WO2024003360A1 - Biomarkers and uses thereof for the treatment of neuroblastoma - Google Patents

Biomarkers and uses thereof for the treatment of neuroblastoma Download PDF

Info

Publication number
WO2024003360A1
WO2024003360A1 PCT/EP2023/068023 EP2023068023W WO2024003360A1 WO 2024003360 A1 WO2024003360 A1 WO 2024003360A1 EP 2023068023 W EP2023068023 W EP 2023068023W WO 2024003360 A1 WO2024003360 A1 WO 2024003360A1
Authority
WO
WIPO (PCT)
Prior art keywords
cells
hla
gene
neuroblastoma
molecule
Prior art date
Application number
PCT/EP2023/068023
Other languages
French (fr)
Inventor
Isabelle JANOUEIX-LEROSEY
Cécile THIRANT
Ana COSTA
Olivier Delattre
Original Assignee
Institut Curie
Institut National de la Santé et de la Recherche Médicale
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Institut Curie, Institut National de la Santé et de la Recherche Médicale filed Critical Institut Curie
Publication of WO2024003360A1 publication Critical patent/WO2024003360A1/en

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K16/00—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies
    • C07K16/18—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans
    • C07K16/28—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants
    • C07K16/2803—Immunoglobulins [IGs], e.g. monoclonal or polyclonal antibodies against material from animals or humans against receptors, cell surface antigens or cell surface determinants against the immunoglobulin superfamily
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/569—Immunoassay; Biospecific binding assay; Materials therefor for microorganisms, e.g. protozoa, bacteria, viruses
    • G01N33/56966—Animal cells
    • G01N33/56972—White blood cells
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/574—Immunoassay; Biospecific binding assay; Materials therefor for cancer
    • G01N33/57407—Specifically defined cancers
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N2800/00—Detection or diagnosis of diseases
    • G01N2800/52—Predicting or monitoring the response to treatment, e.g. for selection of therapy based on assay results in personalised medicine; Prognosis

Definitions

  • the invention relates to biomarkers and uses thereof for the treatment of neuroblastoma.
  • Tumor microenvironment represents a key component of the tumor ecosystem the complexity of which has to be accurately understood to define selective targeting opportunities, including immune-base therapies.
  • the molecule is an antibody, preferably an antagonist antibody.
  • the subject has an overexpression of TIGIT, LAG3, CTLA4, TIM3, and/or PD-1 on T cells of the neuroblastoma sample.
  • the molecule targets, modulates or inhibits CXCR2, CXCR1 or PTSG2/COX2, preferably CXCR2 or PTSG2/COX2, even more preferably CXCR2.
  • the molecule targets, modulates or inhibits TGF-beta.
  • the at least one cytotoxic T cells are detected by detection or quantification in the T-cells of at least one gene selected from the group consisting of IL7R, LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, OXNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, ITM2A, FAU, TRAF3
  • the cytotoxic T-cells are detected or quantified by detection in the T-cells of at least one gene selected from the group consisting of the LAG3 gene, the TIGIT gene, the CTLA4 gene, the HAVCR2/TIM3 gene, and the PDCD1/PDL1 gene or the expression product thereof,
  • the Myeloid-Derived Suppressor Cells are detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1 A gene and the PTGS2/COX2 gene, or the expression product thereof,
  • NK cells Natural killer cells are detected by detection in the NK cells of the presence of the
  • the macrophages are detected by detection at the macrophage cells surface of the presence of at least one protein selected from the group consisting of the CD68 protein and the APOE protein, or by detection in the macrophages of the corresponding CD68 and APOE genes.
  • the neuroblastoma is a metastatic or pre-metastatic neuroblastoma, wherein the neuroblastoma is a high risk neuroblastoma or wherein the neuroblastoma is selected from refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma.
  • the method of the invention further comprises, after the detection step(s), a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group.
  • the invention also concerns an in vitro method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment, comprising a step of implementing an in vitro method for classifying or identifying a patient according to any one of claims 11 to 14, a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group, the membership of the subject to a specific group being predictive of the responsiveness of said subject to a specific treatment.
  • the cells detected in the classification step are Cytotoxic T cells as disclosed above, and the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PD1/PDL1 inhibitors.
  • the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PD1/PDL1 inhibitors.
  • the cells detected in the classification step are MDSC as disclosed above, and the specific treatment comprises the administration of at least one antibody or small molecule targeting at least one protein encoded by the above-listed genes, such as an anti- CXCR2 targeting small molecule or antibody.
  • the invention also concerns an in vitro method for determining a suitable treatment for a subject, said method comprising a step of implementing an in vitro method for classifying a patient according to the invention, a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group, and a step of determining a suitable treatment.
  • the invention also concerns an in vitro method for detecting or quantifying immunosuppressive MDSC in a neuroblastoma sample from a subject, wherein the method comprises detecting or quantifying at least one gene or gene product of Table 4J or at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1A gene and the PTGS2/COX2 gene, or the expression product thereof, the overexpression of said genes or gene products being indicative of immunosuppressive MDSC.
  • the at least one gene or gene product is selected from the group consisting of CXCR2, FCGR3B, CMTM2, SIOOP, CSF3R, CXCR1, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CDA, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP
  • the invention also concerns a method of treatment of neuroblastoma in a subject in need thereof, comprising the administration a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4A, 4J, 4B, 4H, 41, 4M or 4E, preferably 4A, 4J, 4B, 4H, 41, more preferably 4A or 4J.
  • the invention finally concerns the use of a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4 A, 4 J, 4B, 4H, 41, 4M or 4E, preferably 4 A, 4J, 4B, 4H, 41, more preferably 4A or 4J for the manufacture of a medicament, for the treatment of neuroblastoma.
  • FIG. 1 Deciphering the cellular ecosystem of the TH-MYCN mouse neuroblastoma model, (a) Uniform Manifold Approximation and Projection (UMAP) of the 5,650 cells obtained after the integration by Seurat of the three tumors, (b) Macrophages and other myeloid cells are a major component of the TME as shown by the repartition of the eight TME subpopulations identified by scRNA-seq. (c) Representative images of the staining of macrophages (F4/80) and T lymphocytes (CD3) by IHC on the same tumor. Scale bar: 50 pm. (d) Inverse correlation between the number of CD19 CD3' cells corresponding to myeloid and NK cells and CD3 + CD19‘ cells being T cells obtained by FACS analysis on 7 tumors and normalized to CD45 + cells.
  • UMAP Uniform Manifold Approximation and Projection
  • FIG. 1 Macrophage heterogeneity and Myeloid-Derived Suppressor Cells (MDSCs) in TH-MYCN mouse tumors, (a) Dotplot showing the expression of marker genes highlighting the differences between three macrophage subsets, (b) Representative image of the staining of S100a8 by IHC obtained on the same tumor as the one showed in Figure 1c. Scale bar: 50 pm. (c) Detection of cells expressing Ly6C and Ly6G by FACS amongst CD45 + CD1 lb + cells in 8 TH-MYCN tumors.
  • MDSCs Myeloid-Derived Suppressor Cells
  • FIG. 3 Characterization of the TME in a cohort of 10 neuroblastoma biopsies by singlecell transcriptomic analysis, (a) UMAP of 3,785 cells obtained after the integration of the 10 biopsies and clustering of non-tumor cells only. Tumor cells were defined by the expression of PHOX2B and presence of genomic alterations inferred from scRNA-seq data, (b) Plots showing the expression of APOE, CSF1R and CD33 that defines three different macrophages subsets, (c) Dotplot showing the expression of genes defining the different myeloid cell populations, (e) scVelo analysis indicating that macrophages from clusters 8 and 9 likely derive from macrophages of cluster 2.
  • T cells in human neuroblastoma are dysfunctional, (a) Clusters 0 and 1 of T cells correspond to CD4 + and CD8 + cells, respectively, (b) Heatmap showing that all T cells express at least one inhibitory receptor, (c) Expression of the T cell effectors IL2, TNF, IFNG and GZMB is absent or low in T cells.
  • the MDSC population identified in the mouse TME is conserved in human TME.
  • a signature including the top 20 genes upregulated in the mouse MDCS population (cluster 5) is strongly expressed in cluster 10 of the human TME.
  • Signatures of the three macrophage clusters defined in MYCN-driven mouse neuroblastoma are evaluated on the human myeloid cells of patient tumors.
  • Figure 6 Exhausted phenotype of T cells and immunosuppressive activity of MDSCs from TH-MYCN mouse neuroblastoma, (a) FACS analysis showing that TH-MYCN neuroblastoma tumors exhibit more T cells expressing inhibitory receptors compared to spleen of wild-type mice, (b) CSFE proliferation profiles are shown for CD4 + and CD8 + cells after 3 days of co-culture with CD45+CD1 lb + Ly6G + Ly6C low cells or CD45+CD1 lb + Ly6G'Ly6C hlgh cells of a representative TH-MYCN tumor.
  • the grey histogram corresponds to activated T cells only, the blue and red curves correspond to the histograms of T cells incubated with the two fractions purified from wild-type mouse spleen or TH-MYCN mouse tumor, respectively.
  • Figure 8 (a) and (b) Cells of each cluster were colored in the UMAP according to the MYCN status of the corresponding tumors or according to the status of the patient at the time of analysis (diagnosis or relapse), respectively.
  • the term “detection” of a substance refers to the detection of the presence of said substance in any amount, or of its presence in an amount higher than a threshold.
  • the term “detection” relating to a substance may also encompass the quantification of said substance.
  • cancer refers to the presence of cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, and/or immortality, and/or metastatic potential, and/or rapid growth and/or proliferation rate, and/or certain characteristic morphological features.
  • This term refers to any type of malignancy (primary or metastases) in any type of subject. It may refer to solid tumor as well as hematopoietic tumor.
  • the terms “subject”, “individual” or “patient” are interchangeable and refer to an animal, preferably to a mammal, even more preferably to a human.
  • the term “subject” can also refer to non-human animals, in particular mammals such as dogs, cats, horses, cows, pigs, sheep and non-human primates, among others.
  • the term “marker” or “biomarker” refers to a measurable biological parameter that helps to predict the occurrence of a cancer, such as neuroblastoma, the efficiency of a cancer treatment or the presence of immunosuppressive cells.
  • diagnosis refers to the determination as to whether a subject is likely to be affected by a cancer, in particular neuroblastoma. The skilled artisan often makes a diagnosis on the basis of one or more diagnosis markers, the presence, absence, or amount of which is indicative of the presence or absence of the cancer. By “diagnosis”, it is also intended to refer to the provision of information useful for diagnosis.
  • treatment refers to any act intended to ameliorate the health status of patients such as therapy, prevention, prophylaxis and retardation of the disease. In certain embodiments, such term refers to the amelioration or eradication of a disease or symptoms associated with a disease. In other embodiments, this term refers to minimizing the spread or worsening of the disease resulting from the administration of one or more therapeutic agents to a subject with such a disease.
  • treatment of neuroblastoma or the like is mentioned with reference to the pharmaceutical composition of the invention or an active ingredient, there is meant: a) a method for treating neuroblastoma, said method comprising administering a pharmaceutical composition or an active ingredient of the invention to a subject in need of such treatment; b) the use of a pharmaceutical composition or an active ingredient of the invention for the treatment of neuroblastoma; c) the use of a pharmaceutical composition or an active ingredient of the invention for the manufacture of a medicament for the treatment of neuroblastoma; and/or d) a pharmaceutical composition or an active ingredient of the invention for use in the treatment of neuroblastoma.
  • the term “immunotherapy”, “immunotherapeutic agent” or “immunotherapy treatment” refers to a cancer therapeutic treatment using the immune system to reject cancer, in particular neuroblastoma.
  • the therapeutic treatment stimulates the patient's immune system to attack the malignant tumor cells. It includes immunization of the patient with tumor antigens (e.g. by administering a cancer vaccine), in which case the patient's own immune system is trained to recognize tumor cells as targets to be destroyed, or administration of molecules stimulating the immune system such as cytokines, or administration of therapeutic antibodies as drugs, in which case the patient's immune system is recruited by the therapeutic antibodies to destroy tumor cells.
  • tumor antigens e.g. by administering a cancer vaccine
  • molecules stimulating the immune system such as cytokines
  • therapeutic antibodies as drugs
  • the patient's immune system is recruited by the therapeutic antibodies to destroy tumor cells.
  • antibodies are directed against specific antigens such as the unusual antigens that are presented on the surfaces of tumors.
  • immune checkpoint inhibitor treatment refers to an immunotherapy that targets these checkpoints in order to allow or facilitate the attack of cancer cells by the immune system.
  • percentage is used interchangeably herein and may refer to an absolute quantification of a molecule or a cell in a sample, or to a relative quantification of a molecule or a cell in a sample, i.e., relative to another value such as relative to a reference value as taught herein.
  • + refers to a cell, especially a fibroblast or a macrophage, expressing a marker.
  • CD68+ refers to a cell that expresses CD68 higher than or above a reference level.
  • CD68- refers to a cell, in particular a macrophage, that does not express CD68 or that expresses CD68 less or under a reference level.
  • compositions refers to a preparation of one or more of the active agents, with optional other chemical components such as physiologically suitable carriers and excipients.
  • the purpose of a pharmaceutical composition is to facilitate administration of the active agent to an organism.
  • Compositions of the present invention can be in a form suitable for any conventional route of administration or use.
  • a “composition” typically intends a combination of the active agent, e.g., compound or composition, and a naturally-occurring or non-naturally-occurring carrier, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like and include pharmaceutically acceptable carriers.
  • an "acceptable vehicle” or “acceptable carrier” as referred to herein, is any known compound or combination of compounds that are known to those skilled in the art to be useful in formulating pharmaceutical compositions.
  • active principle As used herein, the terms "active principle”, “active ingredient” “active pharmaceutical ingredient”, “therapeutic agent”, “antitumor compound”, and “antitumor agent” are equivalent and refer to a component having a therapeutic effect.
  • the term “therapeutic effect” refers to an effect induced by an active ingredient or by a pharmaceutical composition according to the invention, capable to prevent or to delay the appearance or the development of a cancer, or to cure or to attenuate the effects of a cancer.
  • “An effective amount” or a “therapeutic effective amount” as used herein refers to the amount of active agent required to confer therapeutic effect on the subject, either alone or in combination with one or more other active agents, e.g. the amount of active agent that is needed to treat the targeted disease or disorder, or to produce the desired effect.
  • the “effective amount” will vary depending on the agent(s), the disease and its severity, the characteristics of the subject to be treated including age, physical condition, size, gender and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment.
  • kit defines especially a "kit of parts” in the sense that the combination partners (a) and (b), as defined in the present application can be dosed independently or by use of different fixed combinations with distinguished amounts of the combination partners (a) and (b), i.e. simultaneously or at different time points.
  • the parts of the kit of parts can then be administered simultaneously or chronologically staggered, that is at different time points for any part of the kit of parts.
  • the ratio of the total amounts of the combination partner (a) to the combination partner (b) to be administered in the combined preparation can be varied.
  • the combination partners (a) and (b) can be administered by the same route or by different routes.
  • the term “simultaneous” refers to a pharmaceutical composition, a kit, a product or a combined preparation according to the invention in which the active ingredients are used or administered simultaneously, i.e. at the same time.
  • the term “sequential” refers to a pharmaceutical composition, a kit, a product or a combined preparation according to the invention in which the active ingredients are used or administered sequentially, i.e. one after the other.
  • the active ingredients are used or administered sequentially, i.e. one after the other.
  • all the active ingredients are administered in less than about an hour, preferably less than about 10 minutes, even more preferably in less than about a minute.
  • the term “separate” refers to a pharmaceutical composition, a kit, a product or a combined preparation according to the invention in which the active ingredients are used or administered at distinct time of the day.
  • the active ingredients are administered with an interval of about 1 hour to about 24 hours, preferably with an interval of about 1 hour and 15 hours, more preferably with an interval of about 1 hour and 8 hours, even more preferably with an interval of about 1 hour and 4 hours.
  • the term “and/or” as used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other.
  • a and/or B is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually.
  • the term “a” or “an” can refer to one of or a plurality of the elements it modifies (e.g., “a reagent” can mean one or more reagents) unless it is contextually clear either one of the elements or more than one of the elements is described.
  • overexpressed or “overexpression” it is referred to an expression level measured at the nucleic acid level, especially mRNA level. It can be measured by any method known by the person skilled in the art. A gene is overexpressed when its expression is increased, at least by a log2, when compared to a level of reference.
  • the level of reference can be the expression of the gene in a control or referenced cell or cells. Control or reference cells can be for instance healthy cell.
  • the expression level can also be measured at the protein level.
  • gene product is intended the protein encoded by the gene.
  • mRNA can be detected by hybridization (e. g., Northern blot analysis) in particular by the Nanostring method and/or by amplification (e.g., RT-PCR), in particular by quantitative or semi-quantitative RT-PCR.
  • amplification e.g., RT-PCR
  • Other methods of Amplification include ligase chain reaction (LCR), transcription-mediated amplification (TMA), strand displacement amplification (SDA) and nucleic acid sequence-based amplification (NASBA).
  • LCR ligase chain reaction
  • TMA transcription-mediated amplification
  • SDA strand displacement amplification
  • NASBA nucleic acid sequence-based amplification
  • Real-time quantitative or semi- quantitative RT-PCR is particularly advantageous. Taqman probes specific of the protein of interest transcript may be used.
  • quantitative RT-PCR As used herein, the terms “quantitative RT-PCR”, “qRT-PCR”, “Real time RT-PCR” and “quantitative Real time RT-PCR” are equivalent and can be used interchangeably. Any of a variety of published quantitative RT-PCR protocols can be used (and modified as needed) for use in the present method. Suitable quantitative RT-PCR procedures include but are not limited to those presented in U.S. Pat. No. 5,618,703 and in U.S. Patent Application No. 2005/0048542, which are hereby incorporated by reference.
  • the quantity of gene products or proteins may be measured by semi-quantitative Western blots, enzyme-labeled and mediated immunoassays, such as ELISAs, biotin/avidin type assays, radioimmunoassay, immunohistochemistry, immunoelectrophoresis or immunoprecipitation, protein or antibody arrays, or flow cytometry, such as Fluorescence-activated cell sorting (FACS).
  • the reactions generally include revealing labels such as fluorescent, chemoluminescent, radioactive, enzymatic labels or dye molecules, or other methods for detecting the formation of a complex between the antigen and the antibody or antibodies reacted therewith.
  • the protein expression level is assessed by FACS or by immunohi stochemi stry .
  • FACS Fluorescence-activated cell sorting
  • Immunohistochemistry refers to the process of selectively imaging antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues. Visualizing the antibody-antigen interaction can be accomplished in a number of ways, well known by the man skilled in the art. In the most common instance, an antibody is conjugated to an enzyme, such as peroxidase, that can catalyze a color-producing reaction or is tagged by a fluorophore, such as fluorescein or rhodamine. Immunohistochemistry can be divided into two phases: sample preparation and sample labeling.
  • enzyme such as peroxidase
  • “about 1, 2 and 3” refers to about 1, about 2 and about 3). Further, when a listing of values is described herein (e.g. about 50%, 60%, 70%, 80%, 85% or 86%) the listing includes all intermediate and fractional values thereof (e.g., 54%, 85.4%).
  • the methods of the invention as disclosed below may be in vivo, ex vivo or in vitro methods, preferably in vitro or ex vivo methods.
  • the present invention relates to the characterization of the population of cells of the immune microenvironment of neuroblastoma.
  • the present invention first relates to an in vitro method for classifying, stratifying or identifying a subject, said subject suffering from neuroblastoma, the method comprising the detection and/or the quantification in a neuroblastoma sample obtained from the patient of at least one among: a) Cytotoxic T cells, b) Myeloid-Derived Suppressor Cells (MDSC), c) Natural killer cells (NK cells), and d) Macrophages cells.
  • a) Cytotoxic T cells obtained from the patient of at least one among: a) Cytotoxic T cells, b) Myeloid-Derived Suppressor Cells (MDSC), c) Natural killer cells (NK cells), and d) Macrophages cells.
  • MDSC Myeloid-Derived Suppressor Cells
  • NK cells Natural killer cells
  • Macrophages cells a) Cytotoxic T cells
  • Cytotoxic T cells are CD8-positive cells and/or CD4-positive cells.
  • cytotoxic T-cells may be detected or quantified by detection in the T-cells of at least one gene selected from the group consisting of the LAG3 gene, the TIGIT gene, the CTL A4 gene, the HAV CR2/TIM3 gene, and the PDCD 1/PDL 1 gene, or a gene product thereof.
  • cytotoxic T-cells may be detected or quantified by detection in the T-cells of at least one gene or gene product of Table 4A, in particular selected from the group consisting of IL7R, LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, 0XNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, I
  • said genes are up-regulated or overexpressed in T cells from a neuroblastoma sample, in particular in comparison to a reference level.
  • a reference level is preferably the expression of the same gene in T cells from a normal or non-cancerous sample.
  • This list of overexpressed genes in neuroblastoma can also be used to define a new therapeutic strategy by using a molecule targeting, modulating or inhibiting one of these overexpressed genes or a combination thereof.
  • This strategy is specific of the T cells present in the subject neuroblastoma and is further detailed below.
  • the T cells of neuroblastoma overexpressed immune inhibitory receptors especially the immune checkpoint such as LAG3, TIGIT, CTLA4, TIM3, and/or PD- 1, it helps to predict a response of a subject suffering from neuroblastoma to an immunotherapy treatment or to assess the possible therapeutic benefit of the subject and then to select a subject for the most appropriate treatment.
  • MDSC Myeloid-Derived Suppressor Cells
  • Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, and the FCGR3B gene, or a gene product thereof.
  • the combination of two or three among S100A8 gene, the S100A9 gene and the FCGR3B gene is used to detect and quantify MDSC.
  • the combination of the three is used.
  • Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the CXCR1 gene, the TREM1 gene, the HIF1 A gene and/or the PTGS2/COX2 gene, or a gene product thereof.
  • Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1A gene and the PTGS2/COX2 gene, or a gene product thereof.
  • the detected Myeloid-Derived Suppressor Cells do not present any HLA- DRB1 protein.
  • Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene or gene product selected in Table 4 J, preferably selected from the group consisting of CXCR2, CXCR1, FCGR3B, CMTM2, SIOOP, CSF3R, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CDA, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B
  • said genes are up-regulated or overexpressed in MDSC cells from a neuroblastoma sample, in particular in comparison to a reference level.
  • a reference level is preferably the expression of the same gene in MDSC cells from a normal or non-cancerous sample.
  • the MDSCs of interest are PMN-MDSCs characterized by a CD 1 lb + Ly6G + Ly6C low phenotype and/or M-MDSCs characterized by a CD1 lb + Ly6G'Ly6C h,gh phenotype.
  • such MDSCs exhibit i) a high level of at least one gene selected from the group consisting of CXCR2, S100a8, S100a9 and Mmp9, preferably of CXCR2, S100a8, S100a9 and Mmp9; and optionally ii) an absent or low expression of Cd68 and/or H2-Aa.
  • MDSCs may be detected by detection in the MDSC of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes, preferably at least 200 genes, preferably at least 300 genes among the list of the previous paragraph, or to the detection of the same numbers of proteins among the proteins obtained by expression of said genes and no more than 500, 400, 300, 200, 100 or 50 genes.
  • NK cells Natural killer cells Natural killer (NK) cells may be detected for instance by detection in the NK cells of the presence of the Natural Killer Cell Granule Protein 7, or a gene product thereof.
  • NK Cells may be detected by detection in the cells of at least one gene selected from the group consisting of KLRF1, TRDC, KLRD1, GNLY, KLRC1, CTSW, PRF1, NKG7, GZMB, IL2RB, KLRB1, FGFBP2, CD7, HOPX, PTGDR, XCL2, CLIC3, CST7, XCL1, CD247, TXK, CCL5, MATK, NCR3, ADGRG1, GZMA, HCST, SPON2, PLAC8, CX3CR1, PYHIN1, GZMM, CMC1, TTC38, CCL4, SAMD3, SH2D2A, APOBEC3G, GZMH, SYTL3, PTPN4, RUNX3, ZAP70, EVL, CHST2, CHST12, MBP, ABHD17A, CD38, IRF1, RARRES3, TBC1D10C, APMAP, HLA-B, CD69, DENND2D, CDC42SE
  • said genes are up-regulated or overexpressed in NK cells from a neuroblastoma sample, in particular in comparison to a reference level.
  • a reference level is preferably the expression of the same gene in NK cells from a normal or non-cancerous sample.
  • NK cells may be detected by detection in the NK cells of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes among the list of the previous paragraph, or to the detection of the same numbers of proteins among the proteins obtained by expression of said genes, and no more than 500, 400, 300, 200, 100 or 50 genes.
  • macrophage cells may be detected by detection at the macrophage cells surface of the presence of the CD68 protein, or a gene product thereof.
  • the inventors identified 4 different clusters of macrophage in human, especially clusters 2, 8, 9 and 16.
  • the clusters 2, 8 and 9 could be of higher interest in the present invention.
  • macrophage cells may be detected by detection at the macrophage cells surface of the presence of at least one protein selected from the group consisting of the APOE protein and the CSF1R protein, or gene products thereof.
  • APOE and CSF1R can be detected in clusters 2, 8 and 9.
  • macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of Cl QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL 18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, AD
  • macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of C1QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB
  • macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of C1QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB
  • macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of APOE, APOCI, Cl QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81,
  • macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, ST14, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HM0X1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9,
  • said genes are up-regulated or overexpressed in macrophages from a neuroblastoma sample, in particular in comparison to a reference level.
  • a reference level is preferably the expression of the same gene in macrophages from a normal or non-cancerous sample.
  • macrophages may be detected by detection in the macrophages of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes, preferably at least 200 genes, preferably at least 300 genes, preferably at least 500 genes, among the list of the previous paragraph, or a gene product thereof and no more than 500, 400, 300, 200, 100 or 50 genes.
  • the in vitro method for classifying, stratifying or selecting a subject according to the invention may further comprise, after the detection step(s), a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group.
  • Each specific group of subjects may correspond to a group of subjects which has a high probability of obtaining a positive response to a specific treatment, to predict the prognosis, for instance a poor or good outcome.
  • the patients stratification can be useful in clinical trials to conduct the results analysis or for defining subpopulation of patients of interest for a particular treatment.
  • the in vitro method for classifying a patient according to the invention may be used among others in a method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment or for selecting a subject as having a therapeutic benefit to be treated a particular treatment such as an immunotherapy treatment.
  • the present invention relates on the identification of neuroblastoma that comprises immunosuppressive Myeloid-Derived Suppressor Cells (MDSC) and its use for determining the patient prognosis, its response to a treatment or the most appropriate therapeutic strategy.
  • MDSC Immunopressive Myeloid-Derived Suppressor Cells
  • the present invention relates on the observation that the T cells of neuroblastoma overexpress at least one of the 5 well-described inhibitory receptors, being LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PD-L1 and its use for determining the patient prognosis, its response to a treatment or the most appropriate therapeutic strategy.
  • a further object of the invention is a method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment, comprising a step of implementing an in vitro method for classifying a patient according to the invention, a step of comparing the number and/or type of detected cells to reference numbers and/or types of detected cells, in order to assign the subject to a specific group, the membership of the subject to a specific group being predictive of the responsiveness of said subject to a specific treatment.
  • the cells detected in the classification step are Cytotoxic T cells as disclosed above, and the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PDL1 inhibitors.
  • the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PDL1 inhibitors.
  • the cells detected in the classification step are MDSC as disclosed above, and the specific treatment comprises the administration of at least one antibody or small molecule targeting at least one protein encoded by the above-listed genes, such as an anti- CXCR2 or CXCR1 targeting small molecule or antibody, preferably an anti-CXCR2 targeting small molecule or antibody. It is within the skills in the art to determine such antibodies or small molecules.
  • the cells detected in the classification step are NK cells as disclosed above, and the specific treatment comprises new therapeutic strategy targeting one or several of the overexpressed genes or to select already known therapeutic molecules targeting one or several of the overexpressed genes.
  • Another object of the present invention is a method for determining a suitable treatment for a subject, said method comprising a step of implementing an in vitro method for classifying a patient according to the invention, a step of comparing the number and/or type of detected cells to reference numbers and/or types of detected cells, in order to assign the subject to a specific group, and a step of determining a suitable treatment.
  • the method for determining a suitable treatment according to the invention may be implemented after or simultaneously with the method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment according to the invention.
  • Another object of the present invention is a compound targeting at least one gene and/or protein disclosed above, for use in the treatment of neuroblastoma.
  • the compound targets, modulates or inhibits one gene and/or protein that is overexpressed in neuroblastoma.
  • the gene or protein can be selected in any of the Tables 4A to 4Q. Indeed, Tables 4A to 4Q provide a list of overexpressed genes in neuroblastoma, such genes being a target of interest for developing a treatment of neuroblastoma.
  • the overexpressed gene and/or protein is overexpressed in T cells, preferably cytotoxic T cells, and the gene or protein can be selected in Table 4A.
  • the compound targets TIGIT (T cell immunoreceptor with Ig and ITIM domains), LAG3 (lymphocyte-activation protein 3), CTLA4 (cytotoxic T lymphocyte antigen 4), HAVCR2/TIM3 (T-cell immunoglobulin mucin domain-3), or PD1/PDL1 (programmed cell death protein 1).
  • TIGIT T cell immunoreceptor with Ig and ITIM domains
  • LAG3 lymphocyte-activation protein 3
  • CTLA4 cytotoxic T lymphocyte antigen 4
  • HAVCR2/TIM3 T-cell immunoglobulin mucin domain-3
  • PD1/PDL1 programmed cell death protein 1
  • the compound can be used in combination, for instance a combination of two compounds targeting two proteins selected in the group consisting of TIGIT, LAG3, CTLA4, TIM3 and PD1.
  • the compound targets TIGIT.
  • TIGIT or T-cell immunoreceptor with Ig and ITIM domains is for example described under Uniprot accession number Q495A1
  • the compound can be an antibody, especially an antagonist antibody.
  • the compound can be a chemical compound.
  • Antibodies directed against LAG3 and bifunctional or bispecific molecules targeting LAG-3 are also known such as BMS- 986016, IMP701, MGD012 or MGD013 (bispecific PD-1 and LAG-3 antibody).
  • Anti -LAG-3 antibodies are also disclosed in W02008132601, EP2320940, WO19152574.
  • Antibodies directed against TIGIT are also known in the art, such as BMS-986207 or AB 154, BMS-986207 CPA.9.086, CHA.9.547.18, CPA.9.018, CPA.9.027, CPA.9.049, CPA.9.057, CPA.9.059, CPA.9.083, CPA.9.089, CPA.9.093, CPA.9.101, CPA.9.103, CHA.9.536.1, CHAN.536.3, CHA.9.536.4, CHA.9.536.5, CHA.9.536.6, CHA.9.536.7, CHA.9.536.8,
  • Anti-TIGIT antibodies are also disclosed in WO16028656, W016106302, WO16191643, W017030823, W017037707, WO17053748, WO17152088, WO18033798, WO18102536, WO18102746, W018160704, W018200430, WO18204363, W019023504, WO19062832, WO19129221, WO19129261, WO19137548, WO19152574, WO19154415, WO19168382 and WO19215728.
  • Antibodies directed against CTLA-4 and bifunctional or bispecific molecules targeting CTLA- 4 are also known such as ipilimumab, tremelimumab, MK-1308, AGEN-1884, XmAb20717 (Xencor), MEDI5752 (AstraZeneca).
  • Anti-CTLA-4 antibodies are also disclosed in WO18025178, WO19179388, WO19179391, WO19174603, WO19148444, WO19120232, WO19056281, WO19023482, W018209701, WO18165895, WO18160536, WO18156250, WO18106862, WO18106864, WO18068182, W018035710, WO18025178, WO17194265, WO17106372, W017084078, WO17087588, WO16196237, WO16130898, WO16015675, WO12120125, W009100140 and W007008463.
  • Antibodies directed against TIM3 and bifunctional or bispecific molecules targeting TIM3 are also known such as Sym023, TSR-022, MBG453, LY3321367, INCAGN02390, BGTB-A425, LY3321367, RG7769 (Roche).
  • a TFM-3 antibody is as disclosed in International Patent Application Publication Nos. W02013006490, W02016/161270, WO 2018/085469, or WO 2018/129553, WO 2011/155607, U.S. 8,552,156, EP 2581113 and U.S 2014/044728.
  • the anti-PDl antibody can be selected from the group consisting of Pembrolizumab (also known as Keytruda lambrolizumab, MK-3475), Nivolumab (Opdivo, MDX-1106, BMS-936558, ONO-4538), Pidilizumab (CT-011), Cemiplimab (Libtayo), Camrelizumab, AUNP12, AMP-224, lsBGB-A317 (Tisleizumab), PDR001 (spartalizumab), MK-3477, PF-06801591, JNJ-63723283, genolimzumab (CBT-501), LZM-009, BCD-100, SHR-1201, BAT-1306, AK-103 (HX-008), MEDI-0680 (also known as AMP-514) MEDI0608, JS001 (
  • BI-754091 TSR- 042 (also known as ANB011), GLS-010 (also known as WBP3055), AM-0001 (Armo), STI- 1110 (see WO 2014/194302), AGEN2034 (see WO 2017/040790), MGA012 (see WO 2017/19846), or IBI308 (see WO 2017/024465, WO 2017/025016, WO 2017/132825, and WO 2017/133540), monoclonal antibodies 5C4, 17D8, 2D3, 4H1, 4A11, 7D3, and 5F4, described in WO 2006/121168.
  • Bifunctional or bispecific molecules targeting PD-1 are also known such as RG7769 (Roche), XmAb20717 (Xencor), MEDI5752 (AstraZeneca), FS118 (F-star), SL- 279252 (Takeda) and XmAb23104 (Xencor).
  • the subject can be selected by the overexpression of TIGIT, LAG3, CTLA4, TIM3, and/or PD-1 on T cells of the neuroblastoma sample.
  • the overexpressed gene and/or protein is overexpressed in MDSC cells, and the gene or protein can be selected in Table 4 J.
  • the compound targets CXCR2 (i.e., C-X-C motif chemokine receptor 2 or CD 182).
  • CXCR2 is for example described under the Uniprot accession number P25025 and GenelD n°3579.
  • CXCR2 antagonists or inhibitors are well known in the art and available.
  • Exemplary CXCR2 inhibitors include, but are not limited to, AZD5059, reparixin, navarixin, danirixin and SX-682.
  • Danirixin is disclosed, e.g., in Miller et al. Eur J Drug Metab Pharmacokinet (2014) 39: 173-181; and Miller et al., BMC Pharmacology and Toxicology (2015), 16: 18.
  • Reparixin is disclosed, e.g., in Zarbock et al., British Journal of Pharmacology (2008), 1-8.
  • Navarixin is disclosed, e.g., in Ning et al., Mol Cancer Ther. 2012; 11(6): 1353- 64.
  • SX-682 is disclosed, e.g.
  • CXCR2 inhibitors can also be an antibody directed against CXCR2 as disclosed in WO20028479. Accordingly, the present invention relates to a CXCR2 antagonist or inhibitor for use in the treatment of neuroblastoma, in particular in a subject having a neuroblastoma having MDSC, in particular high level of MDSC compared to control.
  • the present invention relates to a method for treating neuroblastoma in a subject in need thereof comprising a) providing a neuroblastoma sample from the subject, b) detecting or quantifying MDSC; and c) administering a therapeutic effective amount of a CXCR2 antagonist or inhibitor to the subject if the level of MDSC is present, in particular higher than in the control.
  • the CXCR2 antagonist or inhibitor is used for treating the subject if CXCR2 is overexpressed by MDSC.
  • the compound targets PTSG2/COX2.
  • COX2 inhibitors are well known in the art and available.
  • the compound can be ATRA (all-trans retinoid acid).
  • TGF-beta inhibitor can be for instance selected from M7824, bintrafusp alfa, galunisertib, SAR439459, NIS793, PF-06952229, vactosertib, AVID200, ARGX-115, ABBV-151, trabedersen, VTX-002, ACE-1332, SRK-181 or a combination thereof.
  • the subject to be treated is a subject having a metastatic or pre-metastatic neuroblastoma or having a relapse.
  • the subject to be treated can be a subject having a high risk neuroblastoma, especially one associated with MYCN gene.
  • the inventors have shown that the following clusters are amplified in MYCN status: MDSC (cluster 10), macrophage of cluster 16 (FABP4+ macrophage), NK cells and non-classical monocytes (cluster 13).
  • the neuroblastoma can be refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma.
  • MDSC cluster 10
  • FABP4+ macrophage macrophage of cluster 16
  • the compounds for use in the treatment of neuroblastoma according to the invention are preferably in combination with another compound for use according to the present invention, and/or in combination with a classical neuroblastoma treatment.
  • the standard-of-care treatment can include one or more of the following: surgery or excision of all or a portion of the tumor, radiation therapy, stem cell transplant, administering a chemotherapeutic agents, differentiation agent, and immunotherapy.
  • classical neuroblastoma treatments can be alkylators (cyclophosphamide, temozolomide, and melphalan hydrochloride), platinum agents (carboplatin, cisplatin, and oxaliplatin), anthracyclines (doxorubicin hydrochloride), topoisomerase I inhibitors (irinotecan and topotecan), and vinca alkaloids (vincristine sulfate).
  • Differentiation agents include isotretinoin (13-e/s- retinoic acid), and immunotherapeutic agents include monoclonal antibodies such GD2 monoclonal antibodies (dinutuximab).
  • Vincristine Vincristine
  • Carboplatin Etoposide Drug
  • Cyclophosphamide Vindesine
  • dacarbazine Ifosfamide
  • Doxorubicin Busulfan
  • Melphalan Melphalan
  • Thiotepa Radiotherapy
  • Dinutuximab Beta Dinutuximab Beta and Cisplatin.
  • the compounds of the invention can be combined with a kinase inhibitor such as an Aurora kinase inhibitor (for instance, as disclosed in WO20112514) or an ALK inhibitor such as lorlatinib, crizotinib, ceritinib, alectinib and brigatinib, preferably Lorlatinib. and biomarkers
  • a last object of the invention is a signature and/or biomarker specific of neuroblastoma that is selected from the overexpressed genes of Table 4.
  • Table 4 comprises the lists of genes described below under Table 4 A to Table 4R.
  • the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4A (T cells).
  • the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4J (MDSC).
  • the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of any one of Tables 4B, Table 4H and Table 41 (macrophages).
  • the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4M (non-classical monocytes).
  • the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4E (non-classical monocytes).
  • a “gene signature” or “gene expression signature” is a single or a group of genes in a cell, with a uniquely characteristic pattern of gene expression.
  • the gene signature corresponds to the deregulation of specific genes, in particular, overexpression of genes.
  • the gene signature may comprise at least 10, 20, 30, 40 or 50 genes but no more than 1500, 1000, 900, 800, 700, 600, 500, 400, 300, 200 or 100 genes, preferably no more than 300, 200 or 100 genes.
  • the present invention further relates to the use of these gene signatures for detecting the a cell population as detailed above, especially MDSC, T cells, macrophages orNK cells, in particular for detecting the presence of immunosuppressive MDSC and potentially determining the prognosis of the neuroblastoma or selecting the most appropriate treatment and/or predicting the response to or the relevance of a treatment by an immunotherapy, a particular a checkpoint inhibitor.
  • High-risk neuroblastoma is a pediatric cancer with still a dismal prognosis, despite multimodal and intensive therapies.
  • Tumor microenvironment represents a key component of the tumor ecosystem the complexity of which has to be accurately understood to define selective targeting opportunities, including immune-base therapies.
  • the inventors combined various approaches including single-cell transcriptomics to dissect the tumor microenvironment of both a transgenic mouse neuroblastoma model and a cohort of 10 biopsies from neuroblastoma patients, either at diagnosis or at relapse.
  • Features of related cells were validated by FACS and functional assays.
  • the inventors showed that the immune microenvironment of MYCN-driven mouse neuroblastoma is characterized by a low content of T cells, several phenotypes of macrophages and a population of cells expressing signatures of myeloid-derived suppressor cells (MDSCs) that are molecularly distinct from the various macrophage subsets. They documented two CAF subsets, one of which corresponding to CAF-S1, known to have immunosuppressive functions. Their data unraveled a complex content in myeloid cells in patient tumors and further document a striking correspondence of the microenvironment populations between both mouse and human tumors. The inventors showed that mouse intratumor T cells exhibit increased expression of inhibitory receptors at the protein level.
  • MDSCs myeloid-derived suppressor cells
  • T cells from patients are characterized by features of exhaustion, expressing inhibitory receptors and showing low expression of effector cytokines. They further functionally demonstrated that MDSCs isolated from mouse neuroblastoma have immunosuppressive properties, impairing the proliferation of T lymphocytes. This study characterizes for the first time the whole cellular composition of the neuroblastoma microenvironment without any prior assumptions on surface markers, both in a relevant and immunocompetent mouse neuroblastoma model and in a cohort of patients, and documents multiple features of immunosuppression.
  • Macrophages (Cd68 + ), other myeloid cells (Cdl4 + ), B cells (Cd79a + ), T cells (Cd3e + ), dendritic cells (Irf8 + ) and NK cells (Nkg7 + ) composed the immune microenvironment of these tumors.
  • CAFs Fenl +
  • endothelial cells (vWF + ) were also detected in these samples.
  • Macrophages and Cdl4 + myeloid cells were the most abundant TME populations ( Figure lb). All annotated cell types were detected in each tumor individually at different proportions ( Figure 7b).
  • clusters 3, 6 and 8 which all expressed a common signature including Cd68, Csflr, CCr2, Cd86, Adgrel (encoding F4/80) and Lgals3 were detected in the TME of MY CN-driven tumors ( Figure 2b) .
  • These three macrophage clusters could be further defined by specific markers as follows: cluster 3 was characterized by high expression of Pecaml and Cd300e; cluster 6 exhibited a high expression level of Ccr2 and Fnl whereas cluster 8 strongly expressed Apoe, Clqb and Cd63 ( Figure2b, Table 2). These clusters were respectively named Pecaml+, Ccr2+ and Apoe+ macrophages.
  • a classification of macrophages has been previously used to distinguish “classically activated” Ml and “alternatively activated” M2 macrophages in response to defined stimuli in vitro and respectively associated with anti- and pro-tumor activity.
  • Signatures have also been proposed to identify angiogenesis and phagocytosis associated phenotypes in macrophages (Table 3). The inventors therefore evaluated these distinct signatures defined in human, on the. murine data. This analysis revealed that Apoe+ macrophages expressed signatures associated with M2 and phagocytosis phenotypes. The Ccr2+ and Pecaml+ clusters were not highlighted by any of these signatures.
  • Pglyrpl and Pagl characterized the Pecaml+ macrophages, whereas a signature including Ccr2, Sell, Vcan. Ly6c2, Fnl and F13al identified Ccr2+ macrophages; a three-gene signature (Apoe. Clqb and Cd63) defined Apoe+ macrophages.
  • Tgfbl known to have a central role in the TME immunosuppression was highly expressed in macrophages, regardless of the subset.
  • the TH-MYCN mouse TME contains a population of myeloid-derived suppressor cells
  • cluster 5 highly expressing Cdl4 ( Figure la).
  • cluster 5 was strongly labelled with a neutrophil signature.
  • Cells from this cluster exhibited high levels of S 100a8, S100a9 and Mmp9, but showed an absent or low expression of Cd68 and H2-Aa, that are typical markers of macrophages .
  • S100a8 (Calgranulin-A) and S100a9 (Calgranulin-B) are calcium- and zinc-binding proteins known to form a stable heterodimer called calprotectin that have prominent role in the regulation of inflammatory processes and immune response.
  • Mmp9 S100a8 and S100a9 are known to be highly expressed by neutrophils.
  • cluster 5 cells also expressed a gene signature defining activated PMN-MDSCs , described in mouse tumors, exhibiting a high expression of S100a8/a9 and characterized by a potent immune suppressive activity.
  • a low expression of a signature of PMC-MDSCs was observed only in a minor fraction of cluster 5 .
  • MDSCs constitute a heterogeneous population of myeloid cells that are pathologically activated and have immunosuppressive properties; they are now recognized as major regulators of immune responses in cancer.
  • MDSCs include two major subsets based on their phenotypic features: PolyMorphoNuclear-MDSCs (also called granulocytic (G)-MDSCs) and monocytic (M)- MDSCs.
  • PMNs Polymorphonuclear neutrophils
  • cluster 5 cells were also characterized by strong expression of a signature common to both PMN-MDSCs and M-MDSCs, recently identified in the mouse MMTV-PyMT mammary tumor model .
  • the concomitant expression of signatures of both neutrophils and PMN- MDSCs by cluster 5 fits with the recent idea that PMN-MDSCs correspond to a neutrophil population with immunosuppressive properties and that PMN-MDSCs and activated PMN-MDSCs represent two populations of neutrophils in tumor-bearing mice.
  • cluster 5 cells strongly expressed II lb and Arg2 that are known to be involved in immunosuppression.
  • a subset of these cells also expressed Csf- 1 (colony-stimulating factor- 1) which may promote macrophage accumulation within tumors and regulate macrophage survival, proliferation and differentiation.
  • CAFs have been shown to constitute an abundant component of the TME. In neuroblastoma, CAFs remain poorly characterized.
  • signatures of CAFs defined in human breast and ovarian cancers one subcluster showed a high expression of a CAF-S1 signature, whereas the other one had a strong signal for a CAF-S4 signature.
  • CAF-S1 and CAF-S4 have been shown to have immunosuppressive function and pro-metastatic function, respectively.
  • the CAF-S1 subcluster also mildly expressed a iCAF (inflammatory CAFs) signature whereas the CAF-S4 subcluster was also highlighted by signatures of stromal cells called perivascular-like (PVL) cells, being either differentiated-PVLs (dPVL - Tagin, Cd9, Mylk and CnnT) and immature PVLs (imPVL - Cd36, NotchS, Rgs5, Rhob and Itgal).
  • a differential analysis between the CAF-S1 and CAF-S4 clusters identified upregulated genes in each subset .
  • the two CAF populations were then validated by FACS (. Interestingly, the inventors’ data revealed that several chemokines including Ccl2, Cxcll and Cxcll2 that have been shown to contribute to immunosuppressive TME are highly expressed by CAF-S1 cells .
  • Single-cell transcriptomics reveals a variety of myeloid cells in the TME of human neuroblastoma
  • the inventors performed single-cell transcriptomic analysis on 10 biopsies of human neuroblastoma obtained at diagnosis or at relapse (Table 1).
  • the integration of the 10 biopsies highlighted tumor cells (PHOX2B+, GATA3+) as well as several populations of the TME.
  • Analysis using the InferCNV tool confirmed that tumor cells exhibited the emblematic genetic alterations of neuroblastoma such as 17q gain. In contrast, no such alteration could be detected in the various TME clusters.
  • the inventors observed that the different clusters expressed CD68 and APOE (Figure 3b-c) and were positive for a M2 signature but did not express the signature defining a Ml phenotype , which is in favor of a pro-tumoral activity. Further analysis of signatures associated with an angiogenesis or phagocytosis phenotype highlighted cluster 9 and cluster 2, respectively. The inventors noticed that CSF1R was expressed only in clusters 2 and 9 and CD33 was not detected in clusters 8 and 9 ( Figure 3b-3c). Cluster 2 specifically expressed FOLR2 ( Figure 3c). Of note, a strong level of FABP4, known to be expressed in lung macrophages was observed in cluster 16 .
  • CAF heterogeneity in their cohort of human neuroblastomas.
  • Analysis of known signatures identified one small subcluster expressing a CAF-S1 signature and a second subcluster was characterized by a strong CAF-S4 signature and was also highlighted by dVPL and imPVL signatures (. These observations are reminiscent of those obtained in the mouse TH-MYCN neuroblastoma model.
  • Seurat did not identify distinct CAF clusters, the inventors further split the two subpopulations using specific signatures . This enabled us to identify CAF-S1 and CAF-S4 clusters.
  • a differential analysis of these two clusters identified upregulated genes in each cluster . Expression of CXCL12 and CCL2 cytokines was clearly detected in human CAF-S1 .
  • T cells in human neuroblastoma exhibit features of dysfunctional cells
  • cytotoxic CD8 + T cells are one of the main effector cell types responsible for anti-tumor immunity.
  • the inventors noticed an important cluster of T cells in their cohort of 10 neuroblastoma patients, including CD4 and CD8 lymphocytes ( Figure 4a). It is now well described that immune suppressive agents in the TME lead to T-cell dysfunction, resulting in T-cell exhaustion. This state is characterized by increased expression of inhibitory receptors and decreased production of effector cytokines.
  • T cells being either CD4 + or CD8 +
  • the inventors indicated that all T cells, being either CD4 + or CD8 + , expressed at least one of the 5 well-described inhibitory receptors, being LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PD-L1 (Figure 4b).
  • a subset of CD8 + cells and few CD4 + cells co-expressed LAG3 and TIGIT, whereas some CD4 + cells co-expressed TIGIT and CTLA4.
  • effector cytokines only sparse expression of IL2, TNF, IFNG and GZMB was observed in patient T cells (Figure 4c).
  • the expression profile of T cells infiltrating human neuroblastoma is therefore consistent with a phenotype of dysfunctional cells.
  • the inventors further investigated similarities in population structure between both organisms. To do so, they first extracted the top 50 genes from each annotated clusters in both species, then got the average expression value of all genes in all clusters and finally performed an unsupervised hierarchical clustering of the genes and the different clusters. The inventors observed that CAFs, endothelial cells, B cells, NKs and T cells of the two species clustered together indicating that their identity imposed the similarity between their gene expression profiles, rather than the analyzed organism. Among immune cells, the similarities in gene expression also reflected ontogeny with lymphoid cells separating from myeloid cells.
  • the inventors next applied the mouse-derived gene signatures from myeloid cell populations in the human TME. Strikingly, a signature including the top 20 genes upregulated in the mouse MDSCs cluster defined in the TH-MYCN model was highly expressed in human cluster 10 and mildly expressed in human cluster 4 ( Figure 5).
  • the mouse Apoe + macrophage (cluster 8) signature overlapped with all three macrophage clusters identified in patient tumors ( Figure 5).
  • the inventors data identified a MDSCs population with high similarity between mouse and human neuroblastoma and revealed a high level of complexity in macrophage subsets from neuroblastoma consistently with recent data showing that macrophage subsets show species-specific patterns.
  • T cells of human tumors displayed increased expression of inhibitory receptors
  • the inventors sought to analyze the phenotype of the rare T cells observed in the TME of TH- MYCN mouse tumors with respect to the expression of such receptors.
  • FACS analysis using antibodies for LAG3, TIGIT, CTLA4 and PD1 indeed showed that more T cells significantly expressed these receptors compared to T cells obtained from spleens of wild-type mice ( Figure 6a), further demonstrating that anti-tumor response relying on T cells is impaired in the TH-MYCN mouse model.
  • MDSCs have been shown to exploit several mechanisms to modulate immune responses, since they can induce the proliferative arrest of antigen-activated T cells and restrain their function.
  • T cells purified from the spleen of wild-type syngenic mice and activated in vitro were incubated with PMN- or M-MDSCs isolated from mouse tumors by FACS sorting as CD45 CD1 lb + Ly6G + Ly6C low cells or CD45 CD1 lb + Ly6G Ly6C hlgh cells. Similar cells purified from spleen of wild-type mice were used as a control. After 3 days of coculture, the proliferation of CFSE-labeled CD8 + and CD4 + T-cells was assessed by FACS.
  • the inventors transcriptomic, IHC, FACS and functional data characterized a population of MDSCs in the TH-MYCN neuroblastoma model that exhibit immunosuppressive activity as demonstrated by the inhibition of T cell proliferation ex vivo and the exhausted state of T lymphocytes.
  • the present data highly suggest that the corresponding population identified in human neuroblastoma exhibits immunosuppressive functions, contributing with macrophages to the malignant phenotype.
  • the inventors’ data obtained by single-cell transcriptomics provide the first comprehensive analysis of mouse and human neuroblastoma microenvironment cells without any prior assumptions on surface markers. They could dissect the entire TME including endothelial cells, immune cells and CAFs, the identity of which could be unambiguously defined with canonical markers and signatures. Only one small cluster of the tumor mouse model (cluster 16) and one of the human TME (cluster 14) remained undefined. Importantly, the present single-cell RNA-seq data of the mouse model, for which material can be easily obtained, were confirmed by FACS and IHC analyses for macrophages, T cells and MDSCs. Analysis of high-quality tumor material from young patients affected with cancer remains challenging. The parallel analysis of the TME of a mouse neuroblastoma model and a cohort of patients is one of the strength of the work presented herein and is particularly valuable to get insights into functional activity of some matched cell populations.
  • the inventors documented a high content of myeloid cells and further deciphered the heterogeneity of these cells, with the description of several phenotypes of macrophages in both organisms and characterization of a population of MDSCs. They demonstrated that, in the TH-MY CN model, PMN -MDSCs are more abundant than M-MDSCs and that both types sorted from the murine model are able to inhibit T cell proliferation in an ex vivo functional assay. Of strong interest, is the similarity between the murine immunosuppressive MDSCs (cluster 5) and the cluster 10 of human cells in the inventors’ hierarchical clustering exploring mouse and human cell clusters.
  • Both populations express high levels of S100A8 and S100A9 that have been shown to greatly accumulate in MDSCs and are now recognized as one of the hallmarks of these cells. Consistently with RNA-seq data, S100A8+ HLA-DRB1- MDSCs could be detected in neuroblastoma patient microbiopsies.
  • the inventors single-cell transcriptomic data clearly document that neuroblastoma MDSCs are molecularly distinct from the various subsets of macrophages described in both species.
  • Targeting MDSCs has been suggested as a therapeutic strategy to reverse immunosuppression and improve clinical outcome in cancer patients. Different approaches have been proposed to regulate MDSCs in tumors, such as reducing their recruitment, accumulation and suppressive functions.
  • the inventors’ present results point out upregulated genes in such cells of the neuroblastoma TME that could orientate their targeting.
  • the present transcriptomic data reveal that PTGS2/COX2 and CXCR2 are among the most upregulated genes in both murine and human MDSCs.
  • Cyclooxygenase 2 is one enzyme involved in the generation of prostaglandin E2, a product of lipid oxygenation that has been shown to accumulate in PMN-MDSCs and mediate the enhanced suppressive activity of such cells.
  • the chemokine receptor CXCR2 has been shown to play a key role in the migration of MDSCs to tumors. Its inhibition by genetic ablation or using small-molecules inhibitors enhanced immunotherapy in several mouse models of cancer.
  • MDSC depletion remains challenging since those cells have shortlifespan in tissues and are constantly replaced.
  • Another approach may rely on MDSC reprogramming using inhibition of various pathways to enhance anti -tumor immunity, such as C0X2 inhibition (Fujita M, Kohanbash G, Fellows-Mayle W, Hamilton RL, Komohara Y, Decker SA, et al. COX-2 blockade suppresses gliomagenesis by inhibiting myeloid-derived suppressor cells. Cancer Res. 2011;71:2664- 74) or treatment with W-i reins retinoic acid (ATRA)(Veglia F, Sanseviero E, Gabrilovich DI.
  • ATRA Myeloid- derived suppressor cells in the era of increasing myeloid cell diversity. Nat Rev Immunol. 2021).
  • Retinoic acid-based therapeutics have been used in patients with neuroblastoma and some benefit has been reported through their ability to suppress tumor growth and promote cell differentiation (Matthay KK, Reynolds CP, Seeger RC, Shimada H, Adkins ES, Haas-Kogan D, et al.
  • the inventors could document that the rare intratumor T cells of TH-MY CN neuroblastoma exhibited increased expression of inhibitory receptors.
  • the correlations between the different populations defined by RNA-seq cannot be evaluated since only small microbiopsies have been analyzed and may not be representative of the full tumors when considered individually.
  • the present results showed that despite their presence in human neuroblastoma, CD4 + and CD8 + T cells exhibit features of exhaustion with the expression of at least one inhibitory checkpoint. The link between exhaustion of tumor infdtrative T-cells and the presence or phenotype of MDSCs remains to be studied.
  • mice CAF-S 1 cells in the TH- MYCN model appear to be an important source of cytokines and may exert immunosuppressive functions as previously described.
  • Patient tumors likely include also CAF-S 1 and CAF-S4.
  • the inventors present work has generated a new data resource through single-cell transcriptomics that provides a better understanding of the neuroblastoma ecosystem and the basis to develop both tumor-targeted and immune-targeted therapies.
  • the degree of commonality between the TH-MY CN mouse model and the series of analyzed patient tumors indicates the relevance of using this animal model to evaluate the function of various populations in tumor progression and explore new immune therapeutic approaches.
  • TH-MYCN mice used in this study have been previously described [Weiss WA, Aidape K, Mohapatra G, Feuerstein BG, Bishop JM. Targeted expression of MYCN causes neuroblastoma in transgenic mice. Embo J. 1997;16:2985-95.].
  • Neuroblastoma samples for single-cell analyses were obtained from patients treated at Institut Curie. Surplus tissues obtained at diagnosis or relapse were processed immediately after receipt at the laboratory for molecular diagnosis (Unite de Genetique Somatique). Written informed consents for this study, including the analysis of surplus tumor tissue were obtained for all patients from parents or guardians.
  • mice on a 129* l/SvJ background were obtained from the NCI mouse repository (http://mouse.ncifcrf.gov/) and further backcrossed on 129S2/SvPasCrl background (abbreviated 129S2, Charles River). Genotyping was performed as previously described (Haraguchi S, Nakagawara A. A simple PCR method for rapid genotype analysis of the TH- MYCN transgenic mouse. PLoS One. 2009;4:e6902.). All analyzed mice were heterozygous for the transgene. Bearing tumor mice for the single-cell RNA-seq analysis (42369, 41884 and 42007) were studied at 62, 79 and 63 days, respectively.
  • RNA-seq Single-cell RNA-seq was performed with the lOx Genomics Chromium Single Cell 3’ Kit (v3.1) according to the standard protocol. Libraries were sequenced on an Illumina HiSeq2500 or NovaSeq 6000 sequencing platform. CellRanger version 3.1.0 (lOx Genomics) was used to demultiplex, align and generate UMI count tables from sequencing reads. Two reference genomes were used to align reads: the mouse reference genome (mmlO) for the 3 MYCN- driven mouse tumors; the human reference genome (hg38/GRCh38) for the 10 patient samples. Ambient mRNA correction
  • SoupX R package vl.4.5 (https://github.com/constantAmateur/SoupX) was used to estimate and correct for ambient mRNA contaminations in both mouse and patient tumors.
  • HBB/HBA immunoglobulin genes
  • these genes were absent from the ambient profile (the top 100 covered genes), the inventors used the automatic mode provided by SoupX to estimate contamination fractions and generate corrected expression matrices. Summary of analyses is shown in Tables 5 and 6. Doublet detection
  • RLP/RPS genes all ribosomal genes (defined as RLP/RPS genes) were removed from the raw expression matrices. Then, coverage thresholds were set for each sample individually; an upper threshold was set to remove outlier cells with coverage greater than the 99th percentile, and a lower threshold was set to remove low quality cells with coverage inferior to the 1st percentile. To avoid cells with low number of genes, the same lower threshold was applied on the number of genes thus defining a minimum number of genes required. Finally, cells with more than 20% of reads mapping mitochondrial genes were removed.
  • UMAP Uniform Manifold Approximation and Projections
  • PCs Principal Components
  • the inventors also generated an umap using the graph structure produced by “FindNeighbors” on which “FindClusters” function detects cell clusters. This umap representation is referred to as “umap. graph” .
  • Marker genes that define cell clusters were identified after differential expression analysis using Seurat “Find AllMarkers” function. Clusters were annotated by comparing their top marker genes to canonical cell type markers from the literature. Additional cell type annotation was performed using singleR vl.0.6 (Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20: 163-72. ) which annotates cells against built-in references datasets. The inventors used the Human Primary Cell Atlas (Mabbott NA, Baillie JK, Brown H, Freeman TC, Hume DA.
  • Seurat v3.1.5 was used to integrate the 3 TH-MYCN mouse tumors and the 10 neuroblastoma patient samples using 3,000 anchor features.
  • the integrated objects were subjected to dimension reduction and clustering as described above. Tumor cells and microenvironment were identified based on the expression of specific marker genes.
  • 3,785 non-tumor cells were extracted from the integration. Raw counts were first normalized using SCTransform function (Seurat) then Harmony vl.O (Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods. 2019; 16: 1289-96. ) was used for data integration.
  • RNA velocity analysis To perform RNA velocity analysis (La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, et al. RNA velocity of single cells. Nature. 2018;560:494-8.), the inventors first used velocyto CLI to annotate spliced /unspliced reads from cell-barcodes sorted bam files. The inventors then used the scVelo package (Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol. 2020;38:1408-14. ) with default parameters and default data preparation procedures to compute steady-state velocities and visualize velocity streamplots on myeloid cell populations.
  • IHC Immunohistochemistry
  • FFPE paraffin embedded paraffin embedded tumors from TH-MYCN mice were cut in sections (4 pm) and prepared for staining using standard protocols for xylene and alcohol gradient for deparafination (Sakura, Tissue-Tek DRS). All stainings were performed in the Lab Vision IHC stainer Autostainer 480 device (Thermo Scientific).
  • the epitope retrieval was performed in EnVision FLEX Target Retrieval Solution low-pH (Dako, #K800521, for CD3 and S100A8) or high-pH (Dako, #K800421, for F4/80) followed by 5 minutes blockade of endogenous peroxidase activity with Dako REAL peroxidase-blocking solution (Dako, #S202386).
  • a blocking step was made using Protein Block (Dako, #X-0909) for 10 min.
  • tissue sections were then incubated with the F4/80 (Abeam, #Ab6640; 1 :2000), CD3 (Dako, #A0452; 1 :200) or S100A8 primary antibody (ThermoFisher, #PA5-79948; 1 : 100) or Rabbit IgG isotype control (Abeam, #Ab 172730) for 1 hour at RT, followed by wash with IX PBST (Dako, #K8000).
  • a goat anti -rabbit antibody VECTOR laboratories, #PK-6101 kit
  • tissue sections were washed using PBST and then signal detection was performed by incubation with avidin-horseradish peroxidase (Vector Laboratories) for 25 minutes and detected with 3,3 ’-diaminobenzidine for 5 min (DAB, Dako, #K3468). Counterstaining was performed with Mayer hematoxylin freshly prepared (Dako, #S3309). Tissue sections were then submitted to serial gradients of xylen and mounted with coverslip in an automatic device (Sakura, Tissue-Tek DRS). Staining overview of the sections was done in the Zeiss Axioplan microscope and slides were then scanned using the Philips Ultra Fast Scanner and visualized at high resolution in the Philips IMS 2.2 software for further analyses and photo acquisition.
  • T cell inhibitory receptors For the analysis of T cell inhibitory receptors, cell suspensions obtained from TH-MYCN mouse tumors as described above were pre-enriched in CD45 + cells by magnetic beads (130- 110-618, Miltenyi Biotec) according the manufacturer’s instructions.
  • CD45+ cells were suspended in buffer (PBS, 1%SVF, 5mM EDTA) and incubated with CD4-eF450, CD8-APC, CD279 (PD1)-PC7, CD152 (CTLA4)-AF700, TIGIT-PE and CD223 (LAG-3)-PerCP-eF710 antibodies for 30 min at 4°C in dark. After staining, cells were washed in PBS. Data were acquired with a BD LSRII flow cytometer and analyzed using Flowjo vlO for the expression of the inhibitory receptors in CD4+ and CD8+ cells.
  • Paraffin-embedded tissue blocks were cut into 5 pm sections. Immunostaining was processed in a Bond RX automated (Leica) with OpalTM 7-Color IHC Kits (Akoya Biosciences, NEL821001KT) according to the manufacturer’s instructions using antibodies anti-HLA Class II DRB1 (Abeam mouse monoclonal, ab212448, l/4000 e , 30min - Opal520) and anti- MRP8/S100A8 (Abeam rabbit monoclonal, ab92331, l/2000 e , 60min - Opal690) Tissue sections were coverslipped with ProlongTM Diamond Antifade Mountant (Thermo Fisher).
  • Tumors were harvested from TH-MYCN mice and mechanically dissociated with a scalpel. Enzymatic dissociation was performed as described above. To enrich for viable cells, the inventors performed a cell debris removal kit (130-109-398, Miltenyi Biotec) according the manufacturer’s instructions. Spleens of wild-type mice were crushed on a 70 pm cell strainer (130-098-462, Miltenyi Biotec). Cell suspensions were washed twice with IX PBS. Viability was measured using Vi-cell XR Viability Analyzer (Beckman Coulter).
  • cell suspensions were pre-enriched in Cd45 + cells using magnetic beads (130-110-618, Miltenyi Biotec) according the manufacturer’s instructions and were resuspended in buffer (PBS supplemented with 1% SVF and 5 mM EDTA). Cell suspensions were incubated for 30 minutes at 4°C in dark with pre-conjugated fluorescent labeled with the following combination: CD45-APC-Cy7, CDl lb-FITC, Ly6G-APC (127614, Biolegend), and Ly6C-Alexa700 antibodies. Flow cytometry sorting was performed with the SH800S cell sorter (Sony). The first gating was based on FSC/SSC.
  • Doublet cells were eliminated by gating on SSC-W7 SSC-H followed by FSC-W7FSC- H. The second gating was based on DAPI negative staining to eliminate dead cells.
  • CD45 + /CDl lb + /Ly6G + /Ly6C low (PMN-MDSC) cells and CD45 + /CD1 lb + /Ly6G7Ly6C high (M-MDSCs) were sorted.
  • T cells were isolated using the mouse Pan T Cell Isolation Kit II (130-095-130, Miltenyi Biotec) according to the manufacturer’s instructions. T cells (up to 10 7 ) were stained using the CellTraceTM CSFE Yellow Cell Proliferation Kit (C34573, Thermofisher Scientific) at 5 pM for 8 minutes at 37°C. The staining was stopped by incubation with 5 volumes of PBS supplemented with 5% heat- inactivated FBS for 10 minutes at 4°C.
  • T cells were washed twice with complete medium (RPMI Glutamax) containing 10% heat-inactivated FBS, 1% Penicillin-Streptomycin, 0.1% P-mercaptoethanol, 1% Non-Essential Amino Acid supplement, 1% Hepes, 1% Sodium Pyruvate) at 4°C.
  • Labeled T cells (10 5 /well) were plated and activated in complete medium with anti-CD28 (553294, BDBiosciences, 1 pg/mL) in a flat bottom 96-well plate previously coated with anti-CD3 (Clone 145-2C11, BDBioscience CD3e, 10 pg/mL, diluted in IX PBS).
  • CD45 + /CDl lb + /Ly6G + /Ly6C low cells and CD45 + /CD1 lb + /Ly6G7Ly6C high cells from TH-MYCN tumors or WT spleens were added to the T cells using a 10: 1 T cells:MDSC sorted cells ratio. After 3 days of culture, cells were collected and stained with fluorescent-conjugated antibodies CD4-PE-Cy7 (BLE100528, Biolegend, 1/100) and CD8-APC (553035, BDBioscience, 1/100) for 25 minutes at 4°C, protected from the light.
  • Y T cells alone] / Y (T cells + MDSC sorted cells) ] X 100.
  • the Y value corresponds to the mean fluorescent intensity of CFSE of the whole T cell population divided by the mean fluorescent intensity of CFSE of undivided T cells.
  • Table 1 Characteristics of the 10 neuroblastoma patients studied by scRNA-seq
  • Table 2A Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Clusters 0 and 1
  • Cluster 0 Tubala, H2afz, Stmn2, Mif, Atpifl, Ppplrl4b, Dut, Tubb2b, Tubb3, Ran, Nmel, Fabp5, Uchll, Bex2, Ube2s, Fkbp3, Mycn, Ube2c, PeglO, Hmgb2, Prdx2, Hspdl, Tubb5, Bexl, Polr2f, Ptma, Npml, Ndufabl, Snrpf, Ranbpl, Hmgnl, Pdapl, Hsp90aal, Ccndl, Ndn, Gml673, Gap43, Nasp, Prmtl, Hintl, Nefl, Hlfx, Cct3, Slc25a4, Stmnl, Bex3, Atp5gl, Nnat, Tubalb, Anp32b, Cct7, Snrpdl, Ppal, Nel, Rnase
  • Cluster 1 H2afz, Tubala, Npml
  • Table 2B Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 2
  • Table 2c Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq.
  • Cluster 3 Fcgr4, Fcerlg, Gngt2, Cst3, Pou2f2, Clec4a3, Tmsb4x, Ms4a6c, Lstl, Cd300e, Id2, Satl, Gpxl, Ftll, B2m, Itgal, Cybb, Clec4al, Fthl, Fyb, Ctss, Csflr, Ear2, Ace, H2-D1, Apls2, Itgb2, Ucp2, Cd47, Cd3001d, Hspalb, Corola, Cebpb, Ptprc, Cyba, Ctsb, Lyz2, Itm2b, Tyrobp, Laptm5, Raplb, Msn, Iqgapl, Treml4, Lyn, Hspala, Fl
  • Table 2D Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq.
  • Cluster 4 mt-Atp6, mt-Co3, mt-Co2, mt-Col, mt-Nd2, mt-Cytb, mt-Nd4, mt-Nd3, mt-Ndl, mt-Nd5, mt- Atp8, mt-Nd41, Mai at 1.
  • Table 2E Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 5
  • Table 2G Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 7 Manf, Fkbp2, Ssr4, H2afz, Histlhlb,
  • Table 2H Lists of genes that are up-regulated in the different clusters identified in the of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 8
  • Table 21 Lists are up-: in the different clusters identified in of three TH-MYCN mouse tumors analyzed by scRNA-seq.
  • Cluster 9 Hbb-bs, Hba-al, Hba-a2, Hbb-bt, Lars2, PeglO, Tubb5, Hmgbl, Hsp90aal, Eeflal, Hnmpa2bl, Ptma, Hnrnpal, TmsblO, Eef2, Nel, Stmnl, AY036118, Atp5al, Hnrnpu, Eif4g2, Tubalb, Eif5, Npml, Ywhae, Serbpl, Hsp90abl, Gnas, Soxl l, Ubb, Pcbp2, Naplll, Dnajal, Tptl, Hnmpc, Set, Rackl, Eeflg, Anp32b, Pkm, Dyncli2, Cct2, Eif3
  • Table 2J Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 10
  • Table 2K Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 11
  • Table 2L Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq .
  • Cluster 12 Trbc2, Cd3d, Trbcl, Etsl, Ms4a4b, H2-K1, Trac, Tptl, Cd3g, I17r, H2-Q7, Cd3e, Shisa5, Malatl, TmsblO, mt-Atp6, mt-Nd2, mt-Co3, Gimap3, mt-Col, mt-Co2, Ltb, Vps37b, Cd28, Lek, Gimapl, Btgl, Smad7, Pdcd4, Slamf6, Gimap6, mt-Cytb, Ccnd2, SlOOalO, Emb, Skapl, Gimap4, Ptpreap, Lefl, Eeflal, Bell lb, Cd2, Ms4a
  • Table 2M Lists of genes that are in the different clusters identified in the of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 13
  • Table 2N Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 14
  • Table 20 Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 15
  • Table 2P Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq.
  • Cluster 16 mt-Atp6, mt-Co2, mt-Co3, mt-Cytb, mt-Nd4, mt-Ndl, mt-Nd2, mt-Nd3, mt-Col, Chgb, mt- Nd41, mt-Nd5, Jund, mt-Atp8.
  • Table 2Q Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq .
  • Cluster 17
  • Table 2R Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 18
  • Table 4 comprises the lists of genes described under Table 4A to Table 4R,
  • Table 4A List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Clusters 0 and 1
  • IL7R LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, 0XNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, ITM2A, FAU, TRAF3IP3, EMB, OCIAD2, NOP53, STK4, SUSD3, PIK3IP1, CD247, PDE3B, CLEC2
  • Table 4B List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 2
  • Table 4C List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 3
  • Table 4D List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 4
  • Table 4E List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 5
  • Table 4F List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 6
  • VWF CLDN5, PLVAP, RAMP2, EGFL7, CLEC14A, SOX18, RAMP3, AQP1, SLC9A3R2, CALCRL, CDH5, TM4SF1, ESAM, ADGRL4, PODXL, PTPRB, NOTCH4, ECSCR, EMCN, MMRN2, KDR, ROBO4, SEMA3F, PALMD, RASIP1, TIE1, SLCO2A1, FLT1, GNG11, PCDH17, BCAM, VWA1, HYAL2, FAM167B, SHANK3, CXorf36, CD34, LDB2, EFNA1, CYYR1, CAVIN2, HSPG2, ARHGAP29, MYCT1, NOSTRIN, S100A16, EPAS1, CAV1, TM4SF18, RAPGEF5, WWTR1, BTNL9, STC1, ID1, EFNB2, KANK3, PCDH12, GALNT18, NFIB, NPDC1, TCIM, PCAT19, J
  • Table 4G List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq.
  • Cluster 7 IGHM, MS4A1, CD79A, IGHD, CD79B, TCL1A, BANK1, VPREB3, RALGPS2, TNFRSF13C, LINC00926, CD22, FAM129C, AFF3, BLK, LINC02397, FCRL1, IGLC2, IGKC, CD19, PAX5, SPIB, FCER2, IGLC3, FAM30A, FCRL5, JCHAIN, FCRL2, GNG7, HLA-DOB, CD37, POU2AF1, MEF2C, BCL11A, HVCN1, ADAM28, LY9, GAPT, BLNK, CXCR5, BCL7A, SMIM14, C16orf74, FCMR, STRBP, POU2F2, PLCG2, EAF2, P2RX5, LTB, BACH2, SW
  • Table 4H List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq.
  • Cluster 8
  • Table 41 List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 9
  • Table 4J List are up-: in the different clusters identified in the i of 10 patient tumors analyzed by scRNA-seq. Cluster 10
  • FCGR3B CMTM2, CXCR2, SIOOP, CSF3R, CXCR1, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CDA, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, S
  • Table 4K List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 11
  • Table 4M List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 13
  • TNFRSF8 GPBAR1, LILRA5, APOBEC3A, SMIM25, LILRA1, SLC24A4, CDH23, TCF7L2, LILRB2, FCN1, ZNF703, C19orfi8, LILRA2, CD300E, UPK3A, FCGR3A, MTMR1 1, P2RX1, LRRC25, CFP, NEURL1, STXBP2, CLEC12A, ADGRE1, PILRA, LST1, SLC11A1, FGR, ICAM4, SERPINA1, MTSS1, CDKN1C, LILRB1, PRAM1, IFI30, MS4A7, CFD, POU2F2, C5AR1, WARS, CX3CR1, FAM110A, HES4, LINC00877, Cl lorf21, AIF1, LMO2, SIGLEC10, CAMK1, BID, TNFRSF1B, MAPKAPK3, SLC31A2, PLAGL2, Clorfl62, GCH1, COTL1, CDA,
  • Table 4N List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 14
  • TUBA1A TUBB
  • GNAS ATP5PF
  • STMN2, HSP90AB1 H2AFZ EEF1A2, NPY, ATP5MC3, SUMO2, TUBA1B, PEBP1, STMN1, RACK1, HNRNPA1, H3F3B, ATP5IF1, PTMA, RAN, DYNLL1, TPI1, SLC25A3, BEX1, MDK, FKBP1A, NDUFS5, COX6A1, MLLT11, ARL6IP4, TMEM258, ACTG1, SEMI, PCSK1N, UQCR10, DNAJA1, TUBB2B, CKB, CCNI, COX6C, ATP5MF, MZT2B, COX7A2, GUK1, HSPE1, MAP1B, TUBB2A, LDHB, CHCHD2, TRIR, HINT1, PSMA7, MARCKSL1, NACA, EEF1B2, CLTA, ATP5F1B,
  • Table 40 List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 15
  • Table 4P List are up-: in the different clusters identified in of 10 patient tumors analyzed by scRNA-seq. Cluster 16
  • Table 4Q List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 17
  • Table 5 Filtering of cells with high quality data for the 3 TH-MYCN tumors
  • Table 6 Filtering of cells with high quality data for the 10 neuroblastoma biopsies.
  • Table 7 Antibodies used in the various panels to characterize immune cells and CAFs of the TH-MYCN tumors by FACS.

Landscapes

  • Health & Medical Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Immunology (AREA)
  • Chemical & Material Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Molecular Biology (AREA)
  • Hematology (AREA)
  • General Health & Medical Sciences (AREA)
  • Urology & Nephrology (AREA)
  • Medicinal Chemistry (AREA)
  • Cell Biology (AREA)
  • Biomedical Technology (AREA)
  • Organic Chemistry (AREA)
  • Biochemistry (AREA)
  • Microbiology (AREA)
  • Biotechnology (AREA)
  • Pathology (AREA)
  • General Physics & Mathematics (AREA)
  • Analytical Chemistry (AREA)
  • Physics & Mathematics (AREA)
  • Food Science & Technology (AREA)
  • General Chemical & Material Sciences (AREA)
  • Biophysics (AREA)
  • Virology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Zoology (AREA)
  • Genetics & Genomics (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Pharmacology & Pharmacy (AREA)
  • Nuclear Medicine, Radiotherapy & Molecular Imaging (AREA)
  • Veterinary Medicine (AREA)
  • Public Health (AREA)
  • Animal Behavior & Ethology (AREA)
  • Hospice & Palliative Care (AREA)
  • Oncology (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)

Abstract

The invention relates to biomarkers and uses thereof for the treatment and diagnosis of neuroblastoma.

Description

BIOMARKERS AND USES THEREOF FOR THE TREATMENT OF NEUROBLASTOMA
TECHNICAL FIELD
The invention relates to biomarkers and uses thereof for the treatment of neuroblastoma.
TECHNICAL BACKGROUND
Neuroblastoma is an embryonal cancer of the sympathetic nervous system observed in early childhood that accounts for 8-10% of pediatric cancers. Even when metastatic, this cancer is characterized by diverse clinical behaviors, ranging from spontaneous regression to fatal outcome. Notably, one out of two children diagnosed with neuroblastoma presents with high- risk clinico-biological features and a 5-year overall survival rate below 40%. Multimodal therapies combine surgery, myeloablative chemotherapy, radiation therapy and immunotherapy with monoclonal antibodies targeting the disialoganglioside GD2, highly expressed at the cell surface of tumor cells. High-risk neuroblastoma is a pediatric cancer with still a dismal prognosis, despite multimodal and intensive therapies.
Tumor microenvironment represents a key component of the tumor ecosystem the complexity of which has to be accurately understood to define selective targeting opportunities, including immune-base therapies.
Thus, there remains a need to provide suitable biomarkers and targets for the treatment of neuroblastomas.
SUMMARY OF THE INVENTION
In this respect, the inventors have identified biomarkers that are specific of the immunosuppressive tumor microenvironment of a neuroblastoma. Therefore, the present invention relates to new therapeutics strategy and methods as claimed.
In a first aspect, the invention concerns a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4 A, 4 J, 4B, 4H, 41, 4M or 4E, preferably 4 A, 4J, 4B, 4H, 41, more preferably 4 A or 4 J, for use in the treatment of neuroblastoma in a subject. Preferably, the molecule targets, modulates or inhibits an immune inhibitory receptor, especially TIGIT (T cell immunoreceptor with Ig and ITIM domains), LAG3 (lymphocyteactivation protein 3), CTLA4 (cytotoxic T lymphocyte antigen 4), HAVCR2/TIM3 (T-cell immunoglobulin mucin domain-3), or PD1/PDL1 (programmed cell death protein 1) or wherein a combination of molecules targeting, modulating or inhibiting at least two among TIGIT, LAG3, CTLA4, TIM3, and PD-1 is used.
In particular, the molecule is an antibody, preferably an antagonist antibody.
Preferably, the subject has an overexpression of TIGIT, LAG3, CTLA4, TIM3, and/or PD-1 on T cells of the neuroblastoma sample.
Preferably, the molecule targets, modulates or inhibits CXCR2, CXCR1 or PTSG2/COX2, preferably CXCR2 or PTSG2/COX2, even more preferably CXCR2.
In particular, the neuroblastoma sample has MDSC, in particular high level of MDSC compared to control, in particular MDSC overexpressing CXCR2.
In some embodiments, the molecule targets, modulates or inhibits TGF-beta.
Particularly, the subject has a metastatic or pre-metastatic neuroblastoma, wherein the neuroblastoma is a high risk neuroblastoma or wherein the neuroblastoma is selected from refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma. In some aspects, the molecule is used in combination with another molecule disclosed herein and/or with a classical neuroblastoma treatment.
The subject has particularly been identified or selected by a method according to the invention. The invention also concerns an in vitro method for classifying or identifying a subject, said subject suffering from neuroblastoma, the method comprising the detection and/or the quantification in a neuroblastoma sample obtained from the patient of at least one cell among: a) Cytotoxic T cells, b) Myeloid-Derived Suppressor Cells (MDSC), c) Natural killer cells (NK cells), and d) Macrophages cells,
And wherein: the at least one cytotoxic T cells are detected by detection or quantification in the T-cells of at least one gene selected from the group consisting of IL7R, LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, OXNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, ITM2A, FAU, TRAF3IP3, EMB, OCIAD2, NOP53, STK4, SUSD3, PIK3IP1, CD247, PDE3B, CLEC2D, SEPT6, STK17A, RHOH, BTG1, COX7C, STK17B, EPB41, AC026979.2, RASGRP1, CD96, FAM102A, SOCS1, FXYD5, NPM1, PABPC1, CYTIP, CD7, CDC42SE2, SIT1, PTPRC, ZFP36L2, COMMD6, AES, RACK1, ABLIM1, HINT1, TNFAIP8, DGKA, PPP2R5C, IL2RG, PDCD4, RARRES3, TNFAIP3, NACA, EVL, GPR171, AP3M2, FYN, TRADD, MZT2A, MALAT1, TMA7, B2M, LIMD2, MT-ND6, TTC39C, ARL4C, SNHG25, RAC2, GMFG, MT-ATP6, ANKRD12, HIST1H1D, CYLD, ARHGAP15, ISG20, SEPTI, CDC14A, FNBP1, DDX24, ICAM3, JUNB, NAP1L4, C12orf57, DDX5, RIPOR2, CD48, UQCRB, SYNE2, FYB1, SLFN5, SNHG8, HLA-C, FAM107B, RGS10, BTF3, ANAPC16, CORO1A, MT-CYB, SF1, GSTK1, HIST1H4C, CXCR4, TBC1D10C, MCUB, BCL2, PSIP1, GYPC, RHOF, EIF3E, CORO1B, SELL, C6orf48, TLK1, S1PR4, MTRNR2L12, GIMAP4, ARID5B, SVIP, IL16, ARHGDIB, CALM1, TNFRSF4, CDKN1B, CCND2, APRT, KIAA1551, ATM, EML4, STAT3, PPP1R2, MZT2B, SNRPD2, ANP32B, IK, SON, TSTD1, G3BP2, VAMP2, HLA-F, EEF2, HIST1H1C, ABRACL, NSD3, SYF2, MT-CO1, GPR183, TPR, MT-ND3, KLF13, GCC2, GTF3A, FBL, SRSF5, 0ST4, JAK1, CIB1, NSA2, MYL12A, HNRNPA1, NSMCE3, MBNL1, COX4I1, SEPT9, N4BP2L2, CBX3, UXT, BIRC3, GPSM3, ITGA4, S100A4, SRRM1, PIK3R1, SOD1, PNISR, MT-CO3, RNF213, ARL6IP5, EIF4B, MT- ND1, EIF3H, CREM, PRMT2, BTG2, RGS1, TSC22D3, KLF2, LINC01871, CKLF, CCL5, CD8A, GZMA, CD8B, GZMK, GZMH, NKG7, CST7, CD3D, CD3G, CD3E, TRAC, GZMM, CD2, IL32, HCST, TRGC2, LINC01871, APOBEC3G, RARRES3, SAMD3, TRBC2, CCL4, CTSW, LAG3, LCK, KLRG1, PRF1, KLRD1, GZMB, CD69, RUNX3, CD52, CD27, LYAR, C12orf75, PPP2R5C, STK17A, PTPRC, MATK, CORO 1 A, EVL, IFNG, TIGIT, ACAP1, LAT, CD247, HOPX, CD7, HLA-B, SKAP1, TNFAIP3, PYHIN1, CD96, PSMB9, TRBC1, IKZF3, CXCR3, B2M, MYL12A, SH2D1A, HLA-A, CLEC2D, TMA7, CD99, SH3BGRL3, TMSB4X, GPR171, TBC1D10C, RAC2, CD6, ZFP36L2, BCL11B, SRSF7, CDC42SE2, ISG20, CALM1, CXCR4, LEPROTL1, SIT1, FYN, DUSP2, PSME1, AES, GBP5, RHOH, TRAF3IP3, CLEC2B, RASAL3, ITGAL, PTPN22, AKNA, GIMAP7, TENT5C, S100A4, BTN3A2, SYNE2, SLC38A1, PDCD4, PTPN7, TUBA4A, RNF213, SLFN5, MT2A, BTG1, EEF1D, CHST12, CD48, AAK1, S0CS1, ETS1, CKLF, GNLY, IKZF1, SUB1, PFN1, OST4, AC026979.2, LIMD2, ARL4C, PIK3R1, ITM2A, MYL12B, STK4, TOMM7, PIP4K2A, ANXA1, PAXX, SEPT6, KIAA1551, ITM2C, MBP, HLA-F, ARPC5L, IRF1, GUK1, DDX24, RGS1, IL2RG, GMFG, ABHD17A, SYNE1, SRSF5, VAMP2, COMMD6, CLIC1, SEPT7, CIB1, SSBP4, ADGRE5, GYPC, JUND, ARHGDIB, APOBEC3C, ATP5MG, TRIR, SNRPD2, DRAP1, GIMAP4, GSTK1, PSMB8, TSC22D3 and ISG15, or the expression product thereof; the MDSC are detected by detection or quantification in the cells of at least one gene selected from the group consisting of CXCR2, CXCR1, FCGR3B, CMTM2, SI OOP, CSF3R, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CD A, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, SDCBP, J AML, MCL1, YPEL3, HSPA6, NCF2, SPI1, LILRB3, TYROBP, DUSP1, FCGR2A, SERPINA1, MYO1F, IVNS1ABP, APOBEC3A, RSAD2, MEGF9, RIPOR2, S100A6, ABTB1, LYN, CREB5, LCP1, ALOX5AP, ZFP36L1, USP10, IER2, CSF2RB, SLC11A1, IFITM3, MX2, RGS18, PYGL, SMIM25, SLC2A3, TRIBI, NCF4, TUBA1A, XPO6, TLE3, ITM2B, TXNIP, EGLN1, LILRA5, GMFG, DDX60L, DENND3, IGF2R, HIST1H2AC, EVI2B, PTPRC, CEBPD, LSP1, OAZ1, GLUL, UBE2B, RARA, PNRC1, CPPED1, TLR2, FOS, NADK, CDKN2D, PDLIM7, ARPC5, PTPRE, FLOT2, PLEK, CD55, GNAI2, ADAM8, PTEN, BRI3, ACTB, LAPTM5, STXBP2, P2RY13, ISG15, LY96, UBN1, VSIR, NABP1, SMAP2, ICAM3, VASP, ALOX5, IFRD1, PELI1, RTN3, NUP214, IL17RA, CNN2, MARCKS, HLA-B, PHC2, SEC14L1, CFLAR, ARHGAP9, SHKBP1, RAB11FIP1, EFHD2, LAMTOR4, PLAUR, KDM6B, RASSF3, UBE2D1, CLEC4E, CAP1, CMTM6, LYST, VMP1, FMNL1, FBXL5, TALDO1, CLEC7A, NINJ1, HLA-E, ITGAX, SSH2, PREXI, ACTN1, MAP3K2, ABHD5, HIF1A, ARRB2, ZFP36, ARHGAP26, CYSTM1, TXN, GPSM3, CDC42EP3, UBE2D3, IRF1, CSRNP1, CYTH4, TNFSF13B, ACAP2, PLXNC1, TNFAIP2, USP15, NOPIO, MX1, C4orf3, JMJD1C, SLA, BACH1, MAP4K4, FOSL2, KIAA1551, CKLF, CARD16, NMI, ADGRE5, OSBPL8, WIPF1, FYB1, FLOT1, ATP6V0B, TNFRSF1B, FKBP8, SKAP2, WAS, PLSCR1, TAGLN2, RAB31, PDE4B, SHISA5, LRP10, CCPG1, FAM49B, ADAR, CD46, TCIRG1, IFI16, SERPINB1, UBALD2, MIDN, NCOA4, GNB2, UBE2R2, CDC42SE1, ZYX, TAGAP, RNF213 and LCP2, or the expression product thereof; the NK cells are detected by detection or quantification in the cells of at least one gene selected from the group consisting of KLRF1, TRDC, KLRD1, GNLY, KLRC1, CTSW, PRF1, NKG7, GZMB, IL2RB, KLRB1, FGFBP2, CD7, HOPX, PTGDR, XCL2, CLIC3, CST7, XCL1, CD247, TXK, CCL5, MATK, NCR3, ADGRG1, GZMA, HCST, SPON2, PLAC8, CX3CR1, PYHIN1, GZMM, CMC1, TTC38, CCL4, SAMD3, SH2D2A, APOBEC3G, GZMH, SYTL3, PTPN4, RUNX3, ZAP70, EVL, CHST2, CHST12, MBP, ABHD17A, CD38, IRF1, RARRES3, TBC1D10C, APMAP, HLA-B, CD69, DENND2D, CDC42SE1, DUSP2, MYL12A, PTPN7, RAC2, HLA-A, FCGR3A, SPN, ARL4C, C12orf75, PTPN22, CCND2, EFHD2, PAXX, BTN3A2, LINC01871, PIP4K2A, FCER1G, ACAP1, IER2, CALM1, BTG1, AKNA, JAK1, BIN2, UBB, ARHGAP9, Clorf56, ADGRE5, RAP1B, CORO1A, ZFP36L2, SRSF5, ATM, IL32, CCND3, METRNL, TGFB1, SEPT7, AREG, PFN1, TXNIP, STK17A, LIMD2, ID2, CLEC2B, JUNE), AES, EIF3G, PIK3R1, CD47, NR4A2 and PLEK, or the expression product thereof; and the macrophages are detected by detection or quantification in the cells of at least one gene selected from the group consisting of Cl QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL 18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, ADAP2, APOCI, GRN, CD84, HLA-DMA, MAFB, PLTP, RNF130, PSAP, CYFIP1, ACP2, BLVRB, ABCA1, CTSB, MS4A7, SDC3, ACP5, RAB20, FCGRT, TSPAN4, C3AR1, CCL3L1, Clorf54, TTYH3, SMPDL3A, CD74, CTSC, ASAHI, MPP1, BMP2K, CD163, TPP1, IL4I1, CTSD, TFEC, HLA-DQA1, NR1H3, CD86, DNASE2, RBM47, CYBB, FGL2, CTSH, LAIR1, CMKLR1, HLA-DRA, HEXA, CXCL16, IL18BP, AP1B1, FCHO2, RARRES1, AIF1, AKR1A1, ABHD12, HM0X1, CAPG, HLA-DPA1, DAPK1, FTL, RGL1, LY96, CTSA, HLA-DOA, NAGK, ATOX1, PRDX1, PPT1, ADA2, HLA-DPB1, TIMP2, MMP9, KCTD12, SCPEP1, PLAU, CCL18, LINC00996, IGF1, FCER1G, HLA-DRB1, AKR1B1, SGK1, TNFSF13B, LY86, RAB42, PTAFR, GLUL, ALDH1A1, CST3, CSF2RA, CCL4L2, DMXL2, MRC1, LAMP1, TCN2, CPM, MERTK, MGST2, CUL9, EBB, PLXNC1, SYNGR2, GAL3ST4, PDE6G, CLEC7A, SERPINF1, TGFBI, SPH, TBXAS1, RAB32, STAB1, NAIP, GNPDA1, GRINA, ATP6AP1, CFD, A2M, CEBPA, SAT1, CTSS, TYROBP, SLC7A8, CD63, BLVRA, LAMP2, GNS, SIRPA, CLEC4E, HLA-DQB1, ICAM1, MAF, SEMA4A, SIGLEC10, NINJ1, LINC01857, RENBP, MCOLN1, CD81, IFNGR2, NRP2, AXL, ATP6V1B2, SLC38A6, MSR1, LGALS3, IDH1, UNC93B1, SIGLEC7, PILRA, MMP14, SLC7A7, LACC1, GLA, SLC29A3, FCGR2A, AO AH, DRAM2, GPR137B, SPP1, NCOA4, QPRT, TNFAIP2, TLR4, SPRED1, MARCKS, CHCHD6, LYZ, SDCBP, TFRC, GPX4, CYB561A3, ITM2B, KLHDC8B, BRI3, HSD17B14, NAAA, FRMD4B, EPB41L3, ATP1B1, MITF, ETV5, ANKH, CYP27A1, SIGLEC1, SCARB2, M6PR, ABCC5, HEXB, NAGA, CLIC2, TNS3, LGALS9, DNASE1L3, MARCH1, PHACTR1, GAA, FMNL2, CSTB, ATP6AP2, FUOM, GNB4, CEBPD, LHFPL2, PDK4, SDSL, ATP6V1A, MMP12, VAMP8, CREBL2, SUCNR1, DPP7, SCARB1, RGS1, RRAGD, ATP6V0B, TM6SF1, TMEM138, CLEC4A, MGLL, LST1, PLBD1, ITPR2, CETP, SQSTM1, DNPH1, PLBD2, PCBD1, PRCP, LRRC25, GUSB, FTH1, HLA-DRB5, CD59, HCK, OAZ2, FAM213A, NCEH1, GSAP, MKNK1, SPINT2, SMS, CCR1, DST, PLA2G15, RNF13, SLC48A1, CLEC10A, PMP22, GLMP, SDS, RNASET2, MYO5A, AIG1, PLEK, VOPP1, ATP6V0A1, EPHX1, ADAM9, TYMP, TOR3A, CD300LF, PLEKHB2, SCD, CHPT1, NCF4, EPB41L2, CD300A, CRYL1, IRF8, ATP6V1F, PRNP, GSN, CYBA, CR1, PLIN2, RPN2, CXCL12, PLXDC2, VSIG4, VCAM1, UCP2, LAP3, WWP1, FUCA2, FRMD4A, NEU1, MGAT4A, SNX5, VEGFB, IL13RA1, HAVCR2, FNIP2, MGAT1, CD83, TREM2, ATP6V1C1, ACER3, AHR, RGS10, RAP2B, CD302, ZFAND5, ANTXR1, NFE2L2, SERPINA1, UGCG, SHTN1, TRIM14, DRAM1, RAB10, MYO9B, SAMHD1, PLAUR, TALDO1, GAS7, NR4A3, CISD2, CHCHD10, RAC1, NCKAP1L, LRP1, GSTP1, ARHGAP18, ATP6V0E1, SERPINB6, SMIM30, ITGB2, SNX2, THEMIS2, CSTA, S0D2, LGALS2, SLC31A2, SLAMF7, ANXA5, ATF5, SCAMP2, P2RY13, RAB31, CANX, SASH1, ATP6V0D1, QKI, RCAN1, TMEM70, AP2A2, LAPTM5, OTULINL, RHOQ, CCDC88A, FERMT3, MLEC, ATF3, PDE4DIP, PEPD, IER3, GNPTAB, SDHD, IFNGR1, PDXK, IFI30, LITAF, CLTA, CLTC, HSD17B4, CALHM6, NANS, NUPR1, BCAP31, UBE2D1, G3BP1, KLHL6, ZFYVE16, CAPZB, COMT, FCGR1A, SPATS2L, RGS2, HERPUD1, NR4A2, S100A11, CAT, LGALS1, COLEC12, SLC16A3, CASP1, TMBIM6, RNASE1, SLC43A2, CNDP2, AP2S1, SKAP2, RHOG, SELENOS, STAT1, FCGR3A, PITHD1, Clorfl62, GALNT1, MCUR1, TIMM8B, LMNA, RAB5C, GPR183, PRDX3, CHMP1B, CCL4, KLF4, H2AFJ, MDH1, PABPC4, EFHD2, TMSB4X, MAT2A, ZEB2, CXCL2, LGALS3BP, GADD45B, IQGAP2, LAMTOR2, ATP1B3, DBI, LRPAP1, APLP2, LIMSI, MAP3K8, TXN, SAMSN1, BEX4, SSR3, RTN4, MYDGF, H2AFY, FABP5, CD53, ANXA2, ZNF331, RNH1, CD36, FYB1, ARL6IP1, HES1, SNX6, YWHAH, AC020656.1, NFKBIA, CALR, TNFRSF4, CXCL8, C15orf48, AKAP9, ID2, ZFP36L1, APOE, APOCI, C1QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81, TUBB2B, LILRB4, TUBA1A, ODC1, GPX4, PLD3, ACP5, PLIN2, STMN2, GNAS, LAMP1, C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, STM, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HMOX1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9, SNX10, FPR3, CXCL8, CD109, PLA2G7, CCR1, LGALS3, ERO1A, APLP2, SIRPA, BLVRB, HEXB, TYROBP, FCGR3A, COLEC12, CNDP2, P4HA1, BRI3, PKM, PSAP, ANPEP, NPC2, TNS3, IL18BP, APOE, LAMP1, TPP1, TIMP2, NPL, ATP6V1B2, VAT1, TTYH3, SOAT1, C5AR1, RNASE1, OLR1, GNS, SLC43A3, NCEH1, CTSH, FCGR2A, GRN, FCGR2B, GRINA, FCER1G, SLC2A1, FNDC3B, CTSZ, TMEM51, EGLN3, IL1RN, CTSA, LGALS1, ENO1, CXCL3, CD163, RAB7B, BNIP3, CCDC88A, DAB2, ATP6V1F, PIK3AP1, RAB20, NCF2, S100A11, NR1H3, PLD3, PTAFR, SPI1, FNIP2, DMXL2, OTOA, ASAHI, VIM, NDRG1, ATP6AP1, CLIP4, SCARB2, BNIP3L, CCL3, SLC15A3, GSTO1, VCAN, PLXDC2, CD36, SGK1, ACP2, SLC7A7, ATP6V1A, PLPP3, RAB42, PLTP, ITGAX, NPC1, ANXA2, SQOR, ITGAM, OSCAR, BCKDK, LGMN, EIF4EBP1, ATF5, H2AFY, RRAGD, VEGFA, SOD2, ARL8B, LACTB, TNS1, HAVCR2, BCAP31, LAPTM5, LRP1, CCL18, ADAM9, BCL2A1, SDC4, DRAM1, SERPINA1, ATP13A3, LYZ, POR, LILRB3, CD300A, SDCBP, S100A10, DUSP3, CD86, RBM47, MCRIP2, KIAA0930, MFSD1, CD14, RAB31, MRC1, TCIRG1, GRB2, GPI, SDSL, TFRC, ENO2, P4HB, FKBP15, AGAP3, ADAM8, MGLL, ABHD2, RAB1A, C1QC, RALA, TUBA1C, NINJ1, LIMSI, MFSD12, PGK1, CD63, DHRS3, TPI1, CD84, IRAKI, RAB10, SLC25A19, HEXA, CXCL2, HLA-DRA, RBPJ, LAIR1, SULF2, ATOX1, SLC48A1, IFNAR1, ANXA5, GAPDH, CYFIP1, CTSS, AIF1, GK, GAA, PDE4DIP, ARHGAP18, MGST1, LAMP2, C2, SQSTM1, C3AR1, FMNL2, MAFB, PRDX1, ABHD12, MS4A4A, M6PR, CCL2, SERF2, CPM, MS4A7, EMILIN2, CSF1R, MMP12, CD82, HSD17B4, PLEKHB2, CEBPB, IFNGR2, FAM 162 A, RETN, SAT1, TYMP, MMP9, CANX, SHTN1, C1QA, QSOX1, RNF13, UPP1, PPT1, SLAMF8, KCTD12, MXI1, ADAP2, PGD, ALCAM, SLCO2B1, ITGB2, TPD52L2, EAF1, RABB, HNMT, CLEC4E, BCL2L1, PAPSS1, ZEB2, ELL2, ADA2, ATP6AP2, CYSTM1, CD74, TFEC, SDC2, RXRA, FCGR1A, MMP14, IDH1, PGAM1, GNB4, ACSL1, HM13, LGALS9, ATP6V1C1, CYBB, GCHFR, ALOX5, VAMP8, ICAM1, Cl QB, COLGALT1, ANXA4, VEGFB, CLEC7A, IGF2R, PILRA, METRNL, BMP2K, ABCG1, UNC93B1, HLA- DMA, KCNAB2, GPX4, TSPAN4, LDHA, RNASET2, SPG21, HLA-DRB1, SYK, MIF, TGFBI, PRNP, RASSF4, RASGEF1B, TMEM176A, LSP1, FCGRT, MARCH1, SH3BGRL3, RNASE6, ALDOA, LYN, LRPAP1, LY96, SCPEP1, GLIPR2, YBX1, GNAQ, HBEGF, CD164, IGSF6, PMP22, RAP2B, FERMT3, GNPTAB, TXN, PEA15, VKORC1, MGST3, ATP6V0B, CITED2, HLA-DQB1, CALM3, Clorfl62, TMEM176B, CHST11, ANKRD28, MYO9B, PFKL, DNASE2, FDX1, TUBGCP2, TMBIM6, RGCC, ATP6V1D, ARRDC3, MYDGF, SMS, ZFYVE16, LGALS3BP, OAZ1, RTN4, UGP2, ATP6V0D1, RNF181, CPEB4, NOP 10, NUCB1, PABPC4, RHEB, PLEKHO1, ZYX, RNH1, CLTC, ZFAND5, TPM4, PHC2, RAB7A, ATF3, DPP7, MAF, DBI, ME2, CD44, FOSL2, CD4, IFI6, LITAF, TNFSF13B, NEAT1, SSR3, AP2S1, TSPO, SRGN, VDAC1, SLC2A3, TALDO1, RDX, AHR, PTTG1IP, STX4, USF2, ELOC, SH3BP5, ACADVL, CHCHD10, FLNA, IER3, LMNA, S100A6, GNG5, CALR, HSPA5, LAP3, STAT1, ALDH2, OSBPL8, ANXA1, FN1, HSP90B1, HSPA1A, ZFP36L1, MT1X, RBP4, GPD1, PARAL1, MLPH, FFAR4, GLDN, AC026369.3, SLC19A3, MIR3945HG, MME, SPOCD1, STAC, C8B, FABP4, DEFBI, MCEMP1, PHLDA3, AL035446.1, PPARG, LPL, ILIA, FAM3B, AGRP, LSAMP, BHLHE41, CXCL5, PCOLCE2, GAPLINC, INHBA, ACOT2, CCL23, HCAR2, FAM89A, RETN, MACC1, APOL4, ZDHHC19, MARCO, ITGB8, TEX14, AMIGO2, LINC02345, CES1, ADAMTSL4, PTGER3, CLDN7, CLDN23, VSIG4, OLR1, ADTRP, ARHGEF28, OSCAR, TREM1, AQP3, GALNT12, TNNI2, NMB, AC025048.4, RMDN3, PNPLA6, HSD3B7, MRC1, FBP1, CXCL3, MSR1, GPA33, ALOX5, RYR1, PTCRA, MYB, AL390036.1, FCGR1A, AVPI1, APIP, S100A13, ALAS1, GCHFR, SVIL, TMEM53, CORO2A, PLA2G16, TGM2, ACO1, PPIC, SMIM25, CYP27A1, FOLR3, OASL, ARRDC4, SLC11A1, ABCG1, TREM2, ITIH5, UBASH3B, B3GNT7, ABHD5, COLEC12, MOB3B, PTPMT1, EDEM2, DNASE2B, CCL18, TCF7L2, SCCPDH, AGPAT2, PHYH, ROGDI, VMO1, PLA2G15, APOC2, SLC27A3, CXCL16, ALDH2, NCEH1, ALDH3A2, TRPV2, C20orf27, RHBDD2, LTA4H, DTX4, B3GNT5, SCD, COROIC, QSOX1, HNMT, LGALS3BP, ALOX5AP, OPN3, CDCP1, ABCG2, SNX10, FLVCR2, NCLN, FDX1, MS4A4A, FN1, MGST1, AKR1C3, SERPINA1, GLIPR2, DECR1, MS4A7, OSBPL11, GAA, THBD, ANXA4, ALDH1A1, GCA, TMEM251, IFIT3, PLBD1, COA6, NCF2, C1QC, MIIP, SLCO2B1, GLRX2, ACP5, DDX60L, CD9, ATP1B1, RETREG1, GLRX, COPRS, PDLIM1, SGMS2, SLC49A3, SMCO4, HDDC2, STAC3, POR, ADGRE1, DPH3, COMT, ENPP4, ARHGAP18, FIG4, TFRC, SNX2, SLC31A2, TP53I3, FUOM, C1QB, TMEM38B, HLA-DRB5, TTC39B, PILRA, SPNS1, SERPING1, CPE, NUPR1, Clorfl62, IL1RN, SORT1, TFPT, CARS2, HCAR3, SPI1, MX1, RGCC, CD300C, UPP1, FCGR3A, MCOLN1, AXL, SIGLEC1, LRP1, IFI6, DOK2, CITED2, SEPTI 1, RASAL2, APOCI, RABB, ALDOA, VAT1, C1QA, PBDC1, LAIR1, FCGR1B, HBEGF, SLC7A7, SCPEP1, USP30-AS1, GK, EGR2, NAA20, FAR2, SYS1, CD 163, STXBP2, CD151, BCL2A1, MGST3, CD68, ATL1, AP5B1, FHL1, DTNA, ETHE1, GSTO1, LRPAP1, CAT, ATP6V0D1, FABP5, MYOF, CA2, CAPG, LGALS3, BST1, PLIN2, TRIP6, TSPO, CEBPB, CYB5A, REEP3, TUBB6, SLC7A8, BLOC1S2, PYCARD, MDH1, HPGDS, MARCH2, SPINT1, G6PD, CD300LF, ANXA2, PROCR, CNIH4, KMO, NCF4, CLEC12A, LAMTOR3, IFIT1, HPGD, TMED5, S100A11, ANXA5, HEXB, LAMTOR1, ARHGAP10, TNFSF12, GPCPD1, SIDT2, VASP, IFI30, SFT2D1, PSMA2, GLUL, PLXDC2, RNH1, S100A6, FCER1G, DAB2, ZNF706, FDX2, TXN, SLC25A19, TSPAN3, NIT2, FPR2, S100A10, ARHGEF10L, REEP5, TOMM40, VPS29, RENBP, LIMA1, MPC2, ZDHHC3, CHP1, SLC3A2, RHOB, SQOR, LSM6, CSTA, BACE1, SH2B2, CYB5R3, HLA-DMA, OAS1, TIGAR, CASP1, DNASE2, TYROBP, TUBA1C, SLC31A1, GNG5, TRIQK, RHEB, SIRPA, OAZ1, CTSL, ATP5MC3, ACADVL, ATP6V0B, CISH, SDCBP, PDXK, CHCHD10, TXNDC17, SLFN11, BTK, MLX, MYL6, GGA2, EMILIN2, VAMP8, PPT1, ATP6V1F, MYDGF, RAB5IF, C7orf50, MRPS35, MRPS15, VEGFB, VAMP3, SPN, CSTB, BAX, MSRA, DESI1, LY6E, RARA, GRN, ATP6V1D, LST1, NOPIO, PPFIA1, BSG, YWHAH, NAGLU, S1PR4, PLIN3, SIOOP, CYBA, CTSC, GSN, LGALS9, FTH1, PGD, ANXA11, AKR1A1, LAP3, CCT5, LACTB2, IGFBP2, OSBPL1A, SLC15A3, PLAUR, TST, HCK, ARPC1B, CARD16, BEX4, RGS19, MMP19, NUCB1, ADAM 17, ACOT13, BRI3, PEBP1, SDHD, FCGRT, TFEC, FCGR2A, AP2S1, COMMD9, GALE, ARL6IP1, SSB, OSTF1, VIM, PAPSS1, GPX4, GON7, CTSH, GPRIN3, SNX3, HLA-DQB1, UBB, FUCA2, IRF8, HK3, NANS, FTL, C5AR1, THEMIS2, LY86, HADH, FKBP15, NDUFB5, ANXA1, ARPC3, UGP2, PPDPF, BLVRA, VDAC1, CD81, IFIT2, TSPAN15, C14orfl l9, MRPL14, CCDC115, CTSD, ACER3, CD276, MNDA, PRDX1, MRPL40, STX12, ATP6AP1, ACOT7, TMBIM1, SLC25A24, POLD4, CD63, RAB11FIP1, IGSF6, MR1, SULT1A1, CDC42EP3, RNPEP, CENPW, JAML, ACVRL1, ECHI, CMC1, HLA-DRB1, HTATIP2, TMED9, MPC1, RNF13, UBE2L6, NPTN, LMNA, HAGH, EIF4EBP1, SMIM14, BCAP31, PTPN6, TCIRG1, HSD17B11, THBS1, SCP2, MINK1, SERF2, LEPROT, TBC1D2, MYD88, COQ2, HSD17B14, NDUFV2, GABARAP, LACTB, WASHC3, CCDC88A, CD58, PEPD, NDUFB3, CTSZ, CYBB, FMNL2, GTF2H5, DDAH2, FBXO6, TMEM91, PDCD6IP, CSF1, GUSB, AK6, SMIM15, GNPTG, CHMP5, LAT2, LYZ, CID, BTF3L4, TAF10, APLP2, SUSD1, S100A4, UBE2A, SLC39A3, YBX1, TM6SF1, TKT, MOSPD2, DNAIA1, ANPEP, DBI, HLA-DRA, ERP44, GRB2, ATP2C1, NDUFA7, DCUN1D5, HLA-DPA1, GRINA, TALDO1, CAPZA2, MTHFS, C9orfl6, ATP6V1E1, CD40, MSRB1, IS0C2, J0SD2, QDPR, CXCL2, MTX2, MRPL13, TXNDC11, HEXA, C18orf32, TIMP2, SEC11A, TMEM219, SCIMP, NEK6, AAED1, ASAHI, FKBP1A, PLSCR1, ECHDC1, HSDL2, RTN4, CD33, DHRS4, MMP24OS, TPMT, VDAC2, AC020656.1, MPV17, MFSD10, MINOS1, CFL1, NENF, RND3, DCTN6, SELENOT, PRKCD, CST3, TSG101, FAM50A, LYAR, CREG1, PCBD1, PSMG1, AKIRIN2, RAB10, CMPK2, HLA-DPB1, TMSB4X, P2RX4, GBP1, AGPS, SSR3, CNDP2, LAMTOR2, CLEC7A, MGAT1, ASGR1, SHTN1, CCND3, TWF2, TMEM173, PDHA1, ARPC5, SDSL, SEPHS2, GLB1, ZBTB8OS, CLTA, EMG1, PSMA7, NDUFA4, HLA-DQA1, CTSA, RAB8A, HIGD1A, RAB5C, CD164, LY96, DUSP23, CLIC1, LSM10, SPG21, HADHB, ITPK1, POLR2K, RAB7A, AIF1, C2orf74, RNF7, EEA1, FAM162A, PSMG2, TCEAL4, ATP6V0E1, SAMM50, HAVCR2, PPCS, PSMD9, PSMA3, POMP, TSFM, TMEM230, EFHD2, DYNLL1, ATP6V1B2, TMEM167A, RER1, TMEM126A, MAN1A1, CMAS, CD52, ACTN1, CYCS, RAB9A, PSMB5, ARPC2, ACAA1, TMEM63A, NDUFAB1, P0P4, RAD23A, PNPLA2, ARL2, PHLDA2, C2, SELENOH, MRPL22, KAT8, ARL1, SRI, HEBP1, COLGALT1, TNF, OSTM1, SAMHD1, CTBS, RRAGD, PYURF, DMAC1, TMEM273, AP1S1, RAB32, HVCN1, ELP5, SHARPIN, ESD, NTAN1, COA4, LSM4, TUBA1B, PTAFR, NRBF2, BID, PSMA5, ARL4A, HPCAL1, UNC50, FGD2, RASGEF1B, DYNLT1, SLC16A3, PLAU, ACOT9, MSRB2, TMEM179B, TYMP, RAP1B, GNB2, STX11, PRDX6, SAP18, EMC7, PARP9, PRDX3, RNF181, ITSN1, IFI35, DYNLRB1, UTP18, LAMTOR5, KLF4, PDCL, ATP5F1C, CDC42BPB, EML4, MAP1LC3B, CD83, ATP1B3, HSBP1, CBWD1, SCARB2, H2AFI, SLC39A10, CAMTAI, RAC1, SH3BGRL3, VAPA, GTF3C6, CYSLTR1, FEZ2, PSMB6, PGP, DNTTIP1, HMOX2, PFN1, IPT1, TMED10, TMBIM6, RNF149, TXNIP, ELOC, PEX16, MYL12A, ANAPC15, CTSS, ACAA2, M6PR, ISG15, ISCU, FAM173A, OTUD1, TCEAL9, RUNX1, ANKRD28, PSMD14, FERMT3, HPS5, CRIP1, MAPKAPK3, CXCL8, CHCHD1, ECHS1, DBNL, MRPS23, ENY2, PSMA4, TRIM14, Clorf43, PRR13, UBE2F, RHOA, CMC2, SMIM37, C19orf70, HERC5, AZI2, MRPL41, PCMT1, TPM4, NDUFA13, TAGLN2, PHB, MDH2, SERPINB1, SLA, SH3BGRL, CDC37, CEBPA, CKLF, ELOB, GLRX3, UQCRFS1, VPS26A, HSD17B12, HINT2, SNF8, JUN, DPP7, NDUFC1, COX7A2L, PSME2, EPSTI1, NDUFB6, LGALS1, TMBIM4, LITAF, MRPL18, TMEM70, APH1A, COPZ1, ATP5MF, PKM, SH3GLB1, TBC1D10C, ATP2B1-AS1, GTF2A2, ARF4, SERTAD1, FLNA, TRAPPC2L, CD74, SUMO3, APEX1, ATRAID, ARRB2, AGTRAP, COX17, CIB1, PSMD8, PPIA, BLOC1S1, PFDN2, GLTP, UQCR10, TXNDC12, NDUFS3, WDR1, BAG1, CAP1, FGR, SNRPG, COPS5, BEX3, NDUFAF3, LMAN2, ITGAX, ADRM1, NDUFB2, ACP2, CTNNB1, IL1B, DDIT3, IRF7, ITM2B, CALM1, NUTF2, HIPK2, TMEM14C, CD47, DOCK8, HMGN3, MTPN, LRRFIP1 and FAM89B, or the expression product thereof.
Particularly:
- the cytotoxic T-cells are detected or quantified by detection in the T-cells of at least one gene selected from the group consisting of the LAG3 gene, the TIGIT gene, the CTLA4 gene, the HAVCR2/TIM3 gene, and the PDCD1/PDL1 gene or the expression product thereof,
- the Myeloid-Derived Suppressor Cells are detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1 A gene and the PTGS2/COX2 gene, or the expression product thereof,
- the Natural killer (NK) cells are detected by detection in the NK cells of the presence of the
Natural Killer Cell Granule Protein 7, and/or
- the macrophages are detected by detection at the macrophage cells surface of the presence of at least one protein selected from the group consisting of the CD68 protein and the APOE protein, or by detection in the macrophages of the corresponding CD68 and APOE genes.
Particularly, the neuroblastoma is a metastatic or pre-metastatic neuroblastoma, wherein the neuroblastoma is a high risk neuroblastoma or wherein the neuroblastoma is selected from refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma.
In some aspects, the method of the invention further comprises, after the detection step(s), a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group.
The invention also concerns an in vitro method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment, comprising a step of implementing an in vitro method for classifying or identifying a patient according to any one of claims 11 to 14, a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group, the membership of the subject to a specific group being predictive of the responsiveness of said subject to a specific treatment.
Preferably, the cells detected in the classification step are Cytotoxic T cells as disclosed above, and the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PD1/PDL1 inhibitors.
Alternatively or additionally, the cells detected in the classification step are MDSC as disclosed above, and the specific treatment comprises the administration of at least one antibody or small molecule targeting at least one protein encoded by the above-listed genes, such as an anti- CXCR2 targeting small molecule or antibody.
The invention also concerns an in vitro method for determining a suitable treatment for a subject, said method comprising a step of implementing an in vitro method for classifying a patient according to the invention, a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group, and a step of determining a suitable treatment.
The invention also concerns an in vitro method for detecting or quantifying immunosuppressive MDSC in a neuroblastoma sample from a subject, wherein the method comprises detecting or quantifying at least one gene or gene product of Table 4J or at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1A gene and the PTGS2/COX2 gene, or the expression product thereof, the overexpression of said genes or gene products being indicative of immunosuppressive MDSC.
Preferably, the at least one gene or gene product is selected from the group consisting of CXCR2, FCGR3B, CMTM2, SIOOP, CSF3R, CXCR1, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CDA, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, SDCBP, JAML, MCL1, YPEL3, HSPA6, NCF2, SPI1, LILRB3, TYROBP, DUSP1, FCGR2A, SERPINA1, MYO IF, IVNS1ABP, APOBEC3A, RSAD2, MEGF9, RIPOR2, S100A6, ABTB1, LYN, CREB5, LCP1, ALOX5AP, ZFP36L1, USP10, IER2, CSF2RB, SLC11A1, IFITM3, MX2, RGS18, PYGL, SMIM25, SLC2A3, TRIBI, NCF4, TUBA1A, XPO6, TLE3, ITM2B, TXNIP, EGLN1, LILRA5, GMFG, DDX60L, DENND3, IGF2R, HIST1H2AC, EVI2B, PTPRC, CEBPD, LSP1, OAZ1, GLUL, UBE2B, RARA, PNRC1, CPPED1, TLR2, FOS, NADK, CDKN2D, PDLIM7, ARPC5, PTPRE, FLOT2, PLEK, CD55, GNAI2, ADAM8, PTEN, BRI3, ACTB, LAPTM5, STXBP2, P2RY13, ISG15, LY96, UBN1, VSIR, NABP1, SMAP2, ICAM3, VASP, ALOX5, IFRD1, PELI1, RTN3, NUP214, IL17RA, CNN2, MARCKS, HLA-B, PHC2, SEC14L1, CFLAR, ARHGAP9, SHKBP1, RAB11FIP1, EFHD2, LAMTOR4, PLAUR, KDM6B, RASSF3, UBE2D1, CLEC4E, CAP1, CMTM6, LYST, VMP1, FMNL1, FBXL5, TALDO1, CLEC7A, NINJ1, HLA-E, ITGAX, SSH2, PREXI, ACTN1, MAP3K2, ABHD5, HIF1A, ARRB2, ZFP36, ARHGAP26, CYSTM1, TXN, GPSM3, CDC42EP3, UBE2D3, IRF1, CSRNP1, CYTH4, TNFSF13B, ACAP2, PLXNC1, TNFAIP2, USP15, NOPIO, MX1, C4orf3, JMJD1C, SLA, BACH1, MAP4K4, FOSL2, KIAA1551, CKLF, CARD16, NMI, ADGRE5, OSBPL8, WIPF1, FYB1, FLOT1, ATP6V0B, TNFRSF1B, FKBP8, SKAP2, WAS, PLSCR1, TAGLN2, RAB31, PDE4B, SHISA5, LRP10, CCPG1, FAM49B, ADAR, CD46, TCIRG1, IFI16, SERPINB1, UBALD2, MIDN, NCOA4, GNB2, UBE2R2, CDC42SE1, ZYX, TAGAP, RNF213 and LCP2.
The invention also concerns a method of treatment of neuroblastoma in a subject in need thereof, comprising the administration a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4A, 4J, 4B, 4H, 41, 4M or 4E, preferably 4A, 4J, 4B, 4H, 41, more preferably 4A or 4J.
The invention finally concerns the use of a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4 A, 4 J, 4B, 4H, 41, 4M or 4E, preferably 4 A, 4J, 4B, 4H, 41, more preferably 4A or 4J for the manufacture of a medicament, for the treatment of neuroblastoma.
BRIEF DESCRIPTION OF THE FIGURES
Figure 1. Deciphering the cellular ecosystem of the TH-MYCN mouse neuroblastoma model, (a) Uniform Manifold Approximation and Projection (UMAP) of the 5,650 cells obtained after the integration by Seurat of the three tumors, (b) Macrophages and other myeloid cells are a major component of the TME as shown by the repartition of the eight TME subpopulations identified by scRNA-seq. (c) Representative images of the staining of macrophages (F4/80) and T lymphocytes (CD3) by IHC on the same tumor. Scale bar: 50 pm. (d) Inverse correlation between the number of CD19 CD3' cells corresponding to myeloid and NK cells and CD3+CD19‘ cells being T cells obtained by FACS analysis on 7 tumors and normalized to CD45+ cells.
Figure 2. Macrophage heterogeneity and Myeloid-Derived Suppressor Cells (MDSCs) in TH-MYCN mouse tumors, (a) Dotplot showing the expression of marker genes highlighting the differences between three macrophage subsets, (b) Representative image of the staining of S100a8 by IHC obtained on the same tumor as the one showed in Figure 1c. Scale bar: 50 pm. (c) Detection of cells expressing Ly6C and Ly6G by FACS amongst CD45+CD1 lb+ cells in 8 TH-MYCN tumors.
Figure 3. Characterization of the TME in a cohort of 10 neuroblastoma biopsies by singlecell transcriptomic analysis, (a) UMAP of 3,785 cells obtained after the integration of the 10 biopsies and clustering of non-tumor cells only. Tumor cells were defined by the expression of PHOX2B and presence of genomic alterations inferred from scRNA-seq data, (b) Plots showing the expression of APOE, CSF1R and CD33 that defines three different macrophages subsets, (c) Dotplot showing the expression of genes defining the different myeloid cell populations, (e) scVelo analysis indicating that macrophages from clusters 8 and 9 likely derive from macrophages of cluster 2.
Figure 4. T cells in human neuroblastoma are dysfunctional, (a) Clusters 0 and 1 of T cells correspond to CD4+ and CD8+ cells, respectively, (b) Heatmap showing that all T cells express at least one inhibitory receptor, (c) Expression of the T cell effectors IL2, TNF, IFNG and GZMB is absent or low in T cells.
Figure 5. The MDSC population identified in the mouse TME is conserved in human TME. A signature including the top 20 genes upregulated in the mouse MDCS population (cluster 5) is strongly expressed in cluster 10 of the human TME. Signatures of the three macrophage clusters defined in MYCN-driven mouse neuroblastoma are evaluated on the human myeloid cells of patient tumors.
Figure 6: Exhausted phenotype of T cells and immunosuppressive activity of MDSCs from TH-MYCN mouse neuroblastoma, (a) FACS analysis showing that TH-MYCN neuroblastoma tumors exhibit more T cells expressing inhibitory receptors compared to spleen of wild-type mice, (b) CSFE proliferation profiles are shown for CD4+ and CD8+ cells after 3 days of co-culture with CD45+CD1 lb+Ly6G+Ly6Clow cells or CD45+CD1 lb+Ly6G'Ly6Chlgh cells of a representative TH-MYCN tumor. The grey histogram corresponds to activated T cells only, the blue and red curves correspond to the histograms of T cells incubated with the two fractions purified from wild-type mouse spleen or TH-MYCN mouse tumor, respectively.
Figure 7: (a) Schematic illustration of the overall procedure. scRNA-seq was performed for three different TH-MYCN tumors, (b) The pie chart depicts the contribution of each mouse tumor to the total number of cells (n= 5,650). (c) The histogram highlights the contribution of the different samples to each cluster.
Figure 8: (a) and (b) Cells of each cluster were colored in the UMAP according to the MYCN status of the corresponding tumors or according to the status of the patient at the time of analysis (diagnosis or relapse), respectively.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
In the present invention, the term “detection” of a substance refers to the detection of the presence of said substance in any amount, or of its presence in an amount higher than a threshold. The term “detection” relating to a substance may also encompass the quantification of said substance.
The term "cancer" or “tumor”, as used herein, refers to the presence of cells possessing characteristics typical of cancer-causing cells, such as uncontrolled proliferation, and/or immortality, and/or metastatic potential, and/or rapid growth and/or proliferation rate, and/or certain characteristic morphological features. This term refers to any type of malignancy (primary or metastases) in any type of subject. It may refer to solid tumor as well as hematopoietic tumor.
As used herein, the terms “subject”, “individual” or “patient” are interchangeable and refer to an animal, preferably to a mammal, even more preferably to a human. However, the term "subject" can also refer to non-human animals, in particular mammals such as dogs, cats, horses, cows, pigs, sheep and non-human primates, among others.
As used herein, the term “marker” or “biomarker” refers to a measurable biological parameter that helps to predict the occurrence of a cancer, such as neuroblastoma, the efficiency of a cancer treatment or the presence of immunosuppressive cells.
As used herein, the term “diagnosis” refers to the determination as to whether a subject is likely to be affected by a cancer, in particular neuroblastoma. The skilled artisan often makes a diagnosis on the basis of one or more diagnosis markers, the presence, absence, or amount of which is indicative of the presence or absence of the cancer. By “diagnosis”, it is also intended to refer to the provision of information useful for diagnosis. As used herein, the term “treatment”, “treat” or “treating” refers to any act intended to ameliorate the health status of patients such as therapy, prevention, prophylaxis and retardation of the disease. In certain embodiments, such term refers to the amelioration or eradication of a disease or symptoms associated with a disease. In other embodiments, this term refers to minimizing the spread or worsening of the disease resulting from the administration of one or more therapeutic agents to a subject with such a disease.
Whenever within this whole specification "treatment of neuroblastoma" or the like is mentioned with reference to the pharmaceutical composition of the invention or an active ingredient, there is meant: a) a method for treating neuroblastoma, said method comprising administering a pharmaceutical composition or an active ingredient of the invention to a subject in need of such treatment; b) the use of a pharmaceutical composition or an active ingredient of the invention for the treatment of neuroblastoma; c) the use of a pharmaceutical composition or an active ingredient of the invention for the manufacture of a medicament for the treatment of neuroblastoma; and/or d) a pharmaceutical composition or an active ingredient of the invention for use in the treatment of neuroblastoma.
As used herein, the term “immunotherapy”, “immunotherapeutic agent” or “immunotherapy treatment” refers to a cancer therapeutic treatment using the immune system to reject cancer, in particular neuroblastoma. The therapeutic treatment stimulates the patient's immune system to attack the malignant tumor cells. It includes immunization of the patient with tumor antigens (e.g. by administering a cancer vaccine), in which case the patient's own immune system is trained to recognize tumor cells as targets to be destroyed, or administration of molecules stimulating the immune system such as cytokines, or administration of therapeutic antibodies as drugs, in which case the patient's immune system is recruited by the therapeutic antibodies to destroy tumor cells. In particular, antibodies are directed against specific antigens such as the unusual antigens that are presented on the surfaces of tumors.
An important part of the immune system is its ability to tell between normal cells in the body and those it sees as “foreign”, in particular cancer cells. This lets the immune system attack the cancer cells while leaving the normal cells alone. To do this, the immune system uses “checkpoints”, these checkpoints are molecules on certain immune cells that need to be activated (or inactivated) to start an immune response. Cancer cells sometimes find ways to use these checkpoints to avoid being attacked by the immune system. As used herein, the term “immune checkpoint inhibitor treatment” refers to an immunotherapy that targets these checkpoints in order to allow or facilitate the attack of cancer cells by the immune system. The terms “percentage”, “quantity,” “number”, “amount,” and “level” are used interchangeably herein and may refer to an absolute quantification of a molecule or a cell in a sample, or to a relative quantification of a molecule or a cell in a sample, i.e., relative to another value such as relative to a reference value as taught herein.
As used herein, “neuroblastoma sample”, refers to a tumor biopsy, especially a bone marrow biopsy, an endoscopic biopsy, a fine-needle aspiration, a core needle biopsy, a vacuum-assisted biopsy, an image-guided biopsy, a shave biopsy, a punch biopsy, an incisional biopsy, an excisional biopsy, or a surgical biopsy.
As used herein “+” refers to a cell, especially a fibroblast or a macrophage, expressing a marker. For instance, CD68+ refers to a cell that expresses CD68 higher than or above a reference level. Alternatively, refers to a cell that does not express the marker. For instance, CD68- refers to a cell, in particular a macrophage, that does not express CD68 or that expresses CD68 less or under a reference level.
As used herein, a “pharmaceutical composition” refers to a preparation of one or more of the active agents, with optional other chemical components such as physiologically suitable carriers and excipients. The purpose of a pharmaceutical composition is to facilitate administration of the active agent to an organism. Compositions of the present invention can be in a form suitable for any conventional route of administration or use. In one embodiment, a “composition” typically intends a combination of the active agent, e.g., compound or composition, and a naturally-occurring or non-naturally-occurring carrier, inert (for example, a detectable agent or label) or active, such as an adjuvant, diluent, binder, stabilizer, buffers, salts, lipophilic solvents, preservative, adjuvant or the like and include pharmaceutically acceptable carriers. An "acceptable vehicle" or “acceptable carrier” as referred to herein, is any known compound or combination of compounds that are known to those skilled in the art to be useful in formulating pharmaceutical compositions.
As used herein, the terms "active principle", "active ingredient" "active pharmaceutical ingredient", "therapeutic agent", “antitumor compound”, and “antitumor agent” are equivalent and refer to a component having a therapeutic effect.
As used herein, the term “therapeutic effect” refers to an effect induced by an active ingredient or by a pharmaceutical composition according to the invention, capable to prevent or to delay the appearance or the development of a cancer, or to cure or to attenuate the effects of a cancer. “An effective amount” or a “therapeutic effective amount” as used herein refers to the amount of active agent required to confer therapeutic effect on the subject, either alone or in combination with one or more other active agents, e.g. the amount of active agent that is needed to treat the targeted disease or disorder, or to produce the desired effect. The “effective amount” will vary depending on the agent(s), the disease and its severity, the characteristics of the subject to be treated including age, physical condition, size, gender and weight, the duration of the treatment, the nature of concurrent therapy (if any), the specific route of administration and like factors within the knowledge and expertise of the health practitioner. These factors are well known to those of ordinary skill in the art and can be addressed with no more than routine experimentation. It is generally preferred that a maximum dose of the individual components or combinations thereof be used, that is, the highest safe dose according to sound medical judgment.
The terms “kit”, “product” or "combined preparation", as used herein, defines especially a "kit of parts" in the sense that the combination partners (a) and (b), as defined in the present application can be dosed independently or by use of different fixed combinations with distinguished amounts of the combination partners (a) and (b), i.e. simultaneously or at different time points. The parts of the kit of parts can then be administered simultaneously or chronologically staggered, that is at different time points for any part of the kit of parts. The ratio of the total amounts of the combination partner (a) to the combination partner (b) to be administered in the combined preparation can be varied. The combination partners (a) and (b) can be administered by the same route or by different routes.
As used herein, the term “simultaneous” refers to a pharmaceutical composition, a kit, a product or a combined preparation according to the invention in which the active ingredients are used or administered simultaneously, i.e. at the same time.
As used herein, the term “sequential” refers to a pharmaceutical composition, a kit, a product or a combined preparation according to the invention in which the active ingredients are used or administered sequentially, i.e. one after the other. Preferably, when the administration is sequential, all the active ingredients are administered in less than about an hour, preferably less than about 10 minutes, even more preferably in less than about a minute.
As used herein, the term “separate” refers to a pharmaceutical composition, a kit, a product or a combined preparation according to the invention in which the active ingredients are used or administered at distinct time of the day. Preferably, when the administration is separate, the active ingredients are administered with an interval of about 1 hour to about 24 hours, preferably with an interval of about 1 hour and 15 hours, more preferably with an interval of about 1 hour and 8 hours, even more preferably with an interval of about 1 hour and 4 hours. The term “and/or” as used herein is to be taken as specific disclosure of each of the two specified features or components with or without the other. For example, “A and/or B” is to be taken as specific disclosure of each of (i) A, (ii) B and (iii) A and B, just as if each is set out individually. The term “a” or “an” can refer to one of or a plurality of the elements it modifies (e.g., “a reagent” can mean one or more reagents) unless it is contextually clear either one of the elements or more than one of the elements is described.
By “overexpressed” or “overexpression” it is referred to an expression level measured at the nucleic acid level, especially mRNA level. It can be measured by any method known by the person skilled in the art. A gene is overexpressed when its expression is increased, at least by a log2, when compared to a level of reference. The level of reference can be the expression of the gene in a control or referenced cell or cells. Control or reference cells can be for instance healthy cell. Optionally, the expression level can also be measured at the protein level.
As used herein, the detection of gene or a gene product can be carried out at mRNA and/or protein level. By gene product is intended the protein encoded by the gene.
Methods for determining the quantity of mRNA in a cell are well known by the man skilled in the art. mRNA can be detected by hybridization (e. g., Northern blot analysis) in particular by the Nanostring method and/or by amplification (e.g., RT-PCR), in particular by quantitative or semi-quantitative RT-PCR. Other methods of Amplification include ligase chain reaction (LCR), transcription-mediated amplification (TMA), strand displacement amplification (SDA) and nucleic acid sequence-based amplification (NASBA). Real-time quantitative or semi- quantitative RT-PCR is particularly advantageous. Taqman probes specific of the protein of interest transcript may be used.
As used herein, the terms “quantitative RT-PCR”, “qRT-PCR”, “Real time RT-PCR” and “quantitative Real time RT-PCR” are equivalent and can be used interchangeably. Any of a variety of published quantitative RT-PCR protocols can be used (and modified as needed) for use in the present method. Suitable quantitative RT-PCR procedures include but are not limited to those presented in U.S. Pat. No. 5,618,703 and in U.S. Patent Application No. 2005/0048542, which are hereby incorporated by reference.
The quantity of gene products or proteins may be measured by semi-quantitative Western blots, enzyme-labeled and mediated immunoassays, such as ELISAs, biotin/avidin type assays, radioimmunoassay, immunohistochemistry, immunoelectrophoresis or immunoprecipitation, protein or antibody arrays, or flow cytometry, such as Fluorescence-activated cell sorting (FACS). The reactions generally include revealing labels such as fluorescent, chemoluminescent, radioactive, enzymatic labels or dye molecules, or other methods for detecting the formation of a complex between the antigen and the antibody or antibodies reacted therewith. Preferably, the protein expression level is assessed by FACS or by immunohi stochemi stry .
“Fluorescence-activated cell sorting” (FACS) is a specialized type of flow cytometry. It provides a method for sorting a heterogeneous mixture of biological cells into two or more containers, one cell at a time, based upon the specific light scattering and fluorescent characteristics of each cell.
“Immunohistochemistry” (IHC) refers to the process of selectively imaging antigens (e.g., proteins) in cells of a tissue section by exploiting the principle of antibodies binding specifically to antigens in biological tissues. Visualizing the antibody-antigen interaction can be accomplished in a number of ways, well known by the man skilled in the art. In the most common instance, an antibody is conjugated to an enzyme, such as peroxidase, that can catalyze a color-producing reaction or is tagged by a fluorophore, such as fluorescein or rhodamine. Immunohistochemistry can be divided into two phases: sample preparation and sample labeling.
The term “about” as used herein in connection with any and all values (including lower and upper ends of numerical ranges) means any value having an acceptable range of deviation of up to +/- 10% (e.g., +/- 0.5%, +/-1 %, +/-1 .5%, +/- 2%, +/- 2.5%, +/- 3%, +/- 3.5%, +/- 4%, +/- 4.5%, +/- 5%, +/- 5.5%, +/- 6%, +/- 6.5%, +/- 7%, +/- 7.5%, +/- 8%, +/- 8.5%, +/- 9%, +/- 9.5%). The use of the term “about” at the beginning of a string of values modifies each of the values (i.e. “about 1, 2 and 3” refers to about 1, about 2 and about 3). Further, when a listing of values is described herein (e.g. about 50%, 60%, 70%, 80%, 85% or 86%) the listing includes all intermediate and fractional values thereof (e.g., 54%, 85.4%).
The methods of the invention as disclosed below may be in vivo, ex vivo or in vitro methods, preferably in vitro or ex vivo methods.
Classification, stratification or identification of subjects
The present invention relates to the characterization of the population of cells of the immune microenvironment of neuroblastoma.
Accordingly, the present invention first relates to an in vitro method for classifying, stratifying or identifying a subject, said subject suffering from neuroblastoma, the method comprising the detection and/or the quantification in a neuroblastoma sample obtained from the patient of at least one among: a) Cytotoxic T cells, b) Myeloid-Derived Suppressor Cells (MDSC), c) Natural killer cells (NK cells), and d) Macrophages cells. a) Cytotoxic T cells
Cytotoxic T cells are CD8-positive cells and/or CD4-positive cells.
In an embodiment, cytotoxic T-cells may be detected by detection at their surface of the presence of the T-cell surface glycoprotein CD3 delta chain, or by detection of the corresponding CD3D gene in the T-cells.
In an aspect, cytotoxic T-cells may be detected or quantified by detection in the T-cells of at least one gene selected from the group consisting of the LAG3 gene, the TIGIT gene, the CTL A4 gene, the HAV CR2/TIM3 gene, and the PDCD 1/PDL 1 gene, or a gene product thereof. In an aspect, cytotoxic T-cells may be detected or quantified by detection in the T-cells of at least one gene or gene product of Table 4A, in particular selected from the group consisting of IL7R, LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, 0XNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, ITM2A, FAU, TRAF3IP3, EMB, OCIAD2, NOP53, STK4, SUSD3, PIK3IP1, CD247, PDE3B, CLEC2D, SEPT6, STK17A, RHOH, BTG1, COX7C, STK17B, EPB41, AC026979.2, RASGRP1, CD96, FAM102A, SOCS1, FXYD5, NPM1, PABPC1, CYTIP, CD7, CDC42SE2, SIT1, PTPRC, ZFP36L2, C0MMD6, AES, RACK1, ABLIM1, HINT1, TNFAIP8, DGKA, PPP2R5C, IL2RG, PDCD4, RARRES3, TNFAIP3, NACA, EVL, GPR171, AP3M2, FYN, TRADD, MZT2A, MALAT1, TMA7, B2M, LIMD2, MT-ND6, TTC39C, ARL4C, SNHG25, RAC2, GMFG, MT-ATP6, ANKRD12, HIST1H1D, CYLD, ARHGAP15, ISG20, SEPTI, CDC14A, FNBP1, DDX24, ICAM3, JUNB, NAP1L4, C12orf57, DDX5, RIPOR2, CD48, UQCRB, SYNE2, FYB1, SLFN5, SNHG8, HLA-C, FAM107B, RGS10, BTF3, ANAPC16, CORO1A, MT-CYB, SF1, GSTK1, HIST1H4C, CXCR4, TBC1D10C, MCUB, BCL2, PSIP1, GYPC, RHOF, EIF3E, CORO1B, SELL, C6orf48, TLK1, S1PR4, MTRNR2L12, GIMAP4, ARID5B, SVIP, IL16, ARHGDIB, CALM1, TNFRSF4, CDKN1B, CCND2, APRT, KIAA1551, ATM, EML4, STAT3, PPP1R2, MZT2B, SNRPD2, ANP32B, IK, SON, TSTD1, G3BP2, VAMP2, HLA-F, EEF2, HIST1H1C, ABRACL, NSD3, SYF2, MT-CO1, GPR183, TPR, MT-ND3, KLF13, GCC2, GTF3A, FBL, SRSF5, OST4, JAK1, CIB1, NSA2, MYL12A, HNRNPA1, NSMCE3, MBNL1, COX4I1, SEPT9, N4BP2L2, CBX3, UXT, BIRC3, GPSM3, ITGA4, S100A4, SRRM1, PIK3R1, SOD1, PNISR, MT-CO3, RNF213, ARL6IP5, EIF4B, MT-ND1, EIF3H, CREM, PRMT2, BTG2, RGS1, TSC22D3, KLF2, LINC01871, CKLF, CCL5, CD8A, GZMA, CD8B, GZMK, GZMH, NKG7, CST7, CD3D, CD3G, CD3E, TRAC, GZMM, CD2, IL32, HCST, TRGC2, LINC01871, APOBEC3G, RARRES3, SAMD3, TRBC2, CCL4, CTSW, LAG3, LCK, KLRG1, PRF1, KLRD1, GZMB, CD69, RUNX3, CD52, CD27, LYAR, C12orf75, PPP2R5C, STK17A, PTPRC, MATK, CORO1A, EVL, IFNG, TIGIT, ACAP1, LAT, CD247, HOPX, CD7, HLA-B, SKAP1, TNFAIP3, PYHIN1, CD96, PSMB9, TRBC1, IKZF3, CXCR3, B2M, MYL12A, SH2D1A, HLA-A, CLEC2D, TMA7, CD99, SH3BGRL3, TMSB4X, GPR171, TBC1D10C, RAC2, CD6, ZFP36L2, BCL11B, SRSF7, CDC42SE2, ISG20, CALM1, CXCR4, LEPROTL1, SIT1, FYN, DUSP2, PSME1, AES, GBP5, RHOH, TRAF3IP3, CLEC2B, RASAL3, ITGAL, PTPN22, AKNA, GIMAP7, TENT5C, S100A4, BTN3A2, SYNE2, SLC38A1, PDCD4, PTPN7, TUBA4A, RNF213, SLFN5, MT2A, BTG1, EEF1D, CHST12, CD48, AAK1, S0CS1, ETS1, CKLF, GNLY, IKZF1, SUB1, PFN1, OST4, AC026979.2, LIMD2, ARL4C, PIK3R1, ITM2A, MYL12B, STK4, TOMM7, PIP4K2A, ANXA1, PAXX, SEPT6, KIAA1551, ITM2C, MBP, HLA-F, ARPC5L, IRF1, GUK1, DDX24, RGS1, IL2RG, GMFG, ABHD17A, SYNE1, SRSF5, VAMP2, COMMD6, CLIC1, SEPT7, CIB1, SSBP4, ADGRE5, GYPC, JUNE), ARHGDIB, APOBEC3C, ATP5MG, TRIR, SNRPD2, DRAP1, GIMAP4, GSTK1, PSMB8, TSC22D3 and ISG15.
Preferably, said genes are up-regulated or overexpressed in T cells from a neuroblastoma sample, in particular in comparison to a reference level. Such reference level is preferably the expression of the same gene in T cells from a normal or non-cancerous sample.
Preferably, cytotoxic T-cells may be detected by detection in the T-cells of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes, preferably at least 200 genes, preferably at least 300 genes among the list of the previous paragraph and no more than 500, 400, 300, 200, 100 or 50 genes.
This list of overexpressed genes in neuroblastoma can also be used to define a new therapeutic strategy by using a molecule targeting, modulating or inhibiting one of these overexpressed genes or a combination thereof. This strategy is specific of the T cells present in the subject neuroblastoma and is further detailed below.
As the inventors observed that the T cells of neuroblastoma overexpressed immune inhibitory receptors, especially the immune checkpoint such as LAG3, TIGIT, CTLA4, TIM3, and/or PD- 1, it helps to predict a response of a subject suffering from neuroblastoma to an immunotherapy treatment or to assess the possible therapeutic benefit of the subject and then to select a subject for the most appropriate treatment. b) Myeloid-Derived Suppressor Cells (MDSC)
In an embodiment, Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, and the FCGR3B gene, or a gene product thereof. In a particular aspect the combination of two or three among S100A8 gene, the S100A9 gene and the FCGR3B gene is used to detect and quantify MDSC. Preferably, the combination of the three is used.
In an embodiment, Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the CXCR1 gene, the TREM1 gene, the HIF1 A gene and/or the PTGS2/COX2 gene, or a gene product thereof.
In an embodiment, Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1A gene and the PTGS2/COX2 gene, or a gene product thereof.
In an embodiment, the detected Myeloid-Derived Suppressor Cells do not present any HLA- DRB1 protein.
In an embodiment, Myeloid-Derived Suppressor Cells may be detected by detection in the cells of at least one gene or gene product selected in Table 4 J, preferably selected from the group consisting of CXCR2, CXCR1, FCGR3B, CMTM2, SIOOP, CSF3R, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CDA, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, SDCBP, JAML, MCL1, YPEL3, HSPA6, NCF2, SPI1, LILRB3, TYROBP, DUSP1, FCGR2A, SERPINA1, MYO1F, IVNS1ABP, APOBEC3A, RSAD2, MEGF9, RIPOR2, S100A6, ABTB1, LYN, CREB5, LCP1, ALOX5AP, ZFP36L1, USP10, IER2, CSF2RB, SLC11A1, IFITM3, MX2, RGS18, PYGL, SMIM25, SLC2A3, TRIBI, NCF4, TUBA1A, XPO6, TLE3, ITM2B, TXNIP, EGLN1, LILRA5, GMFG, DDX60L, DENND3, IGF2R, HIST1H2AC, EVI2B, PTPRC, CEBPD, LSP1, OAZ1, GLUL, UBE2B, RARA, PNRC1, CPPED1, TLR2, FOS, NADK, CDKN2D, PDLIM7, ARPC5, PTPRE, FLOT2, PLEK, CD55, GNAI2, ADAM8, PTEN, BRI3, ACTB, LAPTM5, STXBP2, P2RY13, ISG15, LY96, UBN1, VSIR, NABP1, SMAP2, ICAM3, VASP, ALOX5, IFRD1, PELI1, RTN3, NUP214, IL17RA, CNN2, MARCKS, HLA-B, PHC2, SEC14L1, CFLAR, ARHGAP9, SHKBP1, RAB11FIP1, EFHD2, LAMTOR4, PLAUR, KDM6B, RASSF3, UBE2D1, CLEC4E, CAP1, CMTM6, LYST, VMP1, FMNL1, FBXL5, TALDO1, CLEC7A, NINJ1, HLA-E, ITGAX, SSH2, PREXI, ACTN1, MAP3K2, ABHD5, HIF1A, ARRB2, ZFP36, ARHGAP26, CYSTM1, TXN, GPSM3, CDC42EP3, UBE2D3, IRF1, CSRNP1, CYTH4, TNFSF13B, ACAP2, PLXNC1, TNFAIP2, USP15, NOPIO, MX1, C4orfi, JMJD1C, SLA, BACH1, MAP4K4, FOSL2, KIAA1551, CKLF, CARD16, NMI, ADGRE5, OSBPL8, WIPF1, FYB1, FLOT1, ATP6V0B, TNFRSF1B, FKBP8, SKAP2, WAS, PLSCR1, TAGLN2, RAB31, PDE4B, SHISA5, LRP10, CCPG1, FAM49B, ADAR, CD46, TCIRG1, IFI16, SERPINB1, UBALD2, MIDN, NCOA4, GNB2, UBE2R2, CDC42SE1, ZYX, TAGAP, RNF213 and LCP2.
Preferably, said genes are up-regulated or overexpressed in MDSC cells from a neuroblastoma sample, in particular in comparison to a reference level. Such reference level is preferably the expression of the same gene in MDSC cells from a normal or non-cancerous sample.
In some aspects, the MDSCs of interest are PMN-MDSCs characterized by a CD 1 lb+Ly6G+Ly6Clow phenotype and/or M-MDSCs characterized by a CD1 lb+Ly6G'Ly6Ch,gh phenotype. Preferably, such MDSCs exhibit i) a high level of at least one gene selected from the group consisting of CXCR2, S100a8, S100a9 and Mmp9, preferably of CXCR2, S100a8, S100a9 and Mmp9; and optionally ii) an absent or low expression of Cd68 and/or H2-Aa.
Preferably, MDSCs may be detected by detection in the MDSC of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes, preferably at least 200 genes, preferably at least 300 genes among the list of the previous paragraph, or to the detection of the same numbers of proteins among the proteins obtained by expression of said genes and no more than 500, 400, 300, 200, 100 or 50 genes.
This list of overexpressed genes in neuroblastoma can also be used to define a new therapeutic strategy specific of the immunosuppressive MDSC by using a molecule targeting, modulating or inhibiting one of these overexpressed genes or a combination thereof. This strategy is specific of MDSC present in the subject neuroblastoma and is further detailed below. c) Natural killer cells Natural killer (NK) cells may be detected for instance by detection in the NK cells of the presence of the Natural Killer Cell Granule Protein 7, or a gene product thereof.
In an embodiment, NK Cells may be detected by detection in the cells of at least one gene selected from the group consisting of KLRF1, TRDC, KLRD1, GNLY, KLRC1, CTSW, PRF1, NKG7, GZMB, IL2RB, KLRB1, FGFBP2, CD7, HOPX, PTGDR, XCL2, CLIC3, CST7, XCL1, CD247, TXK, CCL5, MATK, NCR3, ADGRG1, GZMA, HCST, SPON2, PLAC8, CX3CR1, PYHIN1, GZMM, CMC1, TTC38, CCL4, SAMD3, SH2D2A, APOBEC3G, GZMH, SYTL3, PTPN4, RUNX3, ZAP70, EVL, CHST2, CHST12, MBP, ABHD17A, CD38, IRF1, RARRES3, TBC1D10C, APMAP, HLA-B, CD69, DENND2D, CDC42SE1, DUSP2, MYL12A, PTPN7, RAC2, HLA-A, FCGR3A, SPN, ARL4C, C12orf75, PTPN22, CCND2, EFHD2, PAXX, BTN3A2, LINC01871, PIP4K2A, FCER1G, ACAP1, IER2, CALM1, BTG1, AKNA, JAK1, BIN2, UBB, ARHGAP9, Clorf56, ADGRE5, RAP1B, CORO1A, ZFP36L2, SRSF5, ATM, IL32, CCND3, METRNL, TGFB1, SEPT7, AREG, PFN1, TXNIP, STK17A, LIMD2, ID2, CLEC2B, JUND, AES, EIF3G, PIK3R1, CD47, NR4A2 and PLEK.
Preferably, said genes are up-regulated or overexpressed in NK cells from a neuroblastoma sample, in particular in comparison to a reference level. Such reference level is preferably the expression of the same gene in NK cells from a normal or non-cancerous sample.
Preferably, NK cells may be detected by detection in the NK cells of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes among the list of the previous paragraph, or to the detection of the same numbers of proteins among the proteins obtained by expression of said genes, and no more than 500, 400, 300, 200, 100 or 50 genes.
This list of overexpressed genes in neuroblastoma can also be used to define a new therapeutic strategy specific of the NK cells by using a molecule targeting, modulating or inhibiting one of these overexpressed genes or a combination thereof. This strategy is specific of NK present in the subject neuroblastoma and is further detailed below. d) Macrophages cells
In an embodiment, macrophage cells may be detected by detection at the macrophage cells surface of the presence of the CD68 protein, or a gene product thereof.
In a particular aspect, the inventors identified 4 different clusters of macrophage in human, especially clusters 2, 8, 9 and 16. The clusters 2, 8 and 9 could be of higher interest in the present invention. In an embodiment, macrophage cells may be detected by detection at the macrophage cells surface of the presence of at least one protein selected from the group consisting of the APOE protein and the CSF1R protein, or gene products thereof. APOE and CSF1R can be detected in clusters 2, 8 and 9.
In an embodiment, macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of Cl QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL 18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, ADAP2, APOCI, GRN, CD84, HLA-DMA, MAFB, PLTP, RNF130, PSAP, CYFIP1, ACP2, BLVRB, ABCA1, CTSB, MS4A7, SDC3, ACP5, RAB20, FCGRT, TSPAN4, C3AR1, CCL3L1, Clorf54, TTYH3, SMPDL3A, CD74, CTSC, ASAHI, MPP1, BMP2K, CD163, TPP1, IL4I1, CTSD, TFEC, HLA-DQA1, NR1H3, CD86, DNASE2, RBM47, CYBB, FGL2, CTSH, LAIR1, CMKLR1, HLA-DRA, HEXA, CXCL16, IL18BP, AP1B1, FCHO2, RARRES1, AIF1, AKR1A1, ABHD12, HM0X1, CAPG, HLA-DPA1, DAPK1, FTL, RGL1, LY96, CTSA, HLA-DOA, NAGK, ATOX1, PRDX1, PPT1, ADA2, HLA-DPB1, TIMP2, MMP9, KCTD12, SCPEP1, PLAU, CCL18, LINC00996, IGF1, FCER1G, HLA-DRB1, AKR1B1, SGK1, TNFSF13B, LY86, RAB42, PTAFR, GLUL, ALDH1A1, CST3, CSF2RA, CCL4L2, DMXL2, MRC1, LAMP1, TCN2, CPM, MERTK, MGST2, CUL9, EBB, PLXNC1, SYNGR2, GAL3ST4, PDE6G, CLEC7A, SERPINF1, TGFBI, SPI1, TBXAS1, RAB32, STAB1, NAIP, GNPDA1, GRINA, ATP6AP1, CFD, A2M, CEBPA, SAT1, CTSS, TYROBP, SLC7A8, CD63, BLVRA, LAMP2, GNS, SIRPA, CLEC4E, HLA-DQB1, ICAM1, MAF, SEMA4A, SIGLEC10, NINJ1, LINC01857, RENBP, MCOLN1, CD81, IFNGR2, NRP2, AXL, ATP6V1B2, SLC38A6, MSR1, LGALS3, IDH1, UNC93B1, SIGLEC7, PILRA, MMP14, SLC7A7, LACC1, GLA, SLC29A3, FCGR2A, AO AH, DRAM2, GPR137B, SPP1, NCOA4, QPRT, TNFAIP2, TLR4, SPRED1, MARCKS, CHCHD6, LYZ, SDCBP, TFRC, GPX4, CYB561A3, ITM2B, KLHDC8B, BRI3, HSD17B14, NAAA, FRMD4B, EPB41L3, ATP1B1, MITF, ETV5, ANKH, CYP27A1, SIGLEC1, SCARB2, M6PR, ABCC5, HEXB, NAGA, CLIC2, TNS3, LGALS9, DNASE1L3, MARCH1, PHACTR1, GAA, FMNL2, CSTB, ATP6AP2, FUOM, GNB4, CEBPD, LHFPL2, PDK4, SDSL, ATP6V1A, MMP12, VAMP8, CREBL2, SUCNR1, DPP7, SCARB1, RGS1, RRAGD, ATP6V0B, TM6SF1, TMEM138, CLEC4A, MGLL, LST1, PLBD1, ITPR2, CETP, SQSTM1, DNPH1, PLBD2, PCBD1, PRCP, LRRC25, GUSB, FTH1, HLA-DRB5, CD59, HCK, OAZ2, FAM213A, NCEH1, GSAP, MKNK1, SPINT2, SMS, CCR1, DST, PLA2G15, RNF13, SLC48A1, CLEC10A, PMP22, GLMP, SDS, RNASET2, MYO5A, AIG1, PLEK, V0PP1, ATP6V0A1, EPHX1, ADAM9, TYMP, TOR3A, CD300LF, PLEKHB2, SCD, CHPT1, NCF4, EPB41L2, CD300A, CRYL1, IRF8, ATP6V1F, PRNP, GSN, CYBA, CR1, PLIN2, RPN2, CXCL12, PLXDC2, VSIG4, VCAM1, UCP2, LAP3, WWP1, FUCA2, FRMD4A, NEU1, MGAT4A, SNX5, VEGFB, IL13RA1, HAVCR2, FNIP2, MGAT1, CD83, TREM2, ATP6V1C1, ACER3, AHR, RGS10, RAP2B, CD302, ZFAND5, ANTXR1, NFE2L2, SERPINA1, UGCG, SHTN1, TRIM14, DRAM1, RAB10, MYO9B, SAMHD1, PLAUR, TALDO1, GAS7, NR4A3, CISD2, CHCHD10, RAC1, NCKAP1L, LRP1, GSTP1, ARHGAP18, ATP6V0E1, SERPINB6, SMIM30, ITGB2, SNX2, THEMIS2, CSTA, S0D2, LGALS2, SLC31A2, SLAMF7, ANXA5, ATF5, SCAMP2, P2RY13, RAB31, CANX, SASH1, ATP6V0D1, QKI, RCAN1, TMEM70, AP2A2, LAPTM5, OTULINL, RHOQ, CCDC88A, FERMT3, MLEC, ATF3, PDE4DIP, PEPD, IER3, GNPTAB, SDHD, IFNGR1, PDXK, IFI30, LITAF, CLTA, CLTC, HSD17B4, CALHM6, NANS, NUPR1, BCAP31, UBE2D1, G3BP1, KLHL6, ZFYVE16, CAPZB, COMT, FCGR1A, SPATS2L, RGS2, HERPUD1, NR4A2, S100A11, CAT, LGALS1, COLEC12, SLC16A3, CASP1, TMBIM6, RNASE1, SLC43A2, CNDP2, AP2S1, SKAP2, RHOG, SELENOS, STAT1, FCGR3A, PITHD1, Clorfl62, GALNT1, MCUR1, TIMM8B, LMNA, RAB5C, GPR183, PRDX3, CHMP1B, CCL4, KLF4, H2AFJ, MDH1, PABPC4, EFHD2, TMSB4X, MAT2A, ZEB2, CXCL2, LGALS3BP, GADD45B, IQGAP2, LAMTOR2, ATP1B3, DBI, LRPAP1, APLP2, LIMSI, MAP3K8, TXN, SAMSN1, BEX4, SSR3, RTN4, MYDGF, H2AFY, FABP5, CD53, ANXA2, ZNF331, RNH1, CD36, FYB1, ARL6IP1, HES1, SNX6, YWHAH, AC020656.1, NFKBIA, CALR, TNFRSF4, CXCL8, C15orf48, AKAP9, ID2, ZFP36L1, APOE, APOCI, C1QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81, TUBB2B, LILRB4, TUBA1A, ODC1, GPX4, PLD3, ACP5, PLIN2, STMN2, GNAS, LAMP1, C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, STM, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HMOX1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9, SNX10, FPR3, CXCL8, CD109, PLA2G7, CCR1, LGALS3, ERO1A, APLP2, SIRPA, BLVRB, HEXB, TYROBP, FCGR3A, COLEC12, CNDP2, P4HA1, BRI3, PKM, PSAP, ANPEP, NPC2, TNS3, IL18BP, APOE, LAMP1, TPP1, TIMP2, NPL, ATP6V1B2, VAT1, TTYH3, SOAT1, C5AR1, RNASE1, OLR1, GNS, SLC43A3, NCEH1, CTSH, FCGR2A, GRN, FCGR2B, GRINA, FCER1G, SLC2A1, FNDC3B, CTSZ, TMEM51, EGLN3, IL1RN, CTSA, LGALS1, ENO1, CXCL3, CD163, RAB7B, BNIP3, CCDC88A, DAB2, ATP6V1F, PIK3AP1, RAB20, NCF2, S100A11, NR1H3, PLD3, PTAFR, SPI1, FNIP2, DMXL2, OTOA, ASAHI, VIM, NDRG1, ATP6AP1, CLIP4, SCARB2, BNIP3L, CCL3, SLC15A3, GSTO1, VCAN, PLXDC2, CD36, SGK1, ACP2, SLC7A7, ATP6V1A, PLPP3, RAB42, PLTP, ITGAX, NPC1, ANXA2, SQOR, ITGAM, OSCAR, BCKDK, LGMN, EIF4EBP1, ATF5, H2AFY, RRAGD, VEGFA, SOD2, ARL8B, LACTB, TNS1, HAVCR2, BCAP31, LAPTM5, LRP1, CCL18, ADAM9, BCL2A1, SDC4, DRAM1, SERPINA1, ATP13A3, LYZ, POR, LILRB3, CD300A, SDCBP, S100A10, DUSP3, CD86, RBM47, MCRIP2, KIAA0930, MFSD1, CD14, RAB31, MRC1, TCIRG1, GRB2, GPI, SDSL, TFRC, ENO2, P4HB, FKBP15, AGAP3, ADAM8, MGLL, ABHD2, RAB1A, C1QC, RALA, TUBA1C, NINJ1, LIMSI, MFSD12, PGK1, CD63, DHRS3, TPI1, CD84, IRAKI, RAB10, SLC25A19, HEXA, CXCL2, HLA-DRA, RBPJ, LAIR1, SULF2, ATOX1, SLC48A1, IFNAR1, ANXA5, GAPDH, CYFIP1, CTSS, AIF1, GK, GAA, PDE4DIP, ARHGAP18, MGST1, LAMP2, C2, SQSTM1, C3AR1, FMNL2, MAFB, PRDX1, ABHD12, MS4A4A, M6PR, CCL2, SERF2, CPM, MS4A7, EMILIN2, CSF1R, MMP12, CD82, HSD17B4, PLEKHB2, CEBPB, IFNGR2, FAM162A, RETN, SAT1, TYMP, MMP9, CANX, SHTN1, C1QA, QSOX1, RNF13, UPP1, PPT1, SLAMF8, KCTD12, MXI1, ADAP2, PGD, ALCAM, SLCO2B1, ITGB2, TPD52L2, EAF1, RABB, HNMT, CLEC4E, BCL2L1, PAPSS1, ZEB2, ELL2, ADA2, ATP6AP2, CYSTM1, CD74, TFEC, SDC2, RXRA, FCGR1A, MMP14, IDH1, PGAM1, GNB4, ACSL1, HM13, LGALS9, ATP6V1C1, CYBB, GCHFR, ALOX5, VAMP8, ICAM1, Cl QB, COLGALT1, ANXA4, VEGFB, CLEC7A, IGF2R, PILRA, METRNL, BMP2K, ABCG1, UNC93B1, HLA-DMA, KCNAB2, GPX4, TSPAN4, LDHA, RNASET2, SPG21, HLA-DRB1, SYK, MIF, TGFBI, PRNP, RASSF4, RASGEF1B, TMEM176A, LSP1, FCGRT, MARCH1, SH3BGRL3, RNASE6, ALDOA, LYN, LRPAP1, LY96, SCPEP1, GLIPR2, YBX1, GNAQ, HBEGF, CD164, IGSF6, PMP22, RAP2B, FERMT3, GNPTAB, TXN, PEA15, VKORC1, MGST3, ATP6V0B, CITED2, HLA-DQB1, CALM3, Clorfl62, TMEM176B, CHST11, ANKRD28, MYO9B, PFKL, DNASE2, FDX1, TUBGCP2, TMBIM6, RGCC, ATP6V1D, ARRDC3, MYDGF, SMS, ZFYVE16, LGALS3BP, OAZ1, RTN4, UGP2, ATP6V0D1, RNF181, CPEB4, NOPIO, NUCB1, PABPC4, RHEB, PLEKHO1, ZYX, RNH1, CLTC, ZFAND5, TPM4, PHC2, RAB7A, ATF3, DPP7, MAF, DBI, ME2, CD44, FOSL2, CD4, IFI6, LITAF, TNFSF13B, NEAT1, SSR3, AP2S1, TSPO, SRGN, VDAC1, SLC2A3, TALDO1, RDX, AHR, PTTG1IP, STX4, USF2, ELOC, SH3BP5, ACADVL, CHCHD10, FLNA, IER3, LMNA, S100A6, GNG5, CALR, HSPA5, LAP3, STAT1, ALDH2, OSBPL8, ANXA1, FN1, HSP90B1, HSPA1A, ZFP36L1, MT1X, RBP4, GPD1, PARAL1, MLPH, FFAR4, GLDN, AC026369.3, SLC19A3, MIR3945HG, MME, SPOCD1, STAC, C8B, FABP4, DEFBI, MCEMP1, PHLDA3, AL035446.1, PPARG, LPL, ILIA, FAM3B, AGRP, LSAMP, BHLHE41, CXCL5, PCOLCE2, GAPLINC, INHBA, ACOT2, CCL23, HCAR2, FAM89A, RETN, MACC1, APOL4, ZDHHC19, MARCO, ITGB8, TEX14, AMIGO2, LINC02345, CES1, ADAMTSL4, PTGER3, CLDN7, CLDN23, VSIG4, OLR1, ADTRP, ARHGEF28, OSCAR, TREM1, AQP3, GALNT12, TNNI2, NMB, AC025048.4, RMDN3, PNPLA6, HSD3B7, MRC1, FBP1, CXCL3, MSR1, GPA33, ALOX5, RYR1, PTCRA, MYB, AL390036.1, FCGR1A, AVPI1, APIP, S100A13, ALAS1, GCHFR, SVIL, TMEM53, CORO2A, PLA2G16, TGM2, ACO1, PPIC, SMIM25, CYP27A1, FOLR3, OASL, ARRDC4, SLC11A1, ABCG1, TREM2, ITIH5, UBASH3B, B3GNT7, ABHD5, COLEC12, MOB3B, PTPMT1, EDEM2, DNASE2B, CCL18, TCF7L2, SCCPDH, AGPAT2, PHYH, ROGDI, VMO1, PLA2G15, APOC2, SLC27A3, CXCL16, ALDH2, NCEH1, ALDH3A2, TRPV2, C20orf27, RHBDD2, LTA4H, DTX4, B3GNT5, SCD, COROIC, QSOX1, HNMT, LGALS3BP, ALOX5AP, OPN3, CDCP1, ABCG2, SNX10, FLVCR2, NCLN, FDX1, MS4A4A, FN1, MGST1, AKR1C3, SERPINA1, GLIPR2, DECR1, MS4A7, OSBPL11, GAA, THBD, ANXA4, ALDH1A1, GCA, TMEM251, IFIT3, PLBD1, COA6, NCF2, C1QC, MIIP, SLCO2B1, GLRX2, ACP5, DDX60L, CD9, ATP IB 1, RETREG1, GLRX, COPRS, PDLIM1, SGMS2, SLC49A3, SMCO4, HDDC2, STAC3, POR, ADGRE1, DPH3, COMT, ENPP4, ARHGAP18, FIG4, TFRC, SNX2, SLC31A2, TP53I3, FUOM, C1QB, TMEM38B, HLA- DRB5, TTC39B, PILRA, SPNS1, SERPING1, CPE, NUPR1, Clorfl62, IL1RN, SORT1, TFPT, CARS2, HCAR3, SPI1, MX1, RGCC, CD300C, UPP1, FCGR3A, MCOLN1, AXL, SIGLEC1, LRP1, IFI6, DOK2, CITED2, SEPTI 1, RASAL2, APOCI, RABB, ALDOA, VAT1, C1QA, PBDC1, LAIR1, FCGR1B, HBEGF, SLC7A7, SCPEP1, USP30-AS1, GK, EGR2, NAA20, FAR2, SYS1, CD163, STXBP2, CD151, BCL2A1, MGST3, CD68, ATL1, AP5B1, FHL1, DTNA, ETHE1, GSTO1, LRPAP1, CAT, ATP6V0D1, FABP5, MYOF, CA2, CAPG, LGALS3, BST1, PLIN2, TRIP6, TSPO, CEBPB, CYB5A, REEP3, TUBB6, SLC7A8, BLOC1S2, PYCARD, MDH1, HPGDS, MARCH2, SPINT1, G6PD, CD300LF, ANXA2, PROCR, CNH44, KMO, NCF4, CLEC12A, LAMTOR3, IFIT1, HPGD, TMED5, S100A11, ANXA5, HEXB, LAMTOR1, ARHGAP10, TNFSF12, GPCPD1, SIDT2, VASP, IFI30, SFT2D1, PSMA2, GLUL, PLXDC2, RNH1, S100A6, FCER1G, DAB2, ZNF706, FDX2, TXN, SLC25A19, TSPAN3, NIT2, FPR2, S100A10, ARHGEF10L, REEP5, TOMM40, VPS29, RENBP, LIMA1, MPC2, ZDHHC3, CHP1, SLC3A2, RHOB, SQOR, LSM6, CSTA, BACE1, SH2B2, CYB5R3, HLA-DMA, OAS1, TIGAR, CASP1, DNASE2, TYROBP, TUBA1C, SLC31A1, GNG5, TRIQK, RHEB, SIRPA, OAZ1, CTSL, ATP5MC3, ACADVL, ATP6V0B, CISH, SDCBP, PDXK, CHCHD10, TXNDC17, SLFN11, BTK, MLX, MYL6, GGA2, EMILIN2, VAMP8, PPT1, ATP6V1F, MYDGF, RAB5IF, C7orf50, MRPS35, MRPS15, VEGFB, VAMP3, SPN, CSTB, BAX, MSRA, DESI1, LY6E, RARA, GRN, ATP6V1D, LST1, NOPIO, PPFIA1, BSG, YWHAH, NAGLU, S1PR4, PLIN3, SIOOP, CYBA, CTSC, GSN, LGALS9, FTH1, PGD, ANXA11, AKR1A1, LAP3, CCT5, LACTB2, IGFBP2, OSBPL1A, SLC15A3, PLAUR, TST, HCK, ARPC1B, CARD16, BEX4, RGS19, MMP19, NUCB1, ADAM17, ACOT13, BRI3, PEBP1, SDHD, FCGRT, TFEC, FCGR2A, AP2S1, COMMD9, GALE, ARL6IP1, SSB, 0STF1, VIM, PAPSS1, GPX4, GON7, CTSH, GPRIN3, SNX3, HLA-DQB1, UBB, FUCA2, IRF8, HK3, NANS, FTL, C5AR1, THEMIS2, LY86, HADH, FKBP15, NDUFB5, ANXA1, ARPC3, UGP2, PPDPF, BLVRA, VDAC1, CD81, IFIT2, TSPAN15, C14orfl l9, MRPL14, CCDC115, CTSD, ACER3, CD276, MNDA, PRDX1, MRPL40, STX12, ATP6AP1, ACOT7, TMBIM1, SLC25A24, POLD4, CD63, RAB11FIP1, IGSF6, MR1, SULT1A1, CDC42EP3, RNPEP, CENPW, JAML, ACVRL1, ECHI, CMC1, HLA-DRB1, HTATIP2, TMED9, MPC1, RNF13, UBE2L6, NPTN, LMNA, HAGH, EIF4EBP1, SMIM14, BCAP31, PTPN6, TCIRG1, HSD17B11, THBS1, SCP2, MINK1, SERF2, LEPROT, TBC1D2, MYD88, COQ2, HSD17B14, NDUFV2, GABARAP, LACTB, WASHC3, CCDC88A, CD58, PEPD, NDUFB3, CTSZ, CYBB, FMNL2, GTF2H5, DDAH2, FBXO6, TMEM91, PDCD6IP, CSF1, GUSB, AK6, SMIM15, GNPTG, CHMP5, LAT2, LYZ, CID, BTF3L4, TAF10, APLP2, SUSD1, S100A4, UBE2A, SLC39A3, YBX1, TM6SF1, TKT, MOSPD2, DNAJA1, ANPEP, DBI, HLA-DRA, ERP44, GRB2, ATP2C1, NDUFA7, DCUN1D5, HLA-DPA1, GRINA, TALDO1, CAPZA2, MTHFS, C9orfl6, ATP6V1E1, CD40, MSRB1, IS0C2, J0SD2, QDPR, CXCL2, MTX2, MRPL13, TXNDC11, HEXA, C18orf32, TIMP2, SEC11 A, TMEM219, SCIMP, NEK6, AAED1, ASAHI, FKBP1 A, PLSCR1, ECHDC1, HSDL2, RTN4, CD33, DHRS4, MMP24OS, TPMT, VDAC2, AC020656.1, MPV17, MFSD10, MINOS1, CFL1, NENF, RND3, DCTN6, SELENOT, PRKCD, CST3, TSG101, FAM50A, LYAR, CREG1, PCBD1, PSMG1, AKIRIN2, RAB10, CMPK2, HLA-DPB1, TMSB4X, P2RX4, GBP1, AGPS, SSR3, CNDP2, LAMTOR2, CLEC7A, MGAT1, ASGR1, SHTN1, CCND3, TWF2, TMEM173, PDHA1, ARPC5, SDSL, SEPHS2, GLB1, ZBTB8OS, CLTA, EMG1, PSMA7, NDUFA4, HLA-DQA1, CTSA, RAB8A, HIGD1A, RAB5C, CD164, LY96, DUSP23, CLIC1, LSM10, SPG21, HADHB, ITPK1, POLR2K, RAB7A, AIF1, C2orf74, RNF7, EEA1, FAM162A, PSMG2, TCEAL4, ATP6V0E1, SAMM50, HAVCR2, PPCS, PSMD9, PSMA3, POMP, TSFM, TMEM230, EFHD2, DYNLL1, ATP6V1B2, TMEM167A, RER1, TMEM126A, MAN1A1, CMAS, CD52, ACTN1, CYCS, RAB9A, PSMB5, ARPC2, ACAA1, TMEM63A, NDUFAB1, P0P4, RAD23A, PNPLA2, ARL2, PHLDA2, C2, SELENOH, MRPL22, KAT8, ARL1, SRI, HEBP1, COLGALT1, TNF, OSTM1, SAMHD1, CTBS, RRAGD, PYURF, DMAC1, TMEM273, AP1S1, RAB32, HVCN1, ELP5, SHARPIN, ESD, NTAN1, COA4, LSM4, TUBA1B, PTAFR, NRBF2, BID, PSMA5, ARL4A, HPCAL1, UNC50, FGD2, RASGEF1B, DYNLT1, SLC16A3, PLAU, ACOT9, MSRB2, TMEM179B, TYMP, RAP1B, GNB2, STX11, PRDX6, SAP18, EMC7, PARP9, PRDX3, RNF181, ITSN1, IFI35, DYNLRB1, UTP18, LAMTOR5, KLF4, PDCL, ATP5F1C, CDC42BPB, EML4, MAP1LC3B, CD83, ATP1B3, HSBP1, CBWD1, SCARB2, H2AFJ, SLC39A10, CAMTAI, RAC1, SH3BGRL3, VAPA, GTF3C6, CYSLTR1, FEZ2, PSMB6, PGP, DNTTIP1, HMOX2, PFN1, IPT1, TMED10, TMBIM6, RNF149, TXNIP, ELOC, PEX16, MYL12A, ANAPC15, CTSS, ACAA2, M6PR, ISG15, ISCU, FAM173A, OTUD1, TCEAL9, RUNX1, ANKRD28, PSMD14, FERMT3, HPS5, CRIP1, MAPKAPK3, CXCL8, CHCHD1, ECHS1, DBNL, MRPS23, ENY2, PSMA4, TRIM14, Clorf43, PRR13, UBE2F, RHOA, CMC2, SMIM37, C19orf70, HERC5, AZI2, MRPL41, PCMT1, TPM4, NDUFA13, TAGLN2, PHB, MDH2, SERPINB1, SLA, SH3BGRL, CDC37, CEBPA, CKLF, ELOB, GLRX3, UQCRFS1, VPS26A, HSD17B12, HINT2, SNF8, JUN, DPP7, NDUFC1, COX7A2L, PSME2, EPSTI1, NDUFB6, LGALS1, TMBIM4, LITAF, MRPL18, TMEM70, APH1A, COPZ1, ATP5MF, PKM, SH3GLB1, TBC1D10C, ATP2B1- AS1, GTF2A2, ARF4, SERTAD1, FLNA, TRAPPC2L, CD74, SUMO3, APEX1, ATRAID, ARRB2, AGTRAP, COX17, CIB1, PSMD8, PPIA, BLOC1S1, PFDN2, GLTP, UQCR10, TXNDC12, NDUFS3, WDR1, BAG1, CAP1, FGR, SNRPG, COPS5, BEX3, NDUFAF3, LMAN2, ITGAX, ADRM1, NDUFB2, ACP2, CTNNB1, IL1B, DDIT3, IRF7, ITM2B, CALM1, NUTF2, HIPK2, TMEM14C, CD47, DOCK8, HMGN3, MTPN, LRRFIP1 and FAM89B or a gene product thereof.
In another embodiment, macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of C1QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, ADAP2, APOCI, GRN, CD84, HLA-DMA, MAFB, PLTP, RNF130, PSAP, CYFIP1, ACP2, BLVRB, ABCA1, CTSB, MS4A7, SDC3, ACP5, RAB20, FCGRT, TSPAN4, C3AR1, CCL3L1, Clorf54, TTYH3, SMPDL3A, CD74, CTSC, ASAHI, MPP1, BMP2K, CD163, TPP1, IL4I1, CTSD, TFEC, HLA-DQA1, NR1H3, CD86, DNASE2, RBM47, CYBB, FGL2, CTSH, LAIR1, CMKLR1, HLA-DRA, HEXA, CXCL16, IL18BP, AP1B1, FCHO2, RARRES1, AIF1, AKR1A1, ABHD12, HMOX1, CAPG, HLA-DPA1, DAPK1, FTL, RGL1, LY96, CTSA, HLA-DOA, NAGK, ATOX1, PRDX1, PPT1, ADA2, HLA-DPB1, TIMP2, MMP9, KCTD12, SCPEP1, PLAU, CCL18, LINC00996, IGF1, FCER1G, HLA-DRB1, AKR1B1, SGK1, TNFSF13B, LY86, RAB42, PTAFR, GLUL, ALDH1A1, CST3, CSF2RA, CCL4L2, DMXL2, MRC1, LAMP1, TCN2, CPM, MERTK, MGST2, CUL9, EBB, PLXNC1, SYNGR2, GAL3ST4, PDE6G, CLEC7A, SERPINF1, TGFBI, SPI1, TBXAS1, RAB32, STAB1, NAIP, GNPDA1, GRINA, ATP6AP1, CFD, A2M, CEBPA, SAT1, CTSS, TYROBP, SLC7A8, CD63, BLVRA, LAMP2, GNS, SIRPA, CLEC4E, HLA-DQB1, ICAM1, MAF, SEMA4A, SIGLEC10, NINJ1, LINC01857, RENBP, MCOLN1, CD81, IFNGR2, NRP2, AXL, ATP6V1B2, SLC38A6, MSR1, LGALS3, IDH1, UNC93B1, SIGLEC7, PILRA, MMP14, SLC7A7, LACC1, GLA, SLC29A3, FCGR2A, AO AH, DRAM2, GPR137B, SPP1, NCOA4, QPRT, TNFAIP2, TLR4, SPRED1, MARCKS, CHCHD6, LYZ, SDCBP, TFRC, GPX4, CYB561A3, ITM2B, KLHDC8B, BRI3, HSD17B14, NAAA, FRMD4B, EPB41L3, ATP1B1, MITF, ETV5, ANKH, CYP27A1, SIGLEC1, SCARB2, M6PR, ABCC5, HEXB, NAGA, CLIC2, TNS3, LGALS9, DNASE1L3, MARCH1, PHACTR1, GAA, FMNL2, CSTB, ATP6AP2, FUOM, GNB4, CEBPD, LHFPL2, PDK4, SDSL, ATP6V1A, MMP12, VAMP8, CREBL2, SUCNR1, DPP7, SCARB1, RGS1, RRAGD, ATP6V0B, TM6SF1, TMEM138, CLEC4A, MGLL, LST1, PLBD1, ITPR2, CETP, SQSTM1, DNPH1, PLBD2, PCBD1, PROP, LRRC25, GUSB, FTH1, HLA-DRB5, CD59, HCK, OAZ2, FAM213A, NCEH1, GSAP, MKNK1, SPINT2, SMS, CCR1, DST, PLA2G15, RNF13, SLC48A1, CLEC10A, PMP22, GLMP, SDS, RNASET2, MYO5A, AIG1, PLEK, VOPP1, ATP6V0A1, EPHX1, ADAM9, TYMP, TOR3A, CD300LF, PLEKHB2, SCD, CHPT1, NCF4, EPB41L2, CD300A, CRYL1, IRF8, ATP6V1F, PRNP, GSN, CYBA, CR1, PLIN2, RPN2, CXCL12, PLXDC2, VSIG4, VCAM1, UCP2, LAP3, WWP1, FUCA2, FRMD4A, NEU1, MGAT4A, SNX5, VEGFB, IL13RA1, HAVCR2, FNIP2, MGAT1, CD83, TREM2, ATP6V1C1, ACER3, AHR, RGS10, RAP2B, CD302, ZFAND5, ANTXR1, NFE2L2, SERPINA1, UGCG, SHTN1, TRIM14, DRAM1, RAB10, MYO9B, SAMHD1, PLAUR, TALDO1, GAS7, NR4A3, CISD2, CHCHD10, RAC1, NCKAP1L, LRP1, GSTP1, ARHGAP18, ATP6V0E1, SERPINB6, SMIM30, ITGB2, SNX2, THEMIS2, CSTA, S0D2, LGALS2, SLC31A2, SLAMF7, ANXA5, ATF5, SCAMP2, P2RY13, RAB31, CANX, SASH1, ATP6V0D1, QKI, RCAN1, TMEM70, AP2A2, LAPTM5, OTULINL, RHOQ, CCDC88A, FERMT3, MLEC, ATF3, PDE4DIP, PEPD, IER3, GNPTAB, SDHD, IFNGR1, PDXK, IFI30, LITAF, CLTA, CLTC, HSD17B4, CALHM6, NANS, NUPR1, BCAP31, UBE2D1, G3BP1, KLHL6, ZFYVE16, CAPZB, COMT, FCGR1A, SPATS2L, RGS2, HERPUD1, NR4A2, S100A11, CAT, LGALS1, COLEC12, SLC16A3, CASP1, TMBIM6, RNASE1, SLC43A2, CNDP2, AP2S1, SKAP2, RHOG, SELENOS, STAT1, FCGR3A, PITHD1, Clorfl62, GALNT1, MCUR1, TIMM8B, LMNA, RAB5C, GPR183, PRDX3, CHMP1B, CCL4, KLF4, H2AFJ, MDH1, PABPC4, EFHD2, TMSB4X, MAT2A, ZEB2, CXCL2, LGALS3BP, GADD45B, IQGAP2, LAMTOR2, ATP1B3, DBI, LRPAP1, APLP2, LIMSI, MAP3K8, TXN, SAMSN1, BEX4, SSR3, RTN4, MYDGF, H2AFY, FABP5, CD53, ANXA2, ZNF331, RNH1, CD36, FYB1, ARL6IP1, HES1, SNX6, YWHAH, AC020656.1, NFKBIA, CALR, TNFRSF4, CXCL8, C15orf48, AKAP9, ID2, ZFP36L1, APOE, APOCI, C1QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81, TUBB2B, LILRB4, TUBA1A, ODC1, GPX4, PLD3, ACP5, PLIN2, STMN2, GNAS, LAMP1, C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, STM, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HMOX1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9, SNX10, FPR3, CXCL8, CD109, PLA2G7, CCR1, LGALS3, ERO1A, APLP2, SIRPA, BLVRB, HEXB, TYROBP, FCGR3A, COLEC12, CNDP2, P4HA1, BRI3, PKM, PSAP, ANPEP, NPC2, TNS3, IL18BP, APOE, LAMP1, TPP1, TIMP2, NPL, ATP6V1B2, VAT1, TTYH3, SOAT1, C5AR1, RNASE1, OLR1, GNS, SLC43A3, NCEH1, CTSH, FCGR2A, GRN, FCGR2B, GRINA, FCER1G, SLC2A1, FNDC3B, CTSZ, TMEM51, EGLN3, IL1RN, CTSA, LGALS1, ENO1, CXCL3, CD163, RAB7B, BNIP3, CCDC88A, DAB2, ATP6V1F, PIK3AP1, RAB20, NCF2, S100A11, NR1H3, PLD3, PTAFR, SPH, FNIP2, DMXL2, OTOA, ASAHI, VIM, NDRG1, ATP6AP1, CLIP4, SCARB2, BNIP3L, CCL3, SLC15A3, GSTO1, VCAN, PLXDC2, CD36, SGK1, ACP2, SLC7A7, ATP6V1A, PLPP3, RAB42, PLTP, ITGAX, NPC1, ANXA2, SQOR, ITGAM, OSCAR, BCKDK, LGMN, EIF4EBP1, ATF5, H2AFY, RRAGD, VEGFA, SOD2, ARL8B, LACTB, TNS1, HAVCR2, BCAP31, LAPTM5, LRP1, CCL18, ADAM9, BCL2A1, SDC4, DRAM1, SERPINA1, ATP13A3, LYZ, POR, LILRB3, CD300A, SDCBP, S100A10, DUSP3, CD86, RBM47, MCRIP2, KIAA0930, MFSD1, CD14, RAB31, MRC1, TCIRG1, GRB2, GPI, SDSL, TFRC, ENO2, P4HB, FKBP15, AGAP3, ADAM8, MGLL, ABHD2, RAB1A, C1QC, RALA, TUBA1C, NINJ1, LIMSI, MFSD12, PGK1, CD63, DHRS3, TPI1, CD84, IRAKI, RAB10, SLC25A19, HEXA, CXCL2, HLA-DRA, RBPJ, LAIR1, SULF2, ATOX1, SLC48A1, IFNAR1, ANXA5, GAPDH, CYFIP1, CTSS, AIF1, GK, GAA, PDE4DIP, ARHGAP18, MGST1, LAMP2, C2, SQSTM1, C3AR1, FMNL2, MAFB, PRDX1, ABHD12, MS4A4A, M6PR, CCL2, SERF2, CPM, MS4A7, EMILIN2, CSF1R, MMP12, CD82, HSD17B4, PLEKHB2, CEBPB, IFNGR2, FAM162A, RETN, SAT1, TYMP, MMP9, CANX, SHTN1, C1QA, QSOX1, RNF13, UPP1, PPT1, SLAMF8, KCTD12, MXI1, ADAP2, PGD, ALCAM, SLCO2B1, ITGB2, TPD52L2, EAF1, RABB, HNMT, CLEC4E, BCL2L1, PAPSS1, ZEB2, ELL2, ADA2, ATP6AP2, CYSTM1, CD74, TFEC, SDC2, RXRA, FCGR1A, MMP14, IDH1, PGAM1, GNB4, ACSL1, HM13, LGALS9, ATP6V1C1, CYBB, GCHFR, ALOX5, VAMP8, ICAM1, Cl QB, COLGALT1, ANXA4, VEGFB, CLEC7A, IGF2R, PILRA, METRNL, BMP2K, ABCG1, UNC93B1, HLA-DMA, KCNAB2, GPX4, TSPAN4, LDHA, RNASET2, SPG21, HLA-DRB1, SYK, MIF, TGFBI, PRNP, RASSF4, RASGEF1B, TMEM176A, LSP1, FCGRT, MARCH1, SH3BGRL3, RNASE6, ALDOA, LYN, LRPAP1, LY96, SCPEP1, GLIPR2, YBX1, GNAQ, HBEGF, CD164, IGSF6, PMP22, RAP2B, FERMT3, GNPTAB, TXN, PEA15, VKORC1, MGST3, ATP6V0B, CITED2, HLA-DQB1, CALM3, Clorfl62, TMEM176B, CHST11, ANKRD28, MYO9B, PFKL, DNASE2, FDX1, TUBGCP2, TMBIM6, RGCC, ATP6V1D, ARRDC3, MYDGF, SMS, ZFYVE16, LGALS3BP, OAZ1, RTN4, UGP2, ATP6V0D1, RNF181, CPEB4, NOPIO, NUCB1, PABPC4, RHEB, PLEKHO1, ZYX, RNH1, CLTC, ZFAND5, TPM4, PHC2, RAB7A, ATF3, DPP7, MAF, DBI, ME2, CD44, FOSL2, CD4, IFI6, LITAF, TNFSF13B, NEAT1, SSR3, AP2S1, TSPO, SRGN, VDAC1, SLC2A3, TALDO1, RDX, AHR, PTTG1IP, STX4, USF2, ELOC, SH3BP5, ACADVL, CHCHD10, FLNA, IER3, LMNA, S100A6, GNG5, CALR, HSPA5, LAP3, STAT1, ALDH2, OSBPL8, ANXA1, FN1, HSP90B1, HSPA1A, ZFP36L1, MT1X or a gene product thereof.
In another embodiment, macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of C1QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, ADAP2, APOCI, GRN, CD84, HLA-DMA, MAFB, PLTP, RNF130, PSAP, CYFIP1, ACP2, BLVRB, ABCA1, CTSB, MS4A7, SDC3, ACP5, RAB20, FCGRT, TSPAN4, C3AR1, CCL3L1, Clorf54, TTYH3, SMPDL3A, CD74, CTSC, ASAHI, MPP1, BMP2K, CD163, TPP1, IL4I1, CTSD, TFEC, HLA-DQA1, NR1H3, CD86, DNASE2, RBM47, CYBB, FGL2, CTSH, LAIR1, CMKLR1, HLA-DRA, HEXA, CXCL16, IL18BP, AP1B1, FCHO2, RARRES1, AIF1, AKR1A1, ABHD12, HMOX1, CAPG, HLA-DPA1, DAPK1, FTL, RGL1, LY96, CTSA, HLA-DOA, NAGK, ATOX1, PRDX1, PPT1, ADA2, HLA-DPB1, TIMP2, MMP9, KCTD12, SCPEP1, PLAU, CCL18, LINC00996, IGF1, FCER1G, HLA-DRB1, AKR1B1, SGK1, TNFSF13B, LY86, RAB42, PTAFR, GLUL, ALDH1A1, CST3, CSF2RA, CCL4L2, DMXL2, MRC1, LAMP1, TCN2, CPM, MERTK, MGST2, CUL9, EBB, PLXNC1, SYNGR2, GAL3ST4, PDE6G, CLEC7A, SERPINF1, TGFBI, SPI1, TBXAS1, RAB32, STAB1, NAIP, GNPDA1, GRINA, ATP6AP1, CFD, A2M, CEBPA, SAT1, CTSS, TYROBP, SLC7A8, CD63, BLVRA, LAMP2, GNS, SIRPA, CLEC4E, HLA-DQB1, ICAM1, MAF, SEMA4A, SIGLEC10, NINJ1, LINC01857, RENBP, MCOLN1, CD81, IFNGR2, NRP2, AXL, ATP6V1B2, SLC38A6, MSR1, LGALS3, IDH1, UNC93B1, SIGLEC7, PILRA, MMP14, SLC7A7, LACC1, GLA, SLC29A3, FCGR2A, AO AH, DRAM2, GPR137B, SPP1, NCOA4, QPRT, TNFAIP2, TLR4, SPRED1, MARCKS, CHCHD6, LYZ, SDCBP, TFRC, GPX4, CYB561A3, ITM2B, KLHDC8B, BRI3, HSD17B14, NAAA, FRMD4B, EPB41L3, ATP1B1, MITF, ETV5, ANKH, CYP27A1, SIGLEC1, SCARB2, M6PR, ABCC5, HEXB, NAGA, CLIC2, TNS3, LGALS9, DNASE1L3, MARCH1, PHACTR1, GAA, FMNL2, CSTB, ATP6AP2, FUOM, GNB4, CEBPD, LHFPL2, PDK4, SDSL, ATP6V1A, MMP12, VAMP8, CREBL2, SUCNR1, DPP7, SCARB1, RGS1, RRAGD, ATP6V0B, TM6SF1, TMEM138, CLEC4A, MGLL, LST1, PLBD1, ITPR2, CETP, SQSTM1, DNPH1, PLBD2, PCBD1, PROP, LRRC25, GUSB, FTH1, HLA-DRB5, CD59, HCK, OAZ2, FAM213A, NCEH1, GSAP, MKNK1, SPINT2, SMS, CCR1, DST, PLA2G15, RNF13, SLC48A1, CLEC10A, PMP22, GLMP, SDS, RNASET2, MYO5A, AIG1, PLEK, VOPP1, ATP6V0A1, EPHX1, ADAM9, TYMP, TOR3A, CD300LF, PLEKHB2, SCD, CHPT1, NCF4, EPB41L2, CD300A, CRYL1, IRF8, ATP6V1F, PRNP, GSN, CYBA, CR1, PLIN2, RPN2, CXCL12, PLXDC2, VSIG4, VCAM1, UCP2, LAP3, WWP1, FUCA2, FRMD4A, NEU1, MGAT4A, SNX5, VEGFB, IL13RA1, HAVCR2, FNIP2, MGAT1, CD83, TREM2, ATP6V1C1, ACER3, AHR, RGS10, RAP2B, CD302, ZFAND5, ANTXR1, NFE2L2, SERPINA1, UGCG, SHTN1, TRIM14, DRAM1, RAB10, MYO9B, SAMHD1, PLAUR, TALD01, GAS7, NR4A3, CISD2, CHCHD10, RAC1, NCKAP1L, LRP1, GSTP1, ARHGAP18, ATP6V0E1, SERPINB6, SMIM30, ITGB2, SNX2, THEMIS2, CSTA, S0D2, LGALS2, SLC31A2, SLAMF7, ANXA5, ATF5, SCAMP2, P2RY13, RAB31, CANX, SASH1, ATP6V0D1, QKI, RCAN1, TMEM70, AP2A2, LAPTM5, OTULINL, RHOQ, CCDC88A, FERMT3, MLEC, ATF3, PDE4DIP, PEPD, IER3, GNPTAB, SDHD, IFNGR1, PDXK, IFI30, LITAF, CLTA, CLTC, HSD17B4, CALHM6, NANS, NUPR1, BCAP31, UBE2D1, G3BP1, KLHL6, ZFYVE16, CAPZB, COMT, FCGR1A, SPATS2L, RGS2, HERPUD1, NR4A2, S100A11, CAT, LGALS1, COLEC12, SLC16A3, CASP1, TMBIM6, RNASE1, SLC43A2, CNDP2, AP2S1, SKAP2, RHOG, SELENOS, STAT1, FCGR3A, PITHD1, Clorfl62, GALNT1, MCUR1, TIMM8B, LMNA, RAB5C, GPR183, PRDX3, CHMP1B, CCL4, KLF4, H2AFJ, MDH1, PABPC4, EFHD2, TMSB4X, MAT2A, ZEB2, CXCL2, LGALS3BP, GADD45B, IQGAP2, LAMTOR2, ATP1B3, DBI, LRPAP1, APLP2, LIMSI, MAP3K8, TXN, SAMSN1, BEX4, SSR3, RTN4, MYDGF, H2AFY, FABP5, CD53, ANXA2, ZNF331, RNH1, CD36, FYB1, ARL6IP1, HES1, SNX6, YWHAH, AC020656.1, NFKBIA, CALR, TNFRSF4, CXCL8, C15orf48, AKAP9, ID2, ZFP36L1, or a gene product thereof.
In another embodiment, macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of APOE, APOCI, Cl QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81, TUBB2B, LILRB4, TUBA1 A, ODC1, GPX4, PLD3, ACP5, PLIN2, STMN2, GNAS, LAMP1, or a gene product thereof.
In another embodiment, macrophages may be detected by detection in the cells of at least one gene selected from the group consisting of C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, ST14, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HM0X1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9, SNX10, FPR3, CXCL8, CD 109, PLA2G7, CCR1, LGALS3, ERO1A, APLP2, SIRPA, BLVRB, HEXB, TYROBP, FCGR3A, COLEC12, CNDP2, P4HA1, BRI3, PKM, PSAP, ANPEP, NPC2, TNS3, IL18BP, APOE, LAMP1, TPP1, TIMP2, NPL, ATP6V1B2, VAT1, TTYH3, SOAT1, C5AR1, RNASE1, OLR1, GNS, SLC43A3, NCEH1, CTSH, FCGR2A, GRN, FCGR2B, GRINA, FCER1G, SLC2A1, FNDC3B, CTSZ, TMEM51, EGLN3, IL1RN, CTSA, LGALS1, ENO1, CXCL3, CD163, RAB7B, BNIP3, CCDC88A, DAB2, ATP6V1F, PIK3AP1, RAB20, NCF2, S100A11, NR1H3, PLD3, PTAFR, SPI1, FNIP2, DMXL2, OTOA, ASAHI, VIM, NDRG1, ATP6AP1, CLIP4, SCARB2, BNIP3L, CCL3, SLC15A3, GSTO1, VC AN, PLXDC2, CD36, SGK1, ACP2, SLC7A7, ATP6V1A, PLPP3, RAB42, PLTP, ITGAX, NPC1, ANXA2, SQOR, ITGAM, OSCAR, BCKDK, LGMN, EIF4EBP1, ATF5, H2AFY, RRAGD, VEGFA, SOD2, ARL8B, LACTB, TNS1, HAVCR2, BCAP31, LAPTM5, LRP1, CCL18, ADAM9, BCL2A1, SDC4, DRAM1, SERPINA1, ATP13A3, LYZ, POR, LILRB3, CD300A, SDCBP, S100A10, DUSP3, CD86, RBM47, MCRIP2, KIAA0930, MFSD1, CD14, RAB31, MRC1, TCIRG1, GRB2, GPI, SDSL, TFRC, ENO2, P4HB, FKBP15, AGAP3, ADAM8, MGLL, ABHD2, RAB1A, C1QC, RALA, TUBA1C, NINJ1, LIMSI, MFSD12, PGK1, CD63, DHRS3, TPI1, CD84, IRAKI, RAB10, SLC25A19, HEXA, CXCL2, HLA-DRA, RBPJ, LAIR1, SULF2, ATOX1, SLC48A1, IFNAR1, ANXA5, GAPDH, CYFIP1, CTSS, AIF1, GK, GAA, PDE4DIP, ARHGAP18, MGST1, LAMP2, C2, SQSTM1, C3AR1, FMNL2, MAFB, PRDX1, ABHD12, MS4A4A, M6PR, CCL2, SERF2, CPM, MS4A7, EMILIN2, CSF1R, MMP12, CD82, HSD17B4, PLEKHB2, CEBPB, IFNGR2, FAM 162 A, RETN, SAT1, TYMP, MMP9, CANX, SHTN1, C1QA, QSOX1, RNF13, UPP1, PPT1, SLAMF8, KCTD12, MXI1, ADAP2, PGD, ALCAM, SLCO2B1, ITGB2, TPD52L2, EAF1, RABB, HNMT, CLEC4E, BCL2L1, PAPSS1, ZEB2, ELL2, ADA2, ATP6AP2, CYSTM1, CD74, TFEC, SDC2, RXRA, FCGR1A, MMP14, IDH1, PGAM1, GNB4, ACSL1, HM13, LGALS9, ATP6V1C1, CYBB, GCHFR, ALOX5, VAMP8, ICAM1, Cl QB, COLGALT1, ANXA4, VEGFB, CLEC7A, IGF2R, PILRA, METRNL, BMP2K, ABCG1, UNC93B1, HLA-DMA, KCNAB2, GPX4, TSPAN4, LDHA, RNASET2, SPG21, HLA-DRB1, SYK, MIF, TGFBI, PRNP, RASSF4, RASGEF1B, TMEM176A, LSP1, FCGRT, MARCH1, SH3BGRL3, RNASE6, ALDOA, LYN, LRPAP1, LY96, SCPEP1, GLIPR2, YBX1, GNAQ, HBEGF, CD 164, IGSF6, PMP22, RAP2B, FERMT3, GNPTAB, TXN, PEA15, VKORC1, MGST3, ATP6V0B, CITED2, HLA- DQB1, CALM3, Clorfl62, TMEM176B, CHST11, ANKRD28, MYO9B, PFKL, DNASE2, FDX1, TUBGCP2, TMBIM6, RGCC, ATP6V1D, ARRDC3, MYDGF, SMS, ZFYVE16, LGALS3BP, OAZ1, RTN4, UGP2, ATP6V0D1, RNF181, CPEB4, NOP 10, NUCB1, PABPC4, RHEB, PLEKHO1, ZYX, RNH1, CLTC, ZFAND5, TPM4, PHC2, RAB7A, ATF3, DPP7, MAF, DBI, ME2, CD44, FOSL2, CD4, IFI6, LITAF, TNFSF13B, NEAT1, SSR3, AP2S1, TSPO, SRGN, VDAC1, SLC2A3, TALDO1, RDX, AHR, PTTG1IP, STX4, USF2, ELOC, SH3BP5, ACADVL, CHCHD10, FLNA, IER3, LMNA, S100A6, GNG5, CALR, HSPA5, LAP3, STAT1, ALDH2, OSBPL8, ANXA1, FN1, HSP90B1, HSPA1A, ZFP36L1, MT IX or a gene product thereof.
Preferably, said genes are up-regulated or overexpressed in macrophages from a neuroblastoma sample, in particular in comparison to a reference level. Such reference level is preferably the expression of the same gene in macrophages from a normal or non-cancerous sample.
Preferably, macrophages may be detected by detection in the macrophages of at least two genes, preferably at least 10 genes, preferably at least 50 genes, preferably at least 100 genes, preferably at least 200 genes, preferably at least 300 genes, preferably at least 500 genes, among the list of the previous paragraph, or a gene product thereof and no more than 500, 400, 300, 200, 100 or 50 genes.
This list of overexpressed genes in neuroblastoma can also be used to define a new therapeutic strategy specific of these or one of these macrophages by using a molecule targeting, modulating or inhibiting one of these overexpressed genes or a combination thereof. This strategy is specific of macrophages present in the subject neuroblastoma and is further detailed below.
The in vitro method for classifying, stratifying or selecting a subject according to the invention may further comprise, after the detection step(s), a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group. Each specific group of subjects may correspond to a group of subjects which has a high probability of obtaining a positive response to a specific treatment, to predict the prognosis, for instance a poor or good outcome.
The patients stratification can be useful in clinical trials to conduct the results analysis or for defining subpopulation of patients of interest for a particular treatment.
Method for predicting a response to a subject to an immunotherapy treatment
The in vitro method for classifying a patient according to the invention may be used among others in a method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment or for selecting a subject as having a therapeutic benefit to be treated a particular treatment such as an immunotherapy treatment. In one particular aspect, the present invention relates on the identification of neuroblastoma that comprises immunosuppressive Myeloid-Derived Suppressor Cells (MDSC) and its use for determining the patient prognosis, its response to a treatment or the most appropriate therapeutic strategy. In addition, identifying the genes overexpressed in neuroblastoma MDSC is useful for defining new therapeutic strategy targeting one or several of the overexpressed genes or to select already known therapeutic molecules targeting one or several of the overexpressed genes. In one particular aspect, the present invention relates on the observation that the T cells of neuroblastoma overexpress at least one of the 5 well-described inhibitory receptors, being LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PD-L1 and its use for determining the patient prognosis, its response to a treatment or the most appropriate therapeutic strategy..
Thus, a further object of the invention is a method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment, comprising a step of implementing an in vitro method for classifying a patient according to the invention, a step of comparing the number and/or type of detected cells to reference numbers and/or types of detected cells, in order to assign the subject to a specific group, the membership of the subject to a specific group being predictive of the responsiveness of said subject to a specific treatment. In some embodiments, the cells detected in the classification step are Cytotoxic T cells as disclosed above, and the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PDL1 inhibitors.
In some embodiments, the cells detected in the classification step are MDSC as disclosed above, and the specific treatment comprises the administration of at least one antibody or small molecule targeting at least one protein encoded by the above-listed genes, such as an anti- CXCR2 or CXCR1 targeting small molecule or antibody, preferably an anti-CXCR2 targeting small molecule or antibody. It is within the skills in the art to determine such antibodies or small molecules.
In some embodiments, the cells detected in the classification step are NK cells as disclosed above, and the specific treatment comprises new therapeutic strategy targeting one or several of the overexpressed genes or to select already known therapeutic molecules targeting one or several of the overexpressed genes.
In some embodiments, the cells detected in the classification step are macrophages as disclosed above, and the specific treatment comprises new therapeutic strategy targeting one or several of the overexpressed genes or to select already known therapeutic molecules targeting one or several of the overexpressed genes. In a first aspect, the macrophages are those of cluster 2. In a second aspect, the macrophages are those of cluster 8. In a third aspect, the macrophages are those of cluster 9. In a fourth aspect, the macrophages are those of any combination of clusters 2, 8 and 9.
The above embodiments may of course be advantageously combined, in order to predict a response to a combination treatment.
Method for determining a suitable treatment for a subject
Another object of the present invention is a method for determining a suitable treatment for a subject, said method comprising a step of implementing an in vitro method for classifying a patient according to the invention, a step of comparing the number and/or type of detected cells to reference numbers and/or types of detected cells, in order to assign the subject to a specific group, and a step of determining a suitable treatment.
The method for determining a suitable treatment according to the invention may be implemented after or simultaneously with the method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment according to the invention.
Methods for the treatment of neuroblastoma
Another object of the present invention is a compound targeting at least one gene and/or protein disclosed above, for use in the treatment of neuroblastoma. In a particular aspect, the compound targets, modulates or inhibits one gene and/or protein that is overexpressed in neuroblastoma. The gene or protein can be selected in any of the Tables 4A to 4Q. Indeed, Tables 4A to 4Q provide a list of overexpressed genes in neuroblastoma, such genes being a target of interest for developing a treatment of neuroblastoma.
In a particular aspect, the overexpressed gene and/or protein is overexpressed in T cells, preferably cytotoxic T cells, and the gene or protein can be selected in Table 4A.
In a particular aspect, the compound targets TIGIT (T cell immunoreceptor with Ig and ITIM domains), LAG3 (lymphocyte-activation protein 3), CTLA4 (cytotoxic T lymphocyte antigen 4), HAVCR2/TIM3 (T-cell immunoglobulin mucin domain-3), or PD1/PDL1 (programmed cell death protein 1). The compound can be used in combination, for instance a combination of two compounds targeting two proteins selected in the group consisting of TIGIT, LAG3, CTLA4, TIM3 and PD1. Preferably, the compound targets TIGIT. TIGIT or T-cell immunoreceptor with Ig and ITIM domains is for example described under Uniprot accession number Q495A1 or Gene ID 201633.
In a particular, the compound can be an antibody, especially an antagonist antibody. Alternatively, the compound can be a chemical compound.
Numerous antibodies directed against TIGIT, LAG3, CTLA4, TIM3, and PD-1 have already been described in the art.
Antibodies directed against LAG3 and bifunctional or bispecific molecules targeting LAG-3 are also known such as BMS- 986016, IMP701, MGD012 or MGD013 (bispecific PD-1 and LAG-3 antibody). Anti -LAG-3 antibodies are also disclosed in W02008132601, EP2320940, WO19152574.
Antibodies directed against TIGIT are also known in the art, such as BMS-986207 or AB 154, BMS-986207 CPA.9.086, CHA.9.547.18, CPA.9.018, CPA.9.027, CPA.9.049, CPA.9.057, CPA.9.059, CPA.9.083, CPA.9.089, CPA.9.093, CPA.9.101, CPA.9.103, CHA.9.536.1, CHAN.536.3, CHA.9.536.4, CHA.9.536.5, CHA.9.536.6, CHA.9.536.7, CHA.9.536.8,
CHAN.560.1, CHAN.560.3, CHA.9.560.4, CHA.9.560.5, CHA.9.560.6, CHA.9.560.7,
CHAN.560.8, CHA.9.546.1, CHA.9.547.1, CHA.9.547.2, CHA.9.547.3, CHA.9.547.4,
CHAN.547.6, CHA.9.547.7, CHA.9.547.8, CHA.9.547.9, CHA.9.547.13, CHA.9.541.1,
CHAN.541.3, CHA.9.541.4, CHA.9.541.5, CHA.9.541.6, CHA.9.541.7, and CHA.9.541.8 as disclosed in WO19232484. Anti-TIGIT antibodies are also disclosed in WO16028656, W016106302, WO16191643, W017030823, W017037707, WO17053748, WO17152088, WO18033798, WO18102536, WO18102746, W018160704, W018200430, WO18204363, W019023504, WO19062832, WO19129221, WO19129261, WO19137548, WO19152574, WO19154415, WO19168382 and WO19215728.
Antibodies directed against CTLA-4 and bifunctional or bispecific molecules targeting CTLA- 4 are also known such as ipilimumab, tremelimumab, MK-1308, AGEN-1884, XmAb20717 (Xencor), MEDI5752 (AstraZeneca). Anti-CTLA-4 antibodies are also disclosed in WO18025178, WO19179388, WO19179391, WO19174603, WO19148444, WO19120232, WO19056281, WO19023482, W018209701, WO18165895, WO18160536, WO18156250, WO18106862, WO18106864, WO18068182, W018035710, WO18025178, WO17194265, WO17106372, W017084078, WO17087588, WO16196237, WO16130898, WO16015675, WO12120125, W009100140 and W007008463.
Antibodies directed against TIM3 and bifunctional or bispecific molecules targeting TIM3 are also known such as Sym023, TSR-022, MBG453, LY3321367, INCAGN02390, BGTB-A425, LY3321367, RG7769 (Roche). In some aspects, a TFM-3 antibody is as disclosed in International Patent Application Publication Nos. W02013006490, W02016/161270, WO 2018/085469, or WO 2018/129553, WO 2011/155607, U.S. 8,552,156, EP 2581113 and U.S 2014/044728.
Several anti-PD-1 are already clinically approved, and others are still in clinical developments. For instance, the anti-PDl antibody can be selected from the group consisting of Pembrolizumab (also known as Keytruda lambrolizumab, MK-3475), Nivolumab (Opdivo, MDX-1106, BMS-936558, ONO-4538), Pidilizumab (CT-011), Cemiplimab (Libtayo), Camrelizumab, AUNP12, AMP-224, lsBGB-A317 (Tisleizumab), PDR001 (spartalizumab), MK-3477, PF-06801591, JNJ-63723283, genolimzumab (CBT-501), LZM-009, BCD-100, SHR-1201, BAT-1306, AK-103 (HX-008), MEDI-0680 (also known as AMP-514) MEDI0608, JS001 (see Si- Yang Liu et al., J. Hematol. Oncol.10: 136 (2017)), BI-754091, TSR- 042 (also known as ANB011), GLS-010 (also known as WBP3055), AM-0001 (Armo), STI- 1110 (see WO 2014/194302), AGEN2034 (see WO 2017/040790), MGA012 (see WO 2017/19846), or IBI308 (see WO 2017/024465, WO 2017/025016, WO 2017/132825, and WO 2017/133540), monoclonal antibodies 5C4, 17D8, 2D3, 4H1, 4A11, 7D3, and 5F4, described in WO 2006/121168. Bifunctional or bispecific molecules targeting PD-1 are also known such as RG7769 (Roche), XmAb20717 (Xencor), MEDI5752 (AstraZeneca), FS118 (F-star), SL- 279252 (Takeda) and XmAb23104 (Xencor).
Optionally, the subject can be selected by the overexpression of TIGIT, LAG3, CTLA4, TIM3, and/or PD-1 on T cells of the neuroblastoma sample.
In another aspect, the overexpressed gene and/or protein is overexpressed in MDSC cells, and the gene or protein can be selected in Table 4 J.
In a particular aspect, the compound targets CXCR2 (i.e., C-X-C motif chemokine receptor 2 or CD 182). CXCR2 is for example described under the Uniprot accession number P25025 and GenelD n°3579. CXCR2 antagonists or inhibitors are well known in the art and available.
Exemplary CXCR2 inhibitors include, but are not limited to, AZD5059, reparixin, navarixin, danirixin and SX-682. Danirixin is disclosed, e.g., in Miller et al. Eur J Drug Metab Pharmacokinet (2014) 39: 173-181; and Miller et al., BMC Pharmacology and Toxicology (2015), 16: 18. Reparixin is disclosed, e.g., in Zarbock et al., British Journal of Pharmacology (2008), 1-8. Navarixin is disclosed, e.g., in Ning et al., Mol Cancer Ther. 2012; 11(6): 1353- 64. SX-682 is disclosed, e.g. in Liao et al., Cancer Cell, 35(4):559-572 (2019). CXCR2 inhibitors can also be an antibody directed against CXCR2 as disclosed in WO20028479. Accordingly, the present invention relates to a CXCR2 antagonist or inhibitor for use in the treatment of neuroblastoma, in particular in a subject having a neuroblastoma having MDSC, in particular high level of MDSC compared to control.
The present invention relates to a method for treating neuroblastoma in a subject in need thereof comprising a) providing a neuroblastoma sample from the subject, b) detecting or quantifying MDSC; and c) administering a therapeutic effective amount of a CXCR2 antagonist or inhibitor to the subject if the level of MDSC is present, in particular higher than in the control.
In an alternative, the CXCR2 antagonist or inhibitor is used for treating the subject if CXCR2 is overexpressed by MDSC.
In another particular aspect, the compound targets PTSG2/COX2. COX2 inhibitors are well known in the art and available. Alternatively, the compound can be ATRA (all-trans retinoid acid).
Another object of the present invention is a compound targeting TGF-beta, for use in the treatment of neuroblastoma. The TGF-beta inhibitor can be for instance selected from M7824, bintrafusp alfa, galunisertib, SAR439459, NIS793, PF-06952229, vactosertib, AVID200, ARGX-115, ABBV-151, trabedersen, VTX-002, ACE-1332, SRK-181 or a combination thereof.
The subject to be treated is a subject having a metastatic or pre-metastatic neuroblastoma or having a relapse. The subject to be treated can be a subject having a high risk neuroblastoma, especially one associated with MYCN gene. Indeed, as shown in Figure 8, the inventors have shown that the following clusters are amplified in MYCN status: MDSC (cluster 10), macrophage of cluster 16 (FABP4+ macrophage), NK cells and non-classical monocytes (cluster 13).
Optionally, the neuroblastoma can be refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma. Indeed, as shown in Figure 8, the inventors have shown that the following clusters are amplified in biopsies at relapse compared to diagnosis: MDSC (cluster 10), and macrophage of cluster 16 (FABP4+ macrophage).
The compounds for use in the treatment of neuroblastoma according to the invention are preferably in combination with another compound for use according to the present invention, and/or in combination with a classical neuroblastoma treatment. The standard-of-care treatment can include one or more of the following: surgery or excision of all or a portion of the tumor, radiation therapy, stem cell transplant, administering a chemotherapeutic agents, differentiation agent, and immunotherapy. For instance, classical neuroblastoma treatments can be alkylators (cyclophosphamide, temozolomide, and melphalan hydrochloride), platinum agents (carboplatin, cisplatin, and oxaliplatin), anthracyclines (doxorubicin hydrochloride), topoisomerase I inhibitors (irinotecan and topotecan), and vinca alkaloids (vincristine sulfate). Differentiation agents include isotretinoin (13-e/s- retinoic acid), and immunotherapeutic agents include monoclonal antibodies such GD2 monoclonal antibodies (dinutuximab).
More specifically, among classical neuroblastoma treatments that may be combined with one or more compounds for use according to the present invention may be cited Vincristine, Carboplatin, Etoposide Drug, Cyclophosphamide, Vindesine, Dacarbazine, Ifosfamide, Doxorubicin, Busulfan, Melphalan, Thiotepa, Radiotherapy, Dinutuximab Beta and Cisplatin. Alternatively, the compounds of the invention can be combined with a kinase inhibitor such as an Aurora kinase inhibitor (for instance, as disclosed in WO20112514) or an ALK inhibitor such as lorlatinib, crizotinib, ceritinib, alectinib and brigatinib, preferably Lorlatinib. and biomarkers
A last object of the invention is a signature and/or biomarker specific of neuroblastoma that is selected from the overexpressed genes of Table 4. Particularly, Table 4 comprises the lists of genes described below under Table 4 A to Table 4R.
In a particular aspect, the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4A (T cells). Alternatively, the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4J (MDSC). Alternatively, the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of any one of Tables 4B, Table 4H and Table 41 (macrophages). Alternatively, the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4M (non-classical monocytes). Alternatively, the signature and/or biomarker specific of neuroblastoma is selected from the overexpressed genes of Table 4E (non-classical monocytes).
A “gene signature” or “gene expression signature” is a single or a group of genes in a cell, with a uniquely characteristic pattern of gene expression. In particular, the gene signature corresponds to the deregulation of specific genes, in particular, overexpression of genes. The gene signature may comprise at least 10, 20, 30, 40 or 50 genes but no more than 1500, 1000, 900, 800, 700, 600, 500, 400, 300, 200 or 100 genes, preferably no more than 300, 200 or 100 genes.
The present invention further relates to the use of these gene signatures for detecting the a cell population as detailed above, especially MDSC, T cells, macrophages orNK cells, in particular for detecting the presence of immunosuppressive MDSC and potentially determining the prognosis of the neuroblastoma or selecting the most appropriate treatment and/or predicting the response to or the relevance of a treatment by an immunotherapy, a particular a checkpoint inhibitor.
The invention will also be described in further detail in the following examples, which are not intended to limit the scope of this invention, as defined by the attached claims.
EXAMPLES
Example 1.
Summary of Example 1
High-risk neuroblastoma is a pediatric cancer with still a dismal prognosis, despite multimodal and intensive therapies. Tumor microenvironment represents a key component of the tumor ecosystem the complexity of which has to be accurately understood to define selective targeting opportunities, including immune-base therapies.
The inventors combined various approaches including single-cell transcriptomics to dissect the tumor microenvironment of both a transgenic mouse neuroblastoma model and a cohort of 10 biopsies from neuroblastoma patients, either at diagnosis or at relapse. Features of related cells were validated by FACS and functional assays.
The inventors showed that the immune microenvironment of MYCN-driven mouse neuroblastoma is characterized by a low content of T cells, several phenotypes of macrophages and a population of cells expressing signatures of myeloid-derived suppressor cells (MDSCs) that are molecularly distinct from the various macrophage subsets. They documented two CAF subsets, one of which corresponding to CAF-S1, known to have immunosuppressive functions. Their data unraveled a complex content in myeloid cells in patient tumors and further document a striking correspondence of the microenvironment populations between both mouse and human tumors. The inventors showed that mouse intratumor T cells exhibit increased expression of inhibitory receptors at the protein level. Consistently, T cells from patients are characterized by features of exhaustion, expressing inhibitory receptors and showing low expression of effector cytokines. They further functionally demonstrated that MDSCs isolated from mouse neuroblastoma have immunosuppressive properties, impairing the proliferation of T lymphocytes. This study characterizes for the first time the whole cellular composition of the neuroblastoma microenvironment without any prior assumptions on surface markers, both in a relevant and immunocompetent mouse neuroblastoma model and in a cohort of patients, and documents multiple features of immunosuppression.
The inventors’ study demonstrated that neuroblastoma tumors have an immunocompromised microenvironment characterized by dysfunctional T-cells and accumulation of immunosuppressive cells. Their work provides a new and precious data resource to better understand the neuroblastoma ecosystem and suggested novel therapeutic strategies, targeting both tumor cells and components of the microenvironment. More particularly, this study suggests novel therapies reversing the immunosuppressive tumor microenvironment in neuroblastoma patients.
Results
Composition of TH-MYCN mouse tumors at the single-cell resolution
To obtain a complete overview of the cell populations composing MYCN-driven mouse neuroblastoma, three independent whole fresh tumors were analyzed by single-cell RNA-seq. Tumors were dissociated into single-cell suspensions, then cells were captured on the Chromium device (lOx Genomics) and sequenced on the Novaseq (Illumina) sequencer (Figure 7a). After integration with Seurat, the inventors obtained 5,650 cells, with an average of 1,883 cells per tumor (Figure 7b). Cluster analysis was performed using Seurat and cell populations were first annotated through the expression of canonical cell type gene markers. In total, eight cell types could be defined in addition to tumor cells represented by several clusters and defined by the expression of the Phox2b transcription factor (Figure la). Macrophages (Cd68+), other myeloid cells (Cdl4+), B cells (Cd79a+), T cells (Cd3e+), dendritic cells (Irf8+) and NK cells (Nkg7+) composed the immune microenvironment of these tumors. CAFs (Fnl+) and endothelial cells (vWF+) were also detected in these samples. Macrophages and Cdl4+ myeloid cells were the most abundant TME populations (Figure lb). All annotated cell types were detected in each tumor individually at different proportions (Figure 7b).
In parallel, the inventors performed immunohistochemistry (IHC) and FACS analyses on distinct tumors of the same model. First, IHC using F4/80 or CD3 antibodies confirmed that macrophages were more abundant in this model as compared to T lymphocytes (Figure lb). Interestingly, by FACS, the inventors observed a strong anti -correlation between the population of CD 3 CD 19" cells, corresponding to myeloid and NK cells and T lymphocytes (CD3+CD19 ) among CD45+ cells (Figure 1c). These observations therefore suggested an immunosuppressive myeloid TME in TH-MYCN mouse tumors.
Heterogeneity of macrophages in mouse neuroblastoma
As shown in Figure la, three clusters of macrophages (clusters 3, 6 and 8) which all expressed a common signature including Cd68, Csflr, CCr2, Cd86, Adgrel (encoding F4/80) and Lgals3 were detected in the TME of MY CN-driven tumors (Figure 2b) . These three macrophage clusters could be further defined by specific markers as follows: cluster 3 was characterized by high expression of Pecaml and Cd300e; cluster 6 exhibited a high expression level of Ccr2 and Fnl whereas cluster 8 strongly expressed Apoe, Clqb and Cd63 (Figure2b, Table 2). These clusters were respectively named Pecaml+, Ccr2+ and Apoe+ macrophages. A classification of macrophages has been previously used to distinguish “classically activated” Ml and “alternatively activated” M2 macrophages in response to defined stimuli in vitro and respectively associated with anti- and pro-tumor activity. Signatures have also been proposed to identify angiogenesis and phagocytosis associated phenotypes in macrophages (Table 3). The inventors therefore evaluated these distinct signatures defined in human, on the. murine data. This analysis revealed that Apoe+ macrophages expressed signatures associated with M2 and phagocytosis phenotypes. The Ccr2+ and Pecaml+ clusters were not highlighted by any of these signatures. These observations are in line with recently published data demonstrating that macrophages exhibit high heterogeneity in different tumor types . The inventors next generated short signatures including a reduced number of genes to detect these three macrophage subsets. A signature including Cd300e, Cd82. Pecaml, 1110, Cd274. Pglyrpl and Pagl characterized the Pecaml+ macrophages, whereas a signature including Ccr2, Sell, Vcan. Ly6c2, Fnl and F13al identified Ccr2+ macrophages; a three-gene signature (Apoe. Clqb and Cd63) defined Apoe+ macrophages. Interestingly, Tgfbl, known to have a central role in the TME immunosuppression was highly expressed in macrophages, regardless of the subset.
The TH-MYCN mouse TME contains a population of myeloid-derived suppressor cells
The inventors next focused on cluster 5 highly expressing Cdl4 (Figure la). When applying SingleR using annotations for mouse cell populations, cluster 5 was strongly labelled with a neutrophil signature. Cells from this cluster exhibited high levels of S 100a8, S100a9 and Mmp9, but showed an absent or low expression of Cd68 and H2-Aa, that are typical markers of macrophages . S100a8 (Calgranulin-A) and S100a9 (Calgranulin-B) are calcium- and zinc-binding proteins known to form a stable heterodimer called calprotectin that have prominent role in the regulation of inflammatory processes and immune response. Together with Mmp9, S100a8 and S100a9 are known to be highly expressed by neutrophils. These observations suggested that cells from cluster 5 may correspond to tumor-associated neutrophils which have recently emerged as an important component of the TME.
Strikingly, cluster 5 cells also expressed a gene signature defining activated PMN-MDSCs , described in mouse tumors, exhibiting a high expression of S100a8/a9 and characterized by a potent immune suppressive activity. A low expression of a signature of PMC-MDSCs was observed only in a minor fraction of cluster 5 . MDSCs constitute a heterogeneous population of myeloid cells that are pathologically activated and have immunosuppressive properties; they are now recognized as major regulators of immune responses in cancer. MDSCs include two major subsets based on their phenotypic features: PolyMorphoNuclear-MDSCs (also called granulocytic (G)-MDSCs) and monocytic (M)- MDSCs. Polymorphonuclear neutrophils (PMNs) have been implicated in antitumor activity and expression signatures have been recently defined that distinguish activated PMN-MDSCs from PMN- MDSCs. Interestingly, cluster 5 cells were also characterized by strong expression of a signature common to both PMN-MDSCs and M-MDSCs, recently identified in the mouse MMTV-PyMT mammary tumor model . The concomitant expression of signatures of both neutrophils and PMN- MDSCs by cluster 5 fits with the recent idea that PMN-MDSCs correspond to a neutrophil population with immunosuppressive properties and that PMN-MDSCs and activated PMN-MDSCs represent two populations of neutrophils in tumor-bearing mice. Of interest, cluster 5 cells strongly expressed II lb and Arg2 that are known to be involved in immunosuppression. A subset of these cells also expressed Csf- 1 (colony-stimulating factor- 1) which may promote macrophage accumulation within tumors and regulate macrophage survival, proliferation and differentiation.
IHC experiments on sections of MYCN-driven mouse tumors confirmed the infiltration of MDSCs highly expressing S100a8 in the tumors (Figure 2b). Next, tumors were analyzed by FACS using cellsurface markers defining PMN-MDSCs and M-MDSCs in mice, with PMN-MDSCs characterized by a CD 1 lb+Ly6G+Ly6Clow phenotype and M-MDSCs being CD 1 lb+Ly6G Ly6Chlgh cells. As shown in Figure 2c, both populations were detected in a series of 8 independent tumors and PMN-MDSCs were more abundant compared to M-MDSC cells. Altogether, these data indicate that cluster 5 cells of TH- MY CN tumors represent a population of immunosuppressive myeloid cells compatible with activated PMN-MDSCs and representing a particular subset of neutrophils.
Two subsets of CAFs are defined in mouse neuroblastoma
In many adult cancers, CAFs have been shown to constitute an abundant component of the TME. In neuroblastoma, CAFs remain poorly characterized. The inventors’ single-cell analysis of murine tumors revealed a cluster of CAFs (cluster 17) characterized by Fnl expression (Figure la) that could further be divided into two subclusters when increasing the resolution in the clustering analysis. Using signatures of CAFs defined in human breast and ovarian cancers, one subcluster showed a high expression of a CAF-S1 signature, whereas the other one had a strong signal for a CAF-S4 signature. CAF-S1 and CAF-S4 have been shown to have immunosuppressive function and pro-metastatic function, respectively. The CAF-S1 subcluster also mildly expressed a iCAF (inflammatory CAFs) signature whereas the CAF-S4 subcluster was also highlighted by signatures of stromal cells called perivascular-like (PVL) cells, being either differentiated-PVLs (dPVL - Tagin, Cd9, Mylk and CnnT) and immature PVLs (imPVL - Cd36, NotchS, Rgs5, Rhob and Itgal). A differential analysis between the CAF-S1 and CAF-S4 clusters identified upregulated genes in each subset . The two CAF populations were then validated by FACS (. Interestingly, the inventors’ data revealed that several chemokines including Ccl2, Cxcll and Cxcll2 that have been shown to contribute to immunosuppressive TME are highly expressed by CAF-S1 cells .
Single-cell transcriptomics reveals a variety of myeloid cells in the TME of human neuroblastoma Next, the inventors performed single-cell transcriptomic analysis on 10 biopsies of human neuroblastoma obtained at diagnosis or at relapse (Table 1). The integration of the 10 biopsies (n=20,296 cells) highlighted tumor cells (PHOX2B+, GATA3+) as well as several populations of the TME. Analysis using the InferCNV tool confirmed that tumor cells exhibited the emblematic genetic alterations of neuroblastoma such as 17q gain. In contrast, no such alteration could be detected in the various TME clusters. To beter discriminate the various TME populations, the inventors then used Harmony to integrate the 10 biopsies after excluding tumor cells (Figure 3a). Expression of canonical cell type gene markers combined with SingleR analysis for human cells allowed to identify the following populations of immune cells: macrophages (CD68 clusters 2, 8, 9 and 16), T cells (CD3D+, clusters 0 and 1), NK cells (NKG7 cluster 5), B cells (MS4A1+ encoding CD20, cluster 7), conventional dendritic cells CD1C cluster 15), monocytes (CD14+, cluster 4), so-called “non-classical monocytes” (CD14mt, FCGR3A+ encoding CD16, cluster 13) and MDSCs (S100A8+, S100A9+, FCGR3B+, cluster 10)( Table 4). Cluster 10 was also highly positive for the neutrophil signature and for a PMN-MDSC signature . These data therefore identified a complexity of macrophages and potential MDSCs in human tumors, as observed in the TH-MYCN model. Additional clusters of CAFs (COIJA I . cluster 3), endothelial cells (VWF+, ENG+, cluster 6), cells expressing lymphatic endothelial markers (LYVE1+, PROXF, PDPN . cluster 17) and cycling cells (MKI67+, clusters 11 and 12) were also part of the TME (Table 4).
Regarding the macrophage populations, the inventors observed that the different clusters expressed CD68 and APOE (Figure 3b-c) and were positive for a M2 signature but did not express the signature defining a Ml phenotype , which is in favor of a pro-tumoral activity. Further analysis of signatures associated with an angiogenesis or phagocytosis phenotype highlighted cluster 9 and cluster 2, respectively. The inventors noticed that CSF1R was expressed only in clusters 2 and 9 and CD33 was not detected in clusters 8 and 9 (Figure 3b-3c). Cluster 2 specifically expressed FOLR2 (Figure 3c). Of note, a strong level of FABP4, known to be expressed in lung macrophages was observed in cluster 16 . This is consistent with the observation that the TR5 sample contributing to this cluster corresponded to a lung biopsy (Table 1) . To further investigate the link between these different macrophage subsets and analyze lineage trajectories of the myeloid populations, the inventors applied the scVelo tool to their RNA-seq data. The obtained trajectories suggested that macrophages of cluster 9 (APOE+CSFlRmed) and cluster 8 (APOE+CSF1R1OW) are derived from APOE+CSF1R+ macrophages of cluster 2.
Since the inventors’ cohort of 10 patient samples included tumors with and without MYCN amplification (5 of each) and tumors at diagnosis or at relapse (5 of each) (Table 1), they asked whether TME cell populations were different in these different categories. Interestingly, they observed that the proportions of MDSCs and non-classical monocytes were higher in the set of tumors with MYCN amplification compared to tumors without this abnormality (Figure 8a). Similarly, they noticed a higher proportion of MDSCs in tumors at relapse compared to tumors at diagnosis (Figure 8b). Of note, B cells and endothelial cells were also more abundant in terms of proportions in relapsed cases. These observations, although obtained on a small series of tumors suggest an accumulation of MDSCs in AfFCA-amplified tumors, known to be aggressive tumors with a poor outcome and also in tumors studied at an advance stage of the disease.
CAF heterogeneity in human neuroblastoma
Consistent with the CAF analyses done in murine neuroblastoma tumors the inventors also addressed CAF heterogeneity in their cohort of human neuroblastomas. Analysis of known signatures identified one small subcluster expressing a CAF-S1 signature and a second subcluster was characterized by a strong CAF-S4 signature and was also highlighted by dVPL and imPVL signatures (. These observations are reminiscent of those obtained in the mouse TH-MYCN neuroblastoma model. As Seurat did not identify distinct CAF clusters, the inventors further split the two subpopulations using specific signatures . This enabled us to identify CAF-S1 and CAF-S4 clusters. A differential analysis of these two clusters identified upregulated genes in each cluster . Expression of CXCL12 and CCL2 cytokines was clearly detected in human CAF-S1 .
T cells in human neuroblastoma exhibit features of dysfunctional cells
Among immune cells, cytotoxic CD8+ T cells are one of the main effector cell types responsible for anti-tumor immunity. The inventors noticed an important cluster of T cells in their cohort of 10 neuroblastoma patients, including CD4 and CD8 lymphocytes (Figure 4a). It is now well described that immune suppressive agents in the TME lead to T-cell dysfunction, resulting in T-cell exhaustion. This state is characterized by increased expression of inhibitory receptors and decreased production of effector cytokines. Interestingly, the inventors’ scRNA-seq data indicated that all T cells, being either CD4+ or CD8+, expressed at least one of the 5 well-described inhibitory receptors, being LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PDCD1/PD-L1 (Figure 4b). A subset of CD8+ cells and few CD4+ cells co-expressed LAG3 and TIGIT, whereas some CD4+ cells co-expressed TIGIT and CTLA4. Regarding effector cytokines, only sparse expression of IL2, TNF, IFNG and GZMB was observed in patient T cells (Figure 4c). The expression profile of T cells infiltrating human neuroblastoma is therefore consistent with a phenotype of dysfunctional cells.
Comparison of cell populations between MYCN-driven mouse neuroblastoma and human tumors reveals striking commonalities and a conserved population of MDSCs
Having defined the TME heterogeneity both in mouse and human neuroblastoma, the inventors further investigated similarities in population structure between both organisms. To do so, they first extracted the top 50 genes from each annotated clusters in both species, then got the average expression value of all genes in all clusters and finally performed an unsupervised hierarchical clustering of the genes and the different clusters. The inventors observed that CAFs, endothelial cells, B cells, NKs and T cells of the two species clustered together indicating that their identity imposed the similarity between their gene expression profiles, rather than the analyzed organism. Among immune cells, the similarities in gene expression also reflected ontogeny with lymphoid cells separating from myeloid cells. Strikingly, a strong similarity between human cluster 10 and mouse cluster 5, previously identified as MDSCs, was observed. Common upregulated genes in both the murine and human populations included S100A8, S100A9, CEBPB, CXCR2 and TREM1 as well as HIF1A and PTGS2/COX2 (Tables 3 and 4) that have been recognized as features of MDSCs. These observations therefore highly suggested that human cells of cluster 10 are MDSCs with immunosuppressive activity. The inventors’ comparison highlighted complex relationships between the three populations of macrophages identified in the mouse model and the three identified in the patients. Indeed mouse cluster 8/Apoe+ macrophages clustered in a common branch with the three human macrophage clusters. Human clusters 4 and 13, annotated as non-classical monocytes and monocytes clustered together in a branch with murine Pecam 1+ macrophages (cluster 3) . To confirm these findings, the inventors next applied the mouse-derived gene signatures from myeloid cell populations in the human TME. Strikingly, a signature including the top 20 genes upregulated in the mouse MDSCs cluster defined in the TH-MYCN model was highly expressed in human cluster 10 and mildly expressed in human cluster 4 (Figure 5). The mouse Apoe+ macrophage (cluster 8) signature overlapped with all three macrophage clusters identified in patient tumors (Figure 5). In contrast, the murine Ccr2+ macrophage signature (cluster 6) rather highlighted human cluster 4 of monocytes (Figure 5) . The murine Pecam 1+ macrophage signature (cluster 3) mapped mostly with human cluster 13 of non- classical monocytes of the human samples (Figure 5). These observations are fully consistent with the aforementioned results of the hierarchical clustering.
Finally, to validate MDSCs in patient microbiopsies by an independent method, the inventors performed immunofluorescence experiments using antibodies against S100A8 and HLA-DRB1 proteins. These two markers allow to distinguish MDSCs (cluster 10) that express S100A8 but not HLA-DRB1 from monocytes (cluster 4) that express both markers (data not shown)). S100A8+ HLA-DRBF cells were observed in several cases, in agreement with the single-cell RNA-seq data.
Overall, the inventors’ data identified a MDSCs population with high similarity between mouse and human neuroblastoma and revealed a high level of complexity in macrophage subsets from neuroblastoma consistently with recent data showing that macrophage subsets show species-specific patterns.
Immunosuppressive activity of MDSCs in the TH-MYCN model
Since the inventors observed that T cells of human tumors displayed increased expression of inhibitory receptors, the inventors sought to analyze the phenotype of the rare T cells observed in the TME of TH- MYCN mouse tumors with respect to the expression of such receptors. FACS analysis using antibodies for LAG3, TIGIT, CTLA4 and PD1 indeed showed that more T cells significantly expressed these receptors compared to T cells obtained from spleens of wild-type mice (Figure 6a), further demonstrating that anti-tumor response relying on T cells is impaired in the TH-MYCN mouse model. MDSCs have been shown to exploit several mechanisms to modulate immune responses, since they can induce the proliferative arrest of antigen-activated T cells and restrain their function. To demonstrate the immunosuppressive property of MDSCs in neuroblastoma, the inventors sought to perform functional assays. Such assays are extremely difficult to setup with human neuroblastoma cells. Indeed, only very limited number of tumor cells are available since patients are of very young age and tumor cells from high-risk patients are obtained in France only from small microbiopsies. Blood samples are also insufficient to obtain enough tumor-matched T cells from the same patient and using T cells from healthy donors would result in allogeneic immune responses. The inventors therefore took advantage of the mouse model to perform immunosuppression assays and evaluate if mouse MDSCs present in TH- MYCN tumors are able to inhibit T cell functional activity. To do so, T cells purified from the spleen of wild-type syngenic mice and activated in vitro were incubated with PMN- or M-MDSCs isolated from mouse tumors by FACS sorting as CD45 CD1 lb+Ly6G+Ly6Clowcells or CD45 CD1 lb+Ly6G Ly6Chlgh cells. Similar cells purified from spleen of wild-type mice were used as a control. After 3 days of coculture, the proliferation of CFSE-labeled CD8+ and CD4+ T-cells was assessed by FACS. This analysis showed that myeloid cells of the two fractions (CD45+CD1 lb+Ly6G+Ly6Glow or CD45+CD1 lb+Ly6G Ly6Chlgh) enriched from tumors significantly suppressed CD4+ and CD8+ T cell proliferation whereas the same fractions from wild-type spleens had no effect (Figure 6b).
Altogether, the inventors’ transcriptomic, IHC, FACS and functional data characterized a population of MDSCs in the TH-MYCN neuroblastoma model that exhibit immunosuppressive activity as demonstrated by the inhibition of T cell proliferation ex vivo and the exhausted state of T lymphocytes. The present data highly suggest that the corresponding population identified in human neuroblastoma exhibits immunosuppressive functions, contributing with macrophages to the malignant phenotype.
Discussion
The inventors’ data, obtained by single-cell transcriptomics provide the first comprehensive analysis of mouse and human neuroblastoma microenvironment cells without any prior assumptions on surface markers. They could dissect the entire TME including endothelial cells, immune cells and CAFs, the identity of which could be unambiguously defined with canonical markers and signatures. Only one small cluster of the tumor mouse model (cluster 16) and one of the human TME (cluster 14) remained undefined. Importantly, the present single-cell RNA-seq data of the mouse model, for which material can be easily obtained, were confirmed by FACS and IHC analyses for macrophages, T cells and MDSCs. Analysis of high-quality tumor material from young patients affected with cancer remains challenging. The parallel analysis of the TME of a mouse neuroblastoma model and a cohort of patients is one of the strength of the work presented herein and is particularly valuable to get insights into functional activity of some matched cell populations.
Both in the mouse neuroblastoma model and primary tumors, the inventors documented a high content of myeloid cells and further deciphered the heterogeneity of these cells, with the description of several phenotypes of macrophages in both organisms and characterization of a population of MDSCs. They demonstrated that, in the TH-MY CN model, PMN -MDSCs are more abundant than M-MDSCs and that both types sorted from the murine model are able to inhibit T cell proliferation in an ex vivo functional assay. Of strong interest, is the similarity between the murine immunosuppressive MDSCs (cluster 5) and the cluster 10 of human cells in the inventors’ hierarchical clustering exploring mouse and human cell clusters. Both populations express high levels of S100A8 and S100A9 that have been shown to greatly accumulate in MDSCs and are now recognized as one of the hallmarks of these cells. Consistently with RNA-seq data, S100A8+ HLA-DRB1- MDSCs could be detected in neuroblastoma patient microbiopsies. The inventors single-cell transcriptomic data clearly document that neuroblastoma MDSCs are molecularly distinct from the various subsets of macrophages described in both species. Targeting MDSCs has been suggested as a therapeutic strategy to reverse immunosuppression and improve clinical outcome in cancer patients. Different approaches have been proposed to regulate MDSCs in tumors, such as reducing their recruitment, accumulation and suppressive functions. The inventors’ present results point out upregulated genes in such cells of the neuroblastoma TME that could orientate their targeting. Notably, the present transcriptomic data reveal that PTGS2/COX2 and CXCR2 are among the most upregulated genes in both murine and human MDSCs. Cyclooxygenase 2 is one enzyme involved in the generation of prostaglandin E2, a product of lipid oxygenation that has been shown to accumulate in PMN-MDSCs and mediate the enhanced suppressive activity of such cells. The chemokine receptor CXCR2 has been shown to play a key role in the migration of MDSCs to tumors. Its inhibition by genetic ablation or using small-molecules inhibitors enhanced immunotherapy in several mouse models of cancer. MDSC depletion remains challenging since those cells have shortlifespan in tissues and are constantly replaced. Another approach may rely on MDSC reprogramming using inhibition of various pathways to enhance anti -tumor immunity, such as C0X2 inhibition (Fujita M, Kohanbash G, Fellows-Mayle W, Hamilton RL, Komohara Y, Decker SA, et al. COX-2 blockade suppresses gliomagenesis by inhibiting myeloid-derived suppressor cells. Cancer Res. 2011;71:2664- 74) or treatment with W-i reins retinoic acid (ATRA)(Veglia F, Sanseviero E, Gabrilovich DI. Myeloid- derived suppressor cells in the era of increasing myeloid cell diversity. Nat Rev Immunol. 2021). Several studies pointed out that ATRA is able to promote the differentiation of M-MDSCs into macrophages and DCs and eradicated PMN-MDSCs in both tumor-bearing mice and patients. Retinoic acid-based therapeutics have been used in patients with neuroblastoma and some benefit has been reported through their ability to suppress tumor growth and promote cell differentiation (Matthay KK, Reynolds CP, Seeger RC, Shimada H, Adkins ES, Haas-Kogan D, et al. Long-term results for children with high-risk neuroblastoma treated on a randomized trial of myeloablative therapy followed by 13-cis-retinoic acid: a children’s oncology group study. J Clin Oncol. 2009;27: 1007-13). Yet, the potential effect of ATRA on tumor MDSCs has not been investigated. Finally, innovative therapies with genetically engineered myeloid cells delivering IL- 12 have been recently used in a mouse model of rhabdomyosarcoma and demonstrated a proof of concept for reversing immunosuppression and activate anti-tumor immunity. The inventors data highlight the complex phenotypes of macrophages in the TME of both mouse and human samples. Whereas three subsets of macrophages could be defined in each organism, signatures of each cluster did not translate into one-to-one correspondence between the two species. These observations are fully consistent with results previously obtained on myeloid cells of adult non-smallcell lung cancer and on a mouse lung adenocarcinoma model documenting that macrophage subsets show species-specific patterns.
The inventors could document that the rare intratumor T cells of TH-MY CN neuroblastoma exhibited increased expression of inhibitory receptors. In the present data of patient tumors, the correlations between the different populations defined by RNA-seq cannot be evaluated since only small microbiopsies have been analyzed and may not be representative of the full tumors when considered individually. Yet, the present results showed that despite their presence in human neuroblastoma, CD4+ and CD8+ T cells exhibit features of exhaustion with the expression of at least one inhibitory checkpoint. The link between exhaustion of tumor infdtrative T-cells and the presence or phenotype of MDSCs remains to be studied.
The present study also highlights different CAF populations both in mouse and human neuroblastoma TME. Although representing small populations in the tumor ecosystem, mouse CAF-S 1 cells in the TH- MYCN model appear to be an important source of cytokines and may exert immunosuppressive functions as previously described. Patient tumors likely include also CAF-S 1 and CAF-S4.
In conclusion, the inventors present work has generated a new data resource through single-cell transcriptomics that provides a better understanding of the neuroblastoma ecosystem and the basis to develop both tumor-targeted and immune-targeted therapies. The degree of commonality between the TH-MY CN mouse model and the series of analyzed patient tumors indicates the relevance of using this animal model to evaluate the function of various populations in tumor progression and explore new immune therapeutic approaches.
For further information, see Costa et al. J Immunother Cancer. 2022; 10(8): e004807, the experiments of which are incorporated herein by reference.
Materials and Methods
TH-MYCN mice used in this study have been previously described [Weiss WA, Aidape K, Mohapatra G, Feuerstein BG, Bishop JM. Targeted expression of MYCN causes neuroblastoma in transgenic mice. Embo J. 1997;16:2985-95.]. Neuroblastoma samples for single-cell analyses were obtained from patients treated at Institut Curie. Surplus tissues obtained at diagnosis or relapse were processed immediately after receipt at the laboratory for molecular diagnosis (Unite de Genetique Somatique). Written informed consents for this study, including the analysis of surplus tumor tissue were obtained for all patients from parents or guardians. Out of the 10 studied patients (Table 1), four patients were enrolled in the MICCHADO study (ClinicalTrials.gov identifier NCT03496402) and four patients in the MAPPYACTS trial (ClinicalTrials.gov identifier NCT02613962), with 2 patients enrolled in both programs. Within these studies, approval of this research was given by the decision of the ethics committees Sud Est VI, reference AU 1388, and He de France III, reference Am7158-2-3272. The study was approved by the Institut Curie’s Institutional Review Board. The technical details of single-cell dissociation, scRNA-seq analysis, immunohistochemistry, FACS analysis, MDSC isolation and T cell suppression assays are provided in the online supplementary methods of Costa et al., J Immunother Cancer. 2022; 10(8): e004807.
TH-MYCN mouse model
Mice on a 129* l/SvJ background were obtained from the NCI mouse repository (http://mouse.ncifcrf.gov/) and further backcrossed on 129S2/SvPasCrl background (abbreviated 129S2, Charles River). Genotyping was performed as previously described (Haraguchi S, Nakagawara A. A simple PCR method for rapid genotype analysis of the TH- MYCN transgenic mouse. PLoS One. 2009;4:e6902.). All analyzed mice were heterozygous for the transgene. Bearing tumor mice for the single-cell RNA-seq analysis (42369, 41884 and 42007) were studied at 62, 79 and 63 days, respectively. The care and use of animals used in this study were strictly applying European and National Regulation in force for the Protection of Vertebrate Animals used for Experimental and other Scientific Purposes (Directive 86/609). Approval for this study was received from Ministere de 1’Education Nationale, de 1’Enseignement Superieur et de la Recherche (authorization number 5524-20 160531 1607151 v5).
Tumor dissociation into single-cell suspension
Mouse tumors and patient samples (biopsies and surgical resections) were cut with scalpels in small fragments. Enzymatic dissociation was performed in GIBCO medium containing 150 pg/mL Liberase™ TL Research Grade (5401020001, Merk) and 150 pg/mL DNase (DN25, Sigma Aldrich), for 30 minutes at 37°C with 400 rpm agitation. Cell suspension was then filtered using a 70 pm cell strainer (130-098-462, Miltenyi Biotec). The cell suspension was washed twice with PBS. Viability was measured using Vi-cell XR Viability Analyzer (Beckman Coulter).
Single-cell RNA-seq experiment and preprocessing of data
Single-cell RNA-seq was performed with the lOx Genomics Chromium Single Cell 3’ Kit (v3.1) according to the standard protocol. Libraries were sequenced on an Illumina HiSeq2500 or NovaSeq 6000 sequencing platform. CellRanger version 3.1.0 (lOx Genomics) was used to demultiplex, align and generate UMI count tables from sequencing reads. Two reference genomes were used to align reads: the mouse reference genome (mmlO) for the 3 MYCN- driven mouse tumors; the human reference genome (hg38/GRCh38) for the 10 patient samples. Ambient mRNA correction
SoupX R package vl.4.5 (https://github.com/constantAmateur/SoupX) was used to estimate and correct for ambient mRNA contaminations in both mouse and patient tumors. First, depending on the expression profile of empty droplets (defined as droplets with UMI count <100), the inventors selected, as recommended, either HBB/HBA or immunoglobulin genes (IGHA1, IGHA2, IGHG1, IGHG2, IGHG3, IGHG4, IGHD, IGHE, IGHM, IGLC1, IGLC2, GLC3, IGLC4, IGLC5, IGLC6, IGLC7, IGKG) as marker genes to estimate contamination fractions. When these genes were absent from the ambient profile (the top 100 covered genes), the inventors used the automatic mode provided by SoupX to estimate contamination fractions and generate corrected expression matrices. Summary of analyses is shown in Tables 5 and 6. Doublet detection
Scrublet vO.2.1 (Wolock SL, Lopez R, Klein AM. Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data. Cell Syst. 2019;8:281-291. e9. ) was used to detect potential doublets using default parameters (expected_doublet_rate=0.06). Cells marked as doublets were removed from subsequent analysis (results in Tables 5 and 6).
Quality control of single-cell data
First, all ribosomal genes (defined as RLP/RPS genes) were removed from the raw expression matrices. Then, coverage thresholds were set for each sample individually; an upper threshold was set to remove outlier cells with coverage greater than the 99th percentile, and a lower threshold was set to remove low quality cells with coverage inferior to the 1st percentile. To avoid cells with low number of genes, the same lower threshold was applied on the number of genes thus defining a minimum number of genes required. Finally, cells with more than 20% of reads mapping mitochondrial genes were removed.
Normalization of single-cell data
Raw UMI counts were normalized using the “SCTransform” function of Seurat v3.1.5 (tuart T, Butler A, Hoffman P, Hafemeister C, Papalexi E, Mauck WM, et al. Comprehensive Integration of Single-Cell Data. Cell. 2019;177: 1888-1902. e21.). Regressed variables included cell coverage, number of features, and the percentage of UMI from mitochondrial genes.
Dimensionality reduction and cluster identification
Normalized count data was subjected to dimensionality reduction keeping the first 30 principal components. Uniform Manifold Approximation and Projections (UMAP) embeddings were calculated using these Principal Components (PCs) as input and cells were clustered using the “FindClusters” function of Seurat. The inventors also generated an umap using the graph structure produced by “FindNeighbors” on which “FindClusters” function detects cell clusters. This umap representation is referred to as “umap. graph” .
Cell type annotation
Marker genes that define cell clusters were identified after differential expression analysis using Seurat “Find AllMarkers” function. Clusters were annotated by comparing their top marker genes to canonical cell type markers from the literature. Additional cell type annotation was performed using singleR vl.0.6 (Aran D, Looney AP, Liu L, Wu E, Fong V, Hsu A, et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol. 2019;20: 163-72. ) which annotates cells against built-in references datasets. The inventors used the Human Primary Cell Atlas (Mabbott NA, Baillie JK, Brown H, Freeman TC, Hume DA. An expression atlas of human primary cells: inference of gene function from coexpression networks. BMC Genomics. 2013; 14:632.) and data from the Immunological Genome Project (Heng TSP, Painter MW, Immunological Genome Project Consortium. The Immunological Genome Project: networks of gene expression in immune cells. Nat Immunol. 2008;9: 1091-4. ) to annotate cells in the human and mouse microenvironment, respectively.
Generation of single-cell signature scores
To plot the expression of gene signatures in single cells, the inventors used the “AddModuleScore” function from Seurat R package with 100 genes in the control gene set. scRNA-seq data integrations
Seurat v3.1.5 was used to integrate the 3 TH-MYCN mouse tumors and the 10 neuroblastoma patient samples using 3,000 anchor features. The integrated objects were subjected to dimension reduction and clustering as described above. Tumor cells and microenvironment were identified based on the expression of specific marker genes. To further study human TME, 3,785 non-tumor cells were extracted from the integration. Raw counts were first normalized using SCTransform function (Seurat) then Harmony vl.O (Korsunsky I, Millard N, Fan J, Slowikowski K, Zhang F, Wei K, et al. Fast, sensitive and accurate integration of single-cell data with Harmony. Nat Methods. 2019; 16: 1289-96. ) was used for data integration.
Copy number analysis
Copy number variations at the single cell level were called with R package InferCNV vl.2.1 (https :// ithub . com/broadinstitute/inferCNV) using default parameters. Cells with fewer than 1000 UMI were excluded and normal cells from the microenvironment of one patient were used as reference cells (n=733).
RNA velocity
To perform RNA velocity analysis (La Manno G, Soldatov R, Zeisel A, Braun E, Hochgerner H, Petukhov V, et al. RNA velocity of single cells. Nature. 2018;560:494-8.), the inventors first used velocyto CLI to annotate spliced /unspliced reads from cell-barcodes sorted bam files. The inventors then used the scVelo package (Bergen V, Lange M, Peidli S, Wolf FA, Theis FJ. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat Biotechnol. 2020;38:1408-14. ) with default parameters and default data preparation procedures to compute steady-state velocities and visualize velocity streamplots on myeloid cell populations.
Immunohistochemistry (IHC) Formalin-fixed paraffin embedded (FFPE) tumors from TH-MYCN mice were cut in sections (4 pm) and prepared for staining using standard protocols for xylene and alcohol gradient for deparafination (Sakura, Tissue-Tek DRS). All stainings were performed in the Lab Vision IHC stainer Autostainer 480 device (Thermo Scientific). The epitope retrieval was performed in EnVision FLEX Target Retrieval Solution low-pH (Dako, #K800521, for CD3 and S100A8) or high-pH (Dako, #K800421, for F4/80) followed by 5 minutes blockade of endogenous peroxidase activity with Dako REAL peroxidase-blocking solution (Dako, #S202386). A blocking step was made using Protein Block (Dako, #X-0909) for 10 min. The tissue sections were then incubated with the F4/80 (Abeam, #Ab6640; 1 :2000), CD3 (Dako, #A0452; 1 :200) or S100A8 primary antibody (ThermoFisher, #PA5-79948; 1 : 100) or Rabbit IgG isotype control (Abeam, #Ab 172730) for 1 hour at RT, followed by wash with IX PBST (Dako, #K8000). Next, a goat anti -rabbit antibody (VECTOR laboratories, #PK-6101 kit) was incubated for 25 minutes at RT for CD3 and S100A8 whereas a rabbit anti-rat antibody was used for F4/80 (Cliniscience, #BA-4001). The tissue sections were washed using PBST and then signal detection was performed by incubation with avidin-horseradish peroxidase (Vector Laboratories) for 25 minutes and detected with 3,3 ’-diaminobenzidine for 5 min (DAB, Dako, #K3468). Counterstaining was performed with Mayer hematoxylin freshly prepared (Dako, #S3309). Tissue sections were then submitted to serial gradients of xylen and mounted with coverslip in an automatic device (Sakura, Tissue-Tek DRS). Staining overview of the sections was done in the Zeiss Axioplan microscope and slides were then scanned using the Philips Ultra Fast Scanner and visualized at high resolution in the Philips IMS 2.2 software for further analyses and photo acquisition.
FACS analysis
Following tumor digestion described in “Tumor dissociation into single-cell suspension section”, 2xl06 cells per sample were stained with Aqua Live/Dead viability dye (Life Technologies) according to the manufacturer’ s instructions. Cells were stained with an antibody panel for immunophenotyping (see Table 7 for a list of antibodies, clones, fluorochromes, manufacturers, and concentrations) for 30 minutes at RT in dark. After staining, cells were washed in PBS supplemented with 2 mM EDTA and 0.5% FBS. Data was acquired with a BD™ LSRII flow cytometer and further analyzed using Flowjo vlO. For the lymphoid panel, CD19+ B cells were gated as CD45+/CD19+, CD3+ T cells as CD45+/CD3+ and CD19 CD3' cells correspond to myeloid and NK cells .
For the analysis of T cell inhibitory receptors, cell suspensions obtained from TH-MYCN mouse tumors as described above were pre-enriched in CD45+ cells by magnetic beads (130- 110-618, Miltenyi Biotec) according the manufacturer’s instructions. CD45+ cells were suspended in buffer (PBS, 1%SVF, 5mM EDTA) and incubated with CD4-eF450, CD8-APC, CD279 (PD1)-PC7, CD152 (CTLA4)-AF700, TIGIT-PE and CD223 (LAG-3)-PerCP-eF710 antibodies for 30 min at 4°C in dark. After staining, cells were washed in PBS. Data were acquired with a BD LSRII flow cytometer and analyzed using Flowjo vlO for the expression of the inhibitory receptors in CD4+ and CD8+ cells.
Mouse-human comparison heatmap
For an unsupervised comparison between mouse and human microenvironment cell populations, only genes with one-to-one translation between human and mouse were considered, as previously defined (Zilionis R, Engblom C, Pfirschke C, Savova V, Zemmour D, Saatcioglu HD, et al. Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species. Immunity. 2019;50: 1317-1334. elO. ). Starting from the two integrations (human and mouse TME), the inventors extracted the top 50 marker genes of each cell population. These markers were filtered for mitochondrial and cell cycle genes. The inventors then retained the intersection between human and mouse marker genes to define the final set of genes used for the inter-species comparison (n=169). The average expression value of these genes within all cell populations was computed and scaled independently within each specie. Finally, the inventors combined the scaled average expression values for human and mouse into a single expression table and used ComplexHeatmap R package (Gu Z, Eils R, Schlesner M. Complex heatmaps reveal patterns and correlations in multidimensional genomic data. Bioinformatics. 2016;32:2847-9.) for visualization. To better highlight expression patterns, the inventors partitioned the heatmap into 7 sub-groups using k-means clustering on rows (selected marker genes) and columns (cell populations). Additional complete hierarchical clustering with Pearson correlation distance was applied to further cluster rows and columns within each sub-group.
Co-immunofluorescence on paraffin-embedded tissues
Paraffin-embedded tissue blocks were cut into 5 pm sections. Immunostaining was processed in a Bond RX automated (Leica) with Opal™ 7-Color IHC Kits (Akoya Biosciences, NEL821001KT) according to the manufacturer’s instructions using antibodies anti-HLA Class II DRB1 (Abeam mouse monoclonal, ab212448, l/4000e, 30min - Opal520) and anti- MRP8/S100A8 (Abeam rabbit monoclonal, ab92331, l/2000e, 60min - Opal690) Tissue sections were coverslipped with Prolong™ Diamond Antifade Mountant (Thermo Fisher). Slides were scanned using the Vectra® 3 automated quantitative pathology imaging system (Vectra 3.0.7; Akoya Biosciences). Multispectral images were unmixed using the inForm Advanced Image Analysis Software (inForm 2.6.0; Akoya Biosciences).
MDSCs isolation from TH-MYCN mouse tumors and mouse WT spleens
Tumors were harvested from TH-MYCN mice and mechanically dissociated with a scalpel. Enzymatic dissociation was performed as described above. To enrich for viable cells, the inventors performed a cell debris removal kit (130-109-398, Miltenyi Biotec) according the manufacturer’s instructions. Spleens of wild-type mice were crushed on a 70 pm cell strainer (130-098-462, Miltenyi Biotec). Cell suspensions were washed twice with IX PBS. Viability was measured using Vi-cell XR Viability Analyzer (Beckman Coulter). Both for tumors and spleens, cell suspensions were pre-enriched in Cd45+ cells using magnetic beads (130-110-618, Miltenyi Biotec) according the manufacturer’s instructions and were resuspended in buffer (PBS supplemented with 1% SVF and 5 mM EDTA). Cell suspensions were incubated for 30 minutes at 4°C in dark with pre-conjugated fluorescent labeled with the following combination: CD45-APC-Cy7, CDl lb-FITC, Ly6G-APC (127614, Biolegend), and Ly6C-Alexa700 antibodies. Flow cytometry sorting was performed with the SH800S cell sorter (Sony). The first gating was based on FSC/SSC. Doublet cells were eliminated by gating on SSC-W7 SSC-H followed by FSC-W7FSC- H. The second gating was based on DAPI negative staining to eliminate dead cells. CD45+/CDl lb+/Ly6G+/Ly6Clow (PMN-MDSC) cells and CD45+/CD1 lb+/Ly6G7Ly6Chigh (M-MDSCs) were sorted.
T cell suppression assay
Cell suspensions from spleens were obtained as described above. T cells were isolated using the mouse Pan T Cell Isolation Kit II (130-095-130, Miltenyi Biotec) according to the manufacturer’s instructions. T cells (up to 107) were stained using the CellTrace™ CSFE Yellow Cell Proliferation Kit (C34573, Thermofisher Scientific) at 5 pM for 8 minutes at 37°C. The staining was stopped by incubation with 5 volumes of PBS supplemented with 5% heat- inactivated FBS for 10 minutes at 4°C. Finally, T cells were washed twice with complete medium (RPMI Glutamax) containing 10% heat-inactivated FBS, 1% Penicillin-Streptomycin, 0.1% P-mercaptoethanol, 1% Non-Essential Amino Acid supplement, 1% Hepes, 1% Sodium Pyruvate) at 4°C. Labeled T cells (105/well) were plated and activated in complete medium with anti-CD28 (553294, BDBiosciences, 1 pg/mL) in a flat bottom 96-well plate previously coated with anti-CD3 (Clone 145-2C11, BDBioscience CD3e, 10 pg/mL, diluted in IX PBS). Sorted CD45+/CDl lb+/Ly6G+/Ly6Clow cells and CD45+/CD1 lb+/Ly6G7Ly6Chigh cells from TH-MYCN tumors or WT spleens were added to the T cells using a 10: 1 T cells:MDSC sorted cells ratio. After 3 days of culture, cells were collected and stained with fluorescent-conjugated antibodies CD4-PE-Cy7 (BLE100528, Biolegend, 1/100) and CD8-APC (553035, BDBioscience, 1/100) for 25 minutes at 4°C, protected from the light. Cells were washed and incubated with DAPI followed by flow cytometry analysis performed with the BD™ LSRII cytometer. The percentage of proliferation was calculated with the following formula [Y (T cells alone] / Y (T cells + MDSC sorted cells) ] X 100. The Y value corresponds to the mean fluorescent intensity of CFSE of the whole T cell population divided by the mean fluorescent intensity of CFSE of undivided T cells.
Figure imgf000063_0001
Table 1 : Characteristics of the 10 neuroblastoma patients studied by scRNA-seq Table 2A: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Clusters 0 and 1
Cluster 0: Tubala, H2afz, Stmn2, Mif, Atpifl, Ppplrl4b, Dut, Tubb2b, Tubb3, Ran, Nmel, Fabp5, Uchll, Bex2, Ube2s, Fkbp3, Mycn, Ube2c, PeglO, Hmgb2, Prdx2, Hspdl, Tubb5, Bexl, Polr2f, Ptma, Npml, Ndufabl, Snrpf, Ranbpl, Hmgnl, Pdapl, Hsp90aal, Ccndl, Ndn, Gml673, Gap43, Nasp, Prmtl, Hintl, Nefl, Hlfx, Cct3, Slc25a4, Stmnl, Bex3, Atp5gl, Nnat, Tubalb, Anp32b, Cct7, Snrpdl, Ppal, Nel, Rnaseh2c, Hspel, Tomm20, Gnas, Cenpv, Hmgb3, Fkbp4, Dctppl, Eif4al, Cox7c, Pclaf, Eif5a, Set, Atp5b, Mrps33, Ndufa5, Atp5o.l, Timm8b, Baspl, Birc5, Histlhlb, Glrx5, Histlh4d, Mrpll2, Clqbp, Cdk4, U2afl, Pebpl, Tfap2b, Maplb, Nhp2, Ybxl, Chchdl, Timml3, Serbpl, Snrpd2, Hsp90abl, Dlkl, Nefrn, Selenoh, Ptovl, Mrpl34, Chchd2, Ppid, Uqcc2, Psmb6, Cacybp, Eif3g, Rtnl, Rfc4, Bex4, Tubb2a, Srm, Bzw2, Eeflg, Cct8, Psma7, Sumo2, AY036118, Ndufs5, Cox7a2, Snrpe, Usmg5, Nedd4, Elavl3, Cdkl, Ttc9b, Clpb, Txnl4a, Hmgbl, Impdh2, Pdcd5, Snul3, Cct5, Atp5e
Cluster 1 : H2afz, Tubala, Npml
Table 2B: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 2
PeglO, Stmnl, Tubb5, Nefl, Tubalb, Hmgb2, Nefrn, Nel, Tubala, Ptma, Uchll, Ccndl, Hsp90aal, Tubb3, Ube2c, Hmgbl, Npml, Set, Top2a, Dut, Nedd4, Mycn, Tubb2b, Nasp, Stmn2, Anp32b, Nucksl, Ube2s, Ranbpl, Ran, Pdapl, Gnas, Cbx3, Hmgnl, Ywhae, Hsp90abl, Hspdl, Dek, Hmgb3, Pclaf, Serbpl, Tfap2b, Slc25a4, Soxl 1, Prdx2, Baspl, Maplb, Nmel, Cenpf, Mif, Bex2, Elavl3, Pebpl, Atp5b, Cct3, Hnrnpab, Eif4al, Cct2, Eif5a, Snrpf, Phox2b, Fabp5, Fkbp4, Snrpdl, Srsf3, Calm2, Dlkl, Hnmpa2bl, Hlfx, Prmtl, H2afz, Fkbp3, Tcpl, Hnrnpal, Hnrnpu, Histlhlb, Rrm2, Mcm7, Birc5, Tcf4, Cct7, Ndn, Atpifl, Ppplrl4b, Smc4, Cdkl, Naplll, Psipl, Cks2, Ybxl, Smarccl, Srm, Cdv3, Hnrnpd, Eif4g2, Gap43, Impdh2, Mdh2, Bex3, G3bpl, Eeflg, Nude, Ppia, Sumo2, Hnrnpk, Rdx, Hlf, Hand2, Isll, Suptl6, Sms, Tubb4b, Cct8, Ptges3, Hnrnpa3, Cdc20, Cdca8, Insm2, Smc2, Bexl, Hintl, Gml673, Srsf7, Bzw2, Atxn713b, Chchd2, Ttc3, Eif2s2, Cct5, Dynlll, Histlh2ap, Ina, Apexl, Cdk4, U2afl, Polr2f, Pa2g4, Ssb, Atp5gl, Vcp, Jptl, Caldl, Tubb2a, Anp32e, Clqbp, Glrx3, Hdgf, Cct4, Smarca5, Snul3, Atp5o.l, Rbm3, Metap2, Sfpq, HnrnpaO, Fscnl, Bex4, Mlltl l, Eidl, Rnfl87, Vdacl, Sf3b2, Ndufabl, Park7, Snrpd2, Rtnl, Hmgn2, Eif3c, Mki67, Nusapl, Eefla2, Ccnbl, Dnmtl, Ptovl, Sox4, Ppal, Dctppl, Cacybp, Hspel, Nnat, Psmb4, Ddx39b, Atp5al, Nop58, Mrfapl, Pik3rl, Smc3, Histlh4d, Pbk, Tpx2, Ligl, Rnpsl, Ssrpl, Calm3, Glrx5, Hnrnpc, Crmpl, Ppplrl7, Lmnbl, Hdac2, Ddc, Cenpa, Ddxl, Mrpl28, Pfdn2, Cbx5, Csnkle, Psma4, Mrpll2, Selenoh, Smarca4, Timml3, Rslldl, Snrpb, Topi, Kifl 1, Pfn2, Plcb4, Alyref, Elavl4, Lyar, Cfl2, Psmc6, Hnmpr, Ckslb, Eif3g, Timm8b, Romol, Bzwl, Eif3d, Srsfl, Matr3, Eif4h, Eif5, Ndufv3, Psma7, Histlhle, Proxl, Mab2112, Pcbp4, Zwint, Cenpv, Ezh2, Stipl, Smarcel, Psmc5, Phb2, Gsptl, Ppid, Fkbpla, Brd3, Psmb5, Agtr2, Polr2m, Rbm8a, Eef2, Psma2, Tomm20, Caprinl, Atp5fl, Nop 10, Chgb, Srsf2, Sei enow, Kif21a, Zfp428, Khdrbs3, Rrml, Dpysl2, Marcksll, Nt5dc2, Cycl, Hsphl, Ccdc34, Dynll2, H2afx, Gnl3, Nhp2, Bub3, Kpnbl, Rbbp4, Atad2, Ndufc2, Swi5, Ube3a, Subl, Snrpe, Hnrnphl, Gnbl, Pbrml, Hnmpm, Anp32a, Usmg5, Spc24, H2afy2, Insml, GrblO, Fam60a, Rangapl, Nsd2, Abcfl, Psmb7, Knopl, Pafahlb2, Stmn3, Trim28, Rcc2, Hells, Mrto4, Mpp6, Clpb, Fbl, Psmdl3, Nolcl, Ndufa5, Psmb6, Lsm4, Mrps33, Ebnalbp2, Ywhaq, Ddxl8, Mybbpla, Zc3hl5, Psmb3, Nono, Nol7, Fxrl, Lsm5, Gsk3b, Atp5g3, Naca, Atp5j, Llph, Smc6, 1110004F10Rik, Atp5g2, Pcbpl, Pak3, Tipin, Ccnb2, Ttc9b, Ccna2, Pdxp, Zfp704, Lmol, Acatl, Ruvbll, Klhdc2, Pcml, Rfc4, Uba2, Pfdn4, Lsm7, Mlf2, Psmcl, Snrpal, Dnajc2, Rbbp7, Txnll, Banfl, Cbxl, Suclgl, Anapc5, Larpl, Snrpd3, Syncrip, Dtymk, Eif3i, Mtchl, Rbxl, Btf3, Atp5j2, Ybx3, Phox2a, Mcm5, Hdgfl3, Celf4, Sytl4, Prpfl9, Gars, Stmn4, Magedl, Gmnn, Garl, Gkapl, Rpa3, Odel, Pafahlb3, Prcl, Myef2, Ak2, Mrpll8, Psmdl, Psmc2, Ndufv2, Snrpe, Rrpl, Ube2n, Dstn, Pfdn6, Pkm, Ewsrl, Psmc3, Hspa9, Mdhl, Hspa8, Mrpl54, Pdcd5, Cycs, Dnaja2, Gapdh, Khdrbsl, Zfp706, Prdx6, Minosl, Atp5h, Snrpg, Cox5a, Eif3a, Mcm2, Ckap5, Snmp40, Dkcl, Faml36a, Parpl, Mbd3, Sael, Eif31, Lsm6, Dazapl, Erh, Nudt21, AtxnlO, Ube2m, Paics, Nop56, Eif3b, Ndufs5, Bcas2, Sumol, Thoc7, Ndufb8, Cox7c, Stubl, Ndufs6, Ldha, Hspa4, G3bp2, Pafahlbl, Ddx21, Ruvbl2, Pmml, Rpf2, Hnrnph3, Sfxnl, Nudcd2, Acpl, Hirip3, Ddah2, Ilf2, Noll2, Actl6a, Ilf3, Lsm2, Exosc8, Cuedc2, Mrpl51, Polr2c, Tceal9, Rheb, Eif4e, Txnl4a, Srsf6, NaalO, Gtf2h5, Eif2sl, Sumo3, Mrpl20, Cetn3, Cfdpl, Dnajc8, Cdk2apl, 2410015M20Rik, Lsm3, Uqcrfsl, Psma5, Ywhag, Eiflax, Tmpo, Atp5cl, Eif4gl, Ywhah, Atp5d, Rab3a, Thoc3, Snrpn, Kars, Pgp, Kdmla, Gstm5, Tsen34, Dnajc9, Magoh, Puml, Rars, Cirbp, Polr2j, Rnaseh2c, Prrc2a, Vdac3, Adh5, Prdxl, Psmd6, Psmd2, Eeflb2, Psma6, Hnmpdl, Fubpl, Dnajb6, Ube2i, Zbtb20, Tardbp, H2afv, Ap2a2, Kif5b, Stl3, Cox7a2.
Table 2c: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 3 Fcgr4, Fcerlg, Gngt2, Cst3, Pou2f2, Clec4a3, Tmsb4x, Ms4a6c, Lstl, Cd300e, Id2, Satl, Gpxl, Ftll, B2m, Itgal, Cybb, Clec4al, Fthl, Fyb, Ctss, Csflr, Ear2, Ace, H2-D1, Apls2, Itgb2, Ucp2, Cd47, Cd3001d, Hspalb, Corola, Cebpb, Ptprc, Cyba, Ctsb, Lyz2, Itm2b, Tyrobp, Laptm5, Raplb, Msn, Iqgapl, Treml4, Lyn, Hspala, Flna, Nr4al, Caimi, Hck, Cd300c2, Stapl, Pla2g7, Bcl2alb, Pecaml, Lcpl, Itga4, Cx3crl, Smpdl3a, Zfp3611, Acp5, Cd9, Ifitm2, Grk3, Ms4a6d, Spil, Adgre5, Pglyrpl, Hesl, Zeb2, Ly6e, Arpc2, Cd52, Spn, Fam46a, Arpclb, Pfnl, Nadk, Ifitm3, Atplal, Lmo4, Malatl, Duspl6, Adgre4, Tlnl, Gm2a, Actb, Myolg, Bcl2ala, Txnl, Bcl2ald, Efhd2, Eno3, Filip 11, Cytip, StklO, Ptpn6, Lampl, Plek, Rgs2, Rhoa, Msrbl, Btgl, Hfe, Pld4, Fgr, Klf4, Mpegl, Samsnl, Tnfrsflb, Myll2b, Ncf4, Polr21, Fabp4, Ifngrl, Prkcd, Vamp8, Psap, Tgm2, Cd300a, Lrpl, Cd68, Plin2, Plac8, Gnai2, Cyth3, Stk38, Limd2, Man2bl, Capzb, Ptpnl, Adgrel, Abi3, Sirpa, Apbblip, Lgals3, Rgsl, Slcl5a3, Tcf712, Metrnl, Gmfg, Arhgefl, Srgn, Ptprj, Slcl lai, Pagl, Hclsl, Ctsa, Rac2, Cd44, Gm42418, Ptpre, Nfkbia, Lilra5, Syk, Fxyd5, Lspl, Cd72, Ezr, Arhgdib, Atp2bl, Fmnll, Stk24, Cd53, Klfl3, Cdc42, Klf2, Jun, Pparg, Laptm4a, Ptp4a2, Atoxl, Siglece, Cyfip2, Prrl3, B4galntl, Nfe212, S100a4, Zfand5, Fam49a, Pilra, Pbxipl, Ccl6, Napsa, Taldol, H2-K1, Smpdl3b, Rbpms, Apobecl, Bin2, Csf2ra, Sh3bgrl, Ankrd44, Gng5, Cd48, Cd83, Tgfbrl, Nfkbiz, Itgbl, Samhdl, Ptp4al, Sh3glbl, Cd244, Lairl, Rassf4, Lcp2, Myolf, I117ra, F10, Mef2a, Rel, Neatl, Capl, Akapl3, Ctsz, Zfp36, Fos, H3f3a, Rassf5, Abcgl, Pip4k2a, Mbp, Rapla, Arhgap30, Clec4e, Dazap2, Actr2, Cdknlb, Klra2, Cd82, Nabpl, Lrrfipl, Socs3, Cfl 1, Nuprl, Fpr2, Rras, Gstml, Cblb, I16ra, Plekho2, Tmed5, Slfn2, Celf2, Ostfl, Fam49b, Gdpd3, Ceacaml, Gm21188, Map3k8, Fcgrt, Nfkbl, Ms4a6b, Tgfbi, Rnfl30, Nripl, Igsf6, Tppp3, Tmccl, Emc2, Lgmn, Clicl, Arpc5, Rsrpl, Gml5987, Abhdl2, Ccl9, Emilin2, Id3, Gpcpdl, Myh9, TmedlO, Myl6, Arl5c, Sema4d, Cyth4, Dock2, Gm, Vasp, Gludl, Ptbp3, Tmbim6, Xist, Actgl, Ddx5, Adrb2, Trafl, Zmizl, Evi, Tgfbi, Rrbpl, Actr3, Gabarap, Capza2, Klf6, Fgd4, Ptk2b, Dusp5, Sgmsl, Clipl, Anxa5, Vmpl, Ccl3, Mell, Ccdc88a, Ssh2, Nmtl, Ier2, Tsc22d3, Themis2, Man2al, Trpsl, Corolb, Ikzfl, Ms4a4c, Clec2d, Mapkapk2, RablO, Duspl, Ahnak, Arpc3, Cxcr4, Wfdcl7, Serf2, Ubc, Rbl, Nfaml, Rin3, Pptl, Cregl, Tpd52, Abracl, Fau, Zfp3612, Prdx5, Gk, Rasa3, Mobla, Ikbkb, Csk, Ctsh, Cdk2ap2, Ywhaz, Rexo2, Tnipl, Acp2, Ifitm6, Camkk2, Mppl, Slc43a2, Pirb, Skap2, Sgkl, Ppp2r5a, Grk2, Ccnd2, Cyp4fl8, Tmem50a, Bnip31, Tkt, Spatal3, Nrlh3, Runxl, Itgam, Adaml7, Zbtb7a, Tet2, Agpat4, Cnn2, Hmoxl, Ehdl, Tmem51, Pilrb2, Hipl, Sipalll, Clecl2a, Fermt3, Lipa, Sqstml, Ubl3, Lamp2, Stat3, Capnsl, Hebpl, Scp2, Vim, Tmeml4c, Rael, Macfl, Arpc4, Ppplcb, Havcr2, Hegl, Arhgef3, Ccrl2, Bcl2, Gprl41, Adcy7, Rab8b, Tlr2, Svil, Klf3, Gpsm3, Unc93bl, Hp, Anxa2, Pitpna, Grb2, Tpm3, Prdxl, Irak3, Susd3, Pidl, Itgax, Rhoq, KlflO, Blvrb, IllOra, Arrdc3, Clec4a2, Wasf2, Atplb3, Dusp2, Atp6vlb2, Kpna4, Brkl, Cotll, Rcanl, Lrrc25, Dok3, Arhgapl7, Fcho2, Tmeml31, Prkcb, Diaphl, Crlf3, Fucal, Tpm4, Sh3bgrl3, Atp6v0b, Mareks, Aldoa, Bcl6, Acer3, Ifi207, Slcl2a2, Adssll, Nckapll, Sh3bp5, Nrros, N4bpl, Sppl2a, Ddit4, Mierl, Irf2, Rafi, Atf3, Arhgdia, mt-Col, Hspa5, Sod2, Gm26825, AC160336.1, Krt80, Tnip3, Lrrc8d, Arapl, Gcnt2, Lifr, Rftnl, Marchl, Clec4n, Snx20, Rhog, AB124611, Sla, Hexa, Taok3, Rnhl, Neurl3, Alox5ap, Cmpkl, Nipbl, Ost4, Fisl, Slpr5, Cd274, Dock5, Naga, Trem3, Vavl, Sirpblc, Irf5, Tm6sfl, Bhlhe40, Ncf2, Fndc3a, Wls, Rbm7, Abil, Gns, Foxpl, Capzal, Rbmsl, Picalm, Plagl2, Ggtal, Lfng, Nuak2, Gm6377, Cat, Ttc7, Cd302, Rnaset2a, Secl411, Htra2, Herc4, Lnpep, Nfat5, Xiap, Rap2a, Wdrl, Cbl, Serpinb6a, Rab5c, Tsc22d4, Dbnl, Mgstl, BC005537, Ppplrl2a, Cripl, Eifl, Slcl6al0, Ldlrad3, Gsap, ArhgeflOl, Tmem38b, Elovl5, Atf6, Slcl5a4, Elmol, Sikl, Ifnar2, Camk2d, Plxnb2, Rilpl2, BC018473, M6pr, Tmcol, Mtpn, AC149090.1, Gnbl, Myll2a, Mrpl52, Ubb, B4galt5, Dram2, Acsl5, Sh3kbpl, Tifab, Asph, Ppplrl5b, Csf2rb, Skil, Vsir, Pycard, Qk, Emp3, Atp6v0dl, Eif4g3, Piml, Ppp2r5c, Pten, mt-Co2, Atp6vlf, Gnb2, Gapdh, P2ryl0b, Ebi3, 6430548M08Rik, Sortl, Abcc5, Gpr35, Acot9, Ehbplll, Zdhhc6, Ddhdl, Pygl, Bachl, Mapkl4, Tnfaip812, Itch, Atp6apl, Tnfaip8, Pknl, Taccl, Nin, Adiporl, Nsd3, Mbnll, Kras, Fam32a, Pdcd4, Eif5b, Nsa2, Pilrbl, Dokl, Map3kl4, Milrl, Sirpblb, Diaph2, Rasa4, Illb, Nedd9, Dock8, Gprl37b, Ptpnl2, Atp2cl, Soatl, Rnfl9b, Snap23, Nptn, Mklnl, Otulin, Nfil3, Eif4ebpl, Fyn, Kctdl2, Ywhag, Mpc2, TaflO, Btg2, Clta, Sh2dlbl, Arid3a, Cdc42ep2, Crybg3, Raplgap2, Sowahc, Lyll, Ppmlh, Hsdl7bl 1, Sgk3, Plcg2, Cers6, Notch2, Alcam, Lilr4b, Fam 168a, Rsul, Napg, Rnfl49, Ifngr2, IllOrb, Dgkz, Tribl, Cyb5a, Pltp, Git2, Add3, Ccnd3, Birc6, Serpl, Ier5, mt-Ndl, Ywhab, Ms4a4a, Apobr, Pik3r5, Rasgrpl, Mkll, Sbno2, Tank, Ncoa3, Cbfa2t3, Fcgr3, Pdcd6ip, Cdc42sel, Slc6a6, Bnip2, Ypel3, Kmt5a, Snx5, Asapl, Spop, Ssr3, Ccdc50, Nufip2, Mtdh, Arfl, Hnrnpf, Ncorl, Ube2d3, Enol, Llcam, G6pdx, Rnfl66, Tlr7, Was, Plbdl, Stat6, Arhgap9, Pde4b, Aupl, Rara, Ogfrll, Gusb, Birc3, Syngr2, 993011 U21Rik2, Magtl, Degsl, Stkl7b, Pgd, Mapk3, Wsbl, Kritl, Tab2, Polr2a, Klhl24, Herpudl, Gadd45b, Mbnl2, Uncl 19, Psenen, Mrpll4, Dyncli2, Gdi2, Atp6v0e, Son, Klhl5, Caspl, Vamp5, Slc8bl, Runx2, Elmo2, Batf, St3gall, Lpcat2, Zfp710, D17Wsu92e, Cflar, Phyh, St3gal4, Myadm, Retregl, Sept9, Taf61, Pold4, Dusp6, Rassf3, Gda, Aldh2, Torlaipl, Bri3bp, Stk4, Med28, Prpf38b, Wdr26, Rtn4, Chmp2a, Chmp4b, Sdcbp, Rabl4, Jund, Nbn, Teskl, Tlrl3, Pik3cg, Zfyve9, Xdh, Scarbl, Sh2b3, Pxn, Dock4, Ceptl, Hexb, Vpsl3c, Cnppdl, Ncfl, Map2kl, Crlf2, Mllt6, Ube2f, Hsdl7bl2, Cmtm7, Faml05a, Slk, Api5, Ggnbp2, Gsr, Abr, Iscu, Xbpl, Wnkl, SlOOal l, Rab8a, Fam96a, Ogt, Pak2, Brd2, Rockl, Arl6ipl, Rhob, Bri3, Pomp, Scandl, Cox7a21, Smagp, A630001G21Rik, Cd3001b, Pitpnml, Slc7a7, Lrrc8c, Etv6, Synj l, Stxbp3, Nabl, Faml29a, Laspi, Zc3havl, N4bp211, Pira2, Cdc42ep3, Ehd4, BC017643, Cast, Cnpy3, Map3kl, Gpr65, Gfptl, Inpp5d, Safb2, Psme2, Tapbp, Serinc3, Asahi, Cmip, Chmp3, Tpp2, Arid4a, Arl4c, Snx3, Thoc2, Pabpcl, Rbm39, Calr, Arhgap27, Arhgap39, Prkch, Gsdmd, P4hal, Mvp, Atpla3, Ctsd, Plod3, Tnfrsfla, Faml74a, Sirt7, Tnrcl8, Slcl2a6, Osbpl8, Cpd, Lyst, Nr3cl, Fam 107b, Kansll, I12rg, Mef2d, Slc44a2, Tm9sf4, Plaur, Copl, Grk6, Znhitl, Galntl, Ashll, 5031439G07Rik, Stag2, Cyfipl, Larp4b, Mknk2, Limsl, Cd2ap, Arf5, Tprgl, Arl6ip5, Syf2, Higd2a, Ccdcl2, Clkl, 1110008F13Rik, Serinci, Atp6vlel, Lars2, Gpil, Minkl, Tmc6, Elf4, Bakl, Tnfaip2, Tppl, Acap2, Fam53b, Lmbrdl, Pik3cd, Stx7, Limdl, Zyx, Chd9, Ppplrl8, Madd, Xprl, Crll, Itsn2, Istl, Sri, Ghitm, Arhgap45, Chpl, Spen, Ankrdl3a, Dnm2, Epnl, Pdhal, Foxn3, Mxil, Ccnll, Emd, Rbm5, Baz2b, Taxlbpl, Plgrkt, Sf3bl, Hectdl, Ralbpl, Kmt2e, Ddx3x, Ankrdl l, Ifrdl, Pfdn5, Mania, Rab32, Stk40, Myolc, Lrmp, Selll, Rap2b, Prexl, SnxlO, DlErtd622e, Flii, Snxl, LrplO, Slc35c2, Ep300, Cntrl, Nfe211, Arf6, Cdc42se2, Map7dl, Mkrnl, Ube2a, Hipkl, Cebpg, Inpp5f, Crk, Tmeml23, Lman2, Ap2bl, Emb, Arfgefl, mt-Co3, Mafg, Aktl, Spag9, Rabla, Rblccl, Ssu72, mt-Nd3, Bazla, Lamtor2, Purb, Ubl5, Pcbp2, Tpr, Uqcrb, Bmt2, Hivep2, Selplg, Epb4112, Rc3hl, Erbin, Wipfl, Foxn2, Nfatc3, Ddi2, Slc29al, Rgsl9, Ets2, Rabi lb, Derll, Glgl, Ppp3rl, Nrbpl, Nfix, Zfand6, Wapl, Jarid2, Oserl, Kdm2a, Vps4b, Mark2, Emc7, Snxl8, Mia2, Ppp4r2, Ctsl, BcllO, Psmel, Tceal, Hook3, Sodl, Tmem234, Tra2a, Dadi, Map4k4, Prpf40a, Oazl, Pkm, Rnase6, Sgpll, Sft2dl, Prep, Myo9b, Litaf, Gltp, Tmed7, Nsf, Ube2ql, Copa, Riok3, Usp8, Faml20a, Ccm2, Vamp4, Vps26a, Cnih4, Sdf4, Phf2011, Jakl, Ppp4r3b, Duspl l, Taokl, Frgl, Kdm6b, Sin3b, Faml04a, Cwcl5, Ttcl4, Tmeml60, PpplrlO, PdcdlO, Cdc51, H2afj, Papola, Luc712, Eif4a2, Morf411, Atp51, Ppp lea, Prrc2c, Ndufa6, Pgaml, Dnajal, Junb, Gmip, Nek7, 1116, Sptlc2, Sorll, Mia3, Ythdf3, Rasgrp2, Ccnt2, Ino80d, Susd6, Marc2, Atpl3a2, Farl, Twf2, Arhgef2, Cdc40, Tmem30a, Baz2a, Snapc5, Cab39, Bdpl, Fam50a, Blvra, Ranbp2, Dlst, Adprh, Bcap31, Ncor2, Selenot, Lbh, Faml l la, Rbm42, Vps35, Brd7, PetlOO, Trappci, Pari, Mapkl, Cnot61, Brd4, Chic2, Histlhlc, Pnisr, Reep5, Selenok, Hnmpul2, Ier3ipl, Phf3, Canx, Rbm25, Cox6al, Fus, Bax, Jptl, Cstb, Cd3001f, 2900097C17Rik, Zmynd8, Arhgapl5, Zmiz2, Tmem259, Rsfl, Aip, Ociadl, Lsml4a, Ap3sl, Csnkld, Tmbim4, Tmem33, Commd6, Ppplrl5a, Arid5b, Upf2, Acaala, Dctn4, Rab7, Ptpnl l, Nrdl, Rtn3, N4bp212, Zfp207, Mycbp2, Supt4a, Tle4, Tra2b, Smchdl, Yyl, Esd, Srrml, Dnajc8, Smdtl, Slc25a5, Selenop, Smgl, Os9, Setd2, Gstol, Rtf2, Stt3b, Hercl, Gnal3, Azinl, Atp6vla, Tripl2, Smiml4, Gatad2b, Sptanl, Gps2, Cite, Mbd2, Tm9sf3, Dbi, Lamtor5, Rabacl, Ankrdl2, Crebbp, Sfrl, Semi. Table 2D: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 4 mt-Atp6, mt-Co3, mt-Co2, mt-Col, mt-Nd2, mt-Cytb, mt-Nd4, mt-Nd3, mt-Ndl, mt-Nd5, mt- Atp8, mt-Nd41, Mai at 1.
Table 2E: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 5
S100a9, S100a8, Cxcl2, Illb, Retnlg, Cdl4, Srgn, G0s2, Cebpb, Hdc, Mxdl, Junb, Ifitml, Duspl, Lcn2, Wfdc21, Mell, Csf3r, Illr2, Msrbl, Tnfaip2, Nfkbia, Ifitm2, SlOOal l, Fthl, Neatl, Btg2, Rnfl49, Cxcr2, Clec4e, Lrgl, Acodl, Hp, Ets2, Fxyd5, Ccrl2, Piml, Grina, Tyrobp, Slcl6a3, Ccrl, Btgl, Treml, Dennd4a, Slc7al l, Lcpl, Plaur, Stkl7b, Actgl, Mmp9, S100a6, Wfdcl7, Tpd52, Gadd45b, Cd3001f, Alox5ap, Cd9, Litaf, Cdk2ap2, Sorll, Zfp36, Samsnl, Zyx, Plek, Egrl, Fos, Cd33, Selplg, Lyst, Plk3, Gcnt2, 2810474019Rik, Cd44, Pglyrpl, Nfkbiz, Spil, Picalm, Clec4d, Ncf2, Rdhl2, Ier3, Ptgs2, BC018473, Kdm6b, Zfp3612, Fosl2, Cyp4fl8, Mmp8, Iqgapl, Lmnbl, Ptprc, Malatl, Adam8, Ndell, Ptafr, Fgl2, Lilr4b, Pnrcl, Mapllc3b, Cd52, Taldol, C5arl, Gdpd3, Mareks, Slfn2, Cxcr4, Stfa211, Csfl, Emilin2, Csrnpl, Adiporl, Slfnl, Nudt4, Nlrp3, Gabarap, Actb, Ncf4, Ccnll, Tribl, March7, Ptpnl, Pygl, Zcchc6, Anxal, Fcerlg, Gmfg, Cdknla, Anxa2, Osm, Asprvl, Cebpd, Klf3, Ftll, Jami, Ncfl, Ppplrl5a, Tmsb4x, Mcempl, Gnai2, Ppplr3b, Fbxl5, Kctdl2, Ddx3x, Arg2, Csf2rb, Rhog, Arpclb, Cd53, Baspl, Isgl5, H2-D1, Tnfrsfla, Fcgr3, Socs3, Capl, Hcar2, Themis2, Ypel3, Slcl5a3, Rac2, Adgre5, Marcksll, Gda, CoqlOb, Ccl6, Atg3, Lstl, Ostfl, Sdcbp, Steap4, Igflr, Entpdl, Snap23, Ogfrll, Vasp, Lspl, Eifl, Pilra, Jdp2, Pla2g7, Klf2, Aldoa, E112, Ssh2, Nfkbid, Ier2, Cd84, Skil, Corola, Prdx5, Illrn, Tspo, Nr4al, Fgr, Neurl3, Cd24a, Tsc22d3, H2-Q10, Snxl8, Ptpn6, Ifitm6, Chill, Nfaml, Fpr2, Ezr, Cotll, Samhdl, H3fib, AC110211.1, Glrx, Tiparp, Pfnl, Gpsm3, Tgfbi, Snx20, Vmpl, Rab7, Clkl, Rab20, 2310001H17Rik, Inpp5d, Pten, Srsf5, Ddx6, Crispld2, Dgatl, Syk, Stat3, Cyba, Ninj l, Myh9, Ier5, Perl, Mirl42hg, Tnfaip3, Arpc3, Arpc2, Hclsl, Rabgefl, Kdm7a, Lyn, Cytip, Klf6, Jund, Slc2al, Pxn, Sbno2, Skap2, Kpna4, Ptp4al, Pptl, Rbmsl, Grk2, Gpcpdl, Myll2b, Slfn4, Smox, Cpeb2, Cardl9, Gadd45a, Glipr2, Retregl, Tlr2, Fmnll, Pde4b, Hipkl, Lamp2, Tpm4, Klfl3, Trem3, Sell, Cd300a, Ppp2r5a, Cd300c2, Ddx5, Rabl lfipl, Igfbp6, Itgam, Ppplrl8, Ptpre, Ehdl, Atf3, Rsrpl, Nktr, Dhrs7, Dmxl2, Il 13ral , Gsn, I117ra, Efhd2, Msn, Spag9, Txnl, Ube2h, Birc3, Apbblip, Laptm5, Atp6vlgl, Atp6v0e, Dhrs9, Sirpblb, Celf2, Gpil, Slc38a2, Siglece, Slc2a3, Vsir, Sh2d3c, Plekho2, Nfil3, Ctsd, Abr, Mrpl33, Atp2bl, Il lf9, Ill rap, Pnpla2, Itgal, Duspl6, Txnip, Clicl, Tra2a, Trim30b, Iqsecl, F6300280 lORik, Stxl l, Hcst, Lilrb4a, Tmccl, Jakl, Raplb, B2m, Coxl7, Selenon, Gm5150, Gm2a, Fam32a, Sf3b 1, 1118rap, Myd88, Rassf3, Pbxipl, Dusp5, Diaphl, Dazap2, Arhgdib, Fam49b, Tmbim6, Cdknlb, Wnkl, Rin3, Cmtm6, Pagl, Ripor2, Tgolnl, Ccnd3, Ptbp3, Taxlbpl, Gng5, Pkm, Cass4, Cfap43, Hdac4, Gpr35, Cdc42sel, Lcp2, Sirpa, Nfe212, Ppplr2, Chd7, Cyth4, Hectdl, H3f3a, Ube2b, Slc40al, Tlrl3, Tcn2, Sntb2, Gliprl, Cpd, AB124611, Igsf6, IllOrb, Oserl, Antxr2, Ltb, Adrb2, Pirb, Jmjdlc, Cuxl, Prrl3, Actr3, Sh3glbl, Slc22al5, Mirtl, Notchl, Slc9a3rl, Arrb2, Lbr, Wipfl, Tet2, Myadm, Pak2, Plin2, Anxal l, Arid5a, Klhl2, Svil, Rcsdl, Nup98, Itgb2, Pgd, Satl, Baz2b, Grb2, Nadk, Arpc5, Rael, Zfand5, Gm26532, Trim30a, I16ra, Sbnol, Mapkapk2, Ubc, Trpm2, Bstl, Cd3001b, Tle3, Sirpblc, Rassf5, Tm6sfl, Csf2ra, Tnrc6b, Tsc22d4, Mbnl2, Cdc42, Akapl3, Fprl, Rbm47, Qsoxl, Map2k3, Tnfrsflb, Myolf, Washc2, Arid4a, Vamp8, Supt4a, Klf7, Kras, Pgkl, Sema4a, Pfkfb4, 1600010M07Rik, Ccpgl, Lpcat2, Tnrcl8, Pira2, Itpkb, Cmip, Slcl lai, Eif4ebpl, Fam 107b, Cnn2, N4bpl, Chmp4b, Id2, Rab44, Mboat7, Ddit3, Susd6, Sikl, Sla, Ankrd44, Por, R3hdm4, Tgm2, Pstpipl, Furin, I14ra, Osbpl9, Nsd3, Vps37b, Cdkn2d, Sri, Sema4d, Pelil, Ncorl, Itga4, Lilra6, Notch2, Cd82, Ill Ora, Snrk, Emb, Rgs2, Myl6, Actr2, Ube2d3, D8Ertd738e, Gcntl, Usp32, Triml2c, Ccng2, Actnl, Rab27a, Cd37, Medl31, Xpo6, Hifla, BcllO, Man2bl, Ogt, Etfl, Enol, Gapdh, Pil6, Fes, Lrrc25, Ptpnl2, Spty2dl, Smap2, Midn, Arhgap45, Pcfl l, Ptk2b, Dennd5a, Cd244, Slc6a6, Rhoa, App, Son, Slpi, Dck, Ttc7, Femlc, DlErtd622e, Rab8b, Lrrfipl, Bin2, Arhgap30, Cd47, Rabacl, Atp6v0b, Pgaml, Cstb, Arhgap9, Arih2, Crebrf, Rnfl67, Msll, Nrros, Fau, Irf2, Gnb2, 1810058I24Rik, Wbpll, Ifitm3, Faml29a, Synj l, Rgs3, Rara, Rnfl l, Dnm2, Sde2, Kdm2a, Serinc3, Ccnl2, Ifnarl, Ppplrl2a, H2afj, Apobr, Dok3, Preb, Nedd9, Laspi, Samd4b, Neul, Nr3cl, Sephs2, Max, Crk, Fyb, Sh3bgrl3, Atp6v0dl, Zfpl06, Clec2d, Arhgap25, Rif, Flotl, Cd3001d, 1116, Pik3cd, Rasa3, Cdl64, Gnai3, Metrnl, Ep300, Lnpep, Rockl, Klhl24, Chmp2a, Kmt2e, Stat6, Tbcldl4, Mknk2, Secl411, Capzal, Tprgl, Stk38, Hnrnph2, Adprh, Atf7ip, Serf2, Ssu72, Ankrdl 1, St3gal4, Vavl, Pknl, Cbl, Ppp3ca, Rafi, Tgfbrl, Emd, Capzb, Irf2bp2, TimmlOb, Myll2a, Nckapll, Reep3, Dnajc5, Atp6ap2, Faml l la, Syf2, Crebbp, Nrdl, BC005537, Prdx6, Slc44a2, Atp6apl, Tapbp, Tpm3, Rsrc2, Mark2, Ankrdl3a, Cregl, Phf2011, Rblccl, Csk, Ubald2, Mob4, Rab8a, Mettl9, Nipbl, Selenok, Ifngrl, Rnfl30, Dock2, Arl4c, Arpc4, Prkcd, Wdrl, Carhspl, Tab2, Tlnl, Bazla, Serpl, Taokl, 1110008F13Rik, Prelidl, Asapl, Bri3, Gpxl, Rabi la, Aff4, Rtn4, Ifi2712a. Table 2F: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 6
Lyz2, S100a4, Ifitm3, Plac8, Cd74, Cripl, H2-Abl, Chil3, H2-Aa, H2-Ebl, Vim, Lgals3, S100a6, Ms4a6c, Ifi2712a, Psap, Hspala, Tyrobp, Cst3, Satl, Tmsb4x, Cybb, Ccr2, Arpclb, Corola, Tgfbi, Cd52, Gpxl, Actb, Cyba, Ctss, Alox5ap, Ccl9, Fnl, Fcerlg, Cebpb, Hspalb, Hp, Ms4a4c, F13al, Lstl, Npc2, Ifitm6, Gngt2, Mafb, Smpdl3a, Polr21, Ifitm2, Actgl, Ctsz, SlOOalO, B2m, Gm2a, Fxyd5, Ahnak, H2-D1, Ctsc, Emp3, Prdx5, Ccl6, Ncf4, Anxa2, Csflr, Arpc2, Fau, Ftll, Fos, Msrbl, Ms4a6b, Lampl, Lspl, Ifngrl, TmsblO, Spil, Atoxl, Pidl, Ms4a6d, Laptm5, Zeb2, Jun, Plbdl, Napsa, Tspo, Slfn2, Pla2g7, F10, Igsf6, Cd300a, Fyb, Rgs2, Lyn, Pitpna, Ptprc, Gnai2, H3f3a, Clec4a3, Gda, Hck, Fam49b, Csf2ra, Raplb, Rhoa, Nr4al, Zfp36, H2-DMbl, Mpegl, SlOOal l, Serf2, Hspa8, Clec4al, H2afj, Actr3, Pfnl, Tptl, Plin2, Nfkbia, Atf3, Tgfbi, Cytip, Cdl4, Ctsh, Ctsb, Samhdl, Taldol, Lrpl, Atplal, Srgn, Capza2, Adgre5, Tpd52, mt-Col, Apls2, Ptpnl, Pld4, Cfll, Cd68, H2-DMa, Myl6, Hmoxl, Ncf2, Emilin2, Prkcd, Flna, Cdc42, Klf4, Arhgdib, Atp2bl, Eifl, Lmo4, Pirb, Ucp2, Gprl41, Wfdcl7, Fgr, Gludl, Neatl, Eeflal, Sec61b, Sirpblc, Gmfg, Tlnl, Rapla, Pabpcl, Pira2, Clec4a2, Cd44, Metrnl, Capzb, Hspa5, Apobecl, Cd300c2, Ostfl, Arpc5, Sh3bgrl3, Eif3f, Tnfrsflb, Cotll, Rnhl, Enol, Plek, Duspl, Illb, Gm21188, Anxa5, Fcgr3, Itgb2, Mell, Gabarap, Btgl, Itgal, Id2, Nadk, Cd47, Itm2b, Fthl, Irf5, Ctsa, Ly6c2, Anxal, Emb, Rael, Sec61g, Mapkapk2, Mgstl, Lgmn, Dbi, Arpc4, Itga4, Clicl, Arpc3, Tkt, Unc93bl, Nfe212, Msn, Ear2, Junb, Calr, Hebpl, Itgam, Fcgr2b, Sirpa, Cx3crl, Aldh2, Cd53, H2-K1, Faml05a, Rassf4, Apbblip, Rrbpl, Mrpl52, Gng5, Zfand5, Gapdh, Vcan, Rnfl30, Vamp8, Psmb8, Lcpl, Iqgapl, Ly6e, Socs3, Ier5, Semi, Cox4il, Klfl3, Soatl, Vsir, Trpsl, Arl5c, Bin2, Sh3bgrl, Lamp2, Capg, Cstb, Atp6v0b, Samsnl, Slc25a5, Rhob, Caimi, Tifab, Nuprl, Clta, Gm9733, Adgre4, Ptpnl8, Prrl3, Eif3h, Cox7a21, mt-Co2, Ifi207, Fucal, Rnfl49, Ccdcl2, Erp29, Atp51, Piml, Pou2f2, Tm6sfl, Arhgap30, Mndal, Trafl, Myll2a, Capl, Arfl, Myolf, Grk3, Efhd2, Kdm7a, Abracl, Nfkbiz, Scandl, Mrpl33, Rackl, C3, Slfn5, Hexa, Corolb, Plekhol, Clec4e, Ace, mt-Co3, Ltb4rl, Csf2rb, Ptpn6, Tppp3, Ssr4, Pdia6, Malatl, Tmeml76b, BC028528, Hopx, I16ra, Fmnll, Nfkbl, Rhog, Hclsl, Arf5, Ier3, Tmeml76a, Tpm3, Zfp3612, Aprt, Ptpro, Snx20, Ccdc88a, Sh3glbl, Brkl, Ppib, Eifik, Gdi2, Nsa2, Klf6, Klf2, Msrl, Ahr, Cd93, Empl, Skap2, Cmtm7, Aifl, Diaphl, Rel, Actr2, Treml4, Sdcbp, Gnb2, Pgkl, Pkm, Evi2a, Tnfrsfla, Mcempl, Myolg, Ly86, Nfaml, AB 124611, Pgd, Pycard, Irf2, Xbpl, Pptl, Tmbim6, Cdk2ap2, Chill, Akrlal, Btg2, Nrros, Man2bl, Gpil, Eifie, Rgsl, Klra2, Lcp2, Sla, I117ra, Shisa5, Pip4k2a, Mtpn, Nabpl, Gdpd3, Mkml, Chmp4b, Nmtl, Bri3, Fam32a, Ptp4a2, Uqcrh, Ier2, S 1 OOal 3, Fermt3, Asahi, Ddhdl, Abi3, Ikbkb, Lilr4b, Ubl3, Ppp2r5a, StklO, Capnsl, Atplb3, Arl4c, Psmel, Itgbl, BC005537, Atp6vlgl, Cox6bl, Btf3, Naca, Sod2, Naaa, Sowahc, Cd302, Tnfaip812, Ptafr, Syngr2, Slk, Cyp4fl8, Tmccl, Cmpkl, Supt4a, Tmem50a, Myll2b, Laptm4a, Picalm, Pdia3, Rsrpl, Slc25a3, Subl, H2afy, Mcub, Ifi204, Plod3, Il 13ral, Rnpep, Ptprj, Gyg, Plekho2, Cebpd, Ikzfl, Zyx, Trf, Slcl5a3, Chmp2a, Atp6vlf, TimmlOb, Ube2d3, Esd, Cox8a, Eef2, Prdxl, Lrrc25, Rap2a, Bachl, Fam49a, Camk2d, Arl6ip5, Nfil3, Ccrl2, Cdknla, Ost4, Grb2, Ccnll, Ndufa6, Hnrnpf, H3f3b, Ifi202b, 1118, Gm5150, Dusp6, Ceacaml, Ifngr2, Rbmsl, Tlr2, Fam46a, Rbm7, Mia2, Reep5, 1110008F13Rik, Tmed2, Ccdc50, Pfdn5, Ywhaz, Gm26825, Pomp, Ms4a8a, Tifa, Jami, Cers6, Torlaipl, Wdrl, Cbl, Filipll, Rtn4, Tmeml4c, TaflO, Smdtl, Atp6v0e, Ywhab, Ubl5, Gm42418, Mefv, Rab32, Cbfa2t3, Magtl, Nckapll, Rnd3, Sppl2a, Cyth4, Myadm, Eif4ebpl, Sri, Psme2, Tnfaip8, Syk, Tmem256, Fam96a, Ccnd3, Atp6vlb2, Snx3, Dazap2, TmedlO, Cops9, Gml0076, Aldoa, Lilra6, ArhgeflOl, Acer3, Cd244, Slpi, Sbno2, Ptpre, Gpr65, Adaml7, P4hb, Ssr3, Bcl2ald, Serpl, Bcl2ala, Tmem258, Ehdl, Akapl3, Ap2a2, Pcbpl, Limd2, Pcbp2, Adssll, Pmaipl, Faml29a, Vpsl3c, Rras, Camkk2, Ube2f, Slcl lal, Lgalsl, Cregl, Mobla, Capzal, Lman2, Hk2, Clec4n, Cope, Slc3a2, App, Snx5, Bnip31, Tmeml67, mt-Nd4, Arhgdia, 2010107E04Rik, Atp5h, Atp5cl, Tagln2, Lyll, Bakl, Sirpblb, Gprl32, Ccr5, Prep, Grn, Stx7, Dok3, Atp6apl, Vamp4, Mppl, Cd48, Derll, Degsl, Sema4d, Pde4b, Jarid2, Spop, Vmpl, Tpm4, Ezr, Mtdh, Hsp90bl, AI839979, Gm6377, Gpr35, Gatm, Epstil, Ehbplll, Itgb7, Ehd4, Clecl2a, Icaml, Stapl, 5031439G07Rik, BcllO, Rpn2, Asapl, mt-Atp6, B930036N10Rik, Canx, Tsc22d3, Arf4, D8Ertd738e, Polrld, Bcl2alb, Cfh, Cyp4fl6, Cebpa, Ifi209, Zfp710, Tlr7, Agpat4, Gpsm3, Taccl, Sdf211, Atp6v0dl, Bazla, Faml l la, Lamtor4, mt-Ndl, Prelidl, Ptbp3, Ptp4al, Cox6al, Mareks, Sf3bl, Eeflb2, Gsdmd, Xdh, Sgk3, Fes, Orail, Slcl5a4, Gusb, Taf61, Runx3, Nptn, Grk2, Snxl, Tmed5, Mef2a, Rab5c, Tmed9, Fisl, Selenof, Kdm6b, Ppplca, Psma7, Jund, AC160336.1, Tmem51, Ralb, Edeml, Dnajbl4, March 1, Hfe, Tmed7, Ill Ora, Dock2, Atpla3, Abil, Arf6, Runxl, M6pr, Gsr, Wls, Lrrfipl, Uba52, Selenos, Sysl, Fosl2, N4bpl, RgslO, Wdr26, Irf2bp2, Edfl, Cox6c, Dusp2, Mycbp2, Stom, Sh3bpl, Scarbl, Hacd4, St3gal4, Tmem38b, Gml5987, Cardl9, Snap23, Faml74a, Adgrel, Pold4, Pnp, Glipr2, Tab2, Atp6ap2, Plaur, Rnfl9b, PsmblO, Limsl, Psenen, PetlOO, Add3, Kpna4, Mrps21, Stk38, Txnip, Tmeml06a, Sqor, Cd86, Sic 16a 10, Necap2, Pik3r5, Rsul, Plcg2, Aupl, Tank, Capn2, Xist, Pepd, Ifnar2, Rbpms, Trim30a, Tet2, Slc6a6, Tmeml31, Lnpep, Sgkl, Stat3, Sdf4, Herpudl, Bnip2, Rac2, Nt5c, Rab7, mt-Nd2, Ninj l, Myh9, Ssh2, Usf2, Spn, Ier3ipl, Ube213, Kmt5a, Ndufal, Oazl, Cox7b, Zeb2os, I830077J02Rik, Nfkbie, Hps3, Zfyve9, Gsap, Mfsdl, Tmem219, Alcam, Slc43a2, Tapbp, Hexb, Rara, Plxnb2, Reep3, Wasf2, BC018473, Wipfl, Stk24, Cnn2, Otulin, Oserl, Iscu, Fbxl5, Klf3, Sgmsl, Cript, Hdlbp, Zbtb7a, Tribl, Mbnll, Scp2, Tmem59, Ndufa3, Rraga, Ppplrl2a, Psmd8, Atp6vlel, Selenok, Dadi, Tmpo, Manf, Arhgap26, Lilrb4a, Ttc7, DlErtd622e, Map3k8, Foxn2, Birc3, BC017643, Rest, Fkbp5, Twf2, Nabl, Rab8b, Glul, DocklO, Snxl8, Bhlhe40, H13, Ppplrl5a, Ube2a, Eloa, Kxdl, mt-Cytb, Dnajc3, Qk, Ssrl, Dnajbl l, Celf2, Atg3, Secl lc, Rbpj, Eif3m, Cnih4, RablO, Rbm39, Son, Nedd8, Ctsl, Caspl, Anxa4, Rp2, Anxa7, Slc7a7, Myd88, Selenop, Mvp, Stat6, Tspanl4, Fgd4, Vavl, Ogfrll, Man2al, Chpl, Atf6, Cast, Ccrl, SplOO, Ifnarl, Ifi203, Emc2, Pknl, Pdcd6ip, Serinc3, Arhgapl7, Rabi a, Surf4, Mbd2, Gadd45b, Uqcrcl, Srp9, Spcs2, Hifla, Cox5b, Adapl, Naga, Milrl, Diaph2, Pdlim5, Fuca2, Esytl, Trafdl, Pik3cd, Taok3, SnxlO, Fcgrt, Itm2c, Spg21, Clec2d, Map7dl, Cisd2, B4galntl, Gml l808, Wsbl, Clintl, Krccl, Cyb5a, Tm9sf3, Tgfbrl, Tomm22, Ppp2r5c, Pten, Mpc2, Vasp, Ppig, Tma7, Uqcrq, Atp5d, Tmem234, Nop53, Krtcap2, Bax, Ubc, Ppplcb, Plekhf2, Irf8, G6pdx, Acot9, Synj l, Ceptl, Tnfaip2, Mfsdl4b, Hpcall, Rap2b, Dock8, Erp44, Scamp2, Sptlc2, Svil, Acaala, Mapkl4, Cyfipl, Tmcol, Mbp, Eif4g3, Rab8a, Cd2ap, Ssu72, Sdhb, Ppp4r2, Eif5b, Atp5e, Psmbl, Uqcrb, Eif4al, Tpil, Was, Bscl2, Cndp2, Gcnt2, Cibl, Cnppdl, Crlf2, Rasa3, Ncfl, Gns, Torla, Arhgap9, Rgsl9, Sh3kbpl, Igbpl, Sorll, Camkid, Cd3001d, Abhdl2, Maltl, Crlf3, Mbnl2, Pbxipl, Bri3bp, Tm2d2, Aphla, Rbm42, Duspl l, Cdc42sel, Nubpl, Fcho2, Eif3j2, Bcap31, Serinci, Ufml, Zmizl, Sec62, Snf8, Dyncli2, Rabl4, Histlhlc, Cuxl, Gnbl, Bola2, Vdac2, Ubb, Pgaml, Tlrl3, Pacsin2, Litaf, Ggal, Notch2, Sirt7, Il 1 Orb, Limdl, Nipa2, Ptpnl2, Rassf5, Map2kl, Hsdl7bl2, Ppp4c, Ebp, I12rg, Arhgap45, Dmacl, Itch, Herc4, Cnpy3, Znrdl, Ptk2b, Stk4, Fndc3a, Epnl, Stkl7b, Syf2, Zfp207, Hsdl7bl0, Copl, Rerl, Yyl, Foxn3, Ap2sl, Tmeml60, Paklipl, Ostc, Sf3b6, Tspanl3, Morf411, Prpf38b, Eif4a2, Tomm7, Atp5g2, LrplO, Adcy7, Vps26a, Ethel, Zfand3, Sirt2, Atp2cl, Ythdf3, Susd6, Cers2, Ankrd44, Ddi2, Adprh, Cdk9, Csk, Nripl, Kdelrl, Gstol, Faml20a, Polb, mt-Nd3, Atp6vla, Srp72, Mctsl, Sdhd, Slc25al l, Dbnl, Ube2d2a, Anxa6, Tceal, PdcdlO, Stxl6, Pak2, 1810037I17Rik, Lamtor2, Rockl, Pari, Ndufal3, Srsf2, Ndufa7, Ifrdl, Selplg, St8sia4, Ctdnepl, Pdhal, Mgat2, Osbpl9, Cebpg, Tgsl, 9930111 J21Rik2, Chmp3, Commd8, Xiap, H2-T23, Epb4114aos, Mknk2, Bbipl, Snx2, Ccdcl24, Tsc22d4, Rexo2, Ppp3ca, Cdc51, Sin3b, Txn2, Usel, Snrpb2, Coxl7, Ubxn4, Cwcl5, Lamtorl, Atp5fl, Pnisr, Spag9, Eif3a, Map4k4, Csnklal, Rbm3, Rin3, Ghitm, Cxcr4, Arrb2, Sap30, Lamtor5, Frgl, Vapa, Mrpl30, Gml6286, Prpf40a, mt-Atp8, Txnl.
Table 2G: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 7 Manf, Fkbp2, Ssr4, H2afz, Histlhlb,
Table 2H: Lists of genes that are up-regulated in the different clusters identified in the of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 8
Apoe, Clqb, Clqa, Ctsd, Clqc, Ctsb, Psap, Lyz2, Selenop, Lgmn, H2-Ebl, Ftll, H2-Abl, H2- Aa, Itm2b, Fthl, Ms4a7, Cd63, Acp5, Vcaml, Ctsz, Cd74, Hmoxl, Lgals3, Cyba, Aifl, Hexb, Wfdcl7, Ctss, Grn, Ctsc, Pltp, Mafb, Cd68, Plin2, Tmsb4x, Gpnmb, Timp2, Lampl, Cregl, Hexa, Pld3, Fcerlg, Mpegl, Ctsh, Hebpl, Fabp5, Cxcll6, Rgsl, Mtl, Npc2, Cstb, Ctsa, Tyrobp, Tgfbi, Cd81, Igfl, Slc40al, Unc93bl, Calr, Sirpa, Trem2, Il 18bp, RgslO, Lipa, Cotll, Gatm, Cd300c2, Glul, Fcgr3, Satl, Prdxl, Maf, Cst3, Ucp2, Tmem86a, Tmeml76b, Sdcbp, Laptm5, Clec4n, Anxa5, Ctsl, Hsp90bl, Serpinb6a, H2-DMbl, Tmeml76a, Pla2g7, Pdia6, Itgb5, Slc43a2, Apobecl, Cfp, Hspa5, B2m, Akrlal, Serf2, Abcal, Gusb, Csflr, Cx3crl, Actb, Tgm2, Blvrb, Ninj l, Man2bl, Gpxl, Abhdl2, Lgalsl, Gabarap, Pdia3, Clta, Stabl, Sdc3, Adgrel, Fcgrt, Lrpl, Lstl, Clec4a2, Lgals3bp, Abcgl, Gns, Gngt2, Cd300a, Sdf211, H2-DMa, Slc7a7, P2rx4, Tppl, Gpr65, Trf, H2-K1, Atp6v0b, Arpclb, Cd38, Gng5, Axl, Anxa4, Atpl3a2, Syngrl, Fcgr2b, Slc3a2, Pfnl, Cfll, Dhrs3, Asahi, Gprl37b, Ms4a6c, Fyb, H2-D1, Rrbpl, Zeb2, Snx5, Cebpa, Faml05a, Ms4a6d, Abcc3, Ly86, Erp29, Bri3, Ptms, Tcn2, H2afj, Ssr4, Nrlh3, Gimp, Itm2c, Tgfbrl, Gapdh, Hpgds, Msrl, Tcirgl, Mgstl, Rnhl, Atoxl, mt-Ndl, Gnal2, Atp6ap2, Lap3, Atp6vlgl, Mertk, Acp2, Mmpl4, Soatl, Sgpll, Atp2bl, Gm2a, Ppib, mt-Co3, Dnase2a, Slcl5a3, Tmem256, Tgfbi, Bcl2alb, Snx3, Capzb, Gnai2, Atp6vlf, Itga9, Cd48, Aldh2, Arl4c, Tmeml4c, mt-Col, Scp2, Aprt, Plbd2, Scarb2, Cd84, Frmd4b, Slcl lal, Csf2ra, Ifnar2, Arl6ipl, mt-Co2, Ncehl, Plekhol, Capg, Comt, Fucal, Slc6a6, Ptpnl8, Rab5c, Cox5a, Cndp2, Cadml, Lamp2, Clec4a3, Lamtorl, Atp6v0e, Tmbim6, Sh3bgrl3, Fuca2, Ubl3, Capza2, Arhgdia, Tmeml60, Aldoa, Atp6apl, Cyth4, Efhd2, Pptl, Reep5, Gdi2, Cd52, Arpc2, mt-Cytb, Fos, Dtnbpl, Corolb, Vamp8, M6pr, mt-Nd3, Sh3glbl, Caimi, Pgkl, Txnl, Cd93, Cd302, Svbp, Cyfipl, Lamtor4, Igsf8, AB124611, Pld4, Atp6vlb2, Laptm4a, Pitpna, Arpc5, Arpc4, Dadi, Gdel, Myl6, Igsf6, Vsir, Mareks, TmedlO, Rael, Psmd8, Manf, Adaml7, Atp6vla, Ostfl, Ifi27, Nfe212, 0610012G03Rik, Atp6v0dl, Cdc42, Canx, Fermt3, Lrpapl, IllOrb, P4hb, Atp6vld, Por, Fkbp2, Prdx5, Arpc3, Clicl, Grb2, Spcs2, mt-Nd4, Arrb2, Psmb8, Rabla, Vim, Dnajbl l, Iscu, Capnsl, Cox4il, Enol, Rnfl30, Trappc21, Cite, Qk, Cops9,
Table 21: Lists
Figure imgf000074_0001
are up-: in the different clusters identified in of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 9 Hbb-bs, Hba-al, Hba-a2, Hbb-bt, Lars2, PeglO, Tubb5, Hmgbl, Hsp90aal, Eeflal, Hnmpa2bl, Ptma, Hnrnpal, TmsblO, Eef2, Nel, Stmnl, AY036118, Atp5al, Hnrnpu, Eif4g2, Tubalb, Eif5, Npml, Ywhae, Serbpl, Hsp90abl, Gnas, Soxl l, Ubb, Pcbp2, Naplll, Dnajal, Tptl, Hnmpc, Set, Rackl, Eeflg, Anp32b, Pkm, Dyncli2, Cct2, Eif3k, Snrpg, Hspel, Hmgb2, Gm42418, Cct5, Eif4al, Atp5b, Ubl5, Atp5k, Rbm3, Mif, Tma7, Nefl, Ptp4a2, HnrnpaO, Pcbpl, Tubb3, Tubala, Naca, Hnrnpk, Capza2, Ywhab, Topi, Eif3a, Snrpb, Morf411, Ppia, Uqcrh, Cnbp, Gpil, Pomp, 2010107E04Rik, Sumo2.
Table 2J: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 10
Cd74, Ebfl, Cd79a, Ighm, Cd79b, Ighd, H2-Aa, H2-Ebl, H2-Abl, Iglc2, Igkc, Btgl, Mef2c, mt-Nd2, Ms4al, Cd37, Fau, Ly6e, Malatl, Ly6d, mt-Co3, mt-Atp6, mt-Ndl, Tptl, mt-Co2, mt-Cytb, mt-Col, mt-Nd3, Etsl, Stkl7b, Iglc3, Foxpl, mt-Nd4, Gm8369, Gm31243, Ralgps2, Dmxll, Gm42418, H2-Ob, Ccr7, Tsc22d3, Lars2, Napsa, Cxcr4, Klf2, Gimap6, Bankl, Cd52, Fcmr, Eeflal, Zfp3611, Tnfrsfl3c, Iglcl, Sorll, Shisa5, Ddx5, H3f3a, Pax5, Gm26825, Serpl, Ptprcap, Zfp3612, H2-DMb2, mt-Nd5, Vpreb3, Satbl, Ltb, Rackl, Hvcnl, H2-K1, Macfl, Pold4, Siglecg, 4930523 C07Rik, Faml07b, Cd83, Gimapl, Syk, Jund, Rhoh, Arhgdib, Hspalb, Scdl, Smad7, Arhgefl, Crlf3, Uba52, Ifi203, Arhgap45, Rel, Clkl, Cd55, H2-DMa, Dusp2, Mbnll, Rbm39, Pdcd4, Fcrla, Zfp318, Ptpnl8, Xist, Ciita, Maltl, Mndal, Inpp5d, Gm30211, Cdl9, ChchdlO, Sell, Smap2, Snx5, Slprl, Arhgapl5, Elfl, Jakl, Pfdn5, Abliml, AC149090.1, Eif3f, Slc38a2, Tra2b, Corola, Eef2, Rasgrp2, Smiml4, Eif4a2, Eifl, Btla, Fchsd2, Rac2, TmsblO, Cd72, Zcchcl l, Son, Ankrdl l, Ly86, Gdi2, 993011 lJ21Rik2, Bell la, Limd2, Bptf, H2-D1, Ier5, Bink, H2-Oa, Gprl83, Mtssl, Csk, Akapl3, Actr3, Ripor2, Klhl24, Hnrnpf, Lmo2, Swap70, Cd69, 1110059E24Rik, SplOO, Tmeml23, mt-Nd41, Cd22, Mzbl, Slamf6, Cox7a21, Serpinbla, Arap2, 112rg, Ssh2, Eeflg, Eeflb2, Btg2, Cd38, Irf8, Snx2, Txnip, Jmjdlc, Neurl3, Zcchc7, Ptbp3, Fcer2a, P2ryl0, Sipal, Gml l808, Tra2a, Gmfg, Cmah, Ptpn22, Samd91, Stapl, Bazla, Foxol, Pik3ipl, Pxk, Rcsdl, Capg, H2-T23, Psmb8, Phip, mt-Atp8, Prrc2c, Pou2afl, Spib, Marchl, Ttcl4, Eefld, Ptp4a2, Pabpcl, Tspan32, 4833420G17Rik, Mania, Pou2f2, Cd53, Snrpg, Eif3e, AY036118, Trib2, Lbh, Itsn2, Farsb, Aldh2, Ankrd44, Irf2, Tnrc6b, Arpc51, Luc712, Cytip, Uqcrh, Nsa2, Cr2, Ikzf3, H2-Q7, Chd2, B2m, Myh9, Laptm5, Ptpn6, Eifih, Ubb, Fcrll, H2-Q6, Cythl, BC018473, Dgkd, Arhgapl7, Kmt2a, Stk24, Dennd4a, Cd47, Kmt2e, Nop53, Srsf5, Tmsb4x, Ddx6, Gml0076, HnrnpaO, Rsrpl, Sh3bp5, Elmol, Etnkl, Ptprc, Grb2, Scafl l, Naca, Rbm25, Srrm2, B3gnt5, Ppplrl6b, Stat4, Crebrf, Rab21, Add3, Pnisr, Nrdl, Pnrcl, Mif4gd, Grap, Map3kl, Prkcb, Filipll, Vps37b, Slc38al, Prpf38b, Atf4, B930036N10Rik, Samhdl, Purb, Ube2d3, Sh3bgrl3, Slcl2a6, Kansll, Ezr, SlOOalO, Zfp292, Wasf2, Zfp644, Msn, Smchdl, Hspala, Pxdcl, Rabgapll, Plekha2, Gga2, Lmbrdl, Smgl, Strbp, Rsbnll, Arhgap30, Tnfaip8, Nipbl, Rhoa, Srsfl l, Tpm3, Cd2, Sesnl, Tnfrsfl3b, Rassf2, Flil, Acadl, Grk6, Tmod3, Ppplrl5a, N4bp212, Rabacl, Pfnl, Wdfy4, Gimap3, H2-Q4, Tmem243, Ptp4a3, Stk4, Unc93bl, Cnn2, Pten, R3hdml, Ddx21, Ubc, Lamb3, Lrrk2, Zdhhcl8, Cnp, DocklO, Dock2, Dennd5b, Ogt, Rapgef6, Tsc22d4, Junb, Tmem234, Sf3bl, Gml0036, Subl, Chst3, Snx29, Gprl71, Gimap4, Lat2, Spl lO, Sdc4, Myole, Itpr2, Birc2, Spl40, Sypl, Tmeml311, Bcl2, Cnot61, Arf6, Kritl, Gnai2, Ddx50, Rbm5, Ashll, Mycbp2, Sec62, Oazl, Bend5, Traf3ip3, Lrmp, Pcmtdl, Nfatc3, 1116, Snhgl2, PpplrlO, Atf7ip, Git2, Setd2, Phf3, Celf2, Prpf4b, Grk2, Wnkl, Kcnqlotl, Tceal, Cnbp, Paip2, Rsrc2, Ncorl, Ifi209, Relb, Escol, Sbkl, Pde7a, St8sia4, Ikbkb, Bini, Camk2d, Herc4, Tcfl2, Limdl, Ifnarl, Foxn3, Hipkl, Aridla, Ahsal, Vars, Otulin, Parpl, Gpbpl, Trp53il l, Prkd2, A630001G21Rik, Arhgefl8, Ppplr21, Slc50al, Retregl, Trim25, Birc3, Tgfbr2, Ptk2b, Pan3, Ep300, Ctsh, Vgll4, Tob2, Kdm7a, Zmyndl l, Arid4b, Lspl, Ankrdl2, Cd24a, Pak2, Clicl, Dnajc7, Smc6, Taxlbpl, Arglul, Acapl, Septi, Gm26740, Rchyl, Plcg2, Ikzfl, Cdkl3, Mknk2, Kdm5a, Tafl5, Aff4, Psenen, Sysl, Senp6, Duspl l, Bodll, Psmel, Top2b, Pnn, Kif21b, Itprl, Acp5, Ms4a4c, Elk4, BC017643, Mirl42hg, Ctse, Tsc22d2, Upf2, Pkig, Swtl, Medl3, Cdc42se2, Iqgapl, Pknl, Birc6, Rp9, Ythdcl, Ppdpf, Serf2, Atp6v0b, Nol7, Chd4, Dnajal, Arhgap4, Abcal, Ublcpl, Lpgatl, Sh3kbpl, Taccl, Eml4, Ifi2712a, Tial, Faml l la, Nsd3, Csnklg3, Nsdl, Tcofl, Rbbp6, SrsflO, Ppp3ca, Hnrnpl, Xrn2, Ctcf, Arl6ipl, Myll2b, Snrnp70, Hnrnpa2bl, Actr2, H3f3b, Eif3k, Ly6a, Myolc, Pagl, Tbcldl, Rest, Alkbhl, Nsf, Ppp4r3a, Snrnp48, Ypel3, Zcchc6, Actb, Sri, Pds5a, Numal, Naal5, Ccnll, Bclafl, Tafld, Pgls, Tcpl ll2, 5031425E22Rik, Mdm4, Cd84, Dok3, Pole4, Nr3cl, Dnajbl, Ncoa3, Lbr, Mark2, Brd9, Gatad2b, Supt20, Syf2, Sf3b3, Chd6, Ccnd3, Tgfbl, Fubpl, Tmbim6, Tnrc6c, Acini, Eif3m, Morf411, Wdr26, Atp5g2, Ier2, I14ra, Ccdc88c, Tmem55b, Marc2, Nfat5, 4932438A13Rik, Mef2d, Crebzf, Crll, Nfkbl, Bcap31, Ranbp2, BC005624, Phf2011, Cwfl912, Rbm26, Supt4a, Rsbnl, Gpatch8, Safb2, Atxn21, Fam49b, Cdkl lb, Arid4a, Faml33b, Rtcb, Arpc2, Tmed9, Matr3, Sbnol, Csdel, Dhx9, Cnot3, Ndufa6, Ppib, Rtfl, Pcbp2, Tpr, H2-DMbl, Uvrag, Pde4b, Leng8, Gpbplll, Zc3havl, Arid5b, Taf61, Dip2b, Mierl, Ppp4r3b, Lyn, Cdkl2, Nudcd3, Trim35, Plgrkt, Tapbp, Poldip3, Wdrl, Kpna4, Zfp207, Plekhol, Sfl, Setd5, Polr2a, Ube2d2a, Mbd2, Yyl, Brd2, Herpudl, Hnmpm, Fus, Sfpq, Hspel, Sgmsl, Runxl, Ccm2, Tox4, Lnpep, Prkacb, Kdm2a, Histlhlc, Fbxw2, Nktr, Nufip2, Uspl5, Mrpl24, Tomm22, Dazap2, Ddxl7, Tle4, Baz2b, Ago2, Rock2, Thoc2, Mtdh, Sec61g, Ywhaz, Tcf25, Eif5, Naplll, Psmb9, Clk4, Ppil4, PdcdlO, Vasp, Kmt2c, Wac, Tmem50a, Fiplll, Cuxl, Evi, Tmed5, Tnrc6a, Cpsf6, Rblccl, Ymelll, Cdc42, Ppplrl l, Polrld, Ppplcc, Gpil, Eif5b, Ddx24, D8Ertd738e, B4galntl, Mat2b, Hclsl, Ppplrl8, Ostfl, Stag2, Xiap, Tm9sf3, Akap9, Rockl, Thrap3, Aes, Tma7, Psmbl.
Table 2K: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 11
Meg3, Xist, Kcnqlotl, Gm26917, Chgb, Tcf4, Auts2, Dlkl, mt-Cytb, Epha5, Gnl3, Tsix, Srrm2, mt-Atp6, Cacna2dl, Mki67, Ncaml, PdelOa, Tafld, Rtnl, mt-Co2, Adarb2, Mirg, mt- Nd4, BC005561, Top2a, Slit2, Ptprs, mt-Nd2, Sfib3, Pnn, Agtr2, Ank3, Zfp644, C130073E24Rik, Rsrcl, Hjurp, Maplb, Alkbhl, Eml5, Fubpl, mt-Ndl, Zbtb20, Celf4, Atrx, Eyal, Snmp70, Nop56, Ttcl4, Stxl6, mt-Co3, D10Wsul02e, Slc24a5, Sytl l, Peg3, Zranb2, Nespas, Adgrb3, Rbm4b, Chd6, Ddx50, Chga, Eprs, Tial, Ktnl, Luc713, Pnisr, Pdcdl l, R3hdml, Snhgl2, mt-Nd41, Ank2, Mytll, Srrm3, Tmeml32a, Nktr, Zdbf2, Tecr, Chd4, Cepl64, Snap25, Kif5c, Phip, Slc38a2, Luc712, Chd3, Mat2a, Ttc3, Ssbp2, Ncapd3, Csppl, Dst, Zfp638, Trim35, Srekl, Prpf4b, Nfasc, Kcnk9, Pbx3, Adgrgl, Crebzf, Pabpnl, Kif21a, Rbm26, Kiflb, Wdr43, Akap9, Pde3a, Meis2, Zfp704, Ahil, Aplp2, Kmt2a, Plcb4, Ddx46, Isll, Pcskln, mt-Nd5, Gm26699, Spata7, Kifl5, Zfp266, Dhx30, Nrp2, 4833420G17Rik, Paxbpl, Pura, Srsfl 1, Zcchcl 1, Slc38al, Selenoi, Tub, Ccnt2, Rere, Podxl2, Ilf2, Smpd3, Nsd2, Srpkl, Ewsrl, SrsflO, Creb5, Cep44, Maml3, Tafl5, Phf3, Fus, Ttcl9, Tmem57, Zfhx2, Enah, Adgrll, Topbpl, Brd8, Srrt, Cpsf6, Stmn2, Bsg, Zfp280d, Odf2, Ppwdl, Zcchc7, Brd9, Kritl, Tmx4, Nisch, Tra2a, Hipk2, Stmn4, Dhx36, Mycbp2, Igsf8, App, Elavl3, Pcml, Nsdl, Bclafl, Cenpf, Stmn3, AC160336.1, Rabl lfip2, Knll, Hells, Mga, Msi2, Ashll, Atad2, Prcl, Zc3hl3, Hirip3, Rbm25, Nnat, Ndn, Ncapd2, Sgce, Tm9sf4, Zfp445, Afdn, Rifl, Gpatch8, Strn4, Rbm5, Ogt, Ubn2, Prdx4, Usp34, Zbtb38, Atp2a2, Phox2b, Ina, Huwel, Tnrc6c, Mdk, Son, Ankrdl l, Hnmphl, Nasp, Cadml, Caldl, Supt20, Ranbp2, Rsbnl, Snrnp48, Hlf, Safb, Map4k4, Cidea, Arglul, Ddx39b, Ubap21, Smcla, Ubap2, Herd, U2surp, Gm26825, Sltm, Nsgl, Dynclhl, Bzw2, Clpb, Mtdh.
Table 2L: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq . Cluster 12 Trbc2, Cd3d, Trbcl, Etsl, Ms4a4b, H2-K1, Trac, Tptl, Cd3g, I17r, H2-Q7, Cd3e, Shisa5, Malatl, TmsblO, mt-Atp6, mt-Nd2, mt-Co3, Gimap3, mt-Col, mt-Co2, Ltb, Vps37b, Cd28, Lek, Gimapl, Btgl, Smad7, Pdcd4, Slamf6, Gimap6, mt-Cytb, Ccnd2, SlOOalO, Emb, Skapl, Gimap4, Ptpreap, Lefl, Eeflal, Bell lb, Cd2, Ms4a6b, Ccr7, AW112010, mt-Nd3, mt-Nd4, Ptpnl8, Fau, Slprl, Tcf7, Satbl, mt-Ndl, Mbnll, Abliml, Crlf3, Txk, B2m, Rackl, Rapgef6, B930036N10Rik, Eeflb2, Atplb3, Limd2, mt-Nd5, Lat, Inpp4b, Arhgefl, Gm42418, Hcst, H2- Dl, Cd52, Rhoh, Saraf, Akapl3, Cd27, Ifi203, Ifi2712a, Rinl, Septi, Arhgapl5, Ddx5, Rac2, Cd4, DusplO, Chd3, Txnip, Lars2, Ptpn22, Xist, Zfp3612, Itk, Dgka, Uba52, Arhgap45, Nsd3, Klf2, Arhgdib, Gm8369, Bcl2, Tra2b, Pnrcl, Clkl, Cd5, Elfl, Statl, Psmb8, Grap2, I12rg, Ptpre, Jakl, Itgb7, Utrn, Pelil, Ankrdl2, Son, Pabpcl, Foxpl, Aes, Rbm39, Eif3h, Nripl, H2- T22, Gprl83, SplOO, Fyn, Prrc2c, Pfdn5, Gimap9, Thyl, H2-T23, Gml l808, Psmel, Smc4, Cd6, Itpkb, Mndal, Tnrc6b, Fyb, Hifla, mt-Atp8, Ankrdl l, Cox7a21, Ubb, Psmb9, Tox, Zc3havl, Gml0076, Junb, Zfp3611, Celf2, Ifngrl, Eif3e, Nsa2, Cd247, Gimap8, Ttcl4, Tnfaip3, 4833420G17Rik, Srpk2, Gm26825, Rgsl, Stkl7b, Corola, Uqcrh, Eifl, Kbtbdl l, Prkca, Myh9, Slc38a2, Vgll4, Arid4a, Faml07b, AC149090.1, Cd53, Prpf4b, Eef2, Tspan32, Ccdc88c, Ripor2, Ikzfl, Tra2a, Tnfaip8, Sdf4, Cnn2, Srrm2, Eif3f, Dnajal, Pfnl, Traf3ip3, Atpl lb, 4932438A13Rik, Chd2, Gramdla, Cnot61, Ogt, Phf2011, Srpkl, Fxyd5, Klf6, Spcs2, Hnmpf, Eefld, Gdpd3, 4930523 C07Rik, Rsbnll, Selplg, Aebp2, Psme2, Naca, Zcchc7, Dock2, Rbm5, RgslO, Sell, mt-Nd41, Clec2d, Ddx24, Sri, Nop53, Bptf, Mycbp2, Abracl, Pak2, Jund, Cast, Ankrd44, Tle4, Dusp2, Ssh2, Tsc22d4, Mbd2, Rockl, Arf5, Rabacl, Sec62, Cytip, AY036118, Myl6, Sh3kbpl, Kritl, Zfp644, Birc6, Arl6ipl, Atrx, Zcchcl 1, Oazl, Stk4, Tnrc6a, Tnrc6c, Pura, Laptm5, Eif3m, Ube2d3, Cd84, Pycard, Nt5c, Eif4ebp2, Nfkbl, Polrld, Prpf38b, Pnisr, Ythdcl, Khdrbsl, Sh3bgrl3, Snhgl2, Ccnd3, Ppplrl8, Vasp, Mierl, Duspl l, Kmt2a, Snrnp70, Evi, Npc2, Snrpg, Atp5h, Btg2, Luc712, Rsrpl, Ly6e, Eeflg, Prdx6, Hspalb, Tsc22d3, Cd37, Usp3, Atf7ip, Kansll, Psenen, Ddx50, Kmt2e, Yyl, Tmem234, Glol, Slc3a2, Bodll, Selenow, Stl3, Ppia, Gmfg, Tpr, Cotll, PpplrlO, Kdm5a, Ypel3, Kiflb, Aff4, Ncorl, Atp5g2, Ptp4a2.
Table 2M: Lists of genes that are
Figure imgf000078_0001
in the different clusters identified in the of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 13
Chgb, Dlkl, Chga, Nnat, Rtnl, Hspdl, Agtr2, Stmn3, Tomm20, Prdx4, Ndufc2, Kif5c, Cidea, Ptprs, Pcskln, Ncaml, Stmn2, Tubala, Nel, Adgrgl, Gml673, Uchll, Ndufb9, Ndn, Stmnl, Ttc3, Tubb5, Mdk, Cd81, Nsgl, Stmn4, Hsp90aal, Bsg, mt-Atp6, Tubb2b, mt-Nd41, H2afz, Tecr, Scg5, Kdelr2, Cacna2dl, Histlh2ap, Bzw2, Prdx2, Fkbp3, Prmtl, Ssr2, Scd2, Nop56, Nmel, Podxl2, Rslldl, Srm, Gnas, Ndufa4, Ndufal3, Sytl l, Gstm5, Fkbp2, Slc24a5, Atp2a2, Dut, Hand2, Cycl, Histlhlb, Timm8b, Slc25a4, Mycn, Ptma, Mrpl28, EmclO, Tubb3, Bex2, PeglO, Manf, Mif, Polr2f, Ranbpl, Ndufv3, Nt5dc2, Histlhle, Clpb, Mtchl, 2410015M20Rik, Ndufb5.
Table 2N: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 14
Igfbp7, Col4al, Sparc, Fabp4, Igfbp3, Col4a2, Plvap, Cdh5, Egfl7, Gngl l, Vim, Eng, Ctla2a, Tm4sfl, Gpihbpl, Pecaml, Ptprb, Hspg2, Emcn, Fltl, Coll8al, Cd93, Prss23, Sparcll, Sptbnl, Serpinhl, mt-Cytb, Ramp2, Kdr, Esam, Aqpl, Plpp3, Cd81, Rbp7, Cd34, Plxndl, Lambl, Aplp2, Bgn, Id3, Igfbp4, Lama4, Hspbl, S100a6, Coll5al, Itgbl, Pcdhl7, Crip2, App, Myl6, Fkbpla, Nrpl, Mmm2, Mgll, Criml, Epasl, Cavl, Mcam, Anxa2, mt-Atp6, Ecscr, Rhoc, Adgrf5, Ltbp4, Lamcl, Cavin2, Cavin3, Gnai2, Cripl, Prex2, Tiel, Esml, Myh9, Tcf4, Gjal, Nfib, Rrbpl, Ly6cl, Hegl, SlOOalO, Ppic, Adgrl4, Nidi, Ednrb, Ly6a, Plec, Dst, Thbsl, Caimi, Caldl, Empl, Ahnak, Pmepal, Lars2, mt-Nd4, Ehd2, Nid2, Timp3, Slprl, Itm2b, Ctnnbl, Cdhl3, Arhgap29, Cd200, Myctl, Fstll, Stabl, Bmpr2, Macfl, Satl, Myll2a, Cavinl, Actn4, Fnl, Itga6, Podxl, Pdliml, mt-Ndl, Pippi, Ecel, Ctnnal, mt-Co3, Tcim, Arhgap31, MyolO, Rflnb, Ly6e, Ctsl, Soxl8, Rhob, Fl lr, Apbb2, Tshz2, Clic4, Mxd4, Atoxl, Lgalsl, Calu, Ehd4, Slc38a2, Clicl, Robo4, S100al6, Icam2, Elk3, Snrk, mt-Col, Wwtrl, Vwal, Anxa3, Serpinb6a, Utrn, Itm2c, Sh3bgrl3, mt-Nd2, Sema6d, S100al3, Slc9a3r2, Mast4, Idl, Hspala, Hsp90bl, Nectin2, Pxdn, Notchl, Insr, Sptanl, Laptm4a, Gm42418, Clecl4a, Cyyrl, Rasipl, Rapgef5, Tnsl, Fermt2, Lrrc58, Txnip, Calr, Malatl, Jun, Slc43a3, Mfge8, Tjpl, Gimap4, Tnfaipl, SlOOal 1, Etsl, Ppib, mt-Co2, Nedd4, Notch4, Luzpl, Pdia3, Anxa5, Hspa5, Ushbpl, Cdl51, Ppfibpl, Cyb5r3, Tspo, Nrp2, Rock2, Tm9sf3, Selenof, Lmna, Arhgefl2, Mmpl4, Tmbim6, Sh3glbl, P4hb, mt-Nd3, Tpm4, Fzd4, Itgal, Ifitm3, Jup, Tgfbl, Tsc22dl, Tagln2, Dysf, Rhoj, Creb312, Pdgfb, Lpar6, Hspalb, Msn, Mafb, Cd9, Mtchl, Tspan9, Wwc2, Dlcl, AdamlO, Rbmsl, Ktnl, H2-K1, Spag9, Serf2, Zbtb20, Sashl, Slfn5, Gimap6, Selenop, H2-D1, Fscnl, Plxna2, Amotll, Myolb, Mprip, Serinc3, Hifla, Tpm3, Rhoa, Mareks, Prdx4, Rsrpl, Atrx, TmsblO, Tptl, Sept4, Hdac7, Nfe211, Klf2, Pnp, Ywhab, Serinci, Itga5, Slc29al, Npdcl, Tcn2, Xist, Galntl, Wnkl, Arpc3, Rtl8a, Nckapl, Degsl, Ptbp3, Rael, Gm26825, Cyb5a, TmedlO, Sox4, 201011 HOlRik, Pik3c2a, Lampl, Tlnl, Afdn, Sdcbp, Mapk3, Arfl, Csnklal, Nisch, Tmed9, Capnsl, Cnn3, Sh3bp5, Dab2ip, Tmeml76a, Secl411, Pitpna, Rabi la, Eif4g2, Map4k4, Pdia6, Prkarla, Ptms, Zebl, Hesl, Mapllc3b, Slk, Jakl, Shisa5, Iqgapl, Fus, Cnot6, Nudt4, Gng5, Mrpl24, Cite, Ddxl7, Sept7, Krtcap2, Arhgef7, Map4, Tpml, Zfp3611, Arpclb, Klf6, mt-Nd5, Abhdl7a, Gnb2, Phf2011, Ppplr2, Slc25a3, Hmg20b, Nfic, mt-Atp8, Ube2d3, Luc712, Limsl, Arglul, Cfll, Ifi27, Fcgrt, Hook3, Mbnll, Git2, Qk, Dynclhl, SfBbl, Rbm39, Flna, Capg, Myll2b, Rabl2, Ubc, Glgl, Arhgdia, Prdxl, Tmem59, Pomp, Gnbl, Ddx5, Eif4gl, Selenok, Fxyd5, Akapl3, Ifngrl, Sipal, Gdi2, Xiap, Sri, GrblO, Rabi 8, Tmem256, Ifitm2, B2m, Ostfl, Cd47, Herc2, Atplal, Clkl, Klf7, Tmeml76b, Bnip2, Capza2, Dyncli2, Mef2a, Ssr2, Rabacl, Cdc42, Capzb, Gdpd3, Cyfipl, Emp3, Taccl, Actgl, Morf411, Wasf2, HnmpaO, Sfpq, Snx3, mt-Nd41, Bst2, Mef2c, Raplb, Prrc2c, Fos, Son, Capl, Actr2, Tmem50a, Gls, Akrlal, Ost4, Atp5j, Rab5c, Tmsb4x, Atp2bl, Ptp4a2, Dnajal, Gapdh.
Table 20: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 15
Siglech, Bst2, Irf8, Cd209d, Ly6d, Rnase6, Plac8, Psap, Ly6c2, St8sia4, Lgalsl, Tyrobp, Tcf4, Cd7, Mpegl, Ctsh, Ctsl, Ly6e, Ctsb, Tagln2, Lairl, Ccr9, Grn, Malatl, Sell, Irf2bp2, Mef2c, Pld4, Cox6a2, Ccl4, Dnajc7, Tspanl3, Pkib, Mbnll, Xist, CleclOa, Dap, Cybb, mt-Col, Klkl, Ighm, Spib, Upbl, Bell la, Lspl, mt-Ndl, Cd8a, Cd74, Unc93bl, Ahnak, P2ryl4, Ly86, Tubgcp5, Klklb27, Runx2, mt-Co3, mt-Co2, Selplg, Cd47, Xbpl, Gm2a, I17r, Atplbl, Clecl2a, Serpl, Fthl, H2-K1, mt-Nd3, Pgls, mt-Nd4, Klral7, Herpudl, Iglc3, H2-T23, Psmb8, Snxl8, H2-Aa, Snx5, RgslO, Slam®, Cadml, Npc2, Relll, Kctdl2, BC018473, Ly6a, Rac2, mt-Atp6, Smim5, Lifr, Fyn, Syngr2, Emp3, Pacsinl, Prkca, Sdc4, Slc44a2, Rampl, Tgfbl, mt- Nd2, H2-D1, Kmo, Rilpl2, mt-Cytb, Pltp, Fyb, Cd8bl, Tmed3, Ccr2, Tsc22dl, Ppfia4, Ifnar2, H2-DMa, Stx7, Laptm5, Hsp90bl, Sec61b, Lag3, Nucb2, Ptprcap, Cdl64, Zfp3611, Bink, Gltp, Cyth4, Ctsz, Mctp2, B2m, Sema4b, Plekhm3, Gsn, Arhgapl7, Zfp3612, Ier5, AC140186.1, Smad7, Flt3, Runx3, Gns, Jun, Ncfl, H2-Abl, Rrbpl, Gm26825, Actb, Tgfbrl, Psmel, Tmem229b, Rabgapll, Rnaset2a, Cst3, Scimp, Gprl71, H13, Btgl, Ikzfl, Slc38al, Ptpn6, Itm2b, Gm42418, Ctse, Cibl, Smiml4, Clec2d, Gdi2, 1830077 J02Rik, Pik3ipl, Echl, Fgfrlop2, Napsa, Mtdh, Dirc2, Npcl, Uvrag, Reep5, Ptms, Hpse, Mzbl, Coro2a, Cd38, Faml74a, Jami, Cd2ap, Sec61g, Tex2, Gprl83, Nptn, Blocls2, Celf2, Itga4, H2-Q7, Gpxl, Ppia, Hspalb, Mvbl2a, Cnp, Pip4k2a, Svbp, Ctss, Gtf2i, Rnd3, Tcfl2, Dbnl, Seel ie, Rapla, Ubxn4, mt-Nd5, Ptprc, Tmbim6, Rsrpl, Arhgef6, Itprl, Mtpn, H2afy, Tptl, Tnfrsfl3b, Evi2a, Tmeml23, Alox5ap, Cd44, mt-Nd41, Lyn, Eif3f, Cacnale, Cmah, Cd69, Ucp2, Dntt, Gnal5, Tbcld8, Abhdl7b, Psmb9, Ifnarl, Plaur, Zeb2, Oazl, Fau, Subl, Lrp8, Atpl3a2, Tapbp, Tmem59, Hspa5, Eepdl, Cardl l, Rab33b, Fam214a, Netl, Septi, Wls, Trim30a, Ctsc, Ptprs, Sptssa, Ssr4, Slc25al2, Hvcnl, Cdl80, Elfl, M6pr, Cbl, Mapkapk2, Bmyc, Serf2, Ubb, Slc29a3, Zc3hl2c, Psme2, Skap2, Inpp5d, Prrl3, Tespal, Ncehl, Adaml9, Itgb7, Sept9, Tmed2, Spcs2, Srsf5, Erp29, Klf2, Csf2rb2, Gm5547, Pmepal, Rftnl, Prep, Cmtm7, Lpgatl, Dnajc3, Taccl, Gnai2, Dadi, Eeflal, Btg2, Leftyl, Ddrl, Irf7, Scpepl, Gnb4, Timp2, Fgr, Asahi, Arhgap30, Ogt, Stkl7b, Gria3, Sla2, Snx9, DocklO, 993011 lJ21Rik2, Limsl, Srpk2, Cd53, Septi 1, Arhgdib, Rhoa, Arpc3, Ubc, Hspala, Paqr5, Klhl42, Rnfl22, Orai3, Pde7a, Selenos, Atplal, Klfl3, Rpgripl, Calcocol, Rasgrp2, TmedlO, Iqgap2, Hivep3, Mgatl, Notchl, H2-Ebl, Adssll, Sikl, Magtl, Dst, Selenot, Tmed5, PpplrlO, Atp6vld, Abhdl7a, Tmem50a, Rbbp6, Manf, Tmsb4x, Gm21762, Cdh5, Them6, H2-DMbl, P2ryl0, Irfl, Traml, Plp2, R3hdm4, Ptpnl8, Ccdc88a, Tnfaip8, Mef2a, Adgre5, H2afj, Pfnl, Gapt, Pir, Slc44al, Hhex, Trim25, Cnpy3, Capg, Cdc42se2, Tribl, Zmiz2, Csk, Foxpl, Pdia3, Ankrdl2, Pafahlb3, Aes, Cdkn2d, Tmem258, Cytip, Nsa2, Inf2, Trp53il3, Ppmlm, Lmo2, Slcl5a4, Ptp4a3, AC149090.1, Manla2, Ssrl, Atp6ap2, Tlnl, Sms, B3gnt8, Nek6, Atp2b4, Gprl37b, Scamp2, Tcf712, Cd48, Dnajbl, Ape, Corola, Macfl, Tmed9, Ube2d3, Eif3h, Krtcap2, Smc6, Cfll, Hs3stl, Inpp4a, Stat2, Itgax, Bmp2k, Cxxc5, Ctsa, Cd68, Arl6ip5, Zmynd8, Pycard, Neatl, Nrdl, Gls, Arpc51, Luc712, Iqgapl, Smdtl, Atp6v0e, Selenow, Pabpcl, Slco4al, 1700017B05Rik, Cdipl, Ahr, Ptprf, Cd33, Frmd4a, Acbd5, Hes6, Trappc5, Cd37, Rcsdl, Foxn3, Vamp8, Ptpre, Zcchc7, Git2, Txnip, Ttcl4, Nktr, Tra2b, Tpm3, Atp2al, Notch3, Pip5klc, Hivepl, Spl40, Arhgap5, Ralgps2, Prkcd, Epstil, Spcs3, Acadl, Etsl, Itm2c, Cyfipl, Hatl, SplOO, Sri, Gng2, Zfp36, Pomp, Gml2253, Man2a2, Ccr5, Lncpint, Rhnol, Emc3, Rnfl3, Gnaq, Slc35c2, Man2bl, Plekhol, Nfkbl, Atp6v0b, Lamtor4, Purb, BC005537, Oserl, Rgsl, Sh3bgrl3, Arhgdia, Fbl, Sh3bgr, Prr5, Klrdl, Gm26759, Pkp3, Fgd2, Fcrla, Phactr2, Bcr, Epsl5, Cldndl, Ubl3, Ddost, Aldh2, Stt3b, Mbd2, Ddit4, Pdcd4, Qk, Hplbp3, Arpc4, Wnkl, Dmxll, Ddx5, Cd209a, Spns3, Kynu, Sec24d, Faml l7a, Adpgk, Pdzd4, Usol, Dctn6, Ncoa4, Lbh, 1110059E24Rik, Kdelrl, Wasf2, Setd2, Faml68b, Jmjdlc, Hexa, Cd82, Cope, Kmt2e, Pdia6, Ybx3, mt-Atp8, Rbm39, Mrpl52, Slc41a2, Rilpll, Slc9a9, Srgap3, Btla, Acapl, Spint2, Arhgap27, Dpyl911, Txndc5, Itsnl, Fam3c, Adipor2, Marchl, Fkbp5, Idil, Lgals3, Taxlbpl, Rnhl, Skil, Akrlal, Scandl, Arpc5, Hspa8, Havcrl, Carmill, Serinc5, Atp2a3, Lat2, Rail, Grap, Fmnl2, BC017643, Leprotll, Limdl, Uggtl, Rmnd5a, Znrf2, Surf4, Arglul, Hnrnpull, Slc3a2, Lamp2, Stk4, Tmeml60, Hmgcsl, Hnrnpf, Rp9, Arhgap27os2, Rgsl8, Zcchc24, Mgat4a, Tagapl, Clcn5, H2-M3, Cbfa2t3, Fam69a, Klhl6, Atg5, Tmem219, H2-T22, Csf2rb, Edem2, Statl, Pcmtdl, Sec61al, Hclsl, Pkig, Rsbnll, Pitpna, Snwl, Sec62, Dhx9, Senp6, Calr, Ppib, Rockl, Tomm7, Eef2, Pfdn5, Fus, Tmeml63, Slpr4, Mtmrl, Scap, Tapi, Gprl8, Ppmlh, Arid3a, Elovl6, Sorll, Etv6, Pdzd8, Clic4, Etnkl, Samsnl, Alkbhl, Stxl6, Abcgl, Hmgn3, Mndal, Kritl, Lman2, Nrros, Actr2, Tsc22d3, Ppplrl l, Clicl, Canx, Ddxl7, Cox7a21, Klf6, Phlpp2, Ctso, Rufyl, Mast4, Coa5, I121r, Spl lO, Golim4, ArhgeflOl, Pcytla, Fnbpl, Arl5c, Ripor2, Dnajbl4, Atf6, Adcy7, Ppp6rl, Copl, MedlO, Atf7ip, Lrrfipl, Setd3, Ikbkb, Chic2, Apbblip, Rnfl49, Scp2, Tm9sf3, PsmblO, Ppdpf, Gabarap, Arfl, Gpil, Rabl4, Gnas, Ywhah, Eif3e, Tor3a, Trp53il l, Tapbpl, Cepl92, Pon2, Vps37a, Anxa7, Ifi35, Sash3, Usp24, Txndcl5, Ddi2, Mfsdl4a, Fuca2, Amfr, Mxd4, Syk, Rpn2, Cyba, Rexo2, B4galntl, Gpcpdl, Grb2, Ccnd3, Nr3cl, Ccdc47, Hnmpl, Exosc5, Mia2, Mrpsl6, Brd4, Srsfl l, Tra2a, Arppl9, Ssr3, Sdhb, Commd6, Atp51, Atp5g2, Jund, Mani cl, H2-Oa, Tomi, Mtmr9, Abcdl, Rbm47, Tm7sf3, Syne2, Rictor, Creb3, Nek7, Lrmp, Map3kl, Srebf2, Mpnd, Pdcd21, Tsix, Sept6, Tex261, IllOrb, Galntl, Sndl, Krccl, Tpd52, Dnajbl l, Son, Nudcd3, Ppplcc, Capzb, Filipll, Zfp706, Med21, Klhll8, Lrchl, Gnptab, Ebpl, H2-Ke6, Tfrc, Hibadh, Dock8, Xrcc6, Maltl, Tspan31, Irf5, Os9, Mlec, Slf2, Arid4a, Xiap, Borcs8, Sp3, Cnn2, Epnl, Osgep, Cnot61, Chd2, EmclO, Cdknlb, Gnal 1, Sdf4, PetlOO, Rab21, Taok3, Chmp4b, Papola, Poldip3, Dpm3, Srpl4, Ndufbl l, Morf411, Polrld, Map4k4, Ifi2712a, Brkl, Zfp398, Nsmaf, Rab3gapl, Nrpl, Srgn, Cripl, Cat, Cnot8, Denndlb, Chd9, Dock2, Slco3al, Nubl, Pmvk, Abi3, Cdc42sel, Commd7, Setd7, Zc3h7a, Tgfbr2, Pknl, Dgkd, Ociadl, Atp6vlh, Safb2, Tsc22d4, Clintl, Ergic3, Bptf, Abracl, Hmgcr, Pnisr, Fosb, Srp9, Zbtb20, Rtraf, Nt5c, Syf2, Prpf 8b, Ubl5, Mat2a, Golga2, Rnpepll, Ccdcl07, Gngl2, Fes, Washc4, Ptpij, Pdpkl, Rhoh, Mirl42hg, Stat3, Tmod3, Farl, Erg28, Bri3bp, 4833420G17Rik, Zbtb7a, Saraf, Jtb, Rnfl30, Fkbp2, Arf5, Ssr2, Bri3, Grk2, Torlaipl, Anapcl l, Vcp, Eif4a2, Sysl, Pcbp2, Prrc2c, Dhxl5, Cox4il, Pak2, 2010107E04Rik, Ccndl, Eefld, Eifl, Hsp90abl, Psmbl, Uqcrh, Sema4d, S100al3, Colgaltl, Plcg2, Adss, Tnfaip812, Tbllx, Arpclb, Snmp48, Pten, Myo5a, Serinc3, Mpcl, Nipbl, N4bp212, Rabacl, Ubnl, Ccnll, RablO, Klhl24, Sin3b, Taldol, Ube2el, Cite, Tceal, Atp6vlgl, Ost4, Kras, Ppig, Snx3, Selenof, Sept7, H3f3b, Mta3, Slc30a5, Kpnal, Spn, Nsmce3, Tmem55b, Clcn3, IllOra, Sec22b, Hadhb, Diaphl, Pold4, LrplO, Gpsm3, Duspl l, Ppp4r3b, Sec63, Spag9, Atplb3, Rbm5, R3hdml, Rtcb, Tnpol, Usp7, Ghitm, Slk, Ube3a, Nop53, Sf3bl, Ap2bl, Psenen, TimmlOb, Mapllc3b, Trmtl l2, Chmp2a, Atp5cl, Rackl, Ndufa6, Ralbpl, Hmgbl, Hnmpa2bl, Topi, Zyx, Cep57, Flii, Pigt, Cerk, Cdk5rap3, Grk6, Chordci, Corolb, Kctd20, Tmem30a, Clkl, Ctbpl, Twf2, Arl6ip4, Ppp2r5c, Adk, Pptl, Ivnslabp, Bcap31, Brd2, Spop, Mrpl38, Ostfl, Samhdl, Bcl7c, Gatadl, Mienl, Zfp91, Arpc2, Rpp21, Coxl4, Sfpq, Aridla, Tmcol, Ywhae, Atrx, Csdel, Ndufal, Eif4b, Cox8a, Cdc3711, Rbckl, Dgcr6, Usel, Cox20, Ncorl, Lnpep, Ccni, Tmem234, Mrps21, Pnn, Ostc, Tmeml67, Psma5, Anp32a, Edfl, Ndufal3, Wdr26, Bzw2. Table 2P: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 16 mt-Atp6, mt-Co2, mt-Co3, mt-Cytb, mt-Nd4, mt-Ndl, mt-Nd2, mt-Nd3, mt-Col, Chgb, mt- Nd41, mt-Nd5, Jund, mt-Atp8.
Table 2Q: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq . Cluster 17
Col3al, Collal, Colla2, Sparc, Mgp, Den, Igfbp7, Acta2, Fnl, Col4al, C3, Rgs5, Bgn, Serpinhl, Tagln, Fstll, Fbnl, Postn, S100a6, Lgalsl, Col4a2, Cripl, Col5a2, Caldl, Hspbl, Vim, Col6a3, Igfbp6, Mfap5, Tpml, Coll4al, Ctgf, Col6al, Serpingl, Aebpl, Timp2, Ccdc80, Timpl, Clec3b, Col5al, Lpl, Gml2840, Nidi, Ccl2, Ctsl, Mtl, Col6a2, Rarres2, Itgal, Gsn, Pcolce, Eln, Cd63, Meg3, Coll5al, Cxcll, Serpinel, Thbsl, Anxal, Egrl, Mt2, Adamts2, Prss23, Timp3, Fabp4, Igfbp4, mt-Cytb, Gasl, Lum, Serpinfl, Loxll, Fos, Cyr61, Tpm2, Lox, Coll8al, Csrp2, Fosb, Tm4sfl, Rrbpl, Fbln2, Sptbnl, Nedd4, Clsl, Sdc4, Ifitm3, Rcn3, Cd248, Dpt, Cd81, Loxl2, Rbpl, Gas6, SlOOalO, Ogn, Col5a3, SlOOal l, Myl6, Hspa5, Pdgfrb, Selenom, Ahnak, Sfrp2, Mmpl4, Cavin3, Tmeml76b, Bsg, Actnl, Lmna, Mfge8, Apoe, Hsp90bl, Cpxml, Ppic, Col8al, Malatl, Mylk, Maged2, Laptm4a, Itgbl, Ptgis, Calu, Lamcl, Jun, Cavinl, Axl, Gpx3, Id3, Cryab, Myl9, Actn4, Pdia3, mt-Nd4, Lhfp, Anxa5, App, Klf4, Myhl 1, Cavl, Rnase4, mt-Co3, Pmepal, Anxa2, Serpine2, Mcam, Nfib, Ptms, Ckap4, mt-Ndl, Calr, Plod2, Plpp3, Lrpl, Clu, Hspg2, P4hb, Sept7, Tmeml76a, Zbtb20, Sulfl, Tnxb, Angptl4, Csrpl, Mprip, Smpd3, S100al6, Cfh, Vcl, Criml, Rhoj, Serpinb6a, Tpm4, Ppib, mt-Nd2, Bmpl, Lama4, Lambl, Lpp, Nenf, Gm42418, Ehd2, Serpina3n, Phldal, Nfix, mt-Col, Htral, Efempl, Efemp2, Adamtsl, Ebfl, Coll2al, Biccl, Plat, Fkbp9, Ecml, Anxa3, Hdlbp, Rock2, Flna, Rhoc, Itih5, Vcan, Errfil, Fermt2, Hegl, Mgstl, Cebpd, Dagl, Notch3, Tagln2, Myll2a, Pdia6, mt-Nd3, mt-Atp6, Gpx8, Mmp2, Pam, Clic4, Dst, Cyb5a, Mmp23, Cygb, Adamts5, Pdgfa, Sparcll, Oat, Arid5b, Olfml2b, Klf9, Septi 1, Myh9, mt-Co2, Ltbp4, Prnp, Nr2f2, Tmed3, Pdliml, Slit3, Limal, Nfia, Ifi27, Myadm, Selenof, Dstn, Clra, Magedl, Emp3, Aspn, Palld, Gngl l, Serf2, Dbi, Creb311, Ifi2712a, Cdl51, Nuprl, Ssr3, Bst2, Arf4, Clqtnf6, Ndufa412, SlOOal, Crip2, Pdia4, Dnajc3, Uapl, Fxydl, Itgb5, Pmp22, S100al3, Myof, Oaf, Jagl, Cd200, 116st, Cyb5r3, Mxd4, Laptm4b, Rcnl, Dadi, Mustnl, Tnsl, Nucbl, Npdcl, Fblnl, Ostc, Cst3, Fthl, Crtap, Mast4, Lgals3bp, Txndc5, Thyl, Kdelr2, Sox4, Ier2, Gata6, Prrxl, Ikbip, Tshz2, Lamb2, Acaa2, Man2al, Aoc3, FkbplO, Fkbp7, Des, Arhgap29, Vkorcl, Serinc3, Plec, Hcfclrl, Cpe, Maf, Canx, Igf2r, Kdelrl, Tceal9, Gpx4, TmsblO, Pxdn, Peakl, Fndc3b, Itgav, Wls, Cnn3, P4hal, Rbmsl, Mfap2, Rpnl, Syne2, Manf, Gucylal, Ltbp3, Pls3, Evalb, Nrpl, Slc39al, Golim4, Dpysl3, Pdlim5, Tmed9, Capnsl, Cnpy2, Ssr4, Tspo, Lbh, Mareks, Mxra8, Amotl2, Fatl, Fkbpl l, Tinagll, Lmanl, Golgbl, Pbxl, Empl, Rpn2, Sdc2, Adgrdl, Flrt2, Gpc6, Dlcl, Epasl, Esyt2, Zfhx3, Nfic, Aplp2, Tmem59, Rtn4, Ktnl, Itm2b, Tmeml l9, Parva, Slc43a3, Plxdc2, Tgfbr3, Ifi202b, Nbeall, Akapl2, Ier3, Tgfbr2, Ifitm2, Ssr2, Gstm2, P3h3, Ctsk, Apbb2, F2r, Mlec, Pde3a, Colgaltl, Atp2a2, Sarla, Rabacl, Prdx4, Npc2, Ddr2, Cdhl l, Dcbld2, Extl, Ctnnal, Rbpms, Surf4, Ddbl, Aril, Morf412, Sec61g, Adamtsl2, Nbll, 2310022B05Rik, Teadl, Sec31a, Sec61al, Pgrmcl, Tsc22dl, Dyncli2, Snhgl8, Medag, Copz2, Mrc2, Twsgl, Mical2, Arhgefl2, Stt3a, Myolc, Mbnl2, Zfp3611, Krtcap2, Illrl, Phldb2, Fgfrl, Colecl2, Csfl, Rras, Sntb2, Nckapl, Comt, Slfn5, Copb2, Tm9sf3, Sec62, Cnn2, Slc25a4, Mxra7, Sept4, Luzpl, Arhgap5, Rnd3, Raphl, Rbms3, Lamp2, Dclkl, Prkarla, mt-Nd41, Fkbpla, Filipll, Maplb, Tns3, Ppfibpl, Gngl2, Tnfrsfl2a, Echl, Gjcl, Itm2c, Rbfox2, Glgl, Ccnd2, Dap, Ergic3, Anxa6, 201011 HOlRik, Vmpl, Ost4, Selenow, Kdelr3, P3h4, Frmd6, Wtip, Il Ural, Amotll, Nucb2, Pcyoxl, Armcx3, Atp2b4, Dnajcl, Kcnqlotl, Selenos, Sh3bgrl, Dynlll, Coll6al, Tgfblil, Faml l4al, Tfpi, Esam, Capn2, Ptk2, Ilk, Gstml, Ctdsp2, Gadd45b, Idh2, Dbnl, TmedlO, Ugp2, Tbrgl, Mtchl, mt-Nd5, Hmgnl, mt-Atp8, Tnkslbpl, Pkdcc, Nectin2, Creb312, Dnajb4, Cdc42bpa, Ryk, Epb4112, 9530068E07Rik, Tm9sf2, Lrrc58, Rabl8, Pnp, Nisch, Utrn, Xist, Zeb2, Fcgrt, Srpr, Nfe211, Creb5, Cyth3, Etfb, Serinci, Ddost, Ssrl, GrblO, Rhob, Jund, Egfr, Vasn, Antxrl, DnajclO, Meis2, Rsul, Tceal8, Copa, Ctnnbl, Dynclhl, Ywhab, Csnklal, Morf411, Ubb, Cmtm3, Adam9, B4galtl, Cd9, Plxnb2, Nfkbiz, Spcsl, Tapbp, Tmed2, Klf6, Flnb, Cttn, Tmem263, Esytl, Peal5a, Pdlim7, Cd302, Nptn, Ttc28, Lrpapl, Ift20, Isynal, Gabarap, Prdxl, Swi5, Mrfapl, Ndufal3, Gaa, Tspan4, Taxlbp3, Ext2, Pofut2, Hl 3, Ptprf, Hesl, Yipf5, Copgl, Thra, Laspi, Tmcol, Cregl, Map4k4, Navi, Bmprla, Slc44al, Leprot, Tmeml65, Copbl, Sri, Traml, Tbllx, Gnb4, Scd2, Eif4gl, Ufml, Mapllc3a, Gng5, Yifla, Idhl, Igflr, Yipf3, Cast, Rnfl l, Bcap31, Tmeml67, Sptanl, Rbbp7, Junb, Ubc, Glol, Txnip, Bagl, Pttglip, Vatl, Rcn2, Ski, Sec63, Smapl, Pkig, Ptprs, Cope, Arf5, Limsl, Tulp4, Vcp, Tpil, Cited2, Eefld, Map4, Ptpra, Mgat2, Yiflb, Rabla, Gorasp2, Pkn2, 2900097C17Rik, Sral, Hsbpl, Acbd3, Aamp, Txndcl7, Fkbp2, Clec2d, Rab2a, Selenok, Bzwl, Elob, Tubb4b, Cox6c, Tvp23b, lahl, Grn, Mia3, Tmem256, Pura, Fucal, Sfxnl, Ddah2, Tbcb, Mrpl52, Hspala, Faml62a, Sec61b, Btg2, Sdf2, Manla2, Tmem30a, Dlgap4, Rab6a, Rexo2, Trim35, Ube2r2, Lrrc59, Reep5, Ptovl, EmclO, Fundc2, Slc38a2, Rhoa, Raly, Sfrl, Hmg20b, Ashll, Sec22b, Eeal, Agpat3, Erp44, Ap3sl, Hook3, Pdcd6ip, Reep3, Oxctl, Arcnl, Gnal l, Ahcyll, Psme2, Rerl, Cite, Eifla, Sapl8, Mtdh, 1810037I17Rik, Cd2ap, Uqcrl l, Eif2s2, Krccl, Anapcl l, Tnfrsfla, Prdx5, Derll, Ifnar2, Serfl, Ubr5, Cfl2, Dpm3, Iscu, Mydgf, Ybx3, Cstb, Edfl, Aprt.
Table 2R: Lists of genes that are up-regulated in the different clusters identified in the integration of three TH-MYCN mouse tumors analyzed by scRNA-seq. Cluster 18
Ccl5, Gzma, AW112010, Nkg7, Gzmb, Klrdl, Prfl, Ms4a4b, I12rb, Klrkl, Serpinb6b, Ncrl, Klrel, Ifngrl, Vps37b, SlOOalO, Serpinb9, Dusp2, Irf8, H2-K1, H2-Q7, Txk, Ahnak, Ctsw, Bcl2, Zfp3612, Klra4, Ptprc, Lgalsl, Etsl, Malatl, Ctla2a, Gimap4, Jakl, Gimapl, Selplg, I118rap, Ccl4, H2-D1, Dennd4a, Shisa5, Sytl3, Gimap6, AC149090.1, Mbnll, mt-Nd2, Ccnd2, Smad7, Trbcl, Bcl2111, Ugcg, Tnfaip3, Wls, Rgsl, Ptpn22, TmsblO, Tmsb4x, Hcst, mt-Atp6, mt-Co2, Btgl, Itgbl, Junb, Ier2, I118rl, Cd52, mt-Co3, Sh2d2a, Gimap3, Ptpnl8, Id2, B930036N10Rik, mt-Col, Stat4, P2ryl0, Runx3, Pdcd4, Cxcr4, Tra2b, Klra7, Ptprcap, mt- Nd3, B2m, Abliml, Klf2, Cmal, I12rg, Rac2, Gimap5, mt-Cytb, Car2, Arhgap45, Cd2, Klhl6, Dock2, Arhgefl, Tagln2, Tptl, H2-Q6, Fyn, Txnip, Klral, Klrbla, Eomes, Septi, Klrblf, mt- Nd5, mt-Nd4, Bhlhe40, Nsd3, Nabpl, Clkl, Rinl, Vgll4, Zcchcl l, Btg2, Lars2, Trdc, Dok2, Prexl, Spn, Pnrcl, Ankrdl l, Slc38a2, Jund, Gimap9, Ccr5, Pitpncl, Ankrd44, SplOO, Bin2, Satbl, Tsc22d3, Dhrs3, Stk24, Ly6c2, mt-Ndl, Akapl3, Pik3rl, Hsdl lbl, Sfibl, Klf6, Rsrc2, Rbm39, Pfnl, Fryl, Tes, Mndal, Ccl3, Pmepal, Nfkbia, Serf2, Ubb, Eeflal, Icaml, I17r, Rgs2, Gm26825, Fasl, Spry2, Gprl71, Cd7, Ppplrl2a, Bptf, Tulp4, Arhgdib, Gm42418, 4930523 C07Rik, Arl6ip5, Rsbnll, Ier5, Tgfbl, Atplbl, Ccnd3, Piml, Spl lO, Itgb7, Laptm5, Luc712, Gem, Skapl, Prkch, Neurl3, March7, Rbm5, 1700025G04Rik, Esytl, Ccr2, Ifi203, Pelil, Ogt, Pycard, Ptp4a2, Xist, Lek, Kif21b, Mxd4, Cd84, BC018473, Faml07b, Kritl, Raplb, Gml9585, Arsb, Samd91, Sell, Nfkbl, Wipfl, Clicl, Aes, Myl6, Nipbl, Sh3bgrl3, Rbl2, Coro2a, Inpp5d, Cnot61, Maltl, Klhl24, Atplb3, Ppplrl5a, Nfkbiz, Taxlbpl, Ncorl, Eif3h, Ddx5, Pabpcl, Klrc2, Tecprl, Lat2, Dnajcl, Flil, Hectdl, Ccdc88c, Tnrc6b, Ssh2, Cd47, Myh9, Prkcq, Ttc39b, Gbp7, Gpr65, Cd37, Tgifl, Ctsd, Anxa6, Celf2, Ptbp3, Tspo, Arpclb, Ppig, Sh2dla, Crybgl, B4galtl, Pik3cd, Mxdl, Kansll, Taccl, Cnn2, Eif4a2, Limd2, Phf3, Reep5, Macfl, Anxa2, Ostfl, Samd3, Peakl, Gramd3, Arap2, Cd82, Lrrfipl, Itgb2, Ikzfl, Nktr, Ankrdl2, Ypel3, Prrc2c, Rsrpl, Gm4070, Gimap8, Chsyl, As3mt, Atpl lb, mt-Atp8, 2810474019Rik, Psmel, Cdc42, Klrblc, Pde2a, Itk, TbcldlOc, Trafl, Plekha2, Adcy7, Fcho2, S100al3, Cntrl, Itgal, Fxyd5, Tpp2, Mknk2, Rhoa, Slpr4, Dusp5, Nfatcl, Pfkp, CoqlOb, Cblb, Psmb8, Tafl5, Zbtb20, Hnmpf, Prkarla, Son, Actb, Jmjdlc, Pde3b, Trbc2, H2-T22, Rnfl38, Heca, Faml05a, Ube2h, Rnaset2a, Cab39, Tm6sfl, Gramdla, Saraf, Mbd2, Kmt2e, Ubald2, Smc4, Sbnol, Vim, M6pr, Sri, Adgre5, Pnisr, Septi 1, Prpf4b, Ifrdl, Ikzf3, Atp2b4, Sirt7, Gpsm3, Arl4c, Dnm2, Borcs7, Cnotl, Sipal, Tpm4, Zyx, 4833420G17Rik, Sec62, Supt4a, Srsf5, Aplp2, Serpina3g, Camk2nl, Lrrkl, Usp48, Zdhhcl8, Ppmlb, Mirl42hg, Irf2, Add3, Snx5, Dnajbl, Tsc22d4, Vasp, Tra2a, Tab2, Iqgapl, Bclafl, Paip2, St8sia4, Ywhaq, Ttcl4, Tpm3, Ube2d3, Arglul, Ubc, Eefld, Oazl, Itga2, Atp2a3, Atp8b4, H2-Q4, Hivep2, Tmem243, Fosl2, Mirtl, Nr2c2, AnkrdlO, Cmcl, Arid5b, Tpst2, Crebzf, B4galntl, Hprt, Kmt2a, Elfl, Pdcd6ip, Rbmsl, mt-Nd41, Arhgap30, Syf2, Pafahlbl, Prkacb, Ppp2ca, Arf4, Jakmipl, Acapl, Pacsl, Ptger4, Sept6, Cd48, Cdkl3, Duspl l, Diaphl, 4932438A13Rik, Marfl, Herd, Arid4a, Arhgapl5, Prrc2b, Ranbp2, Nt5c, Zbtb7a, Gmfg, Rockl, Dnajal, Purb, Trappc8, Ripor2, Sipalll, Gm26740, Esyt2, Emp3, Suco, LrplO, Arhgap9, Slc9a3rl, Emsy, Cyld, Sp3, Zufsp, Rbpms, Traml, Ccntl, Kpna4, Clec2d, Uba52, Evi, Ubl3, Slc3a2, Apbblip, Cwcl5, Btf3, Xm2, Crebbp, Cd53, Cdc37, Srp9, Pla2gl6, Tapi, Elk3, Hbpl, Utrn, Dockl l, Rchyl, Nucbl, DocklO, Ppil4, Cdkl2, Fmnll, Statl, Smap2, Runxl, Gtf2b, Cyth4, Dguok, Gnal3, Cirl, Kat6a, Bini, Chic2, Rab8a, Stat3, Chd3, Acini, Agpat3, Zc3hl3, Mrps24, Dyncli2, 1810037I17Rik, Ashll, Efhd2, Snrnp70, Tyk2, Rabgapll, Sesn3, Sash3, Uimcl, Lbr, Psmb9, Zfp445, Aebp2, Zdhhc20, Plec, Prkcb, 1116, Stk4, Kcmfl, Rbm4b, Znrf2, Npm3, Tmem50a, Bcap31, 1700020114Rik, Psenen, Pabpnl, Yyl, Smapl, Crebl, Eril, Capnsl, Hspa8, Herpudl, Abracl, Cox8a, Serinc3, Dnajb4, Hiplr, Arhgefl8, Nabl, Pole4, Sept9, Lnpep, Smg6, Tbllx, Ppplrl8, Zfand6, Rsfl, Wdrl, Drapl, Actr3, Smgl, PsmblO, Rabacl, Cript, Clintl, Arhgdia, Mapkl, Akap9, Itga4, Kdm6b, Seel la, Rackl, Fus, Ncald, Tyrobp, Cpne3, Fnbpl, Plp2, Cetn2, Idnk, Laspi, Rpp21, Slk, Nfat5, Os9, Gng2, Plek, Cuxl, Chordci, Rasa3, Skil, MlltlO, Gpbpl, Golga4, Wasf2, Trir, Vbpl, Frgl, Kiflb, Thoc2, Srrm2, U2surp, Ppib, Anp32a, Pum2, Pld3, Rhoh, Pde7a, Arid5a, Itsn2, Tmfl, Denndlb, Xrnl, Dctn4, Foxpl, Mysml, Plekhj l, Leprotll, Clcn3, Ptpra, Dadi, Zfp638, Spag9, Dazap2, Pbxipl, Mdhl, Smc3, Celfl, Bcas2, Atf4, Cdc42se2, Edfl, Nsdl, Nop53, Ddx21, Ddxl7, Cdkl lb, Uqcrh, Olfml, Tap2, Gabpb2, Itpr2, Spcs3, Rin3, Rab8b, Emc3, Sla, Tapbp, Cdl64, Slfn2, Lsml4a, Ociadl, Chd7, 2310033P09Rik, Chd2, Arpc2, Zfp207, Vps28, Ubtf, Ahsal, Sptbnl, Usp3, Aridla, Sin3b, Rfc2, Numal, Dnajb6, Stag2, Tprgl, Gsk3b, 1810058I24Rik, H3f3b, Nptn, Sptlc2, Pcmtdl, Vezfl, Ssl8, Amd2, Zc3h7a, Cast, Tial, Wnkl, Msn, H2-T23, Tmbim6, Ywhah, Bazla, Fosb, PpplrlO, Tlnl, Prdx6, Scp2, RablO, Rad21, Polr2e, Prelidl, Pura, Cox7a21, Gpbplll, Ptpn2, BC005624, Cd244, Dnajc3, Commd7, Trim33, Stk38, Ift20, Neatl, Cmpkl, Sap301, Atf7ip, Tmeml60, Tm9sf3, Ggnbp2, Lcpl, Mef2a, Sept7, H2afy, Fam 133b, Eifl, Gpatch8, Actrla, Ppplrl2c, Mklnl, Ppp6r3, Ddx6, Idh3b, Git2, Hsdl7bl0, Fermt3, Hadha, Rassf5, Myolf, Copl, Vps4b, Mat2b, Serinci, Nubpl, Gludl, Rp9, Tle4, Mierl, Eif4e2, Stagl, Tgolnl, Addl, Zcchc6, Tma7, Ikbkb, Cdknlb, Mrpl4, Actgl, Rerl.
For further information on Table 2A to 2R, see Costa etal. JImmunother Cancer. 2022; 10(8): e004807, Supplemental Table 2 incorporated herein by reference.
Table 3 : see Supplementary Table 3 of Costa et al. J Immunother Cancer. 2022; 10(8): e004807, Supplemental Table 2 incorporated herein by reference.
Table 4 comprises the lists of genes described under Table 4A to Table 4R,
Table 4A: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Clusters 0 and 1
Cluster 0:
IL7R, LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, 0XNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, ITM2A, FAU, TRAF3IP3, EMB, OCIAD2, NOP53, STK4, SUSD3, PIK3IP1, CD247, PDE3B, CLEC2D, SEPT6, STK17A, RHOH, BTG1, COX7C, STK17B, EPB41, AC026979.2, RASGRP1, CD96, FAM102A, SOCS1, FXYD5, NPM1, PABPC1, CYTIP, CD7, CDC42SE2, SIT1, PTPRC, ZFP36L2, C0MMD6, AES, RACK1, ABLIM1, HINT1, TNFAIP8, DGKA, PPP2R5C, IL2RG, PDCD4, RARRES3, TNFAIP3, NACA, EVL, GPR171, AP3M2, FYN, TRADD, MZT2A, MALAT1, TMA7, B2M, LIMD2, MT-ND6, TTC39C, ARL4C, SNHG25, RAC2, GMFG, MT-ATP6, ANKRD12, HIST1H1D, CYLD, ARHGAP15, ISG20, SEPTI, CDC14A, FNBP1, DDX24, ICAM3, JUNB, NAP1L4, C12orf57, DDX5, RIPOR2,CD48, UQCRB, SYNE2, FYB1, SLFN5, SNHG8, HLA-C, FAM107B, RGS10, BTF3, ANAPC16, CORO1A, MT-CYB, SF1, GSTK1, HIST1H4C, CXCR4, TBC1D10C, MCUB, BCL2, PSIP1, GYPC, RHOF, EIF3E, CORO1B, SELL, C6orf48, TLK1, S1PR4, MTRNR2L12, GIMAP4, ARID5B, SVIP, IL16, ARHGDIB, CALM1, TNFRSF4, CDKN1B, CCND2, APRT, KIAA1551, ATM, EML4, STAT3, PPP1R2, MZT2B, SNRPD2, ANP32B, IK, SON, TSTD1, G3BP2, VAMP2, HLA-F, EEF2, HIST1H1C, ABRACL, NSD3, SYF2, MT-CO1, GPR183, TPR, MT-ND3, KLF13, GCC2, GTF3A, FBL, SRSF5, OST4, JAK1, CIB1, NSA2, MYL12A, HNRNPA1, NSMCE3, MBNL1, COX4I1, SEPT9, N4BP2L2, CBX3, UXT, BIRC3, GPSM3, ITGA4, S100A4, SRRM1, PIK3R1, SOD1, PNISR, MT-CO3, RNF213, ARL6IP5, EIF4B, MT-NDl, EIF3H, CREM, PRMT2, BTG2, RGS1, TSC22D3, KLF2, LINC01871, CKLF.
Cluster 1 :
TIGIT, CCL5, CD8A, GZMA, CD8B, GZMK, GZMH, NKG7, CST7, CD3D, CD3G, CD3E, TRAC, GZMM, CD2, IL32, HCST, TRGC2, LINC01871, APOBEC3G, RARRES3, SAMD3, TRBC2, CCL4, CTSW, LAG3, LCK, KLRG1, PRF1, KLRD1, GZMB, CD69, RUNX3, CD52, CD27, LYAR, C12orf75, PPP2R5C, STK17A, PTPRC, MATK, CORO1A, EVL, IFNG, ACAP1, LAT, CD247, HOPX, CD7, HLA-B, SKAP1, TNFAIP3, PYHIN1, CD96, PSMB9, TRBC1, IKZF3, CXCR3, B2M, MYL12A, SH2D1A, HLA-A, CLEC2D, TMA7, CD99, SH3BGRL3, TMSB4X, GPR171, TBC1D10C, RAC2, CD6, ZFP36L2, BCL11B, SRSF7, CDC42SE2, ISG20, CALM1, CXCR4, LEPROTL1, SIT1, FYN, DUSP2, PSME1, AES, GBP5, RHOH, TRAF3IP3, CLEC2B, RASAL3, ITGAL, PTPN22, AKNA, GIMAP7, TENT5C, S100A4, BTN3A2, SYNE2, SLC38A1, PDCD4, PTPN7, TUBA4A, RNF213, SLFN5, MT2A, BTG1, EEF1D, CHST12, CD48, AAK1, S0CS1, ETS1, CKLF, GNLY, IKZF1, SUB1, PFN1, OST4, AC026979.2, LIMD2, ARL4C, PIK3R1, ITM2A, MYL12B, STK4, TOMM7, PIP4K2A, ANXA1, PAXX, SEPT6, KIAA1551, ITM2C, MBP, HLA-F, ARPC5L, IRF1, GUK1, DDX24, RGS1, IL2RG, GMFG, ABHD17A, SYNE1, SRSF5, VAMP2, COMMD6, CLIC1, SEPT7, CIB1, SSBP4, ADGRE5, GYPC, JUNE), ARHGDIB, APOBEC3C, ATP5MG, TRIR, SNRPD2, DRAP1, GIMAP4, GSTK1, PSMB8, TSC22D3, ISG15.
Table 4B : List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 2
Cl QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, ADAP2, APOCI, GRN, CD84, HLA- DMA, MAFB, PLTP, RNF130, PSAP, CYFIP1, ACP2, BLVRB, ABCA1, CTSB, MS4A7, SDC3, ACP5, RAB20, FCGRT, TSPAN4, C3AR1, CCL3L1, Clorf54, TTYH3, SMPDL3A, CD74, CTSC, ASAHI, MPP1, BMP2K, CD163, TPP1, IL4I1, CTSD, TFEC, HLA-DQA1, NR1H3, CD86, DNASE2, RBM47, CYBB, FGL2, CTSH, LAIR1, CMKLR1, HLA-DRA, HEXA, CXCL16, IL18BP, AP1B1, FCHO2, RARRES1, AIF1, AKR1A1, ABHD12, HMOX1, CAPG, HLA-DPA1, DAPK1, FTL, RGL1, LY96, CTSA, HLA-DOA, NAGK, ATOX1, PRDX1, PPT1, ADA2, HLA-DPB1, TIMP2, MMP9, KCTD12, SCPEP1, PLAU, CCL18, LINC00996, IGF1, FCER1G, HLA-DRB1, AKR1B1, SGK1, TNFSF13B, LY86, RAB42, PTAFR, GLUL, ALDH1A1, CST3, CSF2RA, CCL4L2, DMXL2, MRC1, LAMP1, TCN2, CPM, MERTK, MGST2, CUL9, EBB, PLXNC1, SYNGR2, GAL3ST4, PDE6G, CLEC7A, SERPINF1, TGFBI, SPH, TBXAS1, RAB32, STAB1, NAIP, GNPDA1, GRINA, ATP6AP1, CFD, A2M, CEBPA, SAT1, CTSS, TYROBP, SLC7A8, CD63, BLVRA, LAMP2, GNS, SIRPA, CLEC4E, HLA-DQB1, ICAM1, MAF, SEMA4A, SIGLEC10, NINJ1, LINC01857, RENBP, MCOLN1, CD81, IFNGR2, NRP2, AXL, ATP6V1B2, SLC38A6, MSR1, LGALS3, IDH1, UNC93B1, SIGLEC7, PILRA, MMP14, SLC7A7, LACC1, GLA, SLC29A3, FCGR2A, AO AH, DRAM2, GPR137B, SPP1, NCOA4, QPRT, TNFAIP2, TLR4, SPRED1, MARCKS, CHCHD6, LYZ, SDCBP, TFRC, GPX4, CYB561A3, ITM2B, KLHDC8B, BRI3, HSD17B14, NAAA, FRMD4B, EPB41L3, ATP1B1, MITF, ETV5, ANKH, CYP27A1, SIGLEC1, SCARB2, M6PR, ABCC5, HEXB, NAGA, CLIC2, TNS3, LGALS9, DNASE1L3, MARCH1, PHACTR1, GAA, FMNL2, CSTB, ATP6AP2, FUOM, GNB4, CEBPD, LHFPL2, PDK4, SDSL, ATP6V1A, MMP12, VAMP8, CREBL2, SUCNR1, DPP7, SCARB1, RGS1, RRAGD, ATP6V0B, TM6SF1, TMEM138, CLEC4A, MGLL, LST1, PLBD1, ITPR2, CETP, SQSTM1, DNPH1, PLBD2, PCBD1, PROP, LRRC25, GUSB, FTH1, HLA-DRB5, CD59, HCK, OAZ2, FAM213A, NCEH1, GSAP, MKNK1, SPINT2, SMS, CCR1, DST, PLA2G15, RNF13, SLC48A1, CLEC10A, PMP22, GLMP, SDS, RNASET2, MYO5A, AIG1, PLEK, VOPP1, ATP6V0A1, EPHX1, ADAM9, TYMP, TOR3A, CD300LF, PLEKHB2, SCD, CHPT1, NCF4, EPB41L2, CD300A, CRYL1, IRF8, ATP6V1F, PRNP, GSN, CYBA, CR1, PLIN2, RPN2, CXCL12, PLXDC2, VSIG4, VCAM1, UCP2, LAP3, WWP1, FUCA2, FRMD4A, NEU1, MGAT4A, SNX5, VEGFB, IL13RA1, HAVCR2, FNIP2, MGAT1, CD83, TREM2, ATP6V1C1, ACER3, AHR, RGS10, RAP2B, CD302, ZFAND5, ANTXR1, NFE2L2, SERPINA1, UGCG, SHTN1, TRIM14, DRAM1, RAB10, MYO9B, SAMHD1, PLAUR, TALDO1, GAS7, NR4A3, CISD2, CHCHD10, RAC1, NCKAP1L, LRP1, GSTP1, ARHGAP18, ATP6V0E1, SERPINB6, SMIM30, ITGB2, SNX2, THEMIS2, CSTA, SOD2, LGALS2, SLC31A2, SLAMF7, ANXA5, ATF5, SCAMP2, P2RY13, RAB31, CANX, SASH1, ATP6V0D1, QKI, RCAN1, TMEM70, AP2A2, LAPTM5, OTULINL, RHOQ, CCDC88A, FERMT3, MLEC, ATF3, PDE4DIP, PEPD, IER3, GNPTAB, SDHD, IFNGR1, PDXK, IFI30, LITAF, CLTA, CLTC, HSD17B4, CALHM6, NANS, NUPR1, BCAP31, UBE2D1, G3BP1, KLHL6, ZFYVE16, CAPZB, COMT, FCGR1A, SPATS2L, RGS2, HERPUD1, NR4A2, S100A11, CAT, LGALS1, COLEC12, SLC16A3, CASP1, TMBIM6, RNASE1, SLC43A2, CNDP2, AP2S1, SKAP2, RHOG, SELENOS, STAT1, FCGR3A, PITHD1, Clorfl62, GALNT1, MCUR1, TIMM8B, LMNA, RAB5C, GPR183, PRDX3, CHMP1B, CCL4, KLF4, H2AFJ, MDH1, PABPC4, EFHD2, TMSB4X, MAT2A, ZEB2, CXCL2, LGALS3BP, GADD45B, IQGAP2, LAMTOR2, ATP1B3, DBI, LRPAP1, APLP2, LIMSI, MAP3K8, TXN, SAMSN1, BEX4, SSR3, RTN4, MYDGF, H2AFY, FABP5, CD53, ANXA2, ZNF331, RNH1, CD36, FYB1, ARL6IP1, HES1, SNX6, YWHAH, AC020656.1, NFKBIA, CALR, TNFRSF4, CXCL8, C15orf48, AKAP9, ID2, ZFP36L1.
Table 4C: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 3
COL1A1, COL1A2, COL3A1, TAGLN, FN1, ACTA2, CALD1, TPM2, DCN, COL6A2, BGN, THY1, COL6A1, MYL9, COL6A3, PDGFRB, PLAC9, AEBP1, PCOLCE, NOTCH3, COL5A1, COL5A2, SOD3, PRRX1, MXRA8, MGP, LHFPL6, NR2F2, CCDC102B, LUM, EMILIN1, COL4A2, MFGE8, COL4A1, PLXDC1, HIGD1B, COL18A1, IGFBP7, CARMN, COL14A1, CD248, FSTL1, SPARC, COL12A1, MYLK, TGFB1I1, TPM1, SEMA5A, CRYAB, SEPT4, EDNRA, C1R, POSTN, ID4, FBN1, CCDC80, FAT1, THBS2, NNMT, UACA, KCNE4, COL5A3, PPP1R14A, SULF1, ASPN, CPE, Cl lorf96, CDH11, SMOC2, GGT5, CTGF, PRKG1, SDC2, CSPG4, SPARCL1, VASN, KCNJ8, SGCE, ABCC9, TIMP3, SNHG18, MMP11, TNC, CAVIN3, IGFBP2, PDLIM3, EHD2, PDGFA, ECM2, ARHGEF17, GUCY1A2, PRSS23, CFH, CDH6, KANK2, SLIT3, TPPP3, ENPEP, SERPINH1, KDELR3, FOXS1, TINAGL1, FKBP10, RCN3, NDUFA4L2, PPIC, DDR2, CAVIN1, CIS, EPS8, AKAP12, TMEM98, CYR61, GJC1, EFEMP2, FOXC2, GUCY1A1, KIRREL1, OLFML2B, CLEC11A, MCAM, FRZB, ADAMTS2, LAMC1, LAMA4, SSPN, DCBLD2, TBX2, CNN3, TFPI, DLC1, LAMB1, ADGRA2, SELENOM, ITGA1, FILIP1L, DKK3, RBPMS, FHL2, MSRB3, GUCY1B1, IGFBP4, RARRES2, CAMK2N1, ECM1, RNF152, PXDN, PGF, CYGB, EBF1, PLS3, EDIL3, COX4I2, CERCAM, COX7A1, GJA4, LAMB2, OLFML3, FBLN1, FHL1, PLEKHH3, CTSK, CAV1, MEG3, GEM, CRISPLD2, OLFML2A, NIDI, LOXL2, INAFM1, AC245595.1, JAG1, GPX8, PALLD, TIMP1, IGFBP6, ELN, YAP1, IGFBP5, ADGRF5, PARVA, FBLIM1, MYO1B, CAV2, CSRP2, C9orfi, NEXN, TNFAIP6, CTTN, GSTM3, MYH11, COPZ2, CHN1, HTRA1, CRIP2, KRT18, PMEPA1, NEURL1B, FAM114A1, ITGB1, FERMT2, ADIRF, ID3, TNFRSF12A, LGALS3BP, SERPING1, ADAMTS1, LRRC32, PLAT, PMP22, BMP1, RGS16, TCEAL9, PHLDB1, FILIP1, LTBP4, NBL1, TNS1, CD 151, PTGIR, ENAH, RBFOX2, RBMS3, ITGAV, SPON2, INHBA, IFITM3, ANTXR1, TUSC1, PTK2, NDN, MAP1B, RND3, NES, PDLIM7, TJP1, PDLIM1, CYBRD1, PPFIBP1, TNS2, MRC2, HES4, LIMA1, DSTN, PHLDA1, VCL, RCN1, LMCD1, AXL, MYH10, CDC42EP5, SGCB, MT1E, NDRG2, PLPP1, EVA1B, MAGED2, SEPTI 1, RAB34, LAPTM4A, CALU, ARHGAP1, CSRP1, RBP1, APP, NFIA, SERPINF1, RRAS, A2M, NT5DC2, AGRN, RABB, LMNA, DNAJB4, GPX3, S100A13, MXRA7, PTMS, NUPR1, FARP1, BEX3, PHLDA2, MAP3K20, EGR1, CD63, LPP, NFIB, FHL3, GSN, EMP2, VC AN, DST, LTBP3, SPTBN1, CKAP4, ACTN1, LGALS1, DBN1, VIM, PEAK1, S0X4, MIR4435- 2HG, CD59, PDLIM2, TUBA1A, TAX1BP3, MY01C, KLF9, MAP1LC3A, RHOC, PRDX4, EPB41L2, THBS1, ABI2, NREP, RHOBTB3, NRP1, MAP4, PELO, S0RBS3, RGS5, F2R, PGRMC1, HCFC1R1, SPRY1, GAS6, TPM4, HSPB1, CLIC4, MPRIP, PPIB, SPATS2L, ROCK2, EMP1, REXO2, METRN, MGST3, SELENOW, CSNK1E, CPQ, TCEAL4, CYTOR, TMEM204, CYB5R3, NFIC, LEPROT, VKORC1, MORF4L2, HSPA1B, RABAC1, ARL3, TSC22D1, IER5L, RRBP1, MT2A, TCF4, PSMB5, SEPT7, PDLIM5, DYNLL1, ITM2C, REEP3, CD99, IKBIP, C12orf57, CD81, LRP1, ILK, ARID5B, KDELR1, ZBTB20, YIF1A, ARF4, GNAS, TGFBI, TUBB, EID1, HDLBP, SLC25A3, KDELR2, CALM2, MMP14, ANXA6, TUBB2A, JUN, IL6ST, TMEM59, ANXA5, PTEN, NDUFS5, P4HB, VMP1, TIMP2, NENF, OSTC, PDIA3, MYH9, PHPT1, FLNA, NPY, ACTG1, TUBB2B, IER3, TUBA1B, ACTN4, HSPA1A, MEF2C, SLC38A2, FOSB, MYL6, MACF1, ODCL
Table 4D: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 4
FCN1, S100A12, CD300E, S100A8, AC020656.1, VCAN, IL1B, APOBEC3A, MNDA, CFP, FPR1, CSTA, LYZ, SERPINA1, SLC11 Al, AC245128.3, S100A9, EREG, C19orf38, NLRP3, FGL2, LST1, ASGR1, CYBB, CSF3R, LILRB2, CTSS, NAMPT, KLF4, PLAUR, TLR2, CLEC7A, LILRA5, CPVL, AP1S2, NCF2, LILRB3, C5AR1, CLEC12A, RETN, Clorfl62, AIF1, IRAK3, G0S2, PRAM1, FGR, CD1D, TREM1, TYROBP, LILRA2, JAML, STXBP2, TYMP, CD93, MPEG1, CST3, TMEM170B, CD36, LGALS2, MS4A6A, PPIF, SRGN, ADGRE2, PLBD1, CD302, GCA, LILRB1, CD 14, COTL1, HBEGF, LRRK2, NEAT1, LTA4H, MXD1, CEBPD, HCK, CPPED1, SLC43A2, BCL2A1, PTPRE, SPI1, ACSL1, DUSP6, TSPO, BST1, TNFRSF1B, TNFSF13B, ANPEP, CLEC4A, SLC7A7, ZNF385A, S100A6, MEGF9, TKT, VSIR, OLR1, RBP7, FTH1, FCER1G, S100A4, SMIM25, PILRA, SIGLEC14, NUP214, ITGAX, CFD, THBS1, STX11, IFI30, ALDH2, OAZ1, ZEB2, LYN, GPCPD1, RGS2, FCGR2A, ATP2B1-AS1, SECTM1, PYCARD, SERPINB1, ITGB2, OGFRL1, P2RY13, DMXL2, THEMIS2, ATF3, S100A11, WARS, OSM, SH3BGRL3, KCTD12, VEGFA, SOD2, MAFB, CXCL8, TRIBI, METRNL, LRP1, IER3, PSAP, AC015912.3, PTGS2, AQP9, FCGR1A, ARRB2, EFHD2, MCL1, MS4A7, PLEK, HRH2, SAT1, SGK1, CD44, ODF3B, KLF10, CASP1, LCP1, C9orf72, PLSCR1, ACTB, AOAH, MARCH1, DSE, RXRA, FGD4, EVI2B, APLP2, NR4A1, IL17RA, SMCO4, TET2, IGSF6, TIMP1, FOSL2, MYD88, H3F3A, EMILIN2, LAPTM5, RNF149, KYNU, RNF130, IL1RN, TNFAIP2, CDKN1A, H2AFY, KDM6B, BACH1, SAMHD1, PLXDC2, ETS2, SERP1, CEBPB, SH3BP2, GLIPR1, FOSB, RIPK2, GK, CCR1, TBXAS1, CNPY3, RAB31, HLA- DRA, IRS2, SERPINB9, BRI3, CYBA, YBX3, CSF1R, ATP13A3, ITGAM, NAIP, RASGEF1B, GNAI2, POU2F2, AHR, GRN, CARD 16, IFNGR2, ADA2, OTUD1, ATP2B1, PPT1, CD55, PRELID1, LY86, ZFAND5, MAPKAPK3, NFIL3, LRRC25, ATG3, DPYD, BLVRB, MYO IF, AGTRAP, GNAQ, CD83, CTSH, LAT2, DUSP1, SNX10, PHACTR1, C3AR1, ATP6V0D1, FAM49A, PIK3AP1, MX2, ARL5B, FLNA, LACTB, IRF2BP2, TALDO1, CMTM6, VASP, HIF1A, NR4A3, PABPC1, ATP6V1B2, WAS, CALHM6, CSRNP1, UBE2D1, NFKBIA, ZYX, BID, QKI, NCF1, PFDN5, ACTR2, TGFBI, RILPL2, NUMB, UPP1, VMP1, CCDC88A, NINJ1, HLA-DRB1, GSTP1, RHOG, NCOA4, SAMSN1, PTP4A2, HSBP1, MAP3K8, METTL9, SORL1, GLRX, PLEKHO1, ARPC3, ZNF106, ATF5, INSIGI, MOB1A, GLIPR2, CXCL2, S0CS3, GRB2, GAPDH, PPP1CB, AREG, CD74, LYST, GLUL, ARPC5, ARPC1B, MAT2A, EMP3, DOCK2, SDCBP, LCP2, LAP3, CTNNB1, FKBP5, TMEM167A, LRRFIP1, GABARAPL1, TNFSF10, SMAP2, PGLS, IFITM3, ATP6V0B, PPP1R15A, GSTO1, PCBP1, FYB1, RNH1, ANXA1, DAZAP2, IFNGR1, MIDN, ADGRE5, NFKBIZ, BNIP3L, NR4A2, MYADM, H3F3B, S100A10, FOS, NABP1, LAMTOR1, PKM, LSP1, ANXA5, SLC2A3, DDX21, LAMTOR4, ZFP36, IFI44L, AHNAK, CHMP1B, SYAP1, MARCKS, GBP1, HLA-DPA1, MX1, GPR183, ZFP36L1, HSPA1A, HLA-DPB1.
Table 4E: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 5
KLRF1, TRDC, KLRD1, GNLY, KLRC1, CTSW, PRF1, NKG7, GZMB, IL2RB, KLRB1, FGFBP2, CD7, HOPX, PTGDR, XCL2, CLIC3, CST7, XCL1, CD247, TXK, CCL5, MATK, NCR3, ADGRG1, GZMA, HCST, SPON2, PLAC8, CX3CR1, PYHIN1, GZMM, CMC1, TTC38, CCL4, SAMD3, SH2D2A, APOBEC3G, GZMH, SYTL3, PTPN4, RUNX3, ZAP70, EVL, CHST2, CHST12, MBP, ABHD17A, CD38, IRF1, RARRES3, TBC1D10C, APMAP, HLA-B, CD69, DENND2D, CDC42SE1, DUSP2, MYL12A, PTPN7, RAC2, HLA-A, FCGR3A, SPN, ARL4C, C12orf75, PTPN22, CCND2, EFHD2, PAXX, BTN3A2, LINC01871, PIP4K2A, FCER1G, ACAP1, IER2, CALM1, BTG1, AKNA, JAK1, BIN2, UBB, ARHGAP9, Clorf56, ADGRE5, RAP1B, CORO1A, ZFP36L2, SRSF5, ATM, IL32, CCND3, METRNL, TGFB1, SEPT7, AREG, PFN1, TXNIP, STK17A, LIMD2, ID2, CLEC2B, JUNE), AES, EIF3G, PIK3R1, CD47, NR4A2, PLEK, CCL3, NFKBIA.
Table 4F : List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 6
VWF, CLDN5, PLVAP, RAMP2, EGFL7, CLEC14A, SOX18, RAMP3, AQP1, SLC9A3R2, CALCRL, CDH5, TM4SF1, ESAM, ADGRL4, PODXL, PTPRB, NOTCH4, ECSCR, EMCN, MMRN2, KDR, ROBO4, SEMA3F, PALMD, RASIP1, TIE1, SLCO2A1, FLT1, GNG11, PCDH17, BCAM, VWA1, HYAL2, FAM167B, SHANK3, CXorf36, CD34, LDB2, EFNA1, CYYR1, CAVIN2, HSPG2, ARHGAP29, MYCT1, NOSTRIN, S100A16, EPAS1, CAV1, TM4SF18, RAPGEF5, WWTR1, BTNL9, STC1, ID1, EFNB2, KANK3, PCDH12, GALNT18, NFIB, NPDC1, TCIM, PCAT19, JAG2, PREX2, IGFBP7, ACVRL1, APLNR, TEK, JAM2, DLL4, TMEM255B, FZD4, IGFBP4, CX3CL1, SMAD6, ADGRL2, HECW2, SOX7, PTPRM, COL4A1, AFAP1L1, PLXNA2, APP, GJA1, CRIP2, BCL6B, MECOM, ESMI, ADGRF5, DOCK6, DCHS1, CAVIN1, IGFBP3, SPARCL1, JCAD, HEG1, FAM69B, TSPAN12, TSPAN18, ENG, ADCY4, CD93, PECAM1, GRB10, ARHGEF15, ITGA2, FLT4, NOVA2, ERG, CASKIN2, INSR, COL4A2, MCAM, SNCG, SHROOM4, TIMP3, DOCK9, COL15A1, HTRA1, MPZL2, SPNS2, ITGA6, SCARF1, IFI27, VEGFC, TJP1, CAV2, CLEC3B, LIFR, EMP2, HEY1, EMP1, PTPRG, EPHB4, NRN1, UNC5B, ACKR3, NPR1, FGD5, LAMA4, ARAP3, ID3, PDGFB, RNASE1, SHE, PON2, SPARC, CNN3, TNS2, SERPINH1, ITGA5, BMPR2, TSPAN9, AGRN, SEMA6A, MYO10, SPRY4, PPFIBP1, MYO6, ADAM15, PLPP1, MAGI1, PLPP3, RHOJ, SPTBN1, LAMB2, A2M, NUAK1, SYNPO, ACE, ADAMTS9, JAM3, CRIM1, FKBP9, PTPN14, IL3RA, PCDH1, LIMS2, TGM2, PXDN, PIK3R3, NRP1, TSPAN7, NCKAP1, CDH13, TMEM204, CMTM8, TFPI, AFDN, LAMA5, PDLIM1, CALD1, LIMCH1, JUP, MMP2, ANGPTL2, TMEM88, CDC42EP5, PKP4, IFITM3, MTUS1, MGP, S100A13, F2R, RAI14, CD59, COX7A1, PLXND1, PLK2, TSPAN15, CAVIN3, LAMB1, MYO1C, LAMC1, PRSS23, PROS1, TSC22D1, ADIRF, FSTL1, SEMA6B, YES1, RABB, LMO2, MPDZ, RBMS2, LRRC8A, MAST4, THBD, DLC1, RGS3, BCAR1, ELK3, FERMT2, IPO11, DGKH, TCF4, ADAMTS1, CTNND1, PLS3, COL18A1, TP53I11, TNFAIP1, NES, ECE1, GNA11, DPYSL3, DEPPI, LOXL2, S1PR1, LRRC32, CLIC4, ICAM2, PROCR, FKBP1A, NIDI, ARHGEF12, CD151, TMEM184B, CDC42BPA, LMCD1, EDNRB, PIK3C2B, JAG1, NFIA, NECTIN2, CTTN, RBPMS, DYSF, NOTCH1, FNBP1L, SMTN, CD9, PCGF2, RHOC, FSCN1, SERPINE1, GRASP, PKIG, SPRY1, BACE2, CTNNAL1, CTNNA1, ITGB1, CTTNBP2NL, CCDC85B, UACA, HDAC7, GAS6, ANGPT2, PTP4A3, ADGRG1, PAM, FLNB, MARCKSL1, SELENON, TINAGL1, LUZP1, PPIC, RASAL2, MGST2, TCEAL9, STOM, IL6ST, PTK2, TNFAIP8L1, SEC14L1, CDC42BPB, ITGA1, SH3BP5, SLC44A2, ETS2, CYR61, SIPA1L2, LXN, RGL2, TGFBR2, RASGRP3, TRIOBP, CD109, VAMP5, FAM198B, FBN1, CYB5R3, Cl lorf96, PPM1F, HES1, RDX, GSN, SEPT10, CD81, EHD4, RHOB, CA2, PLEKHA1, KIAA0355, PIEZO1, MAGED2, MYO1B, CTNNB1, SOX4, RCN1, LAPTM4A, VIM, ACTN4, EVA1B, SERPINB6, TUBB6, TAX1BP3, HDGFL3, TNFSF10, MAP3K11, VGLL4, ZEB1, SHC1, BEX3, MBNL2, NNMT, LEPROT, DAAM1, LIMA1, PTTG1IP, NRP2, SASH1, ROCK2, MXRA7, CD320, ITM2A, HES4, TMEM173, FXYD6, CLU, BST2, SH2D3C, PMEPA1, SNTB2, KLF9, ENTPD1, SNRK, THY1, TCEAL4, APOLD1, MGST3, NEDD9, TMEM109, ITM2B, CD276, MRPL17, PGM2L1, SMURF2, TNFRSF4, MPZL1, VASH1, SELENOM, CCDC50, Clorf54, MACF1, FDPS, ZBTB20, RGCC, CDC37, PROP, LMNA, PTMS, DUSP6, AAMDC, SPTAN1, CCND1, ANXA2, GOLIM4, CD46, PEA15, MYL12B, GNAI2, MEF2C, DPYSL2, RRAS, CARHSP1, PNP, PSMB5, MOB2, HSP90B1, SELENOW, CEMIP2, WARS, RAB11A, SYPL1, SERINC3, YBX3, DSTN, HSPA1B, TUBA1A, GUK1, RAC1, PHACTR2, MARCKS, CALU, PDIA6, DYNLL1, YIPF3, RFLNB, CYB5A, MAP1B, CD99, DADI, YWHAE, TPM4, TNFRSF1A, MYH9, PDIA3, S0CS3, CALR, NDRG1, HSPB1, YWHAH, MAP4K4, BSG, APLP2, GTF2I, PRMT1, GABARAPL2, RABAC1, XAF1, ARHGAP18, NUDT4, HLA-E, SULF2, EFCAB14, MXD4, ARGLU1, EIF4G2, GNAS, HSPA5, PIM3, IFI44L, HNRNPH1, RTN4, CSNK1A1, MIR4435-2HG, LBH, GBP4, IVNS1ABP, CALM1, NEAT1, IFNGR1, HSPA1A, JUN, CYTOR, XIST, DUSP23, IER2, FOXP1.
Table 4G: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 7 IGHM, MS4A1, CD79A, IGHD, CD79B, TCL1A, BANK1, VPREB3, RALGPS2, TNFRSF13C, LINC00926, CD22, FAM129C, AFF3, BLK, LINC02397, FCRL1, IGLC2, IGKC, CD19, PAX5, SPIB, FCER2, IGLC3, FAM30A, FCRL5, JCHAIN, FCRL2, GNG7, HLA-DOB, CD37, POU2AF1, MEF2C, BCL11A, HVCN1, ADAM28, LY9, GAPT, BLNK, CXCR5, BCL7A, SMIM14, C16orf74, FCMR, STRBP, POU2F2, PLCG2, EAF2, P2RX5, LTB, BACH2, SWAP70, GPR18, CDCA7L, HLA-DRB5, NEIL1, CXCR4, FAU, ORAI2, HLA-DRA, HLA-DQB1, CD74, NCF1, CD83, CD72, AC245060.5, TMEM156, RACK1, HLA-DQA1, MT-CO2, CD52, ZCCHC7, STX7, GABPB1-AS1, ARHGAP24, FCRL3, RCSD1, HLA-DPB1, AC025164.1, MT-ND4, PKIG, SELL, MT-ATP6, RIPOR2, BTG1, MT- ND1, HLA-DRB1, MT-CO1, NOP53, QRSL1, MT-ND3, BTK, MALAT1, HLA-DPA1, MT- CO3, MTRNR2L12, CWF19L2, SP140, EEF1B2, HIST1H1E, BIRC3, EEF1A1, CXXC5, HLA-DMB, CLEC2D, PRKCB, RASGRP2, CIITA, PTMA, UBA52, PLAC8, PNN, PNISR, IRF8, RBM38, CD69, GGA2, TPD52, PPM1K, FOXP1, LIMD2, PLEKHA2, JUNE), SNX29, ARGLU1, IKZF3, FCHSD2, TMEM154, TMEM243, PRDM2, EEF1D, NCOA3, SNX2, HERPUD1, REL, RHOH, BOD1L1, STK17A, MT-ND2, SF1, CD24, SNHG7, TSPAN13, MT-CYB, KLF2, TUT4, TCF4, SP100, STK17B, MT-ND4L, LY86, KIAA0040, ST6GAL1, EIF1AY, RERE, PDE4B, BORCS5, SMCHD1, TRIM38, ISG20, MTSS1, HIST1H4C, ZNF791, HIST1H1D, IFT57, CD40, PARP14, CCDC50, SMC6, SYPL1, EZR, NFKBID, DNAJC10, MTRNR2L8, UPF2, MAP4K4, SP110, TAF1D, LAPTM5, ZFAS1, PLPP5, NACA, MBD4, LUC7L3, DDX5, ARID1B, MARCH1, MDM4, TSC22D3, MT-ND5, AC004687.1, HIST1H1C, SLC38A1, SNHG8, STK4, ERP29, PARP1, TAGAP, TNFAIP8, TNRC6B, LSM7, ATM, BTG2, MYCBP2, SMAP2, ZRANB2, PHACTR1, FAM107B, TRA2B, GCC2, TSTD1, EIF3E, MTPN, TCEA1, SRSF5, EEF2, SYF2, NCL, SEC62, TAF7, CIRBP, DDX21, VPS13C, NSA2, NSD3, GPR183, THRAP3, SON, ANKRD12, YBX3, YPEL5.
Table 4H: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 8
APOE, APOCI, Cl QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81, TUBB2B, LILRB4, TUBA1A, ODC1, GPX4, PLD3, ACP5, PLIN2, STMN2, GNAS, LAMP1.
Table 41: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 9
C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, ST14, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HM0X1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9, SNX10, FPR3, CXCL8, CD109, PLA2G7, CCR1, LGALS3, ERO1A, APLP2, SIRPA, BLVRB, HEXB, TYROBP, FCGR3A, COLEC12, CNDP2, P4HA1, BRI3, PKM, PSAP, ANPEP, NPC2, TNS3, IL18BP, APOE, LAMP1, TPP1, TIMP2, NPL, ATP6V1B2, VAT1, TTYH3, SOAT1, C5AR1, RNASE1, OLR1, GNS, SLC43A3, NCEH1, CTSH, FCGR2A, GRN, FCGR2B, GRINA, FCER1G, SLC2A1, FNDC3B, CTSZ, TMEM51, EGLN3, IL1RN, CTSA, LGALS1, ENO1, CXCL3, CD163, RAB7B, BNIP3, CCDC88A, DAB2, ATP6V1F, PIK3AP1, RAB20, NCF2, S100A11, NR1H3, PLD3, PTAFR, SPI1, FNIP2, DMXL2, OTOA, ASAHI, VIM, NDRG1, ATP6AP1, CLIP4, SCARB2, BNIP3L, CCL3, SLC15A3, GSTO1, VC AN, PLXDC2, CD36, SGK1, ACP2, SLC7A7, ATP6V1A, PLPP3, RAB42, PLTP, ITGAX, NPC1, ANXA2, SQOR, ITGAM, OSCAR, BCKDK, LGMN, EIF4EBP1, ATF5, H2AFY, RRAGD, VEGFA, SOD2, ARL8B, LACTB, TNS1, HAVCR2, BCAP31, LAPTM5, LRP1, CCL18, ADAM9, BCL2A1, SDC4, DRAM1, SERPINA1, ATP13A3, LYZ, POR, LILRB3, CD300A, SDCBP, S100A10, DUSP3, CD86, RBM47, MCRIP2, KIAA0930, MFSD1, CD14, RAB31, MRC1, TCIRG1, GRB2, GPI, SDSL, TFRC, ENO2, P4HB, FKBP15, AGAP3, ADAM8, MGLL, ABHD2, RAB1A, C1QC, RALA, TUBA1C, NINJ1, LIMSI, MFSD12, PGK1, CD63, DHRS3, TPI1, CD84, IRAKI, RAB10, SLC25A19, HEXA, CXCL2, HLA-DRA, RBPJ, LAIR1, SULF2, ATOX1, SLC48A1, IFNAR1, ANXA5, GAPDH, CYFIP1, CTSS, AIF1, GK, GAA, PDE4DIP, ARHGAP18, MGST1, LAMP2, C2, SQSTM1, C3AR1, FMNL2, MAFB, PRDX1, ABHD12, MS4A4A, M6PR, CCL2, SERF2, CPM, MS4A7, EMILIN2, CSF1R, MMP12, CD82, HSD17B4, PLEKHB2, CEBPB, IFNGR2, FAM162A, RETN, SAT1, TYMP, MMP9, CANX, SHTN1, C1QA, QSOX1, RNF13, UPP1, PPT1, SLAMF8, KCTD12, MXI1, ADAP2, PGD, ALCAM, SLCO2B1, ITGB2, TPD52L2, EAF1, RABB, HNMT, CLEC4E, BCL2L1, PAPSS1, ZEB2, ELL2, ADA2, ATP6AP2, CYSTM1, CD74, TFEC, SDC2, RXRA, FCGR1A, MMP14, IDH1, PGAM1, GNB4, ACSL1, HM13, LGALS9, ATP6V1C1, CYBB, GCHFR, ALOX5, VAMP8, ICAM1, Cl QB, COLGALT1, ANXA4, VEGFB, CLEC7A, IGF2R, PILRA, METRNL, BMP2K, ABCG1, UNC93B1, HLA-DMA, KCNAB2, GPX4, TSPAN4, LDHA, RNASET2, SPG21, HLA-DRB1, SYK, MIF, TGFBI, PRNP, RASSF4, RASGEF1B, TMEM176A, LSP1, FCGRT, MARCH1, SH3BGRL3, RNASE6, ALDOA, LYN, LRPAP1, LY96, SCPEP1, GLIPR2, YBX1, GNAQ, HBEGF, CD164, IGSF6, PMP22, RAP2B, FERMT3, GNPTAB, TXN, PEA15, VKORC1, MGST3, ATP6V0B, CITED2, HLA-DQB1, CALM3, Clorfl62, TMEM176B, CHST11, ANKRD28, MYO9B, PFKL, DNASE2, FDX1, TUBGCP2, TMBIM6, RGCC, ATP6V1D, ARRDC3, MYDGF, SMS, ZFYVE16, LGALS3BP, OAZ1, RTN4, UGP2, ATP6V0D1, RNF181, CPEB4, NOPIO, NUCB1, PABPC4, RHEB, PLEKHO1, ZYX, RNH1, CLTC, ZFAND5, TPM4, PHC2, RAB7A, ATF3, DPP7, MAF, DBI, ME2, CD44, FOSL2, CD4, IFI6, LITAF, TNFSF13B, NEAT1, SSR3, AP2S1, TSPO, SRGN, VDAC1, SLC2A3, TALDO1, RDX, AHR, PTTG1IP, STX4, USF2, ELOC, SH3BP5, ACADVL, CHCHD10, FLNA, IER3, LMNA, S100A6, GNG5, CALR, HSPA5, LAP3, STAT1, ALDH2, OSBPL8, ANXA1, FN1, HSP90B1, HSPA1A, ZFP36L1, MT1X.
Table 4J: List
Figure imgf000097_0001
are up-:
Figure imgf000097_0002
in the different clusters identified in the i
Figure imgf000097_0003
of 10 patient tumors analyzed by scRNA-seq. Cluster 10
FCGR3B, CMTM2, CXCR2, SIOOP, CSF3R, CXCR1, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CDA, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, SDCBP, JAML, MCL1, YPEL3, HSPA6, NCF2, SPI1, LILRB3, TYROBP, DUSP1, FCGR2A, SERPINA1, MYO IF, IVNS1ABP, APOBEC3A, RSAD2, MEGF9, RIPOR2, S100A6, ABTB1, LYN, CREB5, LCP1, ALOX5AP, ZFP36L1, USP10, IER2, CSF2RB, SLC11A1, IFITM3, MX2, RGS18, PYGL, SMIM25, SLC2A3, TRIBI, NCF4, TUBA1A, XPO6, TLE3, ITM2B, TXNIP, EGLN1, LILRA5, GMFG, DDX60L, DENND3, IGF2R, HIST1H2AC, EVI2B, PTPRC, CEBPD, LSP1, OAZ1, GLUL, UBE2B, RARA, PNRC1, CPPED1, TLR2, FOS, NADK, CDKN2D, PDLIM7, ARPC5, PTPRE, FLOT2, PLEK, CD55, GNAI2, ADAM8, PTEN, BRI3, ACTB, LAPTM5, STXBP2, P2RY13, ISG15, LY96, UBN1, VSIR, NABP1, SMAP2, ICAM3, VASP, ALOX5, IFRD1, PELI1, RTN3, NUP214, IL17RA, CNN2, MARCKS, HLA-B, PHC2, SEC14L1, CFLAR, ARHGAP9, SHKBP1, RAB11FIP1, EFHD2, LAMTOR4, PLAUR, KDM6B, RASSF3, UBE2D1, CLEC4E, CAP1, CMTM6, LYST, VMP1, FMNL1, FBXL5, TALDO1, CLEC7A, NINJ1, HLA-E, ITGAX, SSH2, PREXI, ACTN1, MAP3K2, ABHD5, HIF1A, ARRB2, ZFP36, ARHGAP26, CYSTM1, TXN, GPSM3, CDC42EP3, UBE2D3, IRF1, CSRNP1, CYTH4, TNFSF13B, ACAP2, PLXNC1, TNFAIP2, USP15, NOPIO, MX1, C4orf3, JMJD1C, SLA, BACH1, MAP4K4, FOSL2, KIAA1551, CKLF, CARD16, NMI, ADGRE5, OSBPL8, WIPF1, FYB1, FLOT1, ATP6V0B, TNFRSF1B, FKBP8, SKAP2, WAS, PLSCR1, TAGLN2, RAB31, PDE4B, SHISA5, LRP10, CCPG1, FAM49B, ADAR, CD46, TCIRG1, IFI16, SERPINB1, UBALD2, MIDN, NCOA4, GNB2, UBE2R2, CDC42SE1, ZYX, TAGAP, RNF213, LCP2.
Table 4K: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 11
DLK1, RGS4, RGS5, PAGE2, HAND2, BIRC5, PRCD, BEX1, GNLY, STMN1, HMGB1, CCL5, STMN2, EEF1A2, CD8A, PAGE5, LINC00682, SLC25A4, CDKN1C, UBE2C, CCND1, CDK1, GZMA, CHGA, CKB, HIST1H4C, PHOX2A, CD2, MAD2L1, GMNN, CD8B, CHGB, H3F3B, RUNX3, MDK, NME1, NDUFAF8, GAL, TYMS, CD7, SSRP1, CD3D, PRDX2, TOP2A, HAND2-AS1, PTMA, PHOX2B, CENPF, PCSK1N, GZMK, TUBB2B, GZMH, ANAPC11, GAP43, JPT1, HSP90AA1, UQCRQ, UBE2S, GLCCI1, TUBA1B, MRPL21, HMGN2, GNAS, PTTG1, SUMO2, NPY, CHCHD2, HSP90AB1, KPNA2, CDK6, GAPDH, MAP IB, COX7A2, TUBA4A, SRSF2, MZT2A, HMGB2, SMC4, COX8A, RTF1, MRPS7, TENT5C, ZFP36L2, CKS1B, PTMS, GATA3, TNFAIP3, LSM4, MT-ND2, ACTG1, MARCKSL1, IL32, SNRPF, MRPL12, DUT, SNRPD1, UCHL1, TOBI, HINT1, ACPI, SNRPE, SNRPB, NDUFS6, PSMC5, CBX1, EIF5A, PPP1R14B, NUCKS1, ISG20, SMC2, SNF8, TSTD1, MT-ND5, YWHAQ, UQCRH, TUBB, R0M01, C12orf75, H2AFZ, MLLT11, NOP56, PFDN2, TUBA1A, MZT2B, YPEL5, PA2G4, COX6C, HNRNPAB, C19orf53, STRAP, PHB, CREM, RAN, PCNA, APOBEC3G, LSM3, TMA7, MT-ND3, ITM2C, SEC11C, MANF, DCTN3, SSR4, PSME1, PARP1, SNUB, ATP5PF, SLIRP, MT-ND6, CCT2, H1FX, ATP5MC1, JUN, SERBP1, RANBP1, NASP, SNRPD2, SRSF7, CD52, SEC61G, ID2, SDF2L1, RPA3, ODC1, EIF1AX, CCND2, SRSF9, HMGA1, HIST1H1C, XRCC5, TERF2IP, LMAN1, SUB1, CRELD2, TMEM258, PPIB, LEPROTL1, SPCS2, HSPEL Table 4L: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 12
DLGAP5, MKI67, HMMR, CEP55, CDCA3, ASPM, KIF11, TPX2, NUSAP1, PCLAF, CENPE, CDKN3, TOP2A, AURKB, KNL1, CDC20, KIFC1, TYMS, CCNB2, BIRC5, RRM2, CDK1, CENPF, SPC25, CENPA, PLK1, DEPDC1B, GTSE1, UBE2C, CCNB1, SGO2, ZWINT, TK1, ASF1B, TROAP, NEK2, NCAPG, BUB1, CENPM, CLSPN, KIF14, CENPW, SGO1, DEPDC1, NUF2, BUB IB, KIF23, SHCBP1, HJURP, PTTG1, ARHGAP11A, HMGB3, MAD2L1, MYBL2, FOXM1, ANLN, CENPN, MELK, SPC24, SMC2, H2AFX, BRCA1, TCF19, CDCA8, SMC4, CCNA2, EZH2, PBK, ESCO2, CKS1B, UBE2T, FANCI, AURKA, PHF19, CDT1, MXD3, HMGB2, NDC80, HIST1H1B, DTYMK, NCAPG2, STMN1, DNAJC9, KIF20B, DHFR, CKS2, C21orf58, PCNA, ECT2, RACGAP1, ORC6, SPDL1, MND1, NCAPD2, HMGN2, H2AFV, GMNN, KPNA2, LRR1, TUBA1B, NRM, UBE2S, TACC3, PRR11, FAM111B, H2AFZ, CENPK, GGH, TMPO, TUBB, HMGB1, CCDC34, TTF2, LMNB1, WDR76, RPA3, NUDT1, ATAD2, HIST1H4C, CENPU, DDX39A, ANP32E, CENPH, HELLS, CKAP2, USP1, FEN1, CCDC167, RAD51AP1, TMEM106C, ALYREF, SKA2, FBXO5, KNSTRN, BCL2L12, DUT, SAC3D1, ANP32B, RUVBL2, KIF22, CDKN2C, NUCKS1, RRM1, LSM5, WDR34, TUBB4B, CDCA7, VRK1, CARHSP1, NASP, C12orf75, TUBA1C, MCM3, CRIP1, CDC25B, CDKN2A, PTMA, NCAPD3, SIVA1, RAD21, RAN, CBX5, MCM7, ATAD5, RFC4, MZT2B, CKAP5, TUBA4A, CALM3, HSPB11, PPIA, ZDHHC12, AL441992.1, PFN1, RANBP1, SNRPB, COX8A, CFL1, SMC3, ACAT2, COX17, HDGF, CBX3, MAGOHB, RNASEH2B, DEK, MRPL51, NSD2, PPIH, GAPDH, DBF4, AC084033.3, CDK2AP2, DNMT1, ATP5IF1, IDH2, LSM4, BOLA3, FAM111A, SLC9A3R1, MZT1, HAUS1, HNRNPA2B1, JPT1, MAD2L2, ACTB, YEATS4, HPRT1, HMGA1, HMGN1, SLBP, NUP37, SH2D1A, RBM8A, BUB3, SSRP1, CENPX, TFDP1, SNRPD1, HSP90AA1, SNRPG, PSME2, SNRPF, HAT1, SNRNP25, SLC25A5, CACYBP, SUB1, PSMB9, LSM2, CORO1A, SUZ12, RUVBL1, NDUFB11, CXCR3, HNRNPAB, COX5A, TPRKB, NOP58, RNF167, DCXR, ACYP1, CD3D, RAC2, PLP2, SUPT16H, LDHB, LSM3, PIN1, ACTG1, VDAC3, SMC1 A, NUDT21, FDPS, POP5, PSMC3, STOML2, CHCHD1, PA2G4, CD3G, EIF4A3, CDKN2D, RBBP7, PARP1, HINT1, PSMA5, SRSF3, HNRNPA3, H3F3A, PMAIP1, CD3E, MZT2A, UQCC2, ARHGDIB, MAZ, LBR, SIT1, XRCC6, RALY, TIMM10, RNASEH2C, SRSF10, RNPS1, DCK, EBP, SNRPC, NDUFA6, HP1BP3, NDUFA2, MRPL23, PPP1CA, MAGOH, NAA38, PSMA4, ANAPC11, EIF5A, UBALD2, PSMD14, ATP5MF, CMC2, HNRNPR, LINC01871, COX6A1, HNRNPD, ILF2, COX6C, NDUFS6, PRDX3, COX20, UBB, ELOC, COMMD4, CHCHD2, MIS18BP1, CCT5, ATP5PB, MTF2, CCT2, CD27, YWHAQ, DAZAP1, PSMB2, NDUFB1, RBX1, UBE2N, PDCD5, TRAC, UBE2I, MRPL57, POLE3, ETFB, PPP4C, UCHL5, NUDC, UBE2A, UQCRH, BANF1, HNRNPM, LCK, SNF8, SNRPD3, GLRX5, BRD7, SEMI, PGP, ARPC5L, NOP56, THRAP3, CALM2, PARK7, GZMK, TRBC2, DKC1, PSMB3, TMEM160, ERH, HNRNPF, SNRPE, CKLF, PSME1, CSNK2B, SPN, DCTN3, MCM5, PRDX2, VPS29, GTF2A2, PSMB8, EIF1AX, SNRPA1, UQCRQ, LDHA, CD8A, H1FX, HINT2, HIST1H1C, SSNA1, TMEM258, PPM1G, ATP5PF, CYC1, TRAPPCI, ATP5MC3, NAP1L4, UBE2L3, MRPL22, NOL7, ARL6IP1, MRPL54, TXNDC17, HIST2H2AC, SF3B2, ATP5MG, NONO, PTGES3, SFPQ, KHDRBS1, ENO1, PDAP1, NUCB2, NDUFB3, IFI16, ROMO1, SLIRP, TMEM256, MRPL52, TPI1, PRKDC, TPR, ADRM1, PET100, SEPT6, RBM25, ZNF706, SRP19, YWHAB, NDUFV2, RAB5IF, NDUFB6, RTRAF, NDUFS5, TAPI, EIF2S2, PSMD8, BAX, CD2, GZMA, PSMB6, SDF2L1, LSM7, ATP5F1A, NDUFA4, TMA7, HSPA8, HNRNPA1, ITGB1BP1, YBX1, BLOC1S1, CCT8, PSIP1, RUNX3, EZR, LYAR, S100A10, PSMA2, HIST1H1D, ANAPC5, UQCR10, FBL, PDIA6, DYNLL1, ABRACL, PGAM1, ARHGDIA, CCT7, GTF3C6, UBL5, MANF, COX6B1, SRSF2, SOD1, ARPC2, XRCC5, COX7B, CNTRL, NDUFB8, SF3B5, SRSF4, PSMA3, RBM3, COTL1, RFC1, SET, RHEB, CCT6A, MT2A, YWHAE, ATP5PO, TMSB4X, EIF5B, COX7A2, PSMA7, RGS1, ATP5MD, MPC2, SNHG25, CALM1, CNN2, ATP5F1B, HSPE1, HSPD1, FKBP11, PPA1, IL32, COPE, EMP3, ATP5F1C, TOPI, HIST1H1E, DBI, SPCS1, PSMD7, CD52, CLEC2D, NME1, DDX46, NPM1, MTDH, GTF3A, SERBP1, NCL, PKM, CRELD2, SPCS3, MT-ND6, SEPT7, SRM, ATP5MC1, C1QBP, ZFP36L2, CDV3, CALR, HSPA5, HMGN3, SEC61B, SEC61G, HSP90B1.
Table 4M: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 13
TNFRSF8, GPBAR1, LILRA5, APOBEC3A, SMIM25, LILRA1, SLC24A4, CDH23, TCF7L2, LILRB2, FCN1, ZNF703, C19orfi8, LILRA2, CD300E, UPK3A, FCGR3A, MTMR1 1, P2RX1, LRRC25, CFP, NEURL1, STXBP2, CLEC12A, ADGRE1, PILRA, LST1, SLC11A1, FGR, ICAM4, SERPINA1, MTSS1, CDKN1C, LILRB1, PRAM1, IFI30, MS4A7, CFD, POU2F2, C5AR1, WARS, CX3CR1, FAM110A, HES4, LINC00877, Cl lorf21, AIF1, LMO2, SIGLEC10, CAMK1, BID, TNFRSF1B, MAPKAPK3, SLC31A2, PLAGL2, Clorfl62, GCH1, COTL1, CDA, SLC7A7, OAS1, SPI1, FGL2, FCER1G, LYN, C9orf72, SLC2A6, PPM1N, NR4A1, SECTM1, HCK, NCF2, CTSS, C15orB9, PECAM1, RHOB, KIAA0513, IFITM3, MNDA, MXD3, RXRA, LYST, CPPED1, C5AR2, BCL2A1, CARD16, VSIR, NAAA, TBXAS1, MYO1G, TYROBP, CSF1R, ARRB1, CLEC7A, RRAS, CALHM6, HRH2, TYMP, CSTA, SAT1, CST3, S100A4, TESC, STX11, DOCK5, RGS19, ADGRE2, OAZ1, CASP1, RELT, PTPN6, S100A11, CMTM6, LYL1, TCIRG1, PYCARD, AC096667.1, LFNG, CD300C, LRRK2, IFITM2, ABB, BATF3, PTGIR, AP2A1, PLAUR, KLF4, LTA4H, SMCO4, MBD2, NAMPT, MYD88, HK3, SCIMP, ZEB2, CEBPB, RGS18, RNASET2, SIDT2, TIMP1, CYBB, KDM1B, MS4A4A, ITGAL, MAFB, FPR2, NUP214, ARRB2, S100A6, FRAT2, ITGAX, DUSP1, PLXNB2, FTH1, CD300LF, SLC43A2, CSK, RHOC, TKT, PRKACA, VASP, DUSP6, ARPC3, BRI3, VMO1, ZFAND5, EMP3, BTK, CYSLTR1, FPR1, ARHGAP27, METRNL, EVI2B, NAPRT, RNF144B, UNCI 19, FAM45A, ATG3, TNFSF10, PRELID1, CD55, P2RY13, EHBP1L1, RASGEF1B, PTP4A2, RAB24, GRK3, PIK3AP1, METTL7A, CHST2, IRAK3, TSPO, ASAHI, AL139246.5, ATP2B1-AS1, AP1S2, SERP1, ARPC5, ADA, CYTIP, DEDD2, PTP4A3, RAB8A, FGD2, CD86, SOD2, LGALS9, H3F3A, SPN, RGS2, NFKBIZ, RNH1, RHOG, BLOC1S1, NEAT1, TNFAIP2, CPVL, PSAP, ARPC1B, WAS, LY6E, IL1B, CORO1A, G0S2, RALB, NINJ1, GNAI2, FBP1, THEMIS2, MTPN, LILRB3, RIN3, IGSF6, MX2, GRK2, IRF7, ATG16L2, ARID3A, UBE2R2, PLAC8, PLEK, DRAP1, PPM1F, SH3BP2, RNF149, IFNGR2, CYBA, ARPC2, LIMD2, LPCAT2, IER5, TNFSF13B, HSBP1, PGLS, ACAA1, C20orf27, SSH2, GNG5, NACA, CD83, FTL, CD48, RARA, ADGRE5, GPSM3, BACH1, NMI, TAF10, CNIH4, GMFG, SNX18, IFIT2, ACTB, HACD4, AGTRAP, ARAP1, CTBP2, CD68, OTUD1, VPS29, PABPC4, EIF1, ZNF385A, FAM49A, HHEX, MAP3K1, PAG1, WSB1, ITGB2, EFHD2, CYTH4, ISG15, FLNA, SMAP2, FCGR2A, GCA, ALDO A, CD33, CD37, AKIRIN2, ARL4A, ZNF706, SH3BGRL3, TSPAN14, NUDT16, ITGA4, SH3BP1, RASGRP2, MMP24OS, PTPRC, CNPY3, RAB10, AMPD2, ZBTB7A, SELPLG, ENY2, PAK1, WASF2, MTHFS, VAMP5, C3AR1, ICAM2, TMBIM4, UNC93B1, KYNU, MYO1F, HIGD2A, CEBPA, TSNAX, KLF3, GRK6, NAP1L1, ICAM3, CD300A, S1PR4, MSN, LAMTOR4, LCP1, ZFP36, JAML, GIMAP1, BIN2, POLE4, PKN1, FKBP1A, ANXA5, DOK2, SEPT9, MPEG1, LY96, LRRFIP1, HLA-DPA1, UBE2J1, SEC 11 A, SRGN, JUNB, EIF4E2, TMPO, RHOA, HSD17B11, TPM3, BLVRA, VMP1, ERICH1, TMSB10, MXD1, ATF3, SNHG15, MT2A, PTPN18, MIDN, LSM6, CEBPD, ANKRD13D, RASSF5, RNF130, HCLS1, CHMP4B, SYTL1, RAP1B, YBX1, GLRX, MGAT1, BAZ1A, IFIT1, CDC42EP3, PSMA4, ARPC4, SERPINB1, SH3BGRL, CALM2, CAPZA2, PARVG, TALDO1, SEC14L1, PRKCB, UCP2, SP110, RNF13, GABARAP, PGK1, UTRN, CXCL16, TMSB4X, PLBD1, RAB5IF, ADAM10, STAT2, PSMB9, GSTK1, CUX1, PTGES3, SURF1, PLEKHO1, NDUFB5, CAPNS1, GRB2, PAIP2, TMC6, HBEGF, CHCHD10, RILPL2, PRR13, ARHGAP4, GBP2, GDI2, HES1, PSMB8, SAMHD1, VPS35, KLF2, LPAR6, CD47, PFN1, ABRACL, GBP1, IFI35, M6PR, GNB2, UBC, NAGK, RBX1, PTGER4, TLE4, RABGAP1L, FAM89B, PFDN5, ZNF106, FOS, MX1, ANXA4, IL10RA, DYNLT1, H2AFY, CDC42, UPP1, UBE2L6, UQCRB, CD52, CTNNB1, LSP1, S100A10, IFI6, ARL6IP4, S0CS3, GLIPR1, ATP1B3, SAMSN1, TXNIP, ACTR2, 0STF1, PPP1CB, PPDPF, CHMP1B, PSME2, GBP5.
Table 4N: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 14
UCHL1, TUBA1A, TUBB, GNAS, ATP5PF, STMN2, HSP90AB1, H2AFZ, EEF1A2, NPY, ATP5MC3, SUMO2, TUBA1B, PEBP1, STMN1, RACK1, HNRNPA1, H3F3B, ATP5IF1, PTMA, RAN, DYNLL1, TPI1, SLC25A3, BEX1, MDK, FKBP1A, NDUFS5, COX6A1, MLLT11, ARL6IP4, TMEM258, ACTG1, SEMI, PCSK1N, UQCR10, DNAJA1, TUBB2B, CKB, CCNI, COX6C, ATP5MF, MZT2B, COX7A2, GUK1, HSPE1, MAP1B, TUBB2A, LDHB, CHCHD2, TRIR, HINT1, PSMA7, MARCKSL1, NACA, EEF1B2, CLTA, ATP5F1B, SOX4, ODC1.
Table 40: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 15
IDO1, FLT3, CD1C, CD1E, LGALS2, SIOOB, LAMP3, GPR157, CYP2S1, CSF2RA, PAK1, CIITA, TLR10, ARHGAP22, CLEC10A, HLA-DQB2, SPIB, MYCL, GPAT3, BATF3, IFI30, P2RY14, HLA-DQA2, PLD4, HLA-DQA1, HLA-DOB, DNASE1L3, TSPAN33, P2RY6, HLA-DPB1, HLA-DPA1, HLA-DRA, HLA-DQB1, HLA-DRB1, CPVL, ASB2, HLA-DMA, CBFA2T3, HDAC9, SLAMF7, CD74, C15orf48, NDRG2, ALDH2, SMCO4, SPI1, PPA1, CTSH, PLEKHO1, CST3, FGL2, QPCT, GPR183, SHTN1, GRASP, IL1B, GSTP1, ETV6, HLA-DMB, RGS10, CD83, CFP, RUFY3, PYCARD, UVRAG, SLC8A1, FSCN1, HIC1, GSN, CLIC2, ACTB, HCK, LST1, TMSB10, LYZ, SPINT2, BID, DPYSL2, LSP1, MNDA, KCNK6, JAML, HLA-DRB5, KLF4, PTPRE, COTL1, SERPINB1, AC004687.1, ITGAX, LGALS9, CD40, NR4A3, TMSB4X, RAB11FIP1, APOBR, MCOLN2, SERPINB9, MAP3K8, CALHM6, ITGB2-AS1, CHMP1B, DYNC1LI1, REL, BASP1, TYMP, CLEC7A, SGK1, NR4A1, PGLS, PFN1, IGSF6, CLEC4A, ATG3, DAPP1, ENTPD1, PLEK, CD86, GDI2, CCDC88A, SULF2, COX5A, RAB32, OTULINL, KDM6B, FAM49B, PIM3, Clorfl62, TNFRSF10B, WDFY4, ARPC2, CFL1, NFKBID, IL1R2, P2RY13, CMTM6, PSME2, GRSF1, GLIPR1, RGS2, EIF3M, CD72, MAP3K13, HNRNPAB, PPT1, MARCKSL1, GNA15, ETV3, DSE, MS4A6A, BLOC1S6, TAP2, SUB1, SAMHD1, ATP5F1E, CPPED1, PHACTR1, PTRHD1, LAP3, ADAM19, TPM3, PTP4A2, IFNGR1, PSTPIP2, DUSP5, VASP, MOB1A, UCHL3, VSIR, SLC25A5, Clorf54, SYNGR2, TNFAIP2, EEF1B2, MYD88, BCL2A1, AIF1, SCIMP, MRPL23, NAGK, RNASE6, CTNNBL1, STX11, GCA, C12orf45, PRMT9, AO AH, ARPC3, ATP1B1, PTGER4, NDUFS8, CEBPD, TCTN3, ARPC1B, AREG, UBA52, SLAMF8, UCP2, RGS1, HCLS1, NMI, PEA15, DUSP4, H2AFY, RAB29, ARL5B, LCP1, APEX1, H3F3A, NANS, SNRPF, ARF6, AP1S2, C1QBP, ADAM8, SLC38A1, CLTB, EHBP1L1, STK38L, SLCO3A1, FGD2, PLAUR, ACTR3, ACAA1, LAMTOR1, HLA-DOA, OGFRL1, NFE2L2, AC020656.1, DBI, NMT1, MRPS33, CCT8, PHPT1, ATF3, VRK2, VAMP8, RNH1, NFKB1, SPATS2L, PFDN2, SUMO3, EIF3L, CDK2AP2, CLNS1A, VPS29, SRGN, MAT2A, EIF3H, HERPUD1, CBX6, DENND1B, CSRP1, TWF2, AC103591.3, TAOK3, CKLF, VPS35, FAU, TES, CAT, CDKN1A, SNX3, LAMTOR2, HMGN3, MARCH1, RBM3, VIM, FGR, EFHD2, PRELID1, PSMA4, SNHG8, BAZ1A, GRK3, TMEM14C, PARVG, CEP350, GPR65, CRELD2, PSME1, SFT2D2, APPL1, DDX21, CSTA, RHOG, FTH1, NAAA, FAM129A, CAMTAI, PSMA1, PRR13, DDT, GABARAPL2, RASSF2, PHLDA2, SMDT1, PABPC4, SCAF11, YBX1, PPIA, PPIF, FNBP1, LYSMD2, SAT1, FAM89B, IER5, LMNA, SINHCAF, TAF10, EIF6, DUSP2, UBE2L3, PRPF40A, MPEG1, BTF3, PTPN2, ROCK1, CAMK2D, NR4A2, PSMB8, CASP1, RBX1, IRF8, CD4, CIB1, ID2, SELENOK, ARPC5, HNRNPC, LMO2, APRT, NACA, HIGD2A, TNFSF13B, RASGEF1B, EVI2B, NDUFV2, ACTG1, BIRC3, AP2S1, SSR1, PLSCR1, CYBA, PDIA3, CCND1, NAP1L1, TUBA1B, RUNX3, EPSTI1, PSMA5, SLC25A6, TBCA, SERP1, BHLHE40, WARS, ITGB2, SDF2L1, MLEC, ARL4C, TYROBP, LSM6, GPX4, GBP1, LMO4, PSMB9, TPM4, ZNF331, YWHAH, CPNE3, CCL3L1, ATF5.
Table 4P: List
Figure imgf000103_0002
are up-:
Figure imgf000103_0001
in the different clusters identified in
Figure imgf000103_0003
of 10 patient tumors analyzed by scRNA-seq. Cluster 16
RBP4, GPD1, PARAL1, MLPH, FFAR4, GLDN, AC026369.3, SLC19A3, MIR3945HG, MME, SPOCD1, STAC, C8B, FABP4, DEFBI, MCEMP1, PHLDA3, AL035446.1, PPARG, LPL, ILIA, FAM3B, AGRP, LSAMP, BHLHE41, CXCL5, PCOLCE2, GAPLINC, INHBA, ACOT2, CCL23, HCAR2, FAM89A, RETN, MACC1, APOL4, ZDHHC19, MARCO, ITGB8, TEX14, AMIGO2, LINC02345, CES1, ADAMTSL4, PTGER3, CLDN7, CLDN23, VSIG4, OLR1, ADTRP, ARHGEF28, OSCAR, TREM1, AQP3, GALNT12, TNNI2, NMB, AC025048.4, RMDN3, PNPLA6, HSD3B7, MRC1, FBP1, CXCL3, MSR1, GPA33, ALOX5, RYR1, PTCRA, MYB, AL390036.1, FCGR1A, AVPI1, APIP, S100A13, ALAS1, GCHFR, SVIL, TMEM53, CORO2A, PLA2G16, TGM2, ACO1, PPIC, SMIM25, CYP27A1, FOLR3, OASL, ARRDC4, SLC11A1, ABCG1, TREM2, ITIH5, UBASH3B, B3GNT7, ABHD5, COLEC12, MOB3B, PTPMT1, EDEM2, DNASE2B, CCL18, TCF7L2, SCCPDH, AGPAT2, PHYH, ROGDI, VMO1, PLA2G15, APOC2, SLC27A3, CXCL16, ALDH2, NCEH1, ALDH3A2, TRPV2, C20orf27, RHBDD2, LTA4H, DTX4, B3GNT5, SCD, COROIC, QSOX1, HNMT, LGALS3BP, ALOX5AP, OPN3, CDCP1, ABCG2, SNX10, FLVCR2, NCLN, FDX1, MS4A4A, FN1, MGST1, AKR1C3, SERPINA1, GLIPR2, DECR1, MS4A7, OSBPL11, GAA, THBD, ANXA4, ALDH1A1, GCA, TMEM251, IFIT3, PLBD1, COA6, NCF2, C1QC, MIIP, SLCO2B1, GLRX2, ACP5, DDX60L, CD9, ATP1B1, RETREG1, GLRX, COPRS, PDLIM1, SGMS2, SLC49A3, SMCO4, HDDC2, STAC3, POR, ADGRE1, DPH3, COMT, ENPP4, ARHGAP18, FIG4, TFRC, SNX2, SLC31A2, TP53I3, FUOM, C1QB, TMEM38B, HLA-DRB5, TTC39B, PILRA, SPNS1, SERPING1, CPE, NUPR1, Clorfl62, IL1RN, SORT1, TFPT, CARS2, HCAR3, SPI1, MX1, RGCC, CD300C, UPP1, FCGR3A, MCOLN1, AXL, SIGLEC1, LRP1, IFI6, DOK2, CITED2, SEPTI 1, RASAL2, APOCI, RABB, ALDOA, VAT1, C1QA, PBDC1, LAIR1, FCGR1B, HBEGF, SLC7A7, SCPEP1, USP30-AS1, GK, EGR2, NAA20, FAR2, SYS1, CD163, STXBP2, CD151, BCL2A1, MGST3, CD68, ATL1, AP5B1, FHL1, DTNA, ETHE1, GSTO1, LRPAP1, CAT, ATP6V0D1, FABP5, MYOF, CA2, CAPG, LGALS3, BST1, PLIN2, TRIP6, TSPO, CEBPB, CYB5A, REEP3, TUBB6, SLC7A8, BLOC1S2, PYCARD, MDH1, HPGDS, MARCH2, SPINT1, G6PD, CD300LF, ANXA2, PROCR, CNIH4, KMO, NCF4, CLEC12A, LAMTOR3, IFIT1, HPGD, TMED5, S100A11, ANXA5, HEXB, LAMTOR1, ARHGAP10, TNFSF12, GPCPD1, SIDT2, VASP, IFI30, SFT2D1, PSMA2, GLUL, PLXDC2, RNH1, S100A6, FCER1G, DAB2, ZNF706, FDX2, TXN, SLC25A19, TSPAN3, NIT2, FPR2, S100A10, ARHGEF10L, REEP5, TOMM40, VPS29, RENBP, LIMA1, MPC2, ZDHHC3, CHP1, SLC3A2, RHOB, SQOR, LSM6, CSTA, BACE1, SH2B2, CYB5R3, HLA-DMA, OAS1, TIGAR, CASP1, DNASE2, TYROBP, TUBA1C, SLC31A1, GNG5, TRIQK, RHEB, SIRPA, OAZ1, CTSL, ATP5MC3, ACADVL, ATP6V0B, CISH, SDCBP, PDXK, CHCHD10, TXNDC17, SLFN11, BTK, MLX, MYL6, GGA2, EMILIN2, VAMP8, PPT1, ATP6V1F, MYDGF, RAB5IF, C7orf50, MRPS35, MRPS15, VEGFB, VAMP3, SPN, CSTB, BAX, MSRA, DESI1, LY6E, RARA, GRN, ATP6V1D, LST1, NOPIO, PPFIA1, BSG, YWHAH, NAGLU, S1PR4, PLIN3, SIOOP, CYBA, CTSC, GSN, LGALS9, FTH1, PGD, ANXA11, AKR1A1, LAP3, CCT5, LACTB2, IGFBP2, OSBPL1A, SLC15A3, PLAUR, TST, HCK, ARPC1B, CARD16, BEX4, RGS19, MMP19, NUCB1, ADAM17, ACOT13, BRI3, PEBP1, SDHD, FCGRT, TFEC, FCGR2A, AP2S1, COMMD9, GALE, ARL6IP1, SSB, OSTF1, VIM, PAPSS1, GPX4, GON7, CTSH, GPRIN3, SNX3, HLA-DQB1, UBB, FUCA2, IRF8, HK3, NANS, FTL, C5AR1, THEMIS2, LY86, HADH, FKBP15, NDUFB5, ANXA1, ARPC3, UGP2, PPDPF, BLVRA, VDAC1, CD81, IFIT2, TSPAN15, C14orfll9, MRPL14, CCDC115, CTSD, ACER3, CD276, MNDA, PRDX1, MRPL40, STX12, ATP6AP1, ACOT7, TMBIM1, SLC25A24, POLD4, CD63, RAB11FIP1, IGSF6, MR1, SULT1A1, CDC42EP3, RNPEP, CENPW, JAML, ACVRL1, ECHI, CMC1, HLA-DRB1, HTATIP2, TMED9, MPC1, RNF13, UBE2L6, NPTN, LMNA, HAGH, EIF4EBP1, SMIM14, BCAP31, PTPN6, TCIRG1, HSD17B11, THBS1, SCP2, MINK1, SERF2, LEPROT, TBC1D2, MYD88, COQ2, HSD17B14, NDUFV2, GABARAP, LACTB, WASHC3, CCDC88A, CD58, PEPD, NDUFB3, CTSZ, CYBB, FMNL2, GTF2H5, DDAH2, FBXO6, TMEM91, PDCD6IP, CSF1, GUSB, AK6, SMIM15, GNPTG, CHMP5, LAT2, LYZ, CID, BTF3L4, TAF10, APLP2, SUSD1, S100A4, UBE2A, SLC39A3, YBX1, TM6SF1, TKT, MOSPD2, DNAJA1, ANPEP, DBI, HLA-DRA, ERP44, GRB2, ATP2C1, NDUFA7, DCUN1D5, HLA-DPA1, GRINA, TALDO1, CAPZA2, MTHFS, C9orfl6, ATP6V1E1, CD40, MSRB1, ISOC2, JOSD2, QDPR, CXCL2, MTX2, MRPL13, TXNDC11, HEXA, C18orf32, TIMP2, SEC11 A, TMEM219, SCIMP, NEK6, AAED1, ASAHI, FKBP1 A, PLSCR1, ECHDC1, HSDL2, RTN4, CD33, DHRS4, MMP24OS, TPMT, VDAC2, AC020656.1, MPV17, MFSD10, MINOS1, CFL1, NENF, RND3, DCTN6, SELENOT, PRKCD, CST3, TSG101, FAM50A, LYAR, CREG1, PCBD1, PSMG1, AKIRIN2, RAB10, CMPK2, HLA-DPB1, TMSB4X, P2RX4, GBP1, AGPS, SSR3, CNDP2, LAMTOR2, CLEC7A, MGAT1, ASGR1, SHTN1, CCND3, TWF2, TMEM173, PDHA1, ARPC5, SDSL, SEPHS2, GLB1, ZBTB8OS, CLTA, EMG1, PSMA7, NDUFA4, HLA-DQA1, CTSA, RAB8A, HIGD1A, RAB5C, CD164, LY96, DUSP23, CLIC1, LSM10, SPG21, HADHB, ITPK1, POLR2K, RAB7A, AIF1, C2orf74, RNF7, EEA1, FAM162A, PSMG2, TCEAL4, ATP6V0E1, SAMM50, HAVCR2, PPCS, PSMD9, PSMA3, POMP, TSFM, TMEM230, EFHD2, DYNLL1, ATP6V1B2, TMEM167A, RER1, TMEM126A, MAN1A1, CMAS, CD52, ACTN1, CYCS, RAB9A, PSMB5, ARPC2, ACAA1, TMEM63A, NDUFAB1, POP4, RAD23A, PNPLA2, ARL2, PHLDA2, C2, SELENOH, MRPL22, KAT8, ARL1, SRI, HEBP1, COLGALT1, TNF, OSTM1, SAMHD1, CTBS, RRAGD, PYURF, DMAC1, TMEM273, AP1S1, RAB32, HVCN1, ELP5, SHARPIN, ESD, NTAN1, COA4, LSM4, TUBA1B, PTAFR, NRBF2, BID, PSMA5, ARL4A, HPCAL1, UNC50, FGD2, RASGEF1B, DYNLT1, SLC16A3, PLAU, ACOT9, MSRB2, TMEM179B, TYMP, RAP1B, GNB2, STX11, PRDX6, SAP18, EMC7, PARP9, PRDX3, RNF181, ITSN1, IFI35, DYNLRB1, UTP18, LAMTOR5, KLF4, PDCL, ATP5F1C, CDC42BPB, EML4, MAP1LC3B, CD83, ATP1B3, HSBP1, CBWD1, SCARB2, H2AFJ, SLC39A10, CAMTAI, RAC1, SH3BGRL3, VAPA, GTF3C6, CYSLTR1, FEZ2, PSMB6, PGP, DNTTIP1, HMOX2, PFN1, JPT1, TMED10, TMBIM6, RNF149, TXNIP, ELOC, PEX16, MYL12A, ANAPC15, CTSS, ACAA2, M6PR, ISG15, ISCU, FAM173A, OTUD1, TCEAL9, RUNX1, ANKRD28, PSMD14, FERMT3, HPS5, CRIP1, MAPKAPK3, CXCL8, CHCHD1, ECHS1, DBNL, MRPS23, ENY2, PSMA4, TRIM14, Clorf43, PRR13, UBE2F, RHOA, CMC2, SMIM37, C19orf70, HERC5, AZI2, MRPL41, PCMT1, TPM4, NDUFA13, TAGLN2, PHB, MDH2, SERPINB1, SLA, SH3BGRL, CDC37, CEBPA, CKLF, ELOB, GLRX3, UQCRFS1, VPS26A, HSD17B12, HINT2, SNF8, JUN, DPP7, NDUFC1, COX7A2L, PSME2, EPSTI1, NDUFB6, LGALS1, TMBIM4, LITAF, MRPL18, TMEM70, APH1A, COPZ1, ATP5MF, PKM, SH3GLB1, TBC1D10C, ATP2B1- AS1, GTF2A2, ARF4, SERTAD1, FLNA, TRAPPC2L, CD74, SUMO3, APEX1, ATRAID, ARRB2, AGTRAP, COX17, CIB1, PSMD8, PPIA, BLOC1S1, PFDN2, GLTP, UQCR10, TXNDC12, NDUFS3, WDR1, BAG1, CAP1, FGR, SNRPG, C0PS5, BEX3, NDUFAF3, LMAN2, ITGAX, ADRM1, NDUFB2, ACP2, CTNNB1, IL1B, DDIT3, IRF7, ITM2B, CALM1, NUTF2, HIPK2, TMEM14C, CD47, DOCK8, HMGN3, MTPN, LRRFIP1, FAM89B.
Table 4Q: List of genes that are up-regulated in the different clusters identified in the integration of 10 patient tumors analyzed by scRNA-seq. Cluster 17
TFF3, RELN, TBX1, ACKR2, CCL21, PGM5, PROXI, KCNIP1, FLRT2, STAB2, FAM189A2, FLNC, MMRN1, BHMT2, SEMA3D, NTS, PDPN, SLC26A4, CRTAC1, DSP, TNFAIP8L3, GPR182, ART4, KLHL4, SNCAIP, CNTNAP3B, BMX, RASSF9, LRRN4CL, SLC24A1, PKHD1L1, PARD6G, FLT4, LINC01558, SEMA3A, LAYN, DYNC1I1, CAVIN2, TIE1, TSPAN11, RHOJ, PDE2A, SEMA6A, ABO, TNFRSF11A, CFI, MYCT1, CHRDL1, TM4SF18, F8, NRN1, CYP4X1, EFEMP1, KANK3, ECSCR, BMP6, CGNL1, GJC2, GPM6A, KIAA1324L, CARDIO, NR2F1, ROBO4, CNKSR3, PTX3, SMAD1, PTPN14, S100A16, FABP4, REEP1, CXorf36, TM4SF1, IPO11, GPRC5B, TMEM255B, CTHRC1, SCN3B, ZNF521, PPFIBP1, GLRB, STON2, PLSCR4, LRP5, FAM174B, OAF, LYNX1, RAMP2, RTKN, SNCG, SFRP1, ITGB4, IQCA1, PCAT19, NR2F2, GNG12, EGFL7, NMNAT2, VWF, CRACR2B, PEAR1, BACE2, SLC45A3, UNC5B, GJA1, WFS1, CDC42EP5, MFAP2, NNMT, TFPI, CLDN5, SHE, CLU, TNXB, TMEM54, ELN, LOX, RBP1, SHANK3, CCDC80, WWTR1, ITGA9, CALCRL, LAMA4, ARHGAP29, AFAP1L1, EFNA5, ERG, RAI14, CAV1, GNG11, SOX18, SPHK1, LINC01197, NT5E, CD34, CDH5, MYH10, MTUS1, UBTD1, ACKR3, LYVE1, PTPRB, AKAP12, CAV2, NFIB, PODXL, NXN, ARHGAP23, YAP1, LDB2, THSD1, KLHL3, S100A13, FMOD, TIMP3, ADIRF, MFAP4, ABI3BP, BCAR1, MATN2, HYAL2, ZNF385D, FZD6, OLFM1, LAPTM4B, HSPG2, FILIP1, NINL, MAGI1, MEDAG, PROCR, PON2, ELK3, SELENON, FGFR1, PCSK6, KRT18, CEACAM1, A4GALT, LRP6, KRT8, SHC1, MEGF6, AL022323.4, CALD1, HRCT1, JUP, TSPAN5, SGCE, MDFI, ACKR4, MYZAP, PCDH12, GPR146, LIMCH1, TSPAN18, IGFBP4, ITGA6, CAVIN1, MIR99AHG, C2CD4B, CPXM2, TSPAN7, CNN3, EMIDI, EDNRB, VPS35L, ALPK3, TPBG, EXOC3L1, RAMP3, PLA2G4C, LHFPL6, SEPT10, GALNT18, S1PR1, FBLIM1, PRRG1, PLS3, FLNB, BAALC, TUBB6, RASIP1, ID1, MEIS2, PIEZO2, MSRB3, DTX1, KDR, SGIP1, CYR61, C17orf67, PERP, PPIC, FAM43A, EPHA2, ATP9A, CSGALNACT1, AMOTL2, RARRES2, PALM, IGFBP7, IL33, ADGRA2, NOVA2, SLC9A3R2, IL7, CCDC3, APP, PLEKHA4, TSHZ2, NFIA, STOX2, CD59, LAMB2, EPHX1, KBTBD11, MANI Al, KALRN, BCAM, EFNA1, FAM213A, SULF2, IGF1, FAM89A, NCKAP1, CTTN, PDGFC, RPGR, ADCY4, EHD2, TSPAN9, CBY1, IL1R1, EPHB4, TMEM246, CD9, NBL1, TTC28, TMEM120A, CD151, TSPAN12, AFDN, FXYD6, LAMB1, PRSS23, GRAP, PDLIM1, DYSF, CRIP2, CRIM1, RAPGEF5, CNRIP1, RALGAPA2, EXOC6, SLC22A23, TSPAN6, TGM2, ANGPT2, OLFML2A, SLC39A14, HOXD8, FN1, LMCD1, PRKAR1B, ZFYVE21, THEM6, COLEC12, NIDI, GAS6, SYNM, SHC2, TNFAIP1, SVIL, SPRY1, PLXNA2, CYB5R3, IL6ST, DKK3, RASGRP3, ADGRF5, COX7A1, TMEM204, FHL1, SPR, ATN1, MRC1, EFNB2, NUDT4, RABI 1 A, SPTBN1, RGS3, BCAP29, NFAT5, TINAGL1, CAMSAP2, MEGF8, SELENOM, NEDD4, PDIA5, PPARG, COL4A2, LMO2, BCAR3, TEAD2, TGFBR2, MGST2, PROS1, EMP2, MPDZ, WWC2, KIAA0355, FABP5, CTDSPL, NRP2, JCAD, PLK2, AEBP1, LEPROT, FSCN1, FOXC2, NDN, MXRA7, EBPL, PXDN, TRIOBP, SERPINH1, CD200, SMYD2, CDC42BPA, ATP11A, TULP3, MYO6, RNF152, TJP1, DOCK1, TCEAL9, DLL4, ADM, CISDI, MPP7, FRMD6, REEP3, LTC4S, CTNNAL1, PIEZO1, EMILIN1, FEZ1, RBPMS, MAP7D3, AKR1C3, SH3GL1, DOCK9, DPY19L4, PECAM1, GAS2L1, HTRA1, SMAGP, MCFD2, RABB, ENG, MYO1B, DNAAF5, PTPRE, ZNF273, CPNE8, INSIG2, DHODH, SNX7, SNTB2, FOXCI, EPB41L2, SPSB1, TMEM140, HDGFL3, AC245595.1, SLC43A3, HOMER3, ITGA5, MAP1LC3A, TULP4, ACVRL1, PALD1, FKBP9, TMED1, WLS, RGS16, ABHD17B, C1R, ASAP2, CTGF, FBN1, SYPL1, SNCA, TMEM205, CEP68, YES1, TSPAN15, ARL2, PLPP1, RNF217, HEBP1, ECE1, ZNF467, AC060780.1, FUR, TCF4, JAG1, LAMC1, SLC25A29, PTPRM, GALNT1, PRCP, STAB1, RECK, NPR1, MGP, TLE1, NPDC1, PHACTR2, ZDHHC14, RGL2, LAPTM4A, SERPING1, NTAN1, TSPAN4, TXNL4B, UROD, GNPDA2, MBNL2, HS3ST1, SEPHS1, IFITM3, CARHSP1, PMEPA1, THBS1, C17orf58, ZBTB20, PARVA, NDRG2, ITGA3, COL12A1, DOCK6, ATE1, GFOD2, ADGRL4, MMRN2, BICD1, TSPAN31, BLCAP, GINM1, SDC3, PAM, ABCD4, GYPC, PKIG, TNS1, SSFA2, ANXA2, FILIP1L, PRPSAP1, RCAN1, TMEM115, REXO2, ASPH, TNS2, UACA, PGRMC2, XPOT, NECTIN2, HSPB1, PXMP2, DOCK5, SELENO W, F2R, MARCKSL1, MAP1B, TSTA3, PTMS, ITGAV, DAAM1, EIF5A2, CHST15, DPYSL3, ZEB1, ZNF43, CCND1, TMEM9, ANKRD26, ATP11C, FAM3C, HAPLN3, TRIM5, IGFBP2, PTK2, LUZP1, ARHGAP21, ZNF254, MDK, CTNNA1, TMOD2, CERS2, ARHGEF7, PLA2G16, TSHZ1, ACTN1, HES1, STOM, RHOC, TPD52L2, SLC27A3, UTRN, MARVELD1, RRAS, PLPP3, NDRG1, VIM, LIMSI, CD36, ARL4A, ZC3H7A, LRMDA, MAML2, SLF2, ARPC1A, Clorfl23, NUCB1, ITSN1, PNPLA2, ARID5B, HSD17B12, ZNF33B, CALU, FAF2, ZSCAN18, S100A10, BCR, WDR18, COMT, EMP1, TGFBR3, MARCKS, SPTLC2, ZMYND8, EIF4G3, FERMT2, DEPPI, DBN1, DCTN1, DDX42, FNDC3A, CPD, TNFSF10, CKAP4, DDAH2, FARP1, TIMP1, ODF2L, TP53TG1, NEXN, AC00526L1, EMCN, TCERG1, POLK, ATF6, GCSH, SLC9A9, RABAC1, WARS, ACBD6, FHL3, THBD, FUNDC2, PLEKHO2, ERI3, RFK, MON2, SOX4, MMP2, CERS6, RARS2, PLPP5, TMEM50B, EI24, TPM4, ID3, ITM2C, MRPL32, SIRT2, DLC1, MAP4K5, MSRB2, VGLL4, DADI, YIPF5, BNIP3, DPM2, BMPR2, TCEA2, SBF2, AAED1, MDFIC, UBAP2, ZMYM4, SELENOP, ERICH1, CLCN3, APC, VEZT, CD93, SLC39A1, PEAK1, RYK, RDX, AKAP11, C16orf91, ZDHHC21, PXN, HHEX, PTTG1IP, METTL8, KDSR, EPN2, SEC61A1, DEXI, PTRH1, EIF2B2, NOTCH1, TCEAL4, SYNE1, LRCH3, PAIP1, FKBP1A, YBX3, SDF2, PGRMC1, IFT57, HMBOX1, OSBPL1A, ZNF326, ORMDL2, C4orf48, GRPEL1, TMEM123, TAP2, PINK1, DYNC1I2, EMC2, PGM2L1, PPP2CB, TSC22D1, TANC2, GORASP2, FRMD4B, TMEM59, POLR2L, KRIT1, PLRG1, NARF, TOR1A, CTNND1, DNASE1L3, PLEC, ZNF704, MYL6B, KRTCAP2, ELOVL1, ITGB1, MPST, STMN1, MYL12B, NTPCR, AAMDC, MAPK3, PCID2, TCTN3, GUK1, SLC50A1, SVIP, SPPL3, CCDC82, ATP2B4, NFIC, NAXE, RALGDS, SNX14, DHX29, DNAJB4, YPEL2, C1GALT1C1, NDUFS7, ST6GAL1, PXDC1, AIG1, FAM 102 A, HIPK3, FAM 126 A, UBE2H, SH2D3C, IFT43, CITED4, HDAC7, CUL5, YWHAE, ADD3, SIN3B, MAOA, TM2D2, NRIP1, TMEM50A, KTN1, CFAP298, HIC1, TAX1BP3, MGAT4B, CAPNS1, TBC1D4, DAB2, SEPTI 1, ZC3H7B, PEF1, UNC50, WSB1, CASK, LTBP4, ROCK2, EID1, ACTN4, MEF2C, SLC38A2, XPA, PTAR1, TIMP2, TM9SF3, TP53I3, PPP3CA, APLP2, DCTN6, SPTAN1, TTF1, MSL1, APOLD1, GGT5, CD81, ETS2, MAFF, RCN2, KDELR2, STARD3NL, PMP22, TSN, FOXP1, SCOC, GUCY1A1, BMS1, VAMP5, MAGED2, ADAM10, PDCD6IP, ZFHX3, SLC38A1, CCNL2, CPQ, RAB14, TBC1D9, SLC44A1, ATRAID, PEPD, TMEM87B, IFITM2, ABLIM1, CYB5R1, NUMB, MPRIP, TMBIM4, RRAGA, WDR83OS, DST, DSTN, A2M, SIRPA, MEF2A, TFG, DEGS1, CAPN2, RAB6A, CD99, FCGRT, FDPS, IGFBP5, HLA-E, HMGN3, EDEM2, CHMP3, TMED3, POLR3GL, CFAP97, ATXN3, CNPY2, MOB2, ASAP1, DNAJC10, SERINC3, ITGA1, HSP90B1, PRDX4, LMNA, CTNNB1, ELF2, RAB2A, TMEM30A, BCL7C, HEBP2, DDX1, MEDIO, GNAI2, SCARB2, PSMB5, BORCS7, SREK1, TMEM14C, FTX, TSPAN3, NMT2, ALDH2, PCBD1, ITM2B, CYC1, TMEM141, PTPN11, TMEM173, SUN1, WASF2, MPDU1, GABARAPL2, CD63, OCIAD1, SRSF11, VKORC1, RIF1, VPS28, PIK3C2A, VCP, SLC44A2, PLAC9, CYTOR, LMAN1, NKTR, PPP1R2, C5orf24, GUSB, TUBB4B, MAF, KIF5B, MYL6, SPAG9, SSR4, GIGYF1, ELK4, PEA15, RALBP1, RTN4, TRIP11, RPN2, RHOB, QKI, CD55, CCL2, YWHAQ, TRAPPC6A, ERLEC1, ARL6IP1, AP2A2, LRPAP1, PDLIM7, FKBP2, REEP5, SRI, TMX4, GNAS, ABHD2, DUSP6, KDELR1, CANX, OS9, TXNDC12, MYDGF, RRBP1, PLCG2, APOL3, RAB11FIP1, PDIA6, BEX3, CALR, TMED9, CAST, HADHB, CDC37, HIST1H2AC, MTRNR2L8, ICE2, PRPF6, ALDH1A1, YWHAH, SREK1IP1, IFI6, SEC62, LY96, HLA-A, DDX17, TM2D1.
For further information on Table 4A to 4R, see Costa etal. JImmunother Cancer. 2022; 10(8): e004807, Supplemental Table 4 incorporated herein by reference.
Table 5: Filtering of cells with high quality data for the 3 TH-MYCN tumors
Figure imgf000109_0001
Table 6: Filtering of cells with high quality data for the 10 neuroblastoma biopsies.
Figure imgf000110_0001
Table 7: Antibodies used in the various panels to characterize immune cells and CAFs of the TH-MYCN tumors by FACS.
Catalogue Antibody Dilution Compagny number Clone Species
Figure imgf000110_0002
Figure imgf000111_0001
Panel forT cells
Figure imgf000111_0002

Claims

I l l CLAIMS
1. A molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4A, 4J, 4B, 4H, 41, 4M or 4E, preferably 4A, 4J, 4B, 4H, 41, more preferably 4 A or 4 J, for use in the treatment of neuroblastoma in a subject.
2. The molecule for use according to claim 1, wherein the molecule targets, modulates or inhibits an immune inhibitory receptor, especially TIGIT (T cell immunoreceptor with Ig and ITIM domains), LAG3 (lymphocyte-activation protein 3), CTLA4 (cytotoxic T lymphocyte antigen 4), HAVCR2/TIM3 (T-cell immunoglobulin mucin domain-3), or PD1/PDL1 (programmed cell death protein 1) or wherein a combination of molecules targeting, modulating or inhibiting at least two among TIGIT, LAG3, CTLA4, TIM3, and PD-1 is used.
3. The molecule for use according to claim 2, wherein the molecule is an antibody, preferably an antagonist antibody.
4. The molecule for use according to claim 2 or 3, wherein the subject has an overexpression of TIGIT, LAG3, CTLA4, TIM3, and/or PD-1 on T cells of the neuroblastoma sample.
5. The molecule for use according to claim 1, wherein the molecule targets, modulates or inhibits CXCR2, CXCR1 or PTSG2/COX2, preferably CXCR2 or PTSG2/COX2, even more preferably CXCR2.
6. The molecule for use according to any one of claims 1-5, wherein the neuroblastoma sample has MDSC, in particular high level of MDSC compared to control, in particular MDSC overexpressing CXCR2.
7. The molecule for use according to claim 1, wherein the molecule targets, modulates or inhibits TGF-beta.
8. The molecule for use according to any one of claims 1-7, wherein the subject has a metastatic or pre-metastatic neuroblastoma, wherein the neuroblastoma is a high risk neuroblastoma or wherein the neuroblastoma is selected from refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma.
9. The molecule for use according to any one of claims 1-8, wherein the molecule is used in combination with another molecule as defined in any one of claims 1-5 and/or with a classical neuroblastoma treatment.
10. The molecule for use according to any one of claims 1-9, wherein the subject has been identified or selected by a method according to any of claims 11-19.
11. An in vitro method for classifying or identifying a subject, said subject suffering from neuroblastoma, the method comprising the detection and/or the quantification in a neuroblastoma sample obtained from the patient of at least one cell among: a) Cytotoxic T cells, b) Myeloid-Derived Suppressor Cells (MDSC), c) Natural killer cells (NK cells), and d) Macrophages cells,
And wherein: the at least one cytotoxic T cells are detected by detection or quantification in the T-cells of at least one gene selected from the group consisting of IL7R, LTB, CD3D, TRAC, CD40LG, CD3G, CD2, CD3E, SPOCK2, MAL, RCAN3, TPT1, TRBC1, ICOS, TRBC2, IL32, TRAT1, BCL11B, LCK, TCF7, ETS1, EEF1A1, CD6, PASK, CD27, TNFRSF25, ACAP1, GIMAP7, CD69, CCR7, TC2N, AAK1, AQP3, PBXIP1, LDHB, ITK, EEF1D, OXNAD1, KLRB1, LAT, FLT3LG, SARAF, CAMK4, LEPROTL1, LEF1, CD28, CD5, T0MM7, EEF1B2, UBA52, RORA, SKAP1, NOSIP, CD52, IKZF1, ITM2A, FAU, TRAF3IP3, EMB, OCIAD2, NOP53, STK4, SUSD3, PIK3IP1, CD247, PDE3B, CLEC2D, SEPT6, STK17A, RHOH, BTG1, COX7C, STK17B, EPB41, AC026979.2, RASGRP1, CD96, FAM102A, SOCS1, FXYD5, NPM1, PABPC1, CYTIP, CD7, CDC42SE2, SIT1, PTPRC, ZFP36L2, C0MMD6, AES, RACK1, ABLIM1, HINT1, TNFAIP8, DGKA, PPP2R5C, IL2RG, PDCD4, RARRES3, TNFAIP3, NACA, EVL, GPR171, AP3M2, FYN, TRADD, MZT2A, MALAT1, TMA7, B2M, LIMD2, MT-ND6, TTC39C, ARL4C, SNHG25, RAC2, GMFG, MT-ATP6, ANKRD12, HIST1H1D, CYLD, ARHGAP15, ISG20, SEPTI, CDC14A, FNBP1, DDX24, ICAM3, JUNB, NAP1L4, C12orf57, DDX5, RIPOR2, CD48, UQCRB, SYNE2, FYB1, SLFN5, SNHG8, HLA-C, FAM107B, RGS10, BTF3, ANAPC16, CORO1A, MT-CYB, SF1, GSTK1, HIST1H4C, CXCR4, TBC1D10C, MCUB, BCL2, PSIP1, GYPC, RHOF, EIF3E, CORO1B, SELL, C6orf48, TLK1, S1PR4, MTRNR2L12, GIMAP4, ARID5B, SVIP, IL16, ARHGDIB, CALM1, TNFRSF4, CDKN1B, CCND2, APRT, KIAA1551, ATM, EML4, STAT3, PPP1R2, MZT2B, SNRPD2, ANP32B, IK, SON, TSTD1, G3BP2, VAMP2, HLA-F, EEF2, HIST1H1C, ABRACL, NSD3, SYF2, MT-CO1, GPR183, TPR, MT-ND3, KLF13, GCC2, GTF3A, FBL, SRSF5, OST4, JAK1, CIB1, NSA2, MYL12A, HNRNPA1, NSMCE3, MBNL1, COX4I1, SEPT9, N4BP2L2, CBX3, UXT, BIRC3, GPSM3, ITGA4, S100A4, SRRM1, PIK3R1, SOD1, PNISR, MT-CO3, RNF213, ARL6IP5, EIF4B, MT- ND1, EIF3H, CREM, PRMT2, BTG2, RGS1, TSC22D3, KLF2, LINC01871, CKLF, CCL5, CD8A, GZMA, CD8B, GZMK, GZMH, NKG7, CST7, CD3D, CD3G, CD3E, TRAC, GZMM, CD2, IL32, HCST, TRGC2, LINC01871, APOBEC3G, RARRES3, SAMD3, TRBC2, CCL4, CTSW, LAG3, LCK, KLRG1, PRF1, KLRD1, GZMB, CD69, RUNX3, CD52, CD27, LYAR, C12orf75, PPP2R5C, STK17A, PTPRC, MATK, CORO 1 A, EVL, IFNG, TIGIT, ACAP1, LAT, CD247, HOPX, CD7, HLA-B, SKAP1, TNFAIP3, PYHIN1, CD96, PSMB9, TRBC1, IKZF3, CXCR3, B2M, MYL12A, SH2D1A, HLA-A, CLEC2D, TMA7, CD99, SH3BGRL3, TMSB4X, GPR171, TBC1D10C, RAC2, CD6, ZFP36L2, BCL11B, SRSF7, CDC42SE2, ISG20, CALM1, CXCR4, LEPROTL1, SIT1, FYN, DUSP2, PSME1, AES, GBP5, RHOH, TRAF3IP3, CLEC2B, RASAL3, ITGAL, PTPN22, AKNA, GIMAP7, TENT5C, S100A4, BTN3A2, SYNE2, SLC38A1, PDCD4, PTPN7, TUBA4A, RNF213, SLFN5, MT2A, BTG1, EEF1D, CHST12, CD48, AAK1, S0CS1, ETS1, CKLF, GNLY, IKZF1, SUB1, PFN1, OST4, AC026979.2, LIMD2, ARL4C, PIK3R1, ITM2A, MYL12B, STK4, TOMM7, PIP4K2A, ANXA1, PAXX, SEPT6, KIAA1551, ITM2C, MBP, HLA-F, ARPC5L, IRF1, GUK1, DDX24, RGS1, IL2RG, GMFG, ABHD17A, SYNE1, SRSF5, VAMP2, COMMD6, CLIC1, SEPT7, CIB1, SSBP4, ADGRE5, GYPC, JUNE), ARHGDIB, APOBEC3C, ATP5MG, TRIR, SNRPD2, DRAP1, GIMAP4, GSTK1, PSMB8, TSC22D3 and ISG15, or the expression product thereof; the MDSC are detected by detection or quantification in the cells of at least one gene selected from the group consisting of CXCR2, CXCR1, FCGR3B, CMTM2, SI OOP, CSF3R, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CD A, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, SDCBP, J AML, MCL1, YPEL3, HSPA6, NCF2, SPI1, LILRB3, TYROBP, DUSP1, FCGR2A, SERPINA1, MYO1F, IVNS1ABP, APOBEC3A, RSAD2, MEGF9, RIPOR2, S100A6, ABTB1, LYN, CREB5, LCP1, ALOX5AP, ZFP36L1, USP10, IER2, CSF2RB, SLC11A1, IFITM3, MX2, RGS18, PYGL, SMIM25, SLC2A3, TRIBI, NCF4, TUBA1A, XPO6, TLE3, ITM2B, TXNIP, EGLN1, LILRA5, GMFG, DDX60L, DENND3, IGF2R, HIST1H2AC, EVI2B, PTPRC, CEBPD, LSP1, OAZ1, GLUL, UBE2B, RARA, PNRC1, CPPED1, TLR2, FOS, NADK, CDKN2D, PDLIM7, ARPC5, PTPRE, FLOT2, PLEK, CD55, GNAI2, ADAM8, PTEN, BRI3, ACTB, LAPTM5, STXBP2, P2RY13, ISG15, LY96, UBN1, VSIR, NABP1, SMAP2, ICAM3, VASP, ALOX5, IFRD1, PELI1, RTN3, NUP214, IL17RA, CNN2, MARCKS, HLA-B, PHC2, SEC14L1, CFLAR, ARHGAP9, SHKBP1, RAB11FIP1, EFHD2, LAMTOR4, PLAUR, KDM6B, RASSF3, UBE2D1, CLEC4E, CAP1, CMTM6, LYST, VMP1, FMNL1, FBXL5, TALDO1, CLEC7A, NINJ1, HLA-E, ITGAX, SSH2, PREXI, ACTN1, MAP3K2, ABHD5, HIF1A, ARRB2, ZFP36, ARHGAP26, CYSTM1, TXN, GPSM3, CDC42EP3, UBE2D3, IRF1, CSRNP1, CYTH4, TNFSF13B, ACAP2, PLXNC1, TNFAIP2, USP15, NOPIO, MX1, C4orf3, JMJD1C, SLA, BACH1, MAP4K4, FOSL2, KIAA1551, CKLF, CARD16, NMI, ADGRE5, OSBPL8, WIPF1, FYB1, FLOT1, ATP6V0B, TNFRSF1B, FKBP8, SKAP2, WAS, PLSCR1, TAGLN2, RAB31, PDE4B, SHISA5, LRP10, CCPG1, FAM49B, ADAR, CD46, TCIRG1, IFI16, SERPINB1, UBALD2, MIDN, NCOA4, GNB2, UBE2R2, CDC42SE1, ZYX, TAGAP, RNF213 and LCP2, or the expression product thereof; the NK cells are detected by detection or quantification in the cells of at least one gene selected from the group consisting of KLRF1, TRDC, KLRD1, GNLY, KLRC1, CTSW, PRF1, NKG7, GZMB, IL2RB, KLRB1, FGFBP2, CD7, HOPX, PTGDR, XCL2, CLIC3, CST7, XCL1, CD247, TXK, CCL5, MATK, NCR3, ADGRG1, GZMA, HCST, SPON2, PLAC8, CX3CR1, PYHIN1, GZMM, CMC1, TTC38, CCL4, SAMD3, SH2D2A, APOBEC3G, GZMH, SYTL3, PTPN4, RUNX3, ZAP70, EVL, CHST2, CHST12, MBP, ABHD17A, CD38, IRF1, RARRES3, TBC1D10C, APMAP, HLA-B, CD69, DENND2D, CDC42SE1, DUSP2, MYL12A, PTPN7, RAC2, HLA-A, FCGR3A, SPN, ARL4C, C12orf75, PTPN22, CCND2, EFHD2, PAXX, BTN3A2, LINC01871, PIP4K2A, FCER1G, ACAP1, IER2, CALM1, BTG1, AKNA, JAK1, BIN2, UBB, ARHGAP9, Clorf56, ADGRE5, RAP1B, CORO1A, ZFP36L2, SRSF5, ATM, IL32, CCND3, METRNL, TGFB1, SEPT7, AREG, PFN1, TXNIP, STK17A, LIMD2, ID2, CLEC2B, JUND, AES, EIF3G, PIK3R1, CD47, NR4A2 and PLEK, or the expression product thereof; and the macrophages are detected by detection or quantification in the cells of at least one gene selected from the group consisting of Cl QB, C1QC, SLC40A1, FUCA1, LGMN, MS4A6A, FOLR2, PLA2G7, ADAMDEC1, SLCO2B1, C1QA, GPNMB, IL 18, TMEM176A, TMEM176B, CREG1, MS4A4A, ENPP2, SELENOP, LIPA, NPL, DAB2, FPR3, OTOA, KCNMA1, HLA-DMB, IGSF6, RASSF4, GM2A, TMEM37, C2, SLAMF8, RNASE6, CD14, PLA2G2D, CCL3, CSF1R, MPEG1, CD68, GPR34, APOE, CD4, SGPL1, HNMT, GATM, CD163L1, CTSZ, MFSD1, CPVL, NPC2, SLC15A3, SLC1A3, CTSL, PLD3, LILRB4, ADAP2, APOCI, GRN, CD84, HLA-DMA, MAFB, PLTP, RNF130, PSAP, CYFIP1, ACP2, BLVRB, ABCA1, CTSB, MS4A7, SDC3, ACP5, RAB20, FCGRT, TSPAN4, C3AR1, CCL3L1, Clorf54, TTYH3, SMPDL3A, CD74, CTSC, ASAHI, MPP1, BMP2K, CD163, TPP1, IL4I1, CTSD, TFEC, HLA-DQA1, NR1H3, CD86, DNASE2, RBM47, CYBB, FGL2, CTSH, LAIR1, CMKLR1, HLA-DRA, HEXA, CXCL16, IL18BP, AP1B1, FCHO2, RARRES1, AIF1, AKR1A1, ABHD12, HMOX1, CAPG, HLA-DPA1, DAPK1, FTL, RGL1, LY96, CTSA, HLA-DOA, NAGK, ATOX1, PRDX1, PPT1, ADA2, HLA-DPB1, TIMP2, MMP9, KCTD12, SCPEP1, PLAU, CCL18, LINC00996, IGF1, FCER1G, HLA-DRB1, AKR1B1, SGK1, TNFSF13B, LY86, RAB42, PTAFR, GLUL, ALDH1A1, CST3, CSF2RA, CCL4L2, DMXL2, MRC1, LAMP1, TCN2, CPM, MERTK, MGST2, CUL9, EBB, PLXNC1, SYNGR2, GAL3ST4, PDE6G, CLEC7A, SERPINF1, TGFBI, SPH, TBXAS1, RAB32, STAB1, NAIP, GNPDA1, GRINA, ATP6AP1, CFD, A2M, CEBPA, SAT1, CTSS, TYROBP, SLC7A8, CD63, BLVRA, LAMP2, GNS, SIRPA, CLEC4E, HLA-DQB1, ICAM1, MAF, SEMA4A, SIGLEC10, NINJ1, LINC01857, RENBP, MCOLN1, CD81, IFNGR2, NRP2, AXL, ATP6V1B2, SLC38A6, MSR1, LGALS3, IDH1, UNC93B1, SIGLEC7, PILRA, MMP14, SLC7A7, LACC1, GLA, SLC29A3, FCGR2A, AO AH, DRAM2, GPR137B, SPP1, NCOA4, QPRT, TNFAIP2, TLR4, SPRED1, MARCKS, CHCHD6, LYZ, SDCBP, TFRC, GPX4, CYB561A3, ITM2B, KLHDC8B, BRI3, HSD17B14, NAAA, FRMD4B, EPB41L3, ATP1B1, MITF, ETV5, ANKH, CYP27A1, SIGLEC1, SCARB2, M6PR, ABCC5, HEXB, NAGA, CLIC2, TNS3, LGALS9, DNASE1L3, MARCH1, PHACTR1, GAA, FMNL2, CSTB, ATP6AP2, FUOM, GNB4, CEBPD, LHFPL2, PDK4, SDSL, ATP6V1A, MMP12, VAMP8, CREBL2, SUCNR1, DPP7, SCARB1, RGS1, RRAGD, ATP6V0B, TM6SF1, TMEM138, CLEC4A, MGLL, LST1, PLBD1, ITPR2, CETP, SQSTM1, DNPH1, PLBD2, PCBD1, PROP, LRRC25, GUSB, FTH1, HLA-DRB5, CD59, HCK, OAZ2, FAM213A, NCEH1, GSAP, MKNK1, SPINT2, SMS, CCR1, DST, PLA2G15, RNF13, SLC48A1, CLEC10A, PMP22, GLMP, SDS, RNASET2, MYO5A, AIG1, PLEK, VOPP1, ATP6V0A1, EPHX1, ADAM9, TYMP, TOR3A, CD300LF, PLEKHB2, SCD, CHPT1, NCF4, EPB41L2, CD300A, CRYL1, IRF8, ATP6V1F, PRNP, GSN, CYBA, CR1, PLIN2, RPN2, CXCL12, PLXDC2, VSIG4, VCAM1, UCP2, LAP3, WWP1, FUCA2, FRMD4A, NEU1, MGAT4A, SNX5, VEGFB, IL13RA1, HAVCR2, FNIP2, MGAT1, CD83, TREM2, ATP6V1C1, ACER3, AHR, RGS10, RAP2B, CD302, ZFAND5, ANTXR1, NFE2L2, SERPINA1, UGCG, SHTN1, TRIM14, DRAM1, RAB10, MYO9B, SAMHD1, PLAUR, TALDO1, GAS7, NR4A3, CISD2, CHCHD10, RAC1, NCKAP1L, LRP1, GSTP1, ARHGAP18, ATP6V0E1, SERPINB6, SMIM30, ITGB2, SNX2, THEMIS2, CSTA, SOD2, LGALS2, SLC31A2, SLAMF7, ANXA5, ATF5, SCAMP2, P2RY13, RAB31, CANX, SASH1, ATP6V0D1, QKI, RCAN1, TMEM70, AP2A2, LAPTM5, OTULINL, RHOQ, CCDC88A, FERMT3, MLEC, ATF3, PDE4DIP, PEPD, IER3, GNPTAB, SDHD, IFNGR1, PDXK, IFI30, LITAF, CLTA, CLTC, HSD17B4, CALHM6, NANS, NUPR1, BCAP31, UBE2D1, G3BP1, KLHL6, ZFYVE16, CAPZB, COMT, FCGR1A, SPATS2L, RGS2, HERPUD1, NR4A2, S100A11, CAT, LGALS1, COLEC12, SLC16A3, CASP1, TMBIM6, RNASE1, SLC43A2, CNDP2, AP2S1, SKAP2, RHOG, SELENOS, STAT1, FCGR3A, PITHD1, Clorfl62, GALNT1, MCUR1, TIMM8B, LMNA, RAB5C, GPR183, PRDX3, CHMP1B, CCL4, KLF4, H2AFJ, MDH1, PABPC4, EFHD2, TMSB4X, MAT2A, ZEB2, CXCL2, LGALS3BP, GADD45B, IQGAP2, LAMTOR2, ATP1B3, DBI, LRPAP1, APLP2, LIMSI, MAP3K8, TXN, SAMSN1, BEX4, SSR3, RTN4, MYDGF, H2AFY, FABP5, CD53, ANXA2, ZNF331, RNH1, CD36, FYB1, ARL6IP1, HES1, SNX6, YWHAH, AC020656.1, NFKBIA, CALR, TNFRSF4, CXCL8, C15orf48, AKAP9, ID2, ZFP36L1, APOE, APOCI, C1QB, C1QA, FTL, C1QC, CTSD, CTSB, CD68, SPP1, NPC2, PSAP, CCL18, CTSZ, ATOX1, CSTB, SELENOP, LGMN, GPNMB, FTH1, LIPA, GRN, FABP5, LGALS3, GLUL, CTSC, CD14, MMP12, ASAHI, FCGRT, FUCA1, AIF1, HLA-DQA1, HLA-DPB1, CD74, FCER1G, CTSL, HLA-DPA1, SAT1, BRI3, CREG1, CAPG, MARCKS, ATP6V1F, MMP9, PRDX1, TXN, SLC40A1, SDCBP, TUBB, TUBA1B, CD63, TMEM176B, ANXA5, NUPR1, YBX1, VAMP8, CD81, TUBB2B, LILRB4, TUBA1A, ODC1, GPX4, PLD3, ACP5, PLIN2, STMN2, GNAS, LAMP1, C15orf48, SPP1, GPNMB, FBP1, HK2, CYP27A1, TREM2, LHFPL2, SLC2A5, SCD, CSTB, ACP5, CD68, GSDME, STM, PLIN2, APOCI, VSIG4, FAM20C, LILRB4, ABCA1, SDS, GM2A, CTSD, BCAT1, CXCL16, MMP19, MSR1, HMOX1, PLAUR, CLEC5A, CTSB, SLC16A3, CTSL, MARCO, GLUL, FTL, PDXK, SLC11A1, SMIM25, FTH1, CREG1, NUPR1, IL4I1, HSD3B7, MPP1, MITF, CD9, FABP5, TREM1, LIPA, RNF130, MGAT1, ZNF385A, ADM, CAPG, COROIC, AQP9, SNX10, FPR3, CXCL8, CD109, PLA2G7, CCR1, LGALS3, ERO1A, APLP2, SIRPA, BLVRB, HEXB, TYROBP, FCGR3A, COLEC12, CNDP2, P4HA1, BRI3, PKM, PSAP, ANPEP, NPC2, TNS3, IL18BP, APOE, LAMP1, TPP1, TIMP2, NPL, ATP6V1B2, VAT1, TTYH3, SOAT1, C5AR1, RNASE1, OLR1, GNS, SLC43A3, NCEH1, CTSH, FCGR2A, GRN, FCGR2B, GRINA, FCER1G, SLC2A1, FNDC3B, CTSZ, TMEM51, EGLN3, IL1RN, CTSA, LGALS1, ENO1, CXCL3, CD163, RAB7B, BNIP3, CCDC88A, DAB2, ATP6V1F, PIK3AP1, RAB20, NCF2, S100A11, NR1H3, PLD3, PTAFR, SPI1, FNIP2, DMXL2, OTOA, ASAHI, VIM, NDRG1, ATP6AP1, CLIP4, SCARB2, BNIP3L, CCL3, SLC15A3, GSTO1, VCAN, PLXDC2, CD36, SGK1, ACP2, SLC7A7, ATP6V1A, PLPP3, RAB42, PLTP, ITGAX, NPC1, ANXA2, SQOR, ITGAM, OSCAR, BCKDK, LGMN, EIF4EBP1, ATF5, H2AFY, RRAGD, VEGFA, SOD2, ARL8B, LACTB, TNS1, HAVCR2, BCAP31, LAPTM5, LRP1, CCL18, ADAM9, BCL2A1, SDC4, DRAM1, SERPINA1, ATP13A3, LYZ, POR, LILRB3, CD300A, SDCBP, S100A10, DUSP3, CD86, RBM47, MCRIP2, KIAA0930, MFSD1, CD14, RAB31, MRC1, TCIRG1, GRB2, GPI, SDSL, TFRC, ENO2, P4HB, FKBP15, AGAP3, ADAM8, MGLL, ABHD2, RAB1A, C1QC, RALA, TUBA1C, NINJ1, LIMSI, MFSD12, PGK1, CD63, DHRS3, TPI1, CD84, IRAKI, RAB10, SLC25A19, HEXA, CXCL2, HLA-DRA, RBPJ, LAIR1, SULF2, ATOX1, SLC48A1, IFNAR1, ANXA5, GAPDH, CYFIP1, CTSS, AIF1, GK, GAA, PDE4DIP, ARHGAP18, MGST1, LAMP2, C2, SQSTM1, C3AR1, FMNL2, MAFB, PRDX1, ABHD12, MS4A4A, M6PR, CCL2, SERF2, CPM, MS4A7, EMILIN2, CSF1R, MMP12, CD82, HSD17B4, PLEKHB2, CEBPB, IFNGR2, FAM 162 A, RETN, SAT1, TYMP, MMP9, CANX, SHTN1, C1QA, QSOX1, RNF13, UPP1, PPT1, SLAMF8, KCTD12, MXI1, ADAP2, PGD, ALCAM, SLCO2B1, ITGB2, TPD52L2, EAF1, RABB, HNMT, CLEC4E, BCL2L1, PAPSS1, ZEB2, ELL2, ADA2, ATP6AP2, CYSTM1, CD74, TFEC, SDC2, RXRA, FCGR1A, MMP14, IDH1, PGAM1, GNB4, ACSL1, HM13, LGALS9, ATP6V1C1, CYBB, GCHFR, ALOX5, VAMP8, ICAM1, Cl QB, COLGALT1, ANXA4, VEGFB, CLEC7A, IGF2R, PILRA, METRNL, BMP2K, ABCG1, UNC93B1, HLA- DMA, KCNAB2, GPX4, TSPAN4, LDHA, RNASET2, SPG21, HLA-DRB1, SYK, MIF, TGFBI, PRNP, RASSF4, RASGEF1B, TMEM176A, LSP1, FCGRT, MARCH1, SH3BGRL3, RNASE6, ALDOA, LYN, LRPAP1, LY96, SCPEP1, GLIPR2, YBX1, GNAQ, HBEGF, CD164, IGSF6, PMP22, RAP2B, FERMT3, GNPTAB, TXN, PEA15, VKORC1, MGST3, ATP6V0B, CITED2, HLA-DQB1, CALM3, Clorfl62, TMEM176B, CHST11, ANKRD28, MYO9B, PFKL, DNASE2, FDX1, TUBGCP2, TMBIM6, RGCC, ATP6V1D, ARRDC3, MYDGF, SMS, ZFYVE16, LGALS3BP, OAZ1, RTN4, UGP2, ATP6V0D1, RNF181, CPEB4, NOP 10, NUCB1, PABPC4, RHEB, PLEKHO1, ZYX, RNH1, CLTC, ZFAND5, TPM4, PHC2, RAB7A, ATF3, DPP7, MAF, DBI, ME2, CD44, FOSL2, CD4, IFI6, LITAF, TNFSF13B, NEAT1, SSR3, AP2S1, TSPO, SRGN, VDAC1, SLC2A3, TALDO1, RDX, AHR, PTTG1IP, STX4, USF2, ELOC, SH3BP5, ACADVL, CHCHD10, FLNA, IER3, LMNA, S100A6, GNG5, CALR, HSPA5, LAP3, STAT1, ALDH2, OSBPL8, ANXA1, FN1, HSP90B1, HSPA1A, ZFP36L1, MT1X, RBP4, GPD1, PARAL1, MLPH, FFAR4, GLDN, AC026369.3, SLC19A3, MIR3945HG, MME, SPOCD1, STAC, C8B, FABP4, DEFBI, MCEMP1, PHLDA3, AL035446.1, PPARG, LPL, ILIA, FAM3B, AGRP, LSAMP, BHLHE41, CXCL5, PCOLCE2, GAPLINC, INHBA, ACOT2, CCL23, HCAR2, FAM89A, RETN, MACC1, APOL4, ZDHHC19, MARCO, ITGB8, TEX14, AMIGO2, LINC02345, CES1, ADAMTSL4, PTGER3, CLDN7, CLDN23, VSIG4, OLR1, ADTRP, ARHGEF28, OSCAR, TREM1, AQP3, GALNT12, TNNI2, NMB, AC025048.4, RMDN3, PNPLA6, HSD3B7, MRC1, FBP1, CXCL3, MSR1, GPA33, ALOX5, RYR1, PTCRA, MYB, AL390036.1, FCGR1A, AVPI1, APIP, S100A13, ALAS1, GCHFR, SVIL, TMEM53, CORO2A, PLA2G16, TGM2, ACO1, PPIC, SMIM25, CYP27A1, FOLR3, OASL, ARRDC4, SLC11A1, ABCG1, TREM2, ITIH5, UBASH3B, B3GNT7, ABHD5, COLEC12, MOB3B, PTPMT1, EDEM2, DNASE2B, CCL18, TCF7L2, SCCPDH, AGPAT2, PHYH, ROGDI, VMO1, PLA2G15, APOC2, SLC27A3, CXCL16, ALDH2, NCEH1, ALDH3A2, TRPV2, C20orf27, RHBDD2, LTA4H, DTX4, B3GNT5, SCD, COROIC, QSOX1, HNMT, LGALS3BP, ALOX5AP, OPN3, CDCP1, ABCG2, SNX10, FLVCR2, NCLN, FDX1, MS4A4A, FN1, MGST1, AKR1C3, SERPINA1, GLIPR2, DECR1, MS4A7, OSBPL11, GAA, THBD, ANXA4, ALDH1A1, GCA, TMEM251, IFIT3, PLBD1, COA6, NCF2, C1QC, MIIP, SLCO2B1, GLRX2, ACP5, DDX60L, CD9, ATP1B1, RETREG1, GLRX, COPRS, PDLIM1, SGMS2, SLC49A3, SMCO4, HDDC2, STAC3, POR, ADGRE1, DPH3, COMT, ENPP4, ARHGAP18, FIG4, TFRC, SNX2, SLC31A2, TP53I3, FUOM, C1QB, TMEM38B, HLA-DRB5, TTC39B, PILRA, SPNS1, SERPING1, CPE, NUPR1, Clorfl62, IL1RN, SORT1, TFPT, CARS2, HCAR3, SPI1, MX1, RGCC, CD300C, UPP1, FCGR3A, MCOLN1, AXL, SIGLEC1, LRP1, IFI6, DOK2, CITED2, SEPTI 1, RASAL2, APOCI, RABB, ALDOA, VAT1, C1QA, PBDC1, LAIR1, FCGR1B, HBEGF, SLC7A7, SCPEP1, USP30-AS1, GK, EGR2, NAA20, FAR2, SYS1, CD 163, STXBP2, CD151, BCL2A1, MGST3, CD68, ATL1, AP5B1, FHL1, DTNA, ETHE1, GSTO1, LRPAP1, CAT, ATP6V0D1, FABP5, MYOF, CA2, CAPG, LGALS3, BST1, PLIN2, TRIP6, TSPO, CEBPB, CYB5A, REEP3, TUBB6, SLC7A8, BLOC1S2, PYCARD, MDH1, HPGDS, MARCH2, SPINT1, G6PD, CD300LF, ANXA2, PROCR, CNIH4, KMO, NCF4, CLEC12A, LAMTOR3, IFIT1, HPGD, TMED5, S100A11, ANXA5, HEXB, LAMTOR1, ARHGAP10, TNFSF12, GPCPD1, SIDT2, VASP, IFI30, SFT2D1, PSMA2, GLUL, PLXDC2, RNH1, S100A6, FCER1G, DAB2, ZNF706, FDX2, TXN, SLC25A19, TSPAN3, NIT2, FPR2, S100A10, ARHGEF10L, REEP5, TOMM40, VPS29, RENBP, LIMA1, MPC2, ZDHHC3, CHP1, SLC3A2, RHOB, SQOR, LSM6, CSTA, BACE1, SH2B2, CYB5R3, HLA-DMA, OAS1, TIGAR, CASP1, DNASE2, TYROBP, TUBA1C, SLC31A1, GNG5, TRIQK, RHEB, SIRPA, OAZ1, CTSL, ATP5MC3, ACADVL, ATP6V0B, CISH, SDCBP, PDXK, CHCHD10, TXNDC17, SLFN11, BTK, MLX, MYL6, GGA2, EMILIN2, VAMP8, PPT1, ATP6V1F, MYDGF, RAB5IF, C7orf50, MRPS35, MRPS15, VEGFB, VAMP3, SPN, CSTB, BAX, MSRA, DESI1, LY6E, RARA, GRN, ATP6V1D, LST1, NOPIO, PPFIA1, BSG, YWHAH, NAGLU, S1PR4, PLIN3, SIOOP, CYBA, CTSC, GSN, LGALS9, FTH1, PGD, ANXA11, AKR1A1, LAP3, CCT5, LACTB2, IGFBP2, OSBPL1A, SLC15A3, PLAUR, TST, HCK, ARPC1B, CARD16, BEX4, RGS19, MMP19, NUCB1, ADAM 17, ACOT13, BRI3, PEBP1, SDHD, FCGRT, TFEC, FCGR2A, AP2S1, COMMD9, GALE, ARL6IP1, SSB, OSTF1, VIM, PAPSS1, GPX4, GON7, CTSH, GPRIN3, SNX3, HLA-DQB1, UBB, FUCA2, IRF8, HK3, NANS, FTL, C5AR1, THEMIS2, LY86, HADH, FKBP15, NDUFB5, ANXA1, ARPC3, UGP2, PPDPF, BLVRA, VDAC1, CD81, IFIT2, TSPAN15, C14orfl l9, MRPL14, CCDC115, CTSD, ACER3, CD276, MNDA, PRDX1, MRPL40, STX12, ATP6AP1, ACOT7, TMBIM1, SLC25A24, POLD4, CD63, RAB11FIP1, IGSF6, MR1, SULT1A1, CDC42EP3, RNPEP, CENPW, JAML, ACVRL1, ECHI, CMC1, HLA-DRB1, HTATIP2, TMED9, MPC1, RNF13, UBE2L6, NPTN, LMNA, HAGH, EIF4EBP1, SMIM14, BCAP31, PTPN6, TCIRG1, HSD17B11, THBS1, SCP2, MINK1, SERF2, LEPROT, TBC1D2, MYD88, COQ2, HSD17B14, NDUFV2, GABARAP, LACTB, WASHC3, CCDC88A, CD58, PEPD, NDUFB3, CTSZ, CYBB, FMNL2, GTF2H5, DDAH2, FBXO6, TMEM91, PDCD6IP, CSF1, GUSB, AK6, SMIM15, GNPTG, CHMP5, LAT2, LYZ, CID, BTF3L4, TAF10, APLP2, SUSD1, S100A4, UBE2A, SLC39A3, YBX1, TM6SF1, TKT, MOSPD2, DNAJA1, ANPEP, DBI, HLA-DRA, ERP44, GRB2, ATP2C1, NDUFA7, DCUN1D5, HLA-DPA1, GRINA, TALDO1, CAPZA2, MTHFS, C9orfl6, ATP6V1E1, CD40, MSRB1, ISOC2, JOSD2, QDPR, CXCL2, MTX2, MRPL13, TXNDC11, HEXA, C18orf32, TIMP2, SEC11A, TMEM219, SCIMP, NEK6, AAED1, ASAHI, FKBP1A, PLSCR1, ECHDC1, HSDL2, RTN4, CD33, DHRS4, MMP24OS, TPMT, VDAC2, AC020656.1, MPV17, MFSD10, MINOS1, CFL1, NENF, RND3, DCTN6, SELENOT, PRKCD, CST3, TSG101, FAM50A, LYAR, CREG1, PCBD1, PSMG1, AKIRIN2, RAB10, CMPK2, HLA-DPB1, TMSB4X, P2RX4, GBP1, AGPS, SSR3, CNDP2, LAMTOR2, CLEC7A, MGAT1, ASGR1, SHTN1, CCND3, TWF2, TMEM173, PDHA1, ARPC5, SDSL, SEPHS2, GLB1, ZBTB8OS, CLTA, EMG1, PSMA7, NDUFA4, HLA-DQA1, CTSA, RAB8A, HIGD1A, RAB5C, CD164, LY96, DUSP23, CLIC1, LSM10, SPG21, HADHB, ITPK1, POLR2K, RAB7A, AIF1, C2orf74, RNF7, EEA1, FAM162A, PSMG2, TCEAL4, ATP6V0E1, SAMM50, HAVCR2, PPCS, PSMD9, PSMA3, POMP, TSFM, TMEM230, EFHD2, DYNLL1, ATP6V1B2, TMEM167A, RER1, TMEM126A, MAN1A1, CMAS, CD52, ACTN1, CYCS, RAB9A, PSMB5, ARPC2, ACAA1, TMEM63A, NDUFAB1, POP4, RAD23A, PNPLA2, ARL2, PHLDA2, C2, SELENOH, MRPL22, KAT8, ARL1, SRI, HEBP1, COLGALT1, TNF, OSTM1, SAMHD1, CTBS, RRAGD, PYURF, DMAC1, TMEM273, AP1S1, RAB32, HVCN1, ELP5, SHARPIN, ESD, NTAN1, COA4, LSM4, TUBA1B, PTAFR, NRBF2, BID, PSMA5, ARL4A, HPCAL1, UNC50, FGD2, RASGEF1B, DYNLT1, SLC16A3, PLAU, ACOT9, MSRB2, TMEM179B, TYMP, RAP1B, GNB2, STX11, PRDX6, SAP18, EMC7, PARP9, PRDX3, RNF181, ITSN1, IFI35, DYNLRB1, UTP18, LAMTOR5, KLF4, PDCL, ATP5F1C, CDC42BPB, EML4, MAP1LC3B, CD83, ATP1B3, HSBP1, CBWD1, SCARB2, H2AFJ, SLC39A10, CAMTAI, RAC1, SH3BGRL3, VAPA, GTF3C6, CYSLTR1, FEZ2, PSMB6, PGP, DNTTIP1, HMOX2, PFN1, IPT1, TMED10, TMBIM6, RNF149, TXNIP, ELOC, PEX16, MYL12A, ANAPC15, CTSS, ACAA2, M6PR, ISG15, ISCU, FAM173A, OTUD1, TCEAL9, RUNX1, ANKRD28, PSMD14, FERMT3, HPS5, CRIP1, MAPKAPK3, CXCL8, CHCHD1, ECHS1, DBNL, MRPS23, ENY2, PSMA4, TRIM14, Clorf43, PRR13, UBE2F, RHOA, CMC2, SMIM37, C19orf70, HERC5, AZI2, MRPL41, PCMT1, TPM4, NDUFA13, TAGLN2, PHB, MDH2, SERPINB1, SLA, SH3BGRL, CDC37, CEBPA, CKLF, ELOB, GLRX3, UQCRFS1, VPS26A, HSD17B12, HINT2, SNF8, JUN, DPP7, NDUFC1, COX7A2L, PSME2, EPSTI1, NDUFB6, LGALS1, TMBIM4, LITAF, MRPL18, TMEM70, APH1A, COPZ1, ATP5MF, PKM, SH3GLB1, TBC1D10C, ATP2B1-AS1, GTF2A2, ARF4, SERTAD1, FLNA, TRAPPC2L, CD74, SUMO3, APEX1, ATRAID, ARRB2, AGTRAP, COX17, CIB1, PSMD8, PPIA, BLOC1S1, PFDN2, GLTP, UQCR10, TXNDC12, NDUFS3, WDR1, BAG1, CAP1, FGR, SNRPG, COPS5, BEX3, NDUFAF3, LMAN2, ITGAX, ADRM1, NDUFB2, ACP2, CTNNB1, IL1B, DDIT3, IRF7, ITM2B, CALM1, NUTF2, HIPK2, TMEM14C, CD47, DOCK8, HMGN3, MTPN, LRRFIP1 and FAM89B, or the expression product thereof.
12. The in vitro method for classifying a subject according to claim 11, wherein:
- the cytotoxic T-cells are detected or quantified by detection in the T-cells of at least one gene selected from the group consisting of the LAG3 gene, the TIGIT gene, the CTLA4 gene, the HAVCR2/TIM3 gene, and the PDCD1/PDL1 gene or the expression product thereof, - the Myeloid-Derived Suppressor Cells are detected by detection in the cells of at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1 A gene and the PTGS2/COX2 gene, or the expression product thereof,
- the Natural killer (NK) cells are detected by detection in the NK cells of the presence of the
Natural Killer Cell Granule Protein 7, and/or
- the macrophages are detected by detection at the macrophage cells surface of the presence of at least one protein selected from the group consisting of the CD68 protein and the APOE protein, or by detection in the macrophages of the corresponding CD68 and APOE genes.
13. The in vitro method for classifying a subject according to claim 11 or claim 12, wherein the neuroblastoma is a metastatic or pre-metastatic neuroblastoma, wherein the neuroblastoma is a high risk neuroblastoma or wherein the neuroblastoma is selected from refractory neuroblastoma, relapsed neuroblastoma, or relapsed and refractory neuroblastoma.
14. The in vitro method for classifying a subject according to any one of claims 11 to 13, further comprising, after the detection step(s), a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group.
15. An in vitro method for predicting the response of a subject suffering from neuroblastoma to an immunotherapy treatment, comprising a step of implementing an in vitro method for classifying or identifying a patient according to any one of claims 11 to 14, a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group, the membership of the subject to a specific group being predictive of the responsiveness of said subject to a specific treatment.
16. The in vitro method according to claim 15 for predicting the response of a subj ect suffering from neuroblastoma to an immunotherapy treatment, especially an immunotherapy treatment according to claim 2 or 3, wherein the cells detected in the classification step are Cytotoxic T cells as disclosed above, and the specific treatment comprises the administration of at least one checkpoint inhibitor, preferably selected from the group consisting of LAG3, TIGIT, CTLA4, HAVCR2/TIM3 and PD1/PDL1 inhibitors. The in vitro method according to claim 15 for predicting the response of a subj ect suffering from neuroblastoma to a treatment according to claim 5 or 6, wherein the cells detected in the classification step are MDSC as disclosed above, and the specific treatment comprises the administration of at least one antibody or small molecule targeting at least one protein encoded by the above-listed genes, such as an anti-CXCR2 targeting small molecule or antibody. An in vitro method for determining a suitable treatment for a subject, said method comprising a step of implementing an in vitro method for classifying a patient according to any one of claims 11 to 14, a step of comparing the number and/or type of detected cells to reference or control numbers and/or types of detected cells, in order to assign the subject to a specific group, and a step of determining a suitable treatment. An in vitro method for detecting or quantifying immunosuppressive MDSC in a neuroblastoma sample from a subject, wherein the method comprises detecting or quantifying at least one gene or gene product of Table 4J or at least one gene selected from the group consisting of the S100A8 gene, the S100A9 gene, the CEBPB gene, the CXCR2 gene, the TREM1 gene, the HIF1A gene and the PTGS2/COX2 gene, or the expression product thereof, the overexpression of said genes or gene products being indicative of immunosuppressive MDSC. The method of claim 19, wherein the at least one gene or gene product is selected from the group consisting of CXCR2, FCGR3B, CMTM2, SIOOP, CSF3R, CXCR1, ALPL, S100A8, G0S2, ADGRG3, SLC25A37, VNN2, FFAR2, MNDA, S100A12, PROK2, NAMPT, MXD1, IL1R2, S100A9, PTGS2, FPR1, LRRK2, IFITM2, AQP9, ACSL1, MMP25, GCA, RGS2, NEAT1, SRGN, CD A, STEAP4, BASP1, FPR2, SOD2, CXCL8, BCL2A1, LITAF, RNF149, S100A11, IFIT2, SORL1, H3F3A, CEBPB, TMEM154, FAM129A, NCF1, SAT1, C5AR1, FTH1, H3F3B, MBOAT7, SMCHD1, R3HDM4, IFIT3, SELL, BCL6, MSRB1, ANP32A, TREM1, FRAT2, LST1, IFIT1, RNF24, SDCBP, J AML, MCL1, YPEL3, HSPA6, NCF2, SPI1, LILRB3, TYROBP, DUSP1, FCGR2A, SERPINA1, MY01F, IVNS1ABP, APOBEC3A, RSAD2, MEGF9, RIPOR2, S100A6, ABTB1, LYN, CREB5, LCP1, ALOX5AP, ZFP36L1, USP10, IER2, CSF2RB, SLC11A1, IFITM3, MX2, RGS18, PYGL, SMIM25, SLC2A3, TRIBI, NCF4, TUBA1A, XPO6, TLE3, ITM2B, TXNIP, EGLN1, LILRA5, GMFG, DDX60L, DENND3, IGF2R, HIST1H2AC, EVI2B, PTPRC, CEBPD, LSP1, OAZ1, GLUL, UBE2B, RARA, PNRC1, CPPED1, TLR2, FOS, NADK, CDKN2D, PDLIM7, ARPC5, PTPRE, FLOT2, PLEK, CD55, GNAI2, ADAM8, PTEN, BRI3, ACTB, LAPTM5, STXBP2, P2RY13, ISG15, LY96, UBN1, VSIR, NABP1, SMAP2, ICAM3, VASP, ALOX5, IFRD1, PELI1, RTN3, NUP214, IL17RA, CNN2, MARCKS, HLA-B, PHC2, SEC14L1, CFLAR, ARHGAP9, SHKBP1, RAB11FIP1, EFHD2, LAMTOR4, PLAUR, KDM6B, RASSF3, UBE2D1, CLEC4E, CAP1, CMTM6, LYST, VMP1, FMNL1, FBXL5, TALDO1, CLEC7A, NINJ1, HLA-E, ITGAX, SSH2, PREXI, ACTN1, MAP3K2, ABHD5, HIF1A, ARRB2, ZFP36, ARHGAP26, CYSTM1, TXN, GPSM3, CDC42EP3, UBE2D3, IRF1, CSRNP1, CYTH4, TNFSF13B, ACAP2, PLXNC1, TNFAIP2, USP15, NOPIO, MX1, C4orf3, JMJD1C, SLA, BACH1, MAP4K4, FOSL2, KIAA1551, CKLF, CARD16, NMI, ADGRE5, OSBPL8, WIPF1, FYB1, FLOT1, ATP6V0B, TNFRSF1B, FKBP8, SKAP2, WAS, PLSCR1, TAGLN2, RAB31, PDE4B, SHISA5, LRP10, CCPG1, FAM49B, ADAR, CD46, TCIRG1, IFI16, SERPINB1, UBALD2, MIDN, NCOA4, GNB2, UBE2R2, CDC42SE1, ZYX, TAGAP, RNF213 and LCP2. A method of treatment of neuroblastoma in a subject in need thereof, comprising the administration a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4A, 4J, 4B, 4H, 41, 4M or 4E, preferably 4A, 4J, 4B, 4H, 41, more preferably 4A or 4J. Use of a molecule targeting, modulating or inhibiting a gene or protein selected from Table 4, especially Table 4 A, 4 J, 4B, 4H, 41, 4M or 4E, preferably 4 A, 4 J, 4B, 4H, 41, more preferably 4A or 4J for the manufacture of a medicament, for the treatment of neuroblastoma.
PCT/EP2023/068023 2022-07-01 2023-06-30 Biomarkers and uses thereof for the treatment of neuroblastoma WO2024003360A1 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
EP22305990.8 2022-07-01
EP22305990 2022-07-01

Publications (1)

Publication Number Publication Date
WO2024003360A1 true WO2024003360A1 (en) 2024-01-04

Family

ID=82846405

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/EP2023/068023 WO2024003360A1 (en) 2022-07-01 2023-06-30 Biomarkers and uses thereof for the treatment of neuroblastoma

Country Status (1)

Country Link
WO (1) WO2024003360A1 (en)

Citations (67)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5618703A (en) 1986-08-22 1997-04-08 Hoffmann-La Roche Inc. Unconventional nucleotide substitution in temperature selective RT-PCR
US20050048542A1 (en) 2003-07-10 2005-03-03 Baker Joffre B. Expression profile algorithm and test for cancer prognosis
WO2006121168A1 (en) 2005-05-09 2006-11-16 Ono Pharmaceutical Co., Ltd. Human monoclonal antibodies to programmed death 1(pd-1) and methods for treating cancer using anti-pd-1 antibodies alone or in combination with other immunotherapeutics
WO2007008463A2 (en) 2005-07-07 2007-01-18 Coley Pharmaceutical Group, Inc. Anti-ctla-4 antibody and cpg-motif-containing synthetic oligodeoxynucleotide combination therapy for cancer treatment
WO2008132601A1 (en) 2007-04-30 2008-11-06 Immutep Cytotoxic anti-lag-3 monoclonal antibody and its use in the treatment or prevention of organ transplant rejection and autoimmune disease
WO2009100140A1 (en) 2008-02-04 2009-08-13 Medarex, Inc. Anti-clta-4 antibodies with reduced blocking of binding of ctla-4 to b7 and uses thereof
EP2320940A2 (en) 2008-08-11 2011-05-18 Medarex, Inc. Human antibodies that bind lymphocyte activation gene-3 (lag-3), and uses thereof
WO2011155607A1 (en) 2010-06-11 2011-12-15 協和発酵キリン株式会社 Anti-tim-3 antibody
WO2012120125A1 (en) 2011-03-09 2012-09-13 Antitope Ltd Humanised anti ctla-4 antibodies
WO2013006490A2 (en) 2011-07-01 2013-01-10 Cellerant Therapeutics, Inc. Antibodies that specifically bind to tim3
WO2014194302A2 (en) 2013-05-31 2014-12-04 Sorrento Therapeutics, Inc. Antigen binding proteins that bind pd-1
WO2016015675A1 (en) 2014-08-01 2016-02-04 中山康方生物医药有限公司 Anti-ctla4 monoclonal antibody or antigen binding fragment thereof, medicinal composition and use
WO2016028656A1 (en) 2014-08-19 2016-02-25 Merck Sharp & Dohme Corp. Anti-tigit antibodies
WO2016106302A1 (en) 2014-12-23 2016-06-30 Bristol-Myers Squibb Company Antibodies to tigit
WO2016130898A2 (en) 2015-02-13 2016-08-18 Sorrento Therapeutics, Inc. Antibody therapeutics that bind ctla4
WO2016161270A1 (en) 2015-04-01 2016-10-06 Anaptysbio, Inc. Antibodies directed against t cell immunoglobulin and mucin protein 3 (tim-3)
WO2016191643A2 (en) 2015-05-28 2016-12-01 Oncomed Pharmaceuticals, Inc. Tigit-binding agents and uses thereof
WO2016196237A1 (en) 2015-05-29 2016-12-08 Agenus Inc. Anti-ctla-4 antibodies and methods of use thereof
WO2017019846A1 (en) 2015-07-30 2017-02-02 Macrogenics, Inc. Pd-1-binding molecules and methods use thereof
WO2017025016A1 (en) 2015-08-10 2017-02-16 Innovent Biologics (Suzhou) Co., Ltd. Pd-1 antibodies
WO2017030823A2 (en) 2015-08-14 2017-02-23 Merck Sharp & Dohme Corp. Anti-tigit antibodies
WO2017040790A1 (en) 2015-09-01 2017-03-09 Agenus Inc. Anti-pd-1 antibodies and methods of use thereof
WO2017037707A1 (en) 2015-09-02 2017-03-09 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. Antibodies specific to human t-cell immunoglobulin and itim domain (tigit)
WO2017053748A2 (en) 2015-09-25 2017-03-30 Genentech, Inc. Anti-tigit antibodies and methods of use
WO2017087588A1 (en) 2015-11-18 2017-05-26 Merck Sharp & Dohme Corp. Ctla4 binders
WO2017084078A1 (en) 2015-11-19 2017-05-26 Zeling Cai Ctla-4 antibodies and uses thereof
WO2017106372A1 (en) 2015-12-15 2017-06-22 Oncoimmune, Inc. Chimeric and humanized anti-human ctla4 monoclonal antibodies and uses thereof
WO2017133540A1 (en) 2016-02-02 2017-08-10 Innovent Biologics (Suzhou) Co., Ltd. Pd-1 antibodies
WO2017132825A1 (en) 2016-02-02 2017-08-10 华为技术有限公司 Emission power verification method, user equipment, and base station
WO2017152088A1 (en) 2016-03-04 2017-09-08 JN Biosciences, LLC Antibodies to tigit
WO2017194265A1 (en) 2016-05-10 2017-11-16 Agency For Science, Technology And Research Anti-CTLA-4 Antibodies
WO2018025178A1 (en) 2016-08-02 2018-02-08 Aduro Biotech Holdings, Europe B.V. Antibodies against human ctla-4
WO2018033798A1 (en) 2016-08-17 2018-02-22 Compugen Ltd. Anti-tigit antibodies, anti-pvrig antibodies and combinations thereof
WO2018035710A1 (en) 2016-08-23 2018-03-01 Akeso Biopharma, Inc. Anti-ctla4 antibodies
WO2018068182A1 (en) 2016-10-10 2018-04-19 Crown Bioscience (Taicang) Inc. Novel anti-ctla4 antibodies
WO2018085469A2 (en) 2016-11-01 2018-05-11 Anaptysbio, Inc. Antibodies directed against t cell immunoglobulin and mucin protein 3 (tim-3)
WO2018102746A1 (en) 2016-12-02 2018-06-07 Rigel Pharmaceuticals, Inc. Antigen binding molecules to tigit
WO2018102536A1 (en) 2016-11-30 2018-06-07 Oncomed Pharmaceuticals, Inc. Methods for treatment of cancer comprising tigit-binding agents
WO2018106862A1 (en) 2016-12-07 2018-06-14 Agenus Inc. Anti-ctla-4 antibodies and methods of use thereof
WO2018106864A1 (en) 2016-12-07 2018-06-14 Agenus Inc. Antibodies and methods of use thereof
WO2018129553A1 (en) 2017-01-09 2018-07-12 Tesaro, Inc. Methods of treating cancer with anti-tim-3 antibodies
WO2018156250A1 (en) 2017-02-21 2018-08-30 Remd Biotherapeutics, Inc. Cancer treatment using antibodies that bind cytotoxic t-lymphocyte antigen-4 (ctla-4)
WO2018160536A1 (en) 2017-02-28 2018-09-07 Bristol-Myers Squibb Company Use of anti-ctla-4 antibodies with enhanced adcc to enhance immune response to a vaccine
WO2018160704A1 (en) 2017-02-28 2018-09-07 Adimab Llc Anti-tigit antibodies
WO2018165895A1 (en) 2017-03-15 2018-09-20 苏州银河生物医药有限公司 Ctla4 antibody, pharmaceutical composition and use thereof
WO2018200430A1 (en) 2017-04-26 2018-11-01 Bristol-Myers Squibb Company Methods of antibody production that minimize disulfide bond reduction
WO2018204363A1 (en) 2017-05-01 2018-11-08 Agenus Inc. Anti-tigit antibodies and methods of use thereof
WO2018209701A1 (en) 2017-05-19 2018-11-22 Wuxi Biologics (Shanghai) Co., Ltd. Novel monoclonal antibodies to cytotoxic t-lymphocyte-associated protein 4 (ctla-4)
WO2019023504A1 (en) 2017-07-27 2019-01-31 Iteos Therapeutics Sa Anti-tigit antibodies
WO2019023482A1 (en) 2017-07-27 2019-01-31 Regeneron Pharmaceuticals, Inc. Anti-ctla-4 antibodies and uses thereof
WO2019056281A1 (en) 2017-09-21 2019-03-28 Eucure (Beijing) Biopharma Co., Ltd Anti-ctla4 antibodies and uses thereof
WO2019062832A1 (en) 2017-09-29 2019-04-04 江苏恒瑞医药股份有限公司 Tigit antibody, antigen-binding fragment thereof, and medical use thereof
WO2019120232A1 (en) 2017-12-20 2019-06-27 Harbour Biomed (Shanghai) Co., Ltd Antibodies binding ctla-4 and uses thereof
WO2019129261A1 (en) 2017-12-30 2019-07-04 Beigene, Ltd. Anti-tigit antibodies and their use as therapeutics and diagnostics
WO2019129221A1 (en) 2017-12-28 2019-07-04 Nanjing Legend Biotech Co., Ltd. Single-domain antibodies and variants thereof against tigit
WO2019137548A1 (en) 2018-01-15 2019-07-18 Nanjing Legend Biotech Co., Ltd. Antibodies and variants thereof against tigit
WO2019152574A1 (en) 2018-02-01 2019-08-08 Merck Sharp & Dohme Corp. Methods for treating cancer or infection using a combination of an anti-pd-1 antibody, an anti-lag3 antibody, and an anti-tigit antibody
WO2019148444A1 (en) 2018-02-02 2019-08-08 Adagene Inc. Anti-ctla4 antibodies and methods of making and using the same
WO2019154415A1 (en) 2018-02-06 2019-08-15 I-Mab Antibodies to t cell immunoreceptor with ig and itim domains (tigit) and uses thereof
WO2019168382A1 (en) 2018-02-28 2019-09-06 Yuhan Corporation Anti-tigit antibodies and uses thereof
WO2019174603A1 (en) 2018-03-14 2019-09-19 上海开拓者生物医药有限公司 Antibody targeting ctla-4 , preparation method therefor and use thereof
WO2019179388A1 (en) 2018-03-19 2019-09-26 Wuxi Biologics (Shanghai) Co., Ltd. Novel anti-ctla-4 antibody polypeptide
WO2019179391A1 (en) 2018-03-19 2019-09-26 Wuxi Biologics (Shanghai) Co., Ltd. Novel bispecific pd-1/ctla-4 antibody molecules
WO2019215728A1 (en) 2018-05-09 2019-11-14 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. Antibodies specific to human nectin4
WO2019232484A1 (en) 2018-06-01 2019-12-05 Compugen Ltd Anti-pvrig/anti-tigit bispecific antibodies and methods of use
WO2020028479A1 (en) 2018-08-01 2020-02-06 Cephalon, Inc. Anti-cxcr2 antibodies and uses thereof
WO2020112514A1 (en) 2018-11-30 2020-06-04 Eli Lilly And Company An aurora a kinase inhibitor for use in the treatment of neuroblastoma

Patent Citations (71)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US5618703A (en) 1986-08-22 1997-04-08 Hoffmann-La Roche Inc. Unconventional nucleotide substitution in temperature selective RT-PCR
US20050048542A1 (en) 2003-07-10 2005-03-03 Baker Joffre B. Expression profile algorithm and test for cancer prognosis
WO2006121168A1 (en) 2005-05-09 2006-11-16 Ono Pharmaceutical Co., Ltd. Human monoclonal antibodies to programmed death 1(pd-1) and methods for treating cancer using anti-pd-1 antibodies alone or in combination with other immunotherapeutics
WO2007008463A2 (en) 2005-07-07 2007-01-18 Coley Pharmaceutical Group, Inc. Anti-ctla-4 antibody and cpg-motif-containing synthetic oligodeoxynucleotide combination therapy for cancer treatment
WO2008132601A1 (en) 2007-04-30 2008-11-06 Immutep Cytotoxic anti-lag-3 monoclonal antibody and its use in the treatment or prevention of organ transplant rejection and autoimmune disease
WO2009100140A1 (en) 2008-02-04 2009-08-13 Medarex, Inc. Anti-clta-4 antibodies with reduced blocking of binding of ctla-4 to b7 and uses thereof
EP2320940A2 (en) 2008-08-11 2011-05-18 Medarex, Inc. Human antibodies that bind lymphocyte activation gene-3 (lag-3), and uses thereof
WO2011155607A1 (en) 2010-06-11 2011-12-15 協和発酵キリン株式会社 Anti-tim-3 antibody
EP2581113A1 (en) 2010-06-11 2013-04-17 Kyowa Hakko Kirin Co., Ltd. Anti-tim-3 antibody
US8552156B2 (en) 2010-06-11 2013-10-08 Kyowa Hakko Kirin Co., Ltd Anti-TIM-3 antibody
US20140044728A1 (en) 2010-06-11 2014-02-13 Kyushu University, National University Corporation Anti-tim-3 antibody
WO2012120125A1 (en) 2011-03-09 2012-09-13 Antitope Ltd Humanised anti ctla-4 antibodies
WO2013006490A2 (en) 2011-07-01 2013-01-10 Cellerant Therapeutics, Inc. Antibodies that specifically bind to tim3
WO2014194302A2 (en) 2013-05-31 2014-12-04 Sorrento Therapeutics, Inc. Antigen binding proteins that bind pd-1
WO2016015675A1 (en) 2014-08-01 2016-02-04 中山康方生物医药有限公司 Anti-ctla4 monoclonal antibody or antigen binding fragment thereof, medicinal composition and use
WO2016028656A1 (en) 2014-08-19 2016-02-25 Merck Sharp & Dohme Corp. Anti-tigit antibodies
WO2016106302A1 (en) 2014-12-23 2016-06-30 Bristol-Myers Squibb Company Antibodies to tigit
WO2016130898A2 (en) 2015-02-13 2016-08-18 Sorrento Therapeutics, Inc. Antibody therapeutics that bind ctla4
WO2016161270A1 (en) 2015-04-01 2016-10-06 Anaptysbio, Inc. Antibodies directed against t cell immunoglobulin and mucin protein 3 (tim-3)
WO2016191643A2 (en) 2015-05-28 2016-12-01 Oncomed Pharmaceuticals, Inc. Tigit-binding agents and uses thereof
WO2016196237A1 (en) 2015-05-29 2016-12-08 Agenus Inc. Anti-ctla-4 antibodies and methods of use thereof
WO2017019846A1 (en) 2015-07-30 2017-02-02 Macrogenics, Inc. Pd-1-binding molecules and methods use thereof
WO2017025016A1 (en) 2015-08-10 2017-02-16 Innovent Biologics (Suzhou) Co., Ltd. Pd-1 antibodies
WO2017024465A1 (en) 2015-08-10 2017-02-16 Innovent Biologics (Suzhou) Co., Ltd. Pd-1 antibodies
WO2017030823A2 (en) 2015-08-14 2017-02-23 Merck Sharp & Dohme Corp. Anti-tigit antibodies
WO2017040790A1 (en) 2015-09-01 2017-03-09 Agenus Inc. Anti-pd-1 antibodies and methods of use thereof
WO2017037707A1 (en) 2015-09-02 2017-03-09 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. Antibodies specific to human t-cell immunoglobulin and itim domain (tigit)
WO2017053748A2 (en) 2015-09-25 2017-03-30 Genentech, Inc. Anti-tigit antibodies and methods of use
WO2017087588A1 (en) 2015-11-18 2017-05-26 Merck Sharp & Dohme Corp. Ctla4 binders
WO2017084078A1 (en) 2015-11-19 2017-05-26 Zeling Cai Ctla-4 antibodies and uses thereof
WO2017106372A1 (en) 2015-12-15 2017-06-22 Oncoimmune, Inc. Chimeric and humanized anti-human ctla4 monoclonal antibodies and uses thereof
WO2017133540A1 (en) 2016-02-02 2017-08-10 Innovent Biologics (Suzhou) Co., Ltd. Pd-1 antibodies
WO2017132825A1 (en) 2016-02-02 2017-08-10 华为技术有限公司 Emission power verification method, user equipment, and base station
WO2017152088A1 (en) 2016-03-04 2017-09-08 JN Biosciences, LLC Antibodies to tigit
WO2017194265A1 (en) 2016-05-10 2017-11-16 Agency For Science, Technology And Research Anti-CTLA-4 Antibodies
WO2018025178A1 (en) 2016-08-02 2018-02-08 Aduro Biotech Holdings, Europe B.V. Antibodies against human ctla-4
WO2018033798A1 (en) 2016-08-17 2018-02-22 Compugen Ltd. Anti-tigit antibodies, anti-pvrig antibodies and combinations thereof
WO2018035710A1 (en) 2016-08-23 2018-03-01 Akeso Biopharma, Inc. Anti-ctla4 antibodies
WO2018068182A1 (en) 2016-10-10 2018-04-19 Crown Bioscience (Taicang) Inc. Novel anti-ctla4 antibodies
WO2018085469A2 (en) 2016-11-01 2018-05-11 Anaptysbio, Inc. Antibodies directed against t cell immunoglobulin and mucin protein 3 (tim-3)
WO2018102536A1 (en) 2016-11-30 2018-06-07 Oncomed Pharmaceuticals, Inc. Methods for treatment of cancer comprising tigit-binding agents
WO2018102746A1 (en) 2016-12-02 2018-06-07 Rigel Pharmaceuticals, Inc. Antigen binding molecules to tigit
WO2018106862A1 (en) 2016-12-07 2018-06-14 Agenus Inc. Anti-ctla-4 antibodies and methods of use thereof
WO2018106864A1 (en) 2016-12-07 2018-06-14 Agenus Inc. Antibodies and methods of use thereof
WO2018129553A1 (en) 2017-01-09 2018-07-12 Tesaro, Inc. Methods of treating cancer with anti-tim-3 antibodies
WO2018156250A1 (en) 2017-02-21 2018-08-30 Remd Biotherapeutics, Inc. Cancer treatment using antibodies that bind cytotoxic t-lymphocyte antigen-4 (ctla-4)
WO2018160536A1 (en) 2017-02-28 2018-09-07 Bristol-Myers Squibb Company Use of anti-ctla-4 antibodies with enhanced adcc to enhance immune response to a vaccine
WO2018160704A1 (en) 2017-02-28 2018-09-07 Adimab Llc Anti-tigit antibodies
WO2018165895A1 (en) 2017-03-15 2018-09-20 苏州银河生物医药有限公司 Ctla4 antibody, pharmaceutical composition and use thereof
WO2018200430A1 (en) 2017-04-26 2018-11-01 Bristol-Myers Squibb Company Methods of antibody production that minimize disulfide bond reduction
WO2018204363A1 (en) 2017-05-01 2018-11-08 Agenus Inc. Anti-tigit antibodies and methods of use thereof
WO2018209701A1 (en) 2017-05-19 2018-11-22 Wuxi Biologics (Shanghai) Co., Ltd. Novel monoclonal antibodies to cytotoxic t-lymphocyte-associated protein 4 (ctla-4)
WO2019023504A1 (en) 2017-07-27 2019-01-31 Iteos Therapeutics Sa Anti-tigit antibodies
WO2019023482A1 (en) 2017-07-27 2019-01-31 Regeneron Pharmaceuticals, Inc. Anti-ctla-4 antibodies and uses thereof
WO2019056281A1 (en) 2017-09-21 2019-03-28 Eucure (Beijing) Biopharma Co., Ltd Anti-ctla4 antibodies and uses thereof
WO2019062832A1 (en) 2017-09-29 2019-04-04 江苏恒瑞医药股份有限公司 Tigit antibody, antigen-binding fragment thereof, and medical use thereof
WO2019120232A1 (en) 2017-12-20 2019-06-27 Harbour Biomed (Shanghai) Co., Ltd Antibodies binding ctla-4 and uses thereof
WO2019129221A1 (en) 2017-12-28 2019-07-04 Nanjing Legend Biotech Co., Ltd. Single-domain antibodies and variants thereof against tigit
WO2019129261A1 (en) 2017-12-30 2019-07-04 Beigene, Ltd. Anti-tigit antibodies and their use as therapeutics and diagnostics
WO2019137548A1 (en) 2018-01-15 2019-07-18 Nanjing Legend Biotech Co., Ltd. Antibodies and variants thereof against tigit
WO2019152574A1 (en) 2018-02-01 2019-08-08 Merck Sharp & Dohme Corp. Methods for treating cancer or infection using a combination of an anti-pd-1 antibody, an anti-lag3 antibody, and an anti-tigit antibody
WO2019148444A1 (en) 2018-02-02 2019-08-08 Adagene Inc. Anti-ctla4 antibodies and methods of making and using the same
WO2019154415A1 (en) 2018-02-06 2019-08-15 I-Mab Antibodies to t cell immunoreceptor with ig and itim domains (tigit) and uses thereof
WO2019168382A1 (en) 2018-02-28 2019-09-06 Yuhan Corporation Anti-tigit antibodies and uses thereof
WO2019174603A1 (en) 2018-03-14 2019-09-19 上海开拓者生物医药有限公司 Antibody targeting ctla-4 , preparation method therefor and use thereof
WO2019179388A1 (en) 2018-03-19 2019-09-26 Wuxi Biologics (Shanghai) Co., Ltd. Novel anti-ctla-4 antibody polypeptide
WO2019179391A1 (en) 2018-03-19 2019-09-26 Wuxi Biologics (Shanghai) Co., Ltd. Novel bispecific pd-1/ctla-4 antibody molecules
WO2019215728A1 (en) 2018-05-09 2019-11-14 Yissum Research Development Company Of The Hebrew University Of Jerusalem Ltd. Antibodies specific to human nectin4
WO2019232484A1 (en) 2018-06-01 2019-12-05 Compugen Ltd Anti-pvrig/anti-tigit bispecific antibodies and methods of use
WO2020028479A1 (en) 2018-08-01 2020-02-06 Cephalon, Inc. Anti-cxcr2 antibodies and uses thereof
WO2020112514A1 (en) 2018-11-30 2020-06-04 Eli Lilly And Company An aurora a kinase inhibitor for use in the treatment of neuroblastoma

Non-Patent Citations (26)

* Cited by examiner, † Cited by third party
Title
"The Immunological Genome Project: networks of gene expression in immune cells.", NAT IMMUNOL., vol. 9, 2008, pages 1091 - 4
"Uniprot", Database accession no. P25025
ARAN DLOONEY APLIU LWU EFONG VHSU A ET AL.: "Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage", NAT IMMUNOL., vol. 20, 2019, pages 163 - 72, XP036679985, DOI: 10.1038/s41590-018-0276-y
BERGEN VLANGE MPEIDLI SWOLF FATHEIS FJ: "Generalizing RNA velocity to transient cell states through dynamical modeling.", NAT BIOTECHNOL., vol. 38, 2020, pages 1408 - 14, XP037311068, DOI: 10.1038/s41587-020-0591-3
COSTA ET AL., J IMMUNOTHER CANCER., vol. 10, no. 8, 2022, pages 004807
FROSCH JENNIFER ET AL: "Combined Effects of Myeloid Cells in the Neuroblastoma Tumor Microenvironment", CANCERS, vol. 13, no. 7, 6 April 2021 (2021-04-06), pages 1743, XP093082314, Retrieved from the Internet <URL:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8038814/pdf/cancers-13-01743.pdf> DOI: 10.3390/cancers13071743 *
FUJITA MKOHANBASH GFELLOWS-MAYLE WHAMILTON RLKOMOHARA YDECKER SA ET AL.: "COX-2 blockade suppresses gliomagenesis by inhibiting myeloid-derived suppressor cells.", CANCER RES., vol. 71, 2011, pages 2664 - 74
GU ZEILS RSCHLESNER M: "Complex heatmaps reveal patterns and correlations in multidimensional genomic data", BIOINFORMATICS, vol. 32, 2016, pages 2847 - 9
HAAS-KOGAN D ET AL.: "Long-term results for children with high-risk neuroblastoma treated on a randomized trial of myeloablative therapy followed by 13-cis-retinoic acid: a children's oncology group study.", J CLIN ONCOL., vol. 27, 2009, pages 1007 - 13
HENG TSPPAINTER MW, IMMUNOLOGICAL GENOME PROJECT CONSORTIUM
KORSUNSKY IMILLARD NFAN JSLOWIKOWSKI KZHANG FWEI K ET AL.: "Fast, sensitive and accurate integration of single-cell data with Harmony", NAT METHODS, vol. 16, 2019, pages 1289 - 96, XP037228809, DOI: 10.1038/s41592-019-0619-0
LA MANNO GSOLDATOV RZEISEL ABRAUN EHOCHGERNER HPETUKHOV V ET AL.: "RNA velocity of single cells", NATURE, vol. 560, 2018, pages 494 - 8, XP036573779, DOI: 10.1038/s41586-018-0414-6
LIAO ET AL., CANCER CELL, vol. 35, no. 4, 2019, pages 559 - 572
MABBOTT NABAILLIE JKBROWN HFREEMAN TCHUME DA: "An expression atlas of human primary cells: inference of gene function from coexpression networks", BMC GENOMICS., vol. 14, 2013, pages 632, XP021163126, DOI: 10.1186/1471-2164-14-632
MILLER ET AL., BMC PHARMACOLOGY AND TOXICOLOGY, vol. 16, 2015, pages 18
MILLER ET AL., EUR J DRUG METAB PHARMACOKINET, vol. 39, 2014, pages 173 - 181
NAT REV IMMUNOL., 2021
NINA EISSLER ET AL: "Immune suppression by myeloid-derived suppressor cells, MDSCs, in MYCN-driven neuroblastoma provides a potential target for cancer immunotherapy", JOURNAL FOR IMMUNOTHERAPY OF CANCER, BIOMED CENTRAL, LONDON, GB, vol. 2, no. Suppl 3, 6 November 2014 (2014-11-06), pages P203, XP021202469, ISSN: 2051-1426, DOI: 10.1186/2051-1426-2-S3-P203 *
NING ET AL., MOL CANCER THER., vol. 11, no. 6, 2012, pages 1353 - 64
SI-YANG LIU ET AL., J. HEMATOL. ONCOL., vol. 10, 2017, pages 136
TUART TBUTLER AHOFFMAN PHAFEMEISTER CPAPALEXI EMAUCK WM ET AL.: "Comprehensive Integration of Single-Cell Data", CELL, vol. 177, 2019, pages 1888 - 1902
WEISS WAALDAPE KMOHAPATRA GFEUERSTEIN BGBISHOP JM: "Targeted expression of MYCN causes neuroblastoma in transgenic mice", EMBO J., vol. 16, 1997, pages 2985 - 95, XP002549034, DOI: 10.1093/emboj/16.11.2985
WIENKE JUDITH ET AL: "The immune landscape of neuroblastoma: Challenges and opportunities for novel therapeutic strategies in pediatric oncology", EUROPEAN JOURNAL OF CANCER, ELSEVIER, AMSTERDAM NL, vol. 144, 18 December 2020 (2020-12-18), pages 123 - 150, XP086464946, ISSN: 0959-8049, [retrieved on 20201218], DOI: 10.1016/J.EJCA.2020.11.014 *
WOLOCK SLLOPEZ RKLEIN AM: "Scrublet: Computational Identification of Cell Doublets in Single-Cell Transcriptomic Data", CELL SYST., vol. 8, 2019, pages 281 - 291
ZARBOCK ET AL., BRITISH JOURNAL OF PHARMACOLOGY, 2008, pages 1 - 8
ZILIONIS RENGBLOM CPFIRSCHKE CSAVOVA VZEMMOUR DSAATCIOGLU HD ET AL.: "Single-Cell Transcriptomics of Human and Mouse Lung Cancers Reveals Conserved Myeloid Populations across Individuals and Species", IMMUNITY, vol. 50, 2019, pages 1317 - 1334

Similar Documents

Publication Publication Date Title
US20210047694A1 (en) Methods for predicting outcomes and treating colorectal cancer using a cell atlas
US20210104321A1 (en) Machine learning disease prediction and treatment prioritization
US20190263912A1 (en) Modulation of intestinal epithelial cell differentiation, maintenance and/or function through t cell action
US20230381231A1 (en) Compositions for cancer treatment and methods and uses for cancer treatment and prognosis
US20200347456A1 (en) Methods and compositions for detecting and modulating an immunotherapy resistance gene signature in cancer
US11906511B2 (en) Methods and compositions for treating diseases associated with exhausted T cells
US11644466B2 (en) Methods for treating, preventing and predicting risk of developing breast cancer
US11427869B2 (en) T cell balance gene expression, compositions of matters and methods of use thereof
EP3303636B1 (en) Companion methods for il-2-based therapies and mesenchymal stem cell-based therapies
US7939263B2 (en) Compositions and methods for treating and diagnosing cancer
US8492328B2 (en) Biomarkers and methods for determining sensitivity to insulin growth factor-1 receptor modulators
US20210325387A1 (en) Cell atlas of the healthy and ulcerative colitis human colon
US20210040442A1 (en) Modulation of epithelial cell differentiation, maintenance and/or function through t cell action, and markers and methods of use thereof
US20070099209A1 (en) Compositions and methods for treating and diagnosing cancer
US20120315216A1 (en) Compositions and Methods for Treating and Diagnosing Cancer
AU2010326066A1 (en) Classification of cancers
US20230203485A1 (en) Methods for modulating mhc-i expression and immunotherapy uses thereof
WO2019008412A1 (en) Utilizing blood based gene expression analysis for cancer management
WO2019079647A2 (en) Statistical ai for advanced deep learning and probabilistic programing in the biosciences
WO2019008415A1 (en) Exosome and pbmc based gene expression analysis for cancer management
WO2019008414A1 (en) Exosome based gene expression analysis for cancer management
US20230075965A1 (en) Uses of biomarkers for improving immunotherapy
US20220154282A1 (en) Detection means, compositions and methods for modulating synovial sarcoma cells
WO2023091587A1 (en) Systems and methods for targeting covid-19 therapies
US11815509B2 (en) Cell line and uses thereof

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 23736708

Country of ref document: EP

Kind code of ref document: A1