WO2024119090A2 - Méthodes de traitement de la leucémie myéloïde aiguë - Google Patents

Méthodes de traitement de la leucémie myéloïde aiguë Download PDF

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WO2024119090A2
WO2024119090A2 PCT/US2023/082102 US2023082102W WO2024119090A2 WO 2024119090 A2 WO2024119090 A2 WO 2024119090A2 US 2023082102 W US2023082102 W US 2023082102W WO 2024119090 A2 WO2024119090 A2 WO 2024119090A2
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lsc
aml
identified
cd11b
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WO2024119090A3 (fr
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Craig T. Jordan
Clayton Smith
Austin E. GILLEN
Shanshan Pei
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The Regents Of The University Of Colorado, A Body Corporate
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    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/63—Compounds containing para-N-benzenesulfonyl-N-groups, e.g. sulfanilamide, p-nitrobenzenesulfonyl hydrazide
    • A61K31/635—Compounds containing para-N-benzenesulfonyl-N-groups, e.g. sulfanilamide, p-nitrobenzenesulfonyl hydrazide having a heterocyclic ring, e.g. sulfadiazine
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K31/00—Medicinal preparations containing organic active ingredients
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7052—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides
    • A61K31/706—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom
    • A61K31/7064—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines
    • A61K31/7076—Compounds having saccharide radicals and heterocyclic rings having nitrogen as a ring hetero atom, e.g. nucleosides, nucleotides containing six-membered rings with nitrogen as a ring hetero atom containing condensed or non-condensed pyrimidines containing purines, e.g. adenosine, adenylic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4614—Monocytes; Macrophages
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/462—Cellular immunotherapy characterized by the effect or the function of the cells
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464402—Receptors, cell surface antigens or cell surface determinants
    • A61K39/464429—Molecules with a "CD" designation not provided for elsewhere
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
    • A61P35/00—Antineoplastic agents
    • A61P35/02—Antineoplastic agents specific for leukemia
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • 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
    • G01N33/57426—Specifically defined cancers leukemia
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the cancer treated
    • A61K2239/48—Blood cells, e.g. leukemia or lymphoma
    • 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

  • Acute myeloid leukemia is a blood cancer in which the bone marrow of a subject makes abnormal myeloblasts, red blood cells, or platelets.
  • AML is one of the most common forms of acute leukemia in adults.
  • the build-up of AML cells in bone marrow and blood can rapidly lead to infection, anemia, excessive bleeding and death.
  • BCL-2 inhibitor venetoclax has recently emerged as an important component of therapy for acute myeloid leukemia (AML).
  • venetoclax can induce responses in approximately 60-70% of older previously untreated AML patients, many of whom are unfit for conventional induction therapy.
  • the present disclosure provides a method of treating acute myeloid leukemia (AML) in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression Attorney Docket No.: UNCO-049/001WO (300978-2220) measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) administering to the subject a combination of at least one BCL- 2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent when at least one m-LSC is identified; or administering to the subject a combination of at least one BCL-2 inhibitor and at least one hypomethylating
  • AML acute myeloid leukemia
  • the present disclosure provides a method of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) identifying that the subject will not be responsive to the treatment when the presence of at least one m-LSC is identified; or identifying that the subject will be responsive to the treatment when no m-LSCs are identified.
  • m-LSC monocytic leukemia stem cell
  • step (a) further comprises measuring the expression of at least CD117, CD244 and CD64, wherein a cell is identified as an m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) further comprises measuring the expression of at least CD117, CD244, CD64 and GPR56, wherein a cell is identified as an m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, and GPR56-.
  • the present disclosure provides methods of treating acute myeloid leukemia (AML) in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; and c) administering to the subject a treatment comprising at least one CD70-targeting agent when at least one CD70+ m-LSC is identified, preferably wherein the treatment further comprises at least one BCL-2 inhibitor and at least one hypomethylating agent when no CD70+ m-LSCs are identified.
  • AML acute myeloid leukemia
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a CD70-targeting agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic Attorney Docket No.: UNCO-049/001WO (300978-2220) leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; and c) identifying that the subject will be responsive to the treatment when the presence of at least one CD70+ m-LSC is identified.
  • m-LSC leukemia stem cell
  • step (a) further comprises measuring the expression of at least CD117, CD244 and CD64, wherein a cell is identified as a CD70+ m- LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and CD70+.
  • step (a) further comprises measuring the expression of at least CD117, CD244, CD64, and GPR56- wherein a cell is identified as a CD70+ m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, GPR56-, and CD70+.
  • the at least one CD70-targeting agent is: i) an anti-CD70 antibody, preferably wherein the anti-CD70 antibody is cusatuzumab; ii) an anti-CD70 immunotherapy, preferably wherein the immunotherapy comprises CAR-T and/or NK Cells that are directed specifically at CD70; or iii) an agent that blocks CD70 signaling, preferably wherein the agent that blocks CD70 signaling prevents binding of CD27 and CD70.
  • the at least one m-LSC targeting agent is an agent modulates one-carbon metabolism, is an agent that modulates purine synthesis, is an agent that modulates pyrimidine synthesis, or any combination thereof.
  • the at least one m-LSC targeting agent is selected from methotrexate, brequinar and cladribine.
  • the at least one hypomethylating agent is selected from azacitidine and decitabine.
  • the at least one BCL-2 inhibitor is selected from venetoclax and navitoclax.
  • step (a) comprises performing PCR, high-throughput sequencing, next generation sequencing, Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, [0016] Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • the subject is a subject having AML who has not received any treatment for AML.
  • the subject is a subject having AML who has received previously received at least one AML treatment.
  • the at least one AML treatment comprises a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • identifying that a subject will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent comprises identifying that the subject will have a durable remission after receiving the treatment of a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • identifying that a subject will not be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent comprises identifying that the subject will be refractory to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent and/or that the subject will suffer a relapse after treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • the biological sample comprises blood, a bone marrow biopsy, a bone marrow aspirate, a biopsy of a chloroma, a tissue biopsy, cerebrospinal fluid or any combination thereof.
  • step (a) further comprises performing a transcriptomic analysis of the plurality of cells in the sample; and step (b) further comprises identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on transcriptomic analysis performed in step (a), wherein a cell is identified as an m-LSC based on at least one of the following: i) an upregulation in the expression of at least one of biomarker from Table 5; ii) the expression of at least one biomarker from Table 1A; iii) an upregulation in the expression of at least one GSEA gene signature from Table 1B.
  • m-LSC monocytic leukemia stem cell
  • the transcriptomic analysis is performed using RNA sequencing.
  • CITE- SEQ. is performed using CITE- SEQ.
  • Attorney Docket No.: UNCO-049/001WO (300978-2220) [0027] Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this disclosure belongs. In the Specification, the singular forms also include the plural unless the context clearly dictates otherwise; as examples, the terms “a,” “an,” and “the” are understood to be singular or plural and the term “or” is understood to be inclusive.
  • an element means one or more element.
  • the word “comprising,” or variations such as “comprises” or “comprising,” will be understood to imply the inclusion of a stated element, integer or step, or group of elements, integers or steps, but not the exclusion of any other element, integer or step, or group of elements, integers or steps. About can be understood as within 10%, 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%, 0.5%, 0.1%, 0.05%, or 0.01% of the stated value.
  • FIGS.1A and 1B show the characterization of developmentally heterogeneous LSCs.
  • FIGS.1A and 1B show a summary of engraft% data for Uni-MMP AML-12, AML-08, and AML-14 and Multi-MMP AML-07, and AML-13.
  • Bulk stands for unsorted bulk tumor; prim stands for primitive subpopulation; mono stands for monocytic subpopulation. Each dot represents a mouse.
  • Two-tailed Mann-Whitney tests Attorney Docket No.: UNCO-049/001WO (300978-2220) were used for comparing two groups, Kruskal-Wallis tests were used when comparing more than two groups. ns, not significant.
  • FIGS.2A-2C show the differing nature of disease arising from prim and mono subpopulations of Multi-MMP AMLs.
  • FIG.2A is a diagram depicting workflow used to isolate primitive and monocytic subpopulations of AML-07 for injecting into PDX mice and subsequent determination of their relative sensitivity to the VEN+AZA regimen in vivo.
  • FIG. 2B shows the design of the VEN/AZA in vivo regimen (VEN, 100mg/kg, oral gavage (OG), 5 days/week x 2 weeks; AZA, 3mg/kg, Intraperitoneal injection (IP), 3 days/week x 2 weeks).
  • VEN 100mg/kg
  • OG oral gavage
  • AZA 3mg/kg
  • IP Intraperitoneal injection
  • FIG.3A is a diagram describing the leukemogenesis process of Uni-MMP and Multi-MMP AML patients and their predicted clinical responses to VEN+AZA therapy.
  • FIG.3B, FIG.3C, and FIG.3D are representative cases of Uni-MMP and Multi-MMP AML patients received VEN+AZA therapy.
  • the left panels depict sorting strategies for obtaining diagnosis-prim (Dx-prim) and diagnosis-mono (Dx-mono) subpopulations from diagnosis bulk disease (Dx-bulk), as well as relapse-mono (Rl-mono) subpopulations from relapse bulk disease (Rl-bulk) when applicable.
  • the right panel shows engraftment percentage (engraft%) in NSG-S mice determined by hCD45+/mCD45-% within total viable bone marrow cells. Each dot represents a unique mouse. Median +/- interquartile. Mann-Whitney tests. ns, not significant; *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001.
  • FIG.3C shows Patient 12 (Pt-12), a case of Multi- MMP AML presenting predominant monocytic relapse in 12 months after receiving VEN+AZA therapy.
  • FIG.3D shows Patient 69 (Pt-69), a case of Multi-MMP AML presenting quick relapse in 3 months post VEN+AZA therapy.
  • prim and mono subpopulations were gated using a different sorting strategy based on primitive antigen CD34 and monocytic antigen CD11b.
  • the CD34+/CD11b-, CD34+/CD11b+, and CD34- /CD11b-pp subpopulations were sorted as Dx-prim-A, Dx-prim-B, and Dx-mono Attorney Docket No.: UNCO-049/001WO (300978-2220) subpopulations, respectively.
  • the CD34-/CD11b-pp subpopulation was sorted as the predominant Rl-mono subpopulation.
  • FIG.3G shows remission duration of VEN/AZA relapsed AML patients.
  • the cohort contains five patients who sustained a monocytic phenotype between diagnosis and relapse (mono to mono), four patients transited from a primitive phenotype at diagnosis to monocytic phenotype at relapse (prim to mono), 15 patients sustained a primitive phenotype between diagnosis and relapse (prim to prim), and one patient transited from a monocytic phenotype at diagnosis to primitive phenotype at relapse (mono to prim).
  • Each dot represents a unique patient.
  • Median duration time of both groups are shown in days.
  • FIGS.3B C, D, and F box plots represent median +/- interquartile.
  • FIGS.3B-D Kruskal-Wallis test was used.
  • FIG.3F one-tailed Mann- Whitney test is used. ns, not significant.
  • FIGS.4A-4B show identification of the m-LSC immunophenotype.
  • FIG.4A is stacking bar graphs showing relative proportion of each subcluster within the highlighted “myeloid” region of the UMAP.
  • FIG.4B shows protein expression of surface antigens CD45, CD34, CD4, CD14, CD11b, and CD36.
  • the m-LSC enriched region is highlighted by dotted lines.
  • FIGS.5A-5C show functional validation of m-LSC immunophenotypes.
  • FIGS.5A- 5C show gating strategies for sorting various subpopulations of Mono AML-16, Mono AML-20, and Multi-MMP AML-07 for determining their m-LSC activities using xenograft studies. The sorting is detailed in FIGS.12A-12C. Briefly, for AML-16 and AML-20, FIG.
  • FIG.5A Live/mono
  • FIG.5B Live/mono/CD34-/CD4+/CD14-
  • FIG.5C Live/mono/CD34- /CD4+/CD14+
  • FIG.5D Live/mono/CD34-/CD4+/CD14-/CD11b-CD36-
  • FIG.5E Live/mono/CD34-/CD4+/CD14-/CD11b+CD36+
  • FIG. 6A-6H shows molecular properties and targeting of m-LSCs.
  • FIG. 6A shows impact of TYMS inhibitor methotrexate (MTX), DHODH inhibitor brequinar (BRQ), and purine analogue cladribine (CdA) on colony-forming unit (CFU) potential of CD34+ HSPCs isolated from two normal mobilized peripheral blood samples (MPB-1, 2) versus mono-LSCs isolated from mono AML-20 and mono AML-16.
  • FIG.6B shows representative images of CFU assays measuring the efficacy of CdA on normal CD34+ HSPCs and m-LSCs.
  • FIG. 6D show the impact of chemotherapy agents AraC, DNR, DHODH inhibitor brequinar (BRQ), and TYMS inhibitor methotrexate (MTX) on the CFU potential of m-LSCs, p-LSCs and CD34+ HSPCs.
  • FIG. 6E shows a diagram depicting workflow and design of the regimens used for in vivo treatment. IP, intraperitoneal; OG, oral gavage..
  • FIG.6F shows the impact of in vivo VEN + AZA, CdA, or triple-drug combo treatments on the bone marrow tumor burden of PDX. Engraft% was determined by % of hCD45+/mCD45 ⁇ cells within total viable bone marrow mononuclear cells.
  • FIG. 6G shows the impact of VEN+AZA, CdA or combo treatments on the marrow tumor burden of PDX.
  • hCD45+ count was determined by direct quantification of hCD45+/mCD45- cells within a set volume of marrow harvest using flow cytometry.
  • FIG. 6H shows the impact of VEN+AZA, CdA or combo treatments on the spleen tumor burden of PDX. Engraft% was determined by % of hCD45+/mCD45- cells within total viable spleen mononuclear cells.
  • hCD45+ count was determined by direct quantification of hCD45+/mCD45- cells within a set volume of spleen harvest using flow cytometry. Each dot represents a unique mouse.
  • FIGS.7A-7C show a model depicting interplay between LSC potential, immunophenotype, disease evolution, and clinical response to the venetoclax plus azacitidine therapy in AML patients.
  • FIG.7A shows a first group of AML patients with disease solely driven by p-LSCs captured at various maturation stages with predominant Prim, MMP, and predominant Mono immunophenotypes.
  • FIG.7B shows a second group of AML patients with multi-LSC activities (contains both p-LSCs and m-LSCs) presenting Prim, MMP, or Mono immunophenotypes depending on the relative degrees of maturation and ratio of the two Attorney Docket No.: UNCO-049/001WO (300978-2220) diseases rooted from the two distinct LSC subtypes.
  • FIG.7C shows a last group of AML patients with disease solely driven by m-LSCs usually presenting a predominant mono immunophenotype due to the inherent nature of m-LSCs that are already resting at a relatively more mature promyelocyte-like developmental stage.
  • FIGS.8A-8F show sorting strategies for determining m-LSC immunophenotype.
  • FIGS.8A-8C show the immunophenotyping of A, B, C, D, and E subpopulations sorted from Mono AML-16 (FIG.8A), Mono AML-20 (FIG.8B), and Multi-MMP AML-07 (FIG.8C), and used for injection into NSG-S mice to determine their m-LSC potential.
  • FIGS.8D-8F show the tumor burden in primary and secondary transplants shown by human CD45 and mouse CD45 staining.
  • FIGS.9A and 9B show that M5 but not M4 patients showed significantly higher refractory rate to VEN/AZA therapy.
  • FIG.9A shows a circular pie chart showing numbers of patients identified in different FAB subclasses.
  • FIG.9B shows bar graphs showing percentage of patients had refractory or non-refractory responses to VEN+AZA therapy according to the ELN criteria .
  • FIGS.10A and 10B show the analysis of CD70+ m-LSCs in AML samples.
  • FIG.10A is a graph showing the percentage of total blast cells and percentage of m-LSCs that were CD70+ in the AML samples.
  • FIG.10B shows the percentage of total blast cells and percentage of m-LSCs that were CD70+ in AML samples that were either resistant to treatment with a combination of venetoclax and azacitidine or responsive to treatment with a combination of venetoclax and azacitidine.
  • DETAILED DESCRIPTION OF THE INVENTION [0040] Acute myeloid leukemia is a blood cancer that is one of the most commonly diagnosed types of leukemia in adults. It is estimated that there will be approximately 11,000 deaths from AML in the United States in 2020, along with 20,000 newly diagnosed cases.
  • the average age of a person diagnosed with acute myeloid leukemia is about 68, with most cases occurring after the age of 45.
  • acute myeloid leukemia has also been diagnosed in younger patients, including children.
  • Prognosis for patients diagnosed with acute myeloid leukemia is generally poor, with a long-term survival of only 40-50% in younger patients and a median overall survival of less than one year for older patients.
  • New therapies aimed at supplementing the standard remission induction regimen of infusional Attorney Docket No.: UNCO-049/001WO (300978-2220) cytarabine with intermittent dosing of an anthracycline has provided some improvement to treatment outcomes, but the improvements have been modest.
  • LSCs leukemia stem cells
  • LSCs leukemia stem cells
  • LSCs While multiple strategies derive from robust experimental evidence, as yet improvement of clinical outcomes due to direct eradication of LSCs has remained limited.
  • LSC populations derived from human AML patients demonstrate significant intra- and inter-patient heterogeneity in developmental stages and immunophenotypes, which is thought to be in at least part driven by underlying genetic diversity.
  • recent studies have demonstrated that the existence of heterogeneous underlying LSC populations can mediate differing therapeutic outcomes of conventional chemotherapy and venetoclax-based therapies.
  • the present disclosure is based on, inter alia, the discovery a particular subpopulation of leukemia stems cells, denoted as monocytic leukemia stem cells (m-LSCs) that can be used to predict a subject’s response to treatment with a combination of a BCL-2 inhibitor (e.g. venetoclax) and a hypomethylating agent (e.g. azacitidine, cytarabine and decitabine).
  • a BCL-2 inhibitor e.g. venetoclax
  • a hypomethylating agent e.g. azacitidine, cytarabine and decitabine
  • the present disclosure provides, inter alia, a method of determining if a subject having AML will be responsive to treatment with a combination of at least one BCL- 2 inhibitor and at least one hypomethylating agent based on whether m-LSCs are identified in samples from a subject, as well as methods of treating AML in a subject comprising administering a particular treatment to the subject based on whether a sample from a subject contains m-LSCs.
  • the present disclosure is based on, inter alia, the discovery a particular subpopulation of leukemia stems cells, denoted as CD70+ monocytic leukemia stem cells (m- LSCs) that can be used to predict a subject’s response to treatment with a CD70-targeting agent.
  • CD70+ monocytic leukemia stem cells m- LSCs
  • the present disclosure provides, inter alia, a method of determining if a subject having AML will be responsive to treatment with a CD70-target agent based on whether CD70+ m-LSCs are identified in samples from a subject, as well as methods of treating AML in a subject comprising administering a particular treatment to the subject based on whether a sample from a subject contains CD70+ m-LSCs.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method comprising: a) measuring the expression of at least Attorney Docket No.: UNCO-049/001WO (300978-2220) CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) identifying that the subject will not be responsive to the treatment when the presence of at least one m-LSC is identified; or identifying that the subject will be responsive to the treatment when no m-LSCs are identified.
  • m-LSC monocytic leukemia stem cell
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14 and CD36) and step (b) can further comprise identifying the presence of at least one m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and CD64
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD64+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and GPR56-.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and GPR56
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and GPR56-.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of m-LSCs in the plurality of cells based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) comparing the number and/or percentage of m-LSCs identified in step (b) to a predetermined cutoff value; d) identifying that the subject will not be responsive to the treatment when the number and/or percentage of m-LSCs is equal to or greater than the predetermined cutoff value; or identifying that the subject will be Attorney Docket No.:
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14 and CD36) and step (b) can further comprise identifying the number and/or percentage of m-LSCs in the plurality of cells is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and CD64
  • step (b) can comprise identifying the number and/or percentage of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD64+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and GPR56-.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and GPR56
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and GPR56-.
  • a predetermined cutoff value can be determined by comparing the number and/or percentage of m-LSCs in samples obtained from one or more subjects known to be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent and the number and/or percentage of m-LSCs samples from one or more subjects known to be not responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • the skilled artisan can used methods known in the art to make such comparisons and determine a suitable predetermined cutoff value that will allow for the discrimination between responders and non-responders.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic leukemia stem cell (m- LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ Attorney Docket No.: UNCO-049/001WO (300978-2220) m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; c) identifying that the subject will not be responsive to the treatment when the presence of at least one m-LSC is identified; or identifying that the subject will be responsive to the treatment when no m-LSCs are identified.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14, CD36, and CD70) and step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+, CD117-, CD244- and CD64+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and CD64
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+, and CD64+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+, CD117-, CD244-, CD64+ and GPR56-.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, CD70 and GPR56
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+ and GPR56-.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36, and CD70 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of CD70+ m-LSCs in the plurality of cells based on the expression measured in step (a), wherein a cell is identified as a CD70+ m- LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; c) comparing the number and/or percentage of CD70+ m-LSCs identified in step (b) to a predetermined cutoff value; d) identifying that the subject will not be responsive to the treatment when the number and/or percentage of CD70+ m-LSCs is equal to or greater than the
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14, CD36, and CD70) and step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+, CD117-, CD244- and CD64+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and CD64
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+, and CD64+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+, CD117-, CD244-, CD64+ and GPR56-.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, CD70 and GPR56
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD70+ and GPR56-.
  • a predetermined cutoff value can be determined by comparing the number and/or percentage of CD70+ m-LSCs in samples obtained from one or more subjects known to be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent and the number and/or percentage of CD70+ m-LSCs samples from one or more subjects known to be not responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • the skilled artisan can used methods known in the art to make such comparisons and determine a suitable predetermined cutoff value that will allow for the discrimination between responders and non-responders.
  • the preceding methods can further comprise a step of providing a treatment recommendation to a clinician and/or subject. Accordingly, if a subject is identified as a subject who will not be responsive to a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method can further comprise providing a treatment recommendation that comprises administering an alternative treatment.
  • the alternative treatment can comprise administering to the subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent.
  • the alternative treatment can not include at least one BCL-2 and/or not include at least one hypomethylating agent.
  • identifying that a subject will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent comprises identifying that the subject will have a durable remission after receiving the treatment of a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • identifying that a subject will not be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent comprises identifying that the subject will be refractory to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent and/or that the subject will suffer a relapse after treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a CD70-targeting agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, and CD70+; c) identifying that the subject will be responsive to the treatment when at least one CD70+ m-LSC is identified.
  • m-LSC monocytic leukemia stem cell
  • the preceding method can further comprise identifying that the subject will not be responsive to the treatment when no CD70+ m-LSCs are identified.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14, CD36 and CD70) and step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, CD64 and CD70
  • step (b) can comprise identifying the presence of at least one Attorney Docket No.: UNCO-049/001WO (300978-2220) CD70+ m-LSC, wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD64+ and CD70+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, GPR56- and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, GPR56 and CD70
  • step (b) can comprise identifying the presence of at least one CD70+ m-LSC, wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, GPR56- and CD70+.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a CD70-targeting agent: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of CD70+ m-LSCs in the plurality of cells based on the expression measured in step (a), wherein a cell is identified as a CD70+ m- LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; c) comparing the number and/or percentage of CD70+ m-LSCs identified in step (b) to a predetermined cutoff value; d) identifying that the subject will be responsive to the treatment when the number and/or percentage of CD70+ m-LSCs is greater than or equal to the predetermined cutoff value.
  • the preceding method can further comprise identifying that the subject will not be responsive to the treatment when the number and/or percentage of CD70+ m-LSCs is less than the predetermined cutoff value.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e.
  • step (b) can further comprise identifying the number and/or percentage of CD70+ m-LSCs in the plurality of cells is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and CD70.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, CD64 and CD70
  • step (b) can comprise identifying the number and/or percentage of CD70+ m-LSCs, wherein a cell is identified as a CD70+ m- LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD64+ and CD70.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, GPR56- and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, GPR56 and CD70
  • step (b) can comprise identifying the presence of at least one CD70+ m-LSC, wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, GPR56- and CD70+.
  • a predetermined cutoff value can be determined by comparing the number and/or percentage of CD70+ m-LSCs in samples obtained from one or more subjects known to be responsive to treatment with a CD70- targeting agent and the number and/or percentage of CD70+ m-LSCs samples from one or more subjects known to be not responsive to treatment with a CD70-targeting agent.
  • the skilled artisan can used methods known in the art to make such comparisons and determine a suitable predetermined cutoff value that will allow for the discrimination between responders and non-responders.
  • the preceding methods can further comprise a step of providing a treatment recommendation to a clinician and/or subject.
  • the method can further comprise providing a treatment recommendation that comprises administering a CD70-targeting agent.
  • the treatment recommendation can comprise administering to the subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least CD-70 targeting agent.
  • identifying that a subject will not be responsive to treatment with a CD70-targeting agent comprises identifying that the subject will be refractory to treatment with the at least one CD70-targeting agent and/or that the subject will suffer a relapse after treatment with the at least one CD70-targeting agent.
  • identifying that a subject will be responsive to treatment with a CD70-targeting agent comprises identifying that the subject will have a durable remission after receiving the treatment of at CD70-targeting agent.
  • Methods of treating AML comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), Attorney Docket No.: UNCO-049/001WO (300978-2220) wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) administering to the subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating
  • m-LSC monocytic leukemia stem cell
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14 and CD36) and step (b) can further comprise identifying the presence of at least one m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and CD64
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD64+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and GPR56-.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and GPR56
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and GPR56-.
  • the present disclosure provides methods of treating AML in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of m-LSCs in the plurality of cells based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) comparing the number and/or percentage of m-LSCs identified in step (b) to a predetermined cutoff value; d) administering to the subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent when the number and/or percentage of m-LSCs is equal to or greater than the predetermined cutoff value; or administering to the subject a combination of at least one BCL-2 inhibitor and at
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14 and CD36) and step (b) can further comprise identifying the number and/or percentage of m-LSCs in the plurality of cells is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and CD64
  • step (b) can comprise identifying the number and/or percentage of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD64+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and GPR56-.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36 and GPR56
  • step (b) can comprise identifying the presence of at least m-LSC wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and GPR56-.
  • the present disclosure provides methods of treating a subject having AML, the method comprising administering to the subject having AML a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent.
  • the present disclosure provides methods of treating a subject having AML, wherein the subject has AML that exhibits the presence of at least one m-LSC, the method comprising administering to said subject at least one m-LSC targeting agent.
  • the present disclosure provides a methods of treating a subject having AML, wherein the subject has AML that exhibits a number and/or percentage of m-LSC cells that is greater than or equal to a predetermined cutoff value, the method comprising administering to said subject at least one m-LSC targeting agent.
  • the present disclosure provides methods of treating a subject having AML, wherein the subject has AML that exhibits the presence of at least one m-LSC, the method comprising administering to said subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent.
  • the present disclosure provides a methods of treating a subject having AML, wherein the subject has AML that exhibits a number and/or percentage of m-LSC cells that is greater than or equal to a predetermined cutoff value, the method comprising administering to said Attorney Docket No.: UNCO-049/001WO (300978-2220) subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent.
  • the present disclosure provides methods of treating AML in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; c) administering to the subject a treatment comprising at least one CD70-targeting agent when at least one CD70+ m-LSC is identified.
  • m-LSC monocytic leukemia stem cell
  • the treatment can further comprise at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14, CD36 and CD70+) and step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, CD64 and CD70+
  • step (b) can comprise identifying the presence of at least one CD70+ m-LSC wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD64+ and CD70+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, GPR56- and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, GPR56 and CD70
  • step (b) can comprise identifying the presence of at least one CD70+ m-LSC, wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, GPR56- and CD70+.
  • the present disclosure provides methods of treating AML in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of CD70+ m-LSCs in the plurality of cells based on the expression measured in step (a), wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b- Attorney Docket No.: UNCO-049/001WO (300978-2220) , CD14-, CD36- and CD70+; c) comparing the number and/or percentage of CD70+ m-LSCs identified in step (b) to a predetermined cutoff value; d) administering to the subject treatment comprising at least one CD70-targeting agent when the number and/or percentage of CD70+ m-LSCs is equal to or greater than the predetermined cut
  • the treatment can further comprise at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244 and CD64 (i.e. in addition to CD34, CD4, CD11b, CD14, CD36 and CD70) and step (b) can further comprise identifying the number and/or percentage of CD70+ m-LSCs in the plurality of cells is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, CD64 and CD70
  • step (b) can comprise identifying the number and/or percentage of CD70+ m-LSCs, wherein a cell is identified as a CD70+ m- LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD64+ and CD70+.
  • step (a) can further comprise measuring the expression of at least one of CD117, CD244, CD64, and GPR56 (i.e.
  • step (b) can further comprise identifying the presence of at least one CD70+ m-LSC is identified based on the immunophenotype of CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, GPR56- and CD70+.
  • step (a) can comprise measuring the expression of CD34, CD4, CD11b, CD14, CD36, GPR56 and CD70
  • step (b) can comprise identifying the presence of at least one CD70+ m-LSC, wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, GPR56- and CD70+.
  • the present disclosure provides methods of treating a subject having AML, the method comprising administering to the subject having AML a treatment comprising at least one anti-CD70 target agent, wherein the subject has at least one CD70+ m-LSCs.
  • the treatment further comprises a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • the present disclosure provides methods of treating a subject having AML, the method comprising administering to the subject having AML a treatment comprising at least one anti-CD70 target agent, wherein the subject has AML that exhibits a number of percentage of CD70+ m-LSCs that is greater than or equal to a predetermined cutoff value.
  • the treatment further comprises a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • m-LSCs monocytic leukemia stem cells
  • m-LSCs can be identified based on the novel immunophenotype of: CD34-, CD4+, CD11b-, CD14- and CD36-.
  • this immunophenotype can optionally be further supplemented with one or more makers selected from CD117-, CD244- and CD64+.
  • the user performing the method can measure the expression of CD34, CD4, CD11b, CD14 and CD36 (and optionally one or more of CD117, CD244 and CD64) in cells from a sample from the subject in order to determine whether m-LSCs are present in the sample, and optionally, the percentage and/or number of m-LSCs in the sample.
  • the CD34-, CD4+, CD11b-, CD14- and CD36- immunophenotype can be optionally further supplemented with one or more markers selected from CD117-, CD244-, CD64+ and GPR56.
  • the user performing the method can measure the expression of CD34, CD4, CD11b, CD14 and CD36 (and optionally one or more of CD117, CD244, CD64 and GPR56) in cells from a sample from the subject in order to determine whether m-LSCs are present in the sample, and optionally, the percentage and/or number of m-LSCs in the sample.
  • the expression of the biomarkers described above, or any other biomarker describe herein, can be accomplished using any suitable method known in the art by the skilled artisan.
  • Such methods include, but are not limited to, PCR, high-throughput sequencing, next generation sequencing, Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • PCR high-throughput sequencing
  • next generation sequencing Northern Blot
  • RT-PCR reverse transcription PCR
  • qPCR real-time PCR
  • quantitative PCR quantitative PCR
  • qRT-PCR quantitative PCR
  • flow cytometry flow cytometry
  • mass spectrometry microarray analysis
  • digital droplet PCR Western Blot
  • CITE-SEQ Cellular Indexing of Transcriptomes and Epitopes by Sequencing
  • a transcriptomic feature that identifies an m-LSC can be an upregulation in the expression of at least one of the biomarkers put forth in Table 5. As would be appreciated by the skilled artisan, an upregulation corresponds to an expression level that is greater than a control expression value seen in other types of cells. [00106] In some aspects of the methods of the present disclosure, a transcriptomic feature that identifies an m-LSC can be at least one of the biomarkers, or any combination of the biomarkers, put forth in Table 1A.
  • a transcriptomic feature that identifies an m-LSC can be an upregulation in at least one of the GSEA gene signatures put forth in Table 1B.
  • the skilled artisan would readily appreciate the biomarkers of each of the GSEA gene signatures put forth in Table 1B.
  • Table 1B – GSEA gene signatures upregulated in m-LSCs Any of the transcriptomic features put forth in Tables 1A, 1B and 5 can be combined together in any combination.
  • an m-LSC cell may be identified by the upregulation of two of the biomarkers put forth in Table 1A and three of the biomarkers put forth in Table 5.
  • identifying an m-LSC using the transcriptomic features described herein can comprise measuring the expression of the one or more biomarkers that make up the transcriptomic feature.
  • This measurement of expression can be accomplished using any suitable method known in the art by the skilled artisan.
  • Such methods include, but are not limited to, PCR, high-throughput sequencing, next generation sequencing, Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, RNA sequencing, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • Identifying an m-LSC using the transcriptomic features described herein can also comprise performing a transcriptomic analysis using any of the standard methods known in the art for transcriptomic analysis, including, but not limited to the methods described herein, such as CITE-SEQ.
  • Identification of CD70+ m-LSCs [00114] From the descriptions of the methods presented herein, it is appreciated that the methods of the present disclosure incorporate a step of identifying at least one, the number of, and/or the percentage of CD70+ monocytic leukemia stem cells (m-LSCs) in a plurality of cells in a sample from a subject.
  • a step of identifying at least one CD70+ m-LSC in a plurality of cells can result in the identification of no CD70+ m-LSCs (i.e. the user can determine that there are actually no CD70+ m-LSCs present in the plurality of cells).
  • m-LSCs can be identified based on the novel immunophenotype of: CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+.
  • this immunophenotype can optionally be further supplemented with one or more makers selected from CD117-, CD244- and CD64+.
  • the user performing the method can measure the expression of CD34, CD4, CD11b, CD14, CD36 and CD70 (and optionally one or more of CD117, CD244 and CD64) in cells from a sample from the subject in order to determine whether CD70+ m-LSCs are present in the sample, and optionally, the percentage and/or number of CD70+ m-LSCs in the sample.
  • this immunophenotype can optionally be further supplemented with one or more makers selected from CD117-, CD244-, CD64+, and GPR56-.
  • the user performing the method can measure the expression of CD34, CD4, CD11b, CD14, CD36 and CD70 (and optionally one or more of CD117, CD244, CD64 and GPR56) in cells from a sample from the subject in order to determine whether CD70+ m- LSCs are present in the sample, and optionally, the percentage and/or number of CD70+ m- LSCs in the sample.
  • biomarkers described above, or any other biomarker describe herein can be accomplished using any suitable method known in the art by the skilled artisan. Such methods include, but are not limited to, PCR, high-throughput sequencing, next generation sequencing, Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • CD70+ m-LSCs can be alternatively or further identified by one or more transcriptomic features described herein.
  • a transcriptomic feature that identifies a CD 70+ m-LSC can be an upregulation in the expression of at least one of the biomarkers put forth in Table 5. As would be appreciated by the skilled artisan, an upregulation corresponds to an expression level that is greater than a control expression value seen in other types of cells.
  • a transcriptomic feature that identifies a CD70+ m-LSC can be at least one of the biomarkers, or any combination of the biomarkers, put forth in Table 1A.
  • Any of the transcriptomic features put forth in Tables 1A, 1B and 5 can be combined together in any combination.
  • a CD70+ m-LSC cell may be identified by the upregulation of two of the biomarkers put forth in Table 1A and three of the biomarkers put forth in Table 5, in addition to the measurement of CD70 expression.
  • identifying a CD70+ m-LSC using the transcriptomic features described herein can comprise measuring the expression of the one or more biomarkers that make up the transcriptomic feature. This measurement of expression can be accomplished using any suitable method known in the art by the skilled artisan.
  • Identifying a CD70+ m-LSC using the transcriptomic features described herein can also comprise performing a transcriptomic analysis using any of the standard methods known in the art for transcriptomic analysis, including, but not limited to the methods described herein, such as CITE-SEQ.
  • hypomethylating agents are agents that inhibit DNA methylation.
  • a hypomethylating agent can be selected from azacitidine, cytarabine and decitabine.
  • a hypomethylating agent can be any hypomethylating agent known in the art.
  • a hypomethylating agent can be azacitidine: derivative, salt or ester thereof.
  • azacitidine may be identified by any one of the following names: 5- Azacytidine, Azacytidine, Ladakamycin, 4-Amino-1- ⁇ -D-ribofuranosyl-s-triazin-2(1H)-one, U-18496, CC-486 and 4-Amino-1- ⁇ -D-ribofuranosyl-1,3,5-triazin-2(1H)-one.
  • azacitidine may be identified as CAS No.320-67-2.
  • a hypomethylating agent can be decitabine: , or a pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • decitabine may be identified by any one of the following names: 5-aza-2'- deoxycytidine, 4-Amino-1-(2-deoxy- ⁇ -D-erythro-pentofuranosyl)-1,3,5-triazin-2(1H)-one, 5- Aza-2 ⁇ -deoxycytidine, 5-Azadeoxycytidine, 2-Desoxy-5-azacytidine and 2 ⁇ -Deoxy-5- Attorney Docket No.: UNCO-049/001WO (300978-2220) azacytidine.
  • decitabine may be identified as CAS No.2353-33-5.
  • a hypomethylating agent can be replaced by cytarabine: , or a pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • cytarabine may be identified by any one of the following names: 4-amino-1-[(2R,3S,4S,5R)- 3,4-dihydroxy-5- (hydroxymethyl)oxolan-2-yl] pyrimidin-2-one, Aracytidine and cytosine arabinoside .
  • cytarabine may be identified as CAS No.147-94-4.
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and cytarabine, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m- LSC) based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) identifying that the subject will not be responsive to the treatment when the presence of at least one m-LSC is identified; or identifying that the subject will be responsive to the treatment when no m-LSCs are identified.
  • m- LSC monocytic leukemia stem cell
  • the present disclosure provides methods of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and cytarabine, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of m-LSCs in the plurality of Attorney Docket No.: UNCO-049/001WO (300978-2220) cells based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) comparing the number and/or percentage of m-LSCs identified in step (b) to a predetermined cutoff value; d) identifying that the subject will not be responsive to the treatment when the number and/or percentage of m-LSCs is equal
  • the present disclosure provides methods of treating AML in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) administering to the subject a combination of at least one BCL-2 inhibitor, cytarabine, and at least one m-LSC targeting agent when at least one m-LSC is identified; or administering to the subject a combination of at least one BCL-2 inhibitor and cytarabine when no m-LSCs are identified.
  • m-LSC monocytic leukemia stem cell
  • the present disclosure provides methods of treating AML in a subject, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the number and/or percentage of m-LSCs in the plurality of cells based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) comparing the number and/or percentage of m-LSCs identified in step (b) to a predetermined cutoff value; d) administering to the subject a combination of at least one BCL-2 inhibitor, cytarabine, and at least one m-LSC targeting agent when the number and/or percentage of m-LSCs is equal to or greater than the predetermined cutoff value; or administering to the subject a combination of at least one
  • a BCL-2 inhibitor can be selected from venetoclax and navitoclax. In some aspects of the methods presented herein, a BCL-2 inhibitor can be any BCL-2 inhibitor known in the art. Attorney Docket No.: UNCO-049/001WO (300978-2220) [00136] In some aspects, a BCL-2 inhibitor can be venetoclax: pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • venetoclax may be identified by any one of the following names: GDC-0199, ABT-199, RG-7601, 4-(4- ⁇ [2-(4-Chlorophenyl)-4,4-dimethyl-1- cyclohexen-1-yl]methyl ⁇ -1-piperazinyl)-N-( ⁇ 3-nitro-4-[(tetrahydro-2H-pyran-4- ylmethyl)amino]phenyl ⁇ sulfonyl)-2-(1H-pyrrolo[2,3-b]pyridin-5-yloxy)benzamide, Venclexta and Venclyxto.
  • a BCL-2 inhibitor can be navitoclax: pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • navitoclax may be identified by any one of the following names: ABT263, ABT-263 and 4-(4- ⁇ [2-(4-Chlorophenyl)-5,5- dimethylcyclohex-1-en-1-yl]methyl ⁇ piperazin-1-yl)-N-(4- ⁇ [(2R)-4-(morpholin-4-yl)-1- (phenylsulfanyl)butan-2-yl]amino ⁇ -3-(trifluoromethanesulfonyl)benzene-1- Attorney Docket No.: UNCO-049/001WO (300978-2220) sulfonyl)benzamide.
  • navitoclax may be identified as CAS No.923564-51-6.
  • a BCL-2 inhibitor can be BGB-11417.
  • a BCL-2 inhibitor can be ZN-d5.
  • CD70-targeting agents can be at least one of: i) an anti-CD70 antibody; ii) an anti-CD70 immunotherapy, preferably wherein the immunotherapy comprises CAR-T and/or NK Cells that are directed specifically at CD70; iii) an agent that blocks CD70 signaling, preferably wherein the agent that blocks CD70 signaling prevents binding of CD27 and CD70.
  • a CD70-targeting agent can be cusatuzumab.
  • immunotherapy can comprise administering a therapeutically effective amount of at least one antibody, at least one checkpoint inhibitor, at least one chimeric antigen receptor-modified T-Cell (CAR-T cell), or any combination thereof. Immunotherapy can comprise adoptive cell transfer therapy.
  • an immunotherapy can be an immunotherapy that specifically targets CD70. Accordingly, a non-limiting example of an immunotherapy that specifically targets at least one monocytic antigen can be a CAR-T cell that comprises a chimeric antigen receptor comprising an antigen binding domain that binds to CD70.
  • an m-LSC targeting agent can be an agent that modulates one-carbon metabolism.
  • an m-LSC targeting agent can be an agent that modulates at least one of purine synthesis and pyrimidine synthesis.
  • An agent that modulates one-carbon metabolism is selected from methotrexate, brequinar and cladribine.
  • an m-LSC targeting agent can be cladribine: Attorney Docket No.: UNCO-049/001WO (300978-2220) , or a pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • cladribine may be identified by any one of the following names: 5-(6-Amino- 2-chloro-purin-9-yl)-2-(hydroxymethyl)oxolan-3-ol, 2-Chloro-2 ⁇ -deoxyadenosine, 2-Chloro- 2-Chlorodeoxyadenosine.
  • cladribine may be identified as CAS No.4291-63-8.
  • an m-LSC targeting agent can be brequinar: pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • brequinar may be identified by any one of the following names: 6-fluoro-2- (2'-fluoro-1,1'-biphenyl-4-yl)-3-methyl-4-quinolinecarboxylic acid, Biphenquinate and BPQ. As would be appreciated by the skilled artisan, brequinar may be identified as CAS No. 96187-53-0. Attorney Docket No.: UNCO-049/001WO (300978-2220) [00151]
  • an m-LSC targeting agent can be methotrexate: pharmaceutically acceptable salt, analog, derivative, salt or ester thereof.
  • methotrexate may be identified by any one of the following names: (2S)-2-[(4- ⁇ [(2,4-Diaminopteridin-6- yl)methyl](methyl)amino ⁇ benzoyl)amino]pentanedioic acid, MTX, 4-Amino-N10- methylpteroylglutamic acid and N-[p-[[2,4-Diamino-6- pteridinyl)methyl]methylamino]benzoyl]-L-(+)-glutamic acid.
  • methotrexate may be identified as CAS No.59-05-2.
  • an m-LSC targeting agent can be an agent that inhibits MCL1.
  • agents that inhibit MCL1 are VU661013 and S63845.
  • an m-LSC targeting agent can be an immunotherapy.
  • an m-LSC targeting therapy can be an antifolate.
  • antifolates include methotrexate, pralatrexate and pemetrexed.
  • immunotherapy can comprise administering a therapeutically effective amount of at least one antibody, at least one checkpoint inhibitor, at least one chimeric antigen receptor-modified T-Cell (CAR-T cell), or any combination thereof.
  • Immunotherapy can comprise adoptive cell transfer therapy.
  • an immunotherapy can be an immunotherapy that specifically targets at least one monocytic antigen, including, but not limited to CD64 and LILRB4.
  • a non-limiting example of an immunotherapy that specifically targets at least one monocytic antigen can be a CAR-T cell that comprises a chimeric antigen receptor comprising an antigen binding domain that binds to CD64 and/or LILRB4.
  • antibody herein is used in the broadest sense and encompasses various antibody structures, including but not limited to monoclonal antibodies, polyclonal antibodies, multispecific antibodies (e.g., bispecific antibodies), and antibody fragments so long as they exhibit the desired antigen-binding activity.
  • An antibody that binds to a target Attorney Docket No.: UNCO-049/001WO (300978-2220) refers to an antibody that is capable of binding the target with sufficient affinity such that the antibody is useful as a diagnostic and/or therapeutic agent in targeting the target.
  • an antibody that binds to a target has a dissociation constant (Kd) of ⁇ 1 ⁇ , ⁇ 100 nM, ⁇ 10 nM, ⁇ 1 nM, ⁇ 0.1 nM, ⁇ 0.01 nM, or ⁇ 0.001 nM (e.g. 10 8 M or less, e.g. from 10 8 M to 10 13 M, e.g., from 10 9 M to 10 13 M).
  • Kd dissociation constant
  • an anti-target antibody binds to an epitope of a target that is conserved among different species.
  • a "blocking antibody” or an “antagonist antibody” is one that partially or fully blocks, inhibits, interferes, or neutralizes a normal biological activity of the antigen it binds.
  • an antagonist antibody may block signaling through an immune cell receptor (e.g., a T cell receptor) so as to restore a functional response by T cells (e.g., proliferation, cytokine production, target cell killing) from a dysfunctional state to antigen stimulation.
  • An "agonist antibody” or “activating antibody” is one that mimics, promotes, stimulates, or enhances a normal biological activity of the antigen it binds.
  • Agonist antibodies can also enhance or initiate signaling by the antigen to which it binds.
  • agonist antibodies cause or activate signaling without the presence of the natural ligand.
  • an agonist antibody may increase memory T cell proliferation, increase cytokine production by memory T cells, inhibit regulatory T cell function, and/or inhibit regulatory T cell suppression of effector T cell function, such as effector T cell proliferation and/or cytokine production.
  • An "antibody fragment” refers to a molecule other than an intact antibody that comprises a portion of an intact antibody that binds the antigen to which the intact antibody binds.
  • CAR-T cells are T cells that are genetically modified to stably express at least one chimeric antigen receptor (CAR).
  • a CAR can comprise an extracellular domain, transmembrane domain and a cytoplasmic domain.
  • a CAR can comprise an antigen binding domain.
  • An antigen binding domain can be located in an extracellular domain. In some aspects of the methods of the present disclosure, the antigen binding domain binds to at least one AML cell surface protein.
  • the antigen binding domain binds to CD64 and/or LILRB4.
  • a CAR can also comprise an Attorney Docket No.: UNCO-049/001WO (300978-2220) extracellular spacer (hinge) domain.
  • An extracellular spacer can be located in an extracellular domain.
  • a CAR can comprise a signaling domain.
  • a signaling domain can be a T-cell activation domain.
  • a signaling domain can be located in a cytoplasmic domain.
  • a CAR can comprise at least one costimulatory domain.
  • a CAR can comprise at least two costimulatory domains.
  • a CAR can comprise at least three costimulatory domains.
  • a costimulatory domain can be located in a cytoplasmic domain.
  • CAR-T cells can be autologous with respect to a subject. In some aspects, CAR-T cells can be allogeneic with respect to a subject. [00163] In some aspects of the methods of the present disclosure, CAR-T cells may be administered either alone, or as a pharmaceutical composition in combination with diluents and/or with other components such as IL-2 or other cytokines or cell populations. Briefly, pharmaceutical compositions can comprise a plurality of CAR-T cells in combination with one or more pharmaceutically or physiologically acceptable carriers, diluents or excipients.
  • compositions may comprise buffers such as neutral buffered saline, phosphate buffered saline and the like; carbohydrates such as glucose, mannose, sucrose or dextrans, mannitol; proteins; polypeptides or amino acids such as glycine; antioxidants; chelating agents such as EDTA or glutathione; adjuvants (e.g., aluminum hydroxide); and preservatives.
  • CAR-T cells and related compositions can be administered to a subject intravenously.
  • a CAR-T cell can comprise a chimeric antigen receptor.
  • a chimeric antigen receptor can comprise an antigen binding domain.
  • An antigen binding domain can bind to CD64 and/or LILRB4.
  • the term “subject” includes human and non-human animals, as well as cell lines, cell cultures, tissues, and organs.
  • the subject is a mammal.
  • the mammal can be e.g., a human or appropriate non-human mammal, such as primate, mouse, rat, dog, cat, cow, horse, goat, camel, sheep or a pig.
  • the subject can also be a bird or fowl.
  • the subject is a human.
  • the term “subject in need thereof” refers, both of which refer to a subject having a disease or having an increased risk of developing the disease.
  • a “subject” includes a mammal.
  • the mammal can be e.g., a human or appropriate non-human mammal, such as primate, mouse, rat, dog, cat, cow, horse, goat, camel, sheep or a pig.
  • the subject can also be a bird or fowl.
  • the mammal is a human.
  • a subject in need thereof can be one who has been previously diagnosed or identified as having a disease or disorder Attorney Docket No.: UNCO-049/001WO (300978-2220) disclosed herein.
  • a subject in need thereof can also be one who is suffering from a disease or disorder disclosed herein.
  • a subject in need thereof can be one who has an increased risk of developing such disease or disorder relative to the population at large (i.e., a subject who is predisposed to developing such disorder relative to the population at large).
  • a subject in need thereof can have a refractory or resistant a disease or disorder disclosed herein (i.e., a disease or disorder disclosed herein that does not respond or has not yet responded to treatment). The subject may be resistant at start of treatment or may become resistant during treatment.
  • the subject in need thereof received and failed all known effective therapies for a disease or disorder disclosed herein.
  • the subject in need thereof received at least one prior therapy.
  • the subject is a human.
  • the subject is a subject having AML who has not received any treatment for AML.
  • the subject is a subject having AML who has received previously received at least one AML treatment.
  • the at least one treatment comprises a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • a subject is a subject who has at least one m-LSC present in their population of AML cells.
  • a subject is a subject whose AML cell population contains a percentage of m-LSCs that are greater than a predetermined cutoff percentage.
  • a subject is a subject whose AML cell population contains a number of m-LSCs that are greater than a predetermined cutoff number.
  • a subject is a subject who has at least one CD70+ m-LSC present in their population of AML cells.
  • a subject is a subject whose AML cell population contains a percentage of CD70+ m-LSCs that are greater than a predetermined cutoff percentage.
  • a subject is a subject whose AML cell population contains a number of CD70+ m-LSCs that are greater than a predetermined cutoff number.
  • Attorney Docket No.: UNCO-049/001WO (300978-2220) [00173] Samples [00174] In some aspects of the methods of the present disclosure, a sample can comprise blood, a bone marrow biopsy, a bone marrow aspirate, a biopsy of a chloroma, a tissue biopsy, cerebrospinal fluid or any combination thereof. [00175] In some aspects, a sample can be a bone marrow biopsy. [00176] In some aspects, a sample can be a bone marrow aspirate.
  • a sample can be a biopsy of a chloroma.
  • General Definitions [00179] As used herein, the expressions “one or more of A, B, or C,” “one or more A, B, or C,” “one or more of A, B, and C,” “one or more A, B, and C,” “selected from the group consisting of A, B, and C”, “selected from A, B, and C”, and the like are used interchangeably and all refer to a selection from a group consisting of A, B, and/or C, i.e., one or more As, one or more Bs, one or more Cs, or any combination thereof, unless indicated otherwise.
  • any description of a method of treatment includes use of the agents to provide such treatment as is described herein. It is to be further understood, unless otherwise stated, any description of a method of treatment includes use of the agents to prepare a medicament to treat such condition.
  • the treatment includes treatment of human or non-human animals including rodents and other disease models used herein.
  • the term “treating” or “treat” describes the management and care of a patient for the purpose of combating a disease, condition, or disorder and includes the administration of an agent described in the present disclosure, or a pharmaceutically acceptable salt, polymorph or solvate thereof, to alleviate the symptoms or complications of a disease, condition or disorder, or to eliminate the disease, condition or disorder.
  • the term “treat” can also include treatment of a cell in vitro or an animal model. It is to be appreciated that references to “treating” or “treatment” include the alleviation of established symptoms of a condition.
  • Treating” or “treatment” of a state, disorder or condition therefore includes: (1) preventing the appearance of clinical symptoms of the state or delaying the appearance of clinical symptoms of the state, disorder or condition developing in a human that may be afflicted with or predisposed to the state, disorder or condition but does not yet experience or display clinical or subclinical symptoms of the state, disorder or condition, (2) inhibiting the state, disorder or condition, i.e., arresting, reducing or delaying the development of the disease or a relapse thereof (in case of maintenance treatment) or at least one clinical or Attorney Docket No.: UNCO-049/001WO (300978-2220) subclinical symptom thereof, or (3) relieving or attenuating the disease, i.e., causing regression of the state, disorder or condition or at least one of its clinical or subclinical symptoms.
  • an agent described in the present disclosure can or may also be used to prevent a relevant disease, condition or disorder, or used to identify suitable candidates for such purposes.
  • the term “preventing,” “prevent,” or “protecting against” describes reducing or eliminating the onset of the symptoms or complications of such disease, condition or disorder.
  • the term “pharmaceutically acceptable” refers to those compounds, anions, cations, materials, compositions, carriers, and/or dosage forms which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of human beings and animals without excessive toxicity, irritation, allergic response, or other problem or complication, commensurate with a reasonable benefit/risk ratio.
  • the agents described herein can be administered to a subject in at least one therapeutically effective amount.
  • the term “therapeutically effective amount” refers to an amount of a pharmaceutical agent to treat, ameliorate, or prevent an identified disease or condition, or to exhibit a detectable therapeutic or inhibitory effect.
  • the effect can be detected by any assay method known in the art.
  • the precise effective amount for a subject will depend upon the subject’s body weight, size, and health; the nature and extent of the condition; and the therapeutic or combination of therapeutics selected for administration.
  • Therapeutically effective amounts for a given situation can be determined by routine experimentation that is within the skill and judgment of the clinician.
  • a clinician can also determine the therapeutically effective amounts of the agents described herein using established dosing and administration protocols for the agents described herein.
  • the therapeutically effective amount can be estimated initially either in cell culture assays, e.g., of neoplastic cells, or in animal models, usually rats, mice, rabbits, dogs, or pigs.
  • the animal model may also be used to determine the appropriate concentration range and route of administration. Such information can then be used to determine useful doses and routes for administration in humans.
  • Therapeutic/prophylactic efficacy and toxicity may be determined by standard pharmaceutical procedures in cell cultures or experimental animals, e.g., ED50 (the dose therapeutically effective in 50 % of the population) and LD 50 (the dose lethal to 50 % of the Attorney Docket No.: UNCO-049/001WO (300978-2220) population).
  • the dose ratio between toxic and therapeutic effects is the therapeutic index, and it can be expressed as the ratio, LD50/ED50.
  • Pharmaceutical compositions that exhibit large therapeutic indices are preferred.
  • the dosage may vary within this range depending upon the dosage form employed, sensitivity of the patient, and the route of administration.
  • Dosage and administration are adjusted to provide sufficient levels of the active agent(s) or to maintain the desired effect.
  • Factors which may be taken into account include the severity of the disease state, general health of the subject, age, weight, and gender of the subject, diet, time and frequency of administration, drug combination(s), reaction sensitivities, and tolerance/response to therapy.
  • Long-acting pharmaceutical compositions may be administered every 3 to 4 days, every week, or once every two weeks depending on half-life and clearance rate of the particular formulation.
  • pharmaceutically acceptable salts refer to derivatives of the agents described herein wherein the agent is modified by making acid or base salts thereof.
  • Examples of pharmaceutically acceptable salts include, but are not limited to, mineral or organic acid salts of basic residues such as amines, alkali or organic salts of acidic residues such as carboxylic acids, and the like.
  • the pharmaceutically acceptable salts include the conventional non-toxic salts or the quaternary ammonium salts of the parent agent formed, for example, from non-toxic inorganic or organic acids.
  • such conventional non-toxic salts include, but are not limited to, those derived from inorganic and organic acids selected from 2-acetoxybenzoic, 2-hydroxyethane sulfonic, acetic, ascorbic, benzene sulfonic, benzoic, bicarbonic, carbonic, citric, edetic, ethane disulfonic, 1,2-ethane sulfonic, fumaric, glucoheptonic, gluconic, glutamic, glycolic, glycollyarsanilic, hexylresorcinic, hydrabamic, hydrobromic, hydrochloric, hydroiodic, hydroxymaleic, hydroxynaphthoic, isethionic, lactic, lactobionic, lauryl sulfonic, maleic, malic, mandelic, methane sulfonic, napsylic, nitric, oxalic, pamoic, pantothenic, phenylacetic, phosphoric,
  • the pharmaceutically acceptable salt is a sodium salt, a potassium salt, a calcium salt, a magnesium salt, a diethylamine salt, a choline salt, a meglumine salt, a benzathine salt, a tromethamine salt, an ammonia salt, an arginine salt, or a lysine salt.
  • compositions include hexanoic acid, cyclopentane propionic acid, pyruvic acid, malonic acid, 3-(4-hydroxybenzoyl)benzoic acid, cinnamic acid, 4-chlorobenzenesulfonic acid, 2-naphthalenesulfonic acid, 4-toluenesulfonic Attorney Docket No.: UNCO-049/001WO (300978-2220) acid, camphorsulfonic acid, 4-methylbicyclo-[2.2.2]-oct-2-ene-1-carboxylic acid, 3- phenylpropionic acid, trimethylacetic acid, tertiary butylacetic acid, muconic acid, and the like.
  • the present disclosure also encompasses salts formed when an acidic proton present in the parent agent either is replaced by a metal ion, e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion; or coordinates with an organic base such as ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.
  • a metal ion e.g., an alkali metal ion, an alkaline earth ion, or an aluminum ion
  • organic base such as ethanolamine, diethanolamine, triethanolamine, tromethamine, N-methylglucamine, and the like.
  • the ratio of the agent to the cation or anion of the salt can be 1:1, or any ratio other than 1:1, e.g., 3:1, 2:1, 1:2, or 1:3.
  • references to pharmaceutically acceptable salts include solvent addition forms (solvates) or crystal forms (polymorphs) as defined herein, of the same salt.
  • the term “refractory” as used herein, is used in its broadest sense to refer to instances in which the disease present in a subject does not respond to a particular therapy, i.e. the therapy provides no or decreased clinical benefit to that particular subject.
  • the term “combination therapy” or “co-therapy” includes the administration of an agent disclosed herein, or a pharmaceutically acceptable salt, polymorph or solvate thereof, and at least a second agent as part of a specific treatment regimen intended to provide the beneficial effect from the co-action of these therapeutic agents.
  • the beneficial effect of the combination includes, but is not limited to, pharmacokinetic or pharmacodynamic co-action resulting from the combination of therapeutic agents.
  • the term “temporal proximity” refers to that administration of one therapeutic agent occurs within a time period before or after the administration of another therapeutic agent, such that the therapeutic effect of the one therapeutic agent overlaps with the therapeutic effect of the other therapeutic agent. In some embodiments, the therapeutic effect of the one therapeutic agent completely overlaps with the therapeutic effect of the other therapeutic agent. In some embodiments, “temporal proximity” means that administration of one therapeutic agent occurs within a time period before or after the administration of another therapeutic agent, such that there is a synergistic effect between the one therapeutic agent and the other therapeutic agent.
  • Temporal proximity may vary according to various factors, including but not limited to, the age, gender, weight, genetic background, medical condition, disease history, and treatment history of the subject to which the therapeutic agents are to be administered; the disease or condition to be treated or ameliorated; the therapeutic outcome to be achieved; the dosage, dosing frequency, and dosing duration of the therapeutic agents; the pharmacokinetics and pharmacodynamics of the therapeutic agents; and the route(s) through Attorney Docket No.: UNCO-049/001WO (300978-2220) which the therapeutic agents are administered.
  • “temporal proximity” means within 15 minutes, within 30 minutes, within an hour, within two hours, within four hours, within six hours, within eight hours, within 12 hours, within 18 hours, within 24 hours, within 36 hours, within 2 days, within 3 days, within 4 days, within 5 days, within 6 days, within a week, within 2 weeks, within 3 weeks, within 4 weeks, with 6 weeks, or within 8 weeks.
  • multiple administration of one therapeutic agent can occur in temporal proximity to a single administration of another therapeutic agent.
  • temporal proximity may change during a treatment cycle or within a dosing regimen.
  • a method of treating acute myeloid leukemia (AML) in a subject comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) administering to the subject a combination of at least one BCL-2 inhibitor, at least one hypomethylating agent, and at least one m-LSC targeting agent when at least one m-LSC is identified; or administering to the subject a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent when no m-LSCs are identified.
  • m-LSC monocytic leukemia stem cell
  • Embodiment 2 A method of identifying if a subject having AML will be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14 and CD36 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as an m-LSC if it is at least CD34-, CD4+, CD11b-, CD14- and CD36-; c) identifying that the subject will not be responsive to the treatment when the presence of at least one m-LSC is identified; or identifying that the subject will be responsive to the treatment when no m-LSCs are identified.
  • m-LSC monocytic leukemia stem cell
  • Embodiment 3a The method of embodiment 1 or embodiment 2, wherein step (a) further comprises measuring the expression of at least CD117, CD244 and CD64, wherein a cell is identified as an m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) further comprises measuring the expression of at least CD117, CD244 and CD64, wherein a cell is identified as an m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244- and CD64+.
  • step (a) further comprises measuring the expression of at least CD117, CD244, CD64 and GPR56, wherein a cell is identified as an m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+, and GPR56-.
  • Embodiment 4 The method of any one of the preceding embodiments, wherein the at least one m-LSC targeting agent is an agent modulates one-carbon metabolism, is an agent that modulates purine synthesis, is an agent that modulates pyrimidine synthesis, or any combination thereof.
  • Embodiment 6 The method of any one of the preceding embodiments, wherein the at least one m-LSC targeting agent is selected from methotrexate, brequinar and cladribine.
  • Embodiment 6 The method of any one of the preceding embodiments, wherein the at least one hypomethylating agent is selected from azacitidine and decitabine.
  • Embodiment 7. The method of any one of the preceding embodiments, wherein the at least one BCL-2 inhibitor is selected from venetoclax and navitoclax.
  • step (a) comprises performing PCR, high-throughput sequencing, next generation sequencing, Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • step (a) comprises performing PCR, high-throughput sequencing, next generation sequencing, Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • RT-PCR reverse transcription PCR
  • qPCR real-time PCR
  • quantitative PCR quantitative PCR
  • qRT-PCR quantitative PCR
  • Embodiment 11 The method of embodiment 10, wherein the at least one AML treatment comprises a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • Embodiment 12 The method of any one of the preceding embodiments, wherein identifying that a subject will be responsive to treatment with a combination of at least one Attorney Docket No.: UNCO-049/001WO (300978-2220) BCL-2 inhibitor and at least one hypomethylating agent comprises identifying that the subject will have a durable remission after receiving the treatment of a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • Embodiment 13 The method of any one of the preceding embodiments, wherein identifying that a subject will not be responsive to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent comprises identifying that the subject will be refractory to treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent and/or that the subject will suffer a relapse after treatment with a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • Embodiment 14 Embodiment 14.
  • the biological sample comprises blood, a bone marrow biopsy, a bone marrow aspirate, a biopsy of a chloroma, a tissue biopsy, cerebrospinal fluid or any combination thereof.
  • Embodiment 15 The method of embodiment 14, wherein the sample is a bone marrow biopsy.
  • Embodiment 16 The method of embodiment 14, wherein the sample is a bone marrow aspirate.
  • Embodiment 17. The method of embodiment 14, wherein the sample is a biopsy of a chloroma.
  • step (a) further comprises performing a transcriptomic analysis of the plurality of cells in the sample; and step (b) further comprises identifying the presence of at least one monocytic leukemia stem cell (m-LSC) based on transcriptomic analysis performed in step (a), wherein a cell is identified as an m-LSC based on at least one of the following: i) an upregulation in the expression of at least one of biomarker from Table 5; ii) the expression of at least one biomarker from Table 1A; iii) an upregulation in the expression of at least one GSEA gene signature from Table 1B.
  • m-LSC monocytic leukemia stem cell
  • Embodiment 21 A method of treating acute myeloid leukemia (AML) in a subject, the method comprising: Attorney Docket No.: UNCO-049/001WO (300978-2220) a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic leukemia stem cell (m-LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ m-LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; c) administering to the subject a treatment comprising at least one CD70-
  • AML acute myeloid leukemia
  • Embodiment 22 A method of identifying if a subject having AML will be responsive to treatment with a CD70-targeting agent, the method comprising: a) measuring the expression of at least CD34, CD4, CD11b, CD14, CD36 and CD70 in a plurality of cells in a sample from the subject; b) identifying the presence of at least one CD70+ monocytic leukemia stem cell (m- LSC) based on the expression measured in step (a), wherein a cell is identified as a CD70+ m- LSC if it is at least CD34-, CD4+, CD11b-, CD14-, CD36- and CD70+; c) identifying that the subject will be responsive to the treatment when the presence of at least one CD70+ m-LSC is identified.
  • m- LSC monocytic leukemia stem cell
  • Embodiment 23 The method of embodiment 21 or embodiment 22, wherein step (a) further comprises measuring the expression of at least CD117, CD244 and CD64, wherein a cell is identified as a CD70+ m-LSC is identified if it is at least CD34-, CD4+, CD11b-, CD14-, CD36-, CD117-, CD244-, CD64+ and CD70+.
  • Embodiment 24 Embodiment 24.
  • the at least one CD70-targeting agent is: i) an anti-CD70 antibody, preferably wherein the anti-CD70 antibody is cusatuzumab; ii) an anti-CD70 immunotherapy, preferably wherein the immunotherapy comprises CAR-T and/or NK Cells that are directed specifically at CD70; or iii) an agent that blocks CD70 signaling, preferably wherein the agent that blocks CD70 signaling prevents binding of CD27 and CD70.
  • the at least one hypomethylating agent is selected from azacitidine and decitabine.
  • step (a) comprises performing PCR, high-throughput sequencing, next generation sequencing, Attorney Docket No.: UNCO-049/001WO (300978-2220) Northern Blot, reverse transcription PCR (RT-PCR), real-time PCR (qPCR), quantitative PCR, qRT-PCR, flow cytometry, mass spectrometry, microarray analysis, digital droplet PCR, Western Blot, [00225] Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-SEQ), or any combination thereof.
  • Embodiment 28 The method of any one of the preceding embodiments, wherein the subject is a subject having AML who has not received any treatment for AML.
  • Embodiment 29 The method any one of the preceding embodiments, wherein the subject is a subject having AML who has received previously received at least one AML treatment.
  • Embodiment 30 The method of embodiment 29, wherein the at least one AML treatment comprises a combination of at least one BCL-2 inhibitor and at least one hypomethylating agent.
  • Embodiment 31 Embodiment 31.
  • the biological sample comprises blood, a bone marrow biopsy, a bone marrow aspirate, a biopsy of a chloroma, a tissue biopsy, cerebrospinal fluid or any combination thereof.
  • Embodiment 32 The method of embodiment 31, wherein the sample is a bone marrow biopsy.
  • Embodiment 33 The method of embodiment 31, wherein the sample is a bone marrow aspirate.
  • Embodiment 34 The method of embodiment 31, wherein the sample is a biopsy of a chloroma.
  • Embodiment 35 Embodiment 35.
  • step (a) further comprises performing a transcriptomic analysis of the plurality of cells in the sample; and step (b) further comprises identifying the presence of at least one CD70+ monocytic leukemia stem cell (m-LSC) based on transcriptomic analysis performed in step (a), wherein a cell is identified as a CD70+ m-LSC based on at least one of the following: i) an upregulation in the expression of at least one of biomarker from Table 5; ii) the expression of at least one biomarker from Table 1A; iii) an upregulation in the expression of at least one GSEA gene signature from Table 1B.
  • m-LSC monocytic leukemia stem cell
  • Mono specimens displayed very few blast-like cells ( ⁇ 1%) and a predominant monocyte-like profile (CD45-bright, SSC-high relative to lymphocytes). Mono specimens down-regulated CD34 and CD117, and up-regulated monocytic markers to varying degrees, including CD64. Finally, the MMP specimens were characterized as having discrete blast-like and monocytic-like subpopulations (range, 26%-79% for primitive and 14%-35% for monocytic), which were evident in both the CD45/SSC gate and phenotypic analysis of stem/progenitor makers and monocytic antigens contained a mixture of monocytic and primitive cells, occupying the middle range of the developmental spectrum ().
  • Multi-MMP the second type of MMP AML was Attorney Docket No.: UNCO-049/001WO (300978-2220) designated “Multi-MMP,” where readily detectable LSC activity was evident in both prim and mono subpopulations (FIG.1B).
  • WES whole-exome sequencing
  • Multi-MMP AML arises due to underlying mutational variation, consistent with the understanding that phenotypically distinct subpopulations of LSCs can simultaneously exist in certain patients with AML .
  • Prim vs mono engrafted cells from two representative specimens (AML-07 and AML-13) consistently differed in their developmental spectrum.
  • the prim subpopulation was able to recapitulate the full developmental spectrum of disease, with both prim and mono cells evident in each transplanted mouse.
  • LSCs that initiate and drive disease in the monocytic Attorney Docket No.: UNCO-049/001WO (300978-2220) subpopulation demonstrated a more restricted developmental hierarchy that resides toward the mature end of the myeloid developmental spectrum and distinct resistance to VEN+AZA therapy.
  • This subclass of LSCs was designated as mono-LSCs (m-LSCs).
  • m-LSCs mono-LSCs
  • p-LSCs prim-LSCs
  • these findings demonstrate that heterogeneous LSC subpopulations with distinct developmental phenotypes co-reside in the same patient.
  • LSC heterogeneity gives rise to bulk tumor populations with differing therapeutic response in PDX models, demonstrating clinical significance.
  • Example 2 [00243] In the following non-limiting example, experiments were performed to predict clinical outcomes as a function of m-LSCs. Without wishing to be bound by theory, it was hypothesized that de novo AML patients would differ in pathogenesis and clinical outcome as a function of the presence of m-LSCs. As illustrated schematically in FIG.3A, it was predicted that upon receiving VEN+AZA therapy, Uni-MMP patients that initially presented with only p-LSCs should achieve more durable remission due to intrinsic reliance of p-LSCs on venetoclax target BCL-2. In contrast, Multi-MMP patients with a distinct m-LSC population were predicted to relapse relatively quickly with monocytic disease.
  • Pt-69 had chromosome 11 and 16 duplication events in the prim compartment at diagnosis that were not present at relapse, again consistent with the outgrowth of the genetically distinct monocytic Attorney Docket No.: UNCO-049/001WO (300978-2220) subclone.
  • data from Pt-65 also shows the outgrowth of genetically distinct monocytic clones at relapse marked by two KRAS mutations.
  • both of the KRAS mutations that were dominant at relapse were not readily detectable at 400 ⁇ sequencing depth in the diagnosis specimen and were seen only using higher resolution methods (droplet-digital PCR).
  • Example 3 In the following non-limiting example, m-LSC immunophenotypes were identified and characterized in primary AML specimens. CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by Sequencing) analysis was performed, allowing simultaneous measurement of protein-based surface antigens and RNA-based transcriptome analysis at a single cell level. CITE-seq analysis was performed on a cohort of 27 primary AML specimens containing immunophenotypically defined Prim, MMP, and Mono AMLs (listed in Table 3).
  • CITE-seq Cellular Indexing of Transcriptomes and Epitopes by Sequencing
  • the CITE-seq data was first analyzed using Clustifyr, an application that assigns phenotypes based on comparison to the transcriptome of normal human hematopoiesis (see Fu et al. F1000Res.2020;9:223).
  • This analysis classifies myeloid cells into HSPC, MPP, Early Promyelocyte-like, Late promyelocyte-like, Myelocyte-like, classical monocyte-like, and Nonclassical monocyte-like subclusters, and revealed the myeloid developmental spectrum within primary AML specimens.
  • the MMP group was also further divided into Uni- MMP and Multi-MMP subgroups based on each functional LSC activity, as measured by xenograft assay (FIG.4A).
  • the relative proportion of each myeloid subcluster within Prim, Uni-MMP, Multi-MMP, and Mono groups was highly concordant with expected identity.
  • the Prim group almost exclusively contained the highest proportion of the three LPSC cell types (quiescent, primed, and cycling), which reside at the apex of the myeloid developmental hierarchy.
  • the Mono group presented a developmental hierarchy with almost no LSPC cell types but was rather comprised of a dominant ProMono-like cell type, suggesting the latter could be enriched for m-LSCs.
  • KMT2A-r_LSC_signature A KMT2A-rearranged leukemia-specific LSC signature (KMT2A-r_LSC_signature; Table 4; see Somervailee et al. Cancer Cell 2006;10:257–68; see Somervaille et al.
  • Example 4 [00253] In the following non-limiting example, experiments were performed to functionally validate m-LSCs. A series of flow sorting and transplant studies to functionally validate the m-LSC immunophenotype of the CITE-seq analysis. Two mono specimens AML-16 and AML-20 were employed, from which various subpopulations of cells were isolated using expression of CD45, CD34, CD4, CD14, CD11b, and CD36 (FIGS.5A-B and FIGS.8A-8B). To avoid contamination from conventional CD34+ p-LSCs, the CD34- fraction was gated when validating the m-LSCs.
  • AML-20 some engraftment potential was detected in the CD14-, CD11b+, and CD36+ counterparts (FIG.5E), suggesting that in certain patients the developmental hierarchy of m-LSC-driven AMLs is shallower than others (e.g., AML-16).
  • FIG.5C, FIG.5F, FIG.8C and FIG.8F serial transplant experiments demonstrated that m-LSCs in this Multi-MMP AML were also exclusively enriched by the CD34-, CD14-, CD11b-, and CD36- immunophenotype.
  • CD4 was not included in this sort due to limited cell numbers. Together, these data revealed an m-LSC immunophenotype that was applicable to both Mono and Multi-MMP AMLs, entirely distinct from profiles previously described for the more conventional primitive LSCs (i.e. CD34+ and CD38-). [00255] To further explore the immunophenotype of m-LSCs, analytical flow cytometry was used to evaluate the expression of several additional cell surface antigens associated with stem cell activity. Both CD117 and CD244 have been shown to be frequently expressed specifically in CD34- AML specimens. However, there was no detectable expression of CD117 in any of the seven specimens that underwent functional evaluation for the presence of m-LSCs.
  • CD244 was only detected at low levels in two of seven specimens.
  • Expression of the monocytic marker, CD64 was also investigated, as this antigen was shown Attorney Docket No.: UNCO-049/001WO (300978-2220) to be prevalent in monocytic relapse.
  • CD64 was strongly expressed in six of seven specimens.
  • these results indicated that m- LSCs can be further identified using the immunophenotypic markers of CD117-, CD244-, and CD64+, in addition to those discussed above.
  • expression of another LSC marker, GPR56 was also evaluated. mRNA expression of GPR56 was almost absent in monocytic AML at both bulk and single-cell resolution.
  • Methotrexate (MTX), brequinar (BRQ), and cladribine (CdA) were selected based on their activities in inhibiting one-carbon metabolism enzymes DHFR and TYMS, pyrimidine synthesis enzyme DHODH, and purine-based DNA/RNA synthesis, respectively.
  • Coldrexate (MTX), brequinar (BRQ), and cladribine (CdA) were selected based on their activities in inhibiting one-carbon metabolism enzymes DHFR and TYMS, pyrimidine synthesis enzyme DHODH, and purine-based DNA/RNA synthesis, respectively.
  • Coldy- forming unit assays were performed on m-LSCs and p-LSCs isolated from Mono, Multi-MMP, and Prim specimens, along with normal CD34+ hematopoietic stem and progenitor cells (HSPC) from two healthy donors.
  • HSPC normal CD34+ hematopoietic stem and progenitor cells
  • CdA showed remarkable specificity against m-LSCs while sparing p-LSCs as well as normal HSPC controls. This selectivity was not seen by the other chemotherapy agents cytarabine and daunorubicin (FIG. 6C), suggesting the unique sensitivity of m-LSCs to CdA. In addition, CdA also outperformed BRQ and MTX in potency against m-LSCs (FIG.6D).
  • CdA was selected for in vivo proof-of concept studies in combination Attorney Docket No.: UNCO-049/001WO (300978-2220) with VEN+AZA in two functionally validated MMP AMLs.
  • Fig.6E Multi-MMP AML-13 and AML-07 were transplanted into NSG-S mice and treated with VEN+AZA alone, CdA alone, or the triple-drug combination in vivo.
  • Analysis of AML cells in both bone marrow and spleen demonstrated that the addition of CdA clearly improved the clearance of tumor that was otherwise resistant to VEN + AZA in both PDX models (Fig. 6F-6H).
  • Examples 1-5 describe the identification and characterization of a previously unrecognized type of human acute myeloid leukemia (AML) stem cell defined as “m-LSC.” This particular subclass of LSC is distinguished from more primitive subtypes by virtue of a unique immunophenotype (CD34-, CD4+, CD14-, CD11b-, and CD36-), a relatively narrow developmental profile that is limited to the creation of monocytic progeny, and a gene expression profile that is roughly analogous to normal human promyelocytes.
  • AML acute myeloid leukemia
  • m-LSC is distinct from the CD34- LSC populations described previously, where expression of both CD177 and CD244 were prevalent.
  • the molecular biology of m-LSCs differs from more primitive LSCs in that BCL-2 dependency seems to be largely dispensable, making this type of LSC resistant to treatment with venetoclax and azacytidine.
  • m-LSCs demonstrate selective reliance on one-carbon metabolism and purine/pyrimidine metabolism, adding to the importance of cellular metabolism in the context of AML pathogenesis and therapeutic resistance.
  • m-LSC reliance on purine metabolism mediates increased sensitivity to agents such as cladribine, a well-known purine analogue.
  • FIGS.7A-7C shows the tree as an analogy to describe developmental hierarchy of AML, where the underground roots represent LSCs and the branches above the ground symbolize more differentiated blasts.
  • FIG.7A a single class of more primitive LSCs (p-LSCs) may be present in newly diagnosed AML patients, with varying degrees of monocytic differentiation potential.
  • p-LSCs primitive LSCs
  • FIG.7B some newly diagnosed Multi-MMP AML patients present with at least two distinct subtypes of LSC with primitive vs. monocytic characteristics (p-LSC and m-LSC).
  • p-LSC and m-LSC primitive vs. monocytic characteristics
  • these patients would clinically be expected to respond and then relapse, or to be refractory to venetoclax-based therapies.
  • FIGS.7A-7C show the highest frequency of refractory disease.
  • FAB-M5 monocytic phenotypes
  • FAB-M4 myelomonocytic phenotypes
  • FIGS.7A-7C The novel model described in FIGS.7A-7C can be used to design future therapies.
  • Detection of any m-LSC population at diagnosis in a patient who is being considered for a venetoclax-based therapy may warrant consideration of additional therapies designed to selectively target monocytic population, in the hopes that relapse, which carries a very poor prognosis in this setting, can be avoided.
  • additional therapies designed to selectively target monocytic population, in the hopes that relapse, which carries a very poor prognosis in this setting, can be avoided.
  • Such potential agents include immunotherapies directed towards monocytic antigens such as CD64 and LILRB4, or small molecules that selectively impair unique biology of phenotypically monocytic AML.
  • MCL1 inhibitor drugs appear to be more active in the context of monocytic AML. The results provided herein demonstrate that m-LSCs depend on MCL1 for energy metabolism.
  • Normal CD34+ HSPCs were enriched from thawed MPB samples using the CD34 MicroBead kit (Miltenyi Biotec). Cells were cultured in complete serum-free media (SFM) in 37°C, 5% CO2 incubator. SFM is composed of IMDM (GIBCO), 20% BIT 9500 (STEMCELL Technologies), 10ug/ml LDL (Low Density Lipoprotein, Millipore), 55uM 2-Mercaptoethanol (GIBCO) and 1% Pen/Strep (GIBCO). Complete SFM were made by supplementing the SFM with FLT-3, IL-3 and SCF cytokines (PeproTech), each at 10 ng/ml.
  • SFM complete serum-free media
  • Colony-forming assays Freshly sorted m-LSCs from primary AMLs or prepared CD34+ HSPCs isolated from normal mobilized peripheral samples were plated in human methylcellulose (R&D systems) at about 100K/ml and 2K/ml, respectively. Small molecule inhibitors were directly added into the methylcellulose at the desired final concentration at the plating. Colonies were counted 2- 3 weeks after the initial plating.
  • NSG-S mice (NOD.Cg-Prkdcscid Il2rgtm1Wjl Tg(CMV- IL3,CSF2,KITLG)1Eav/MloySzJ) mice (The Jackson Laboratory) were used for xenograft studies in this study. Male or female mice ranging in age from 6 to 8 weeks were started on experiment. Littermates of the same sex were randomly assigned to experimental groups. NSG-S mice were pre-conditioned 24 hours prior to transplant with 30mg/kg busulfan (Alfa Aesar) via intraperitoneal (IP) injection.
  • busulfan Alfa Aesar
  • the busulfan stock was made fresh at 25 mg/ml in 100% DMSO, then the stock was diluted 1:10 in pre-warmed saline (0.9% NaCl) down to 2.5 mg/ml right before use.
  • the diluted busulfan solution was kept in 37°C water bath before IP injection to prevent precipitation of busulfan due to low solubility.
  • each subpopulation was sorted according to their percentage of total viable cells (detailed in Table 6). When the cell dose was less than 0.5e6/mouse, mononuclear cells isolated from bone marrow and spleens of na ⁇ ve NSG-S mice were used as carrier cells.
  • mice were then washed, pelleted, and resuspended in saline buffer to allow tail vein injection into NSG-S mice at 0.1ml per mouse. Fifteen minutes prior to injection, in vivo anti-human CD3 antibody (BioCell) was added at a final concentration of 1ug/e6 cells to prevent potential graft versus host disease. During all experiments, the weight of mice was approximately 20-30 grams with no animals losing greater than 10% body weight. The mice were kept in ventilated cages and given in vivo treatments when needed in the vivarium at University of Colorado. The majority of the experiments lasted for 6 to 12 weeks. At the end of the experiments, mice were euthanized using carbon dioxide.
  • in vivo anti-human CD3 antibody BioCell
  • Bone marrow and spleen were harvested, subjected to red blood cell lysis, and the mononuclear cells were stained with Attorney Docket No.: UNCO-049/001WO (300978-2220) human CD45, mouse CD45 antibodies, and DAPI to determine percentage of engraftment within viable cells. All animal work were performed in accordance with Institutional Animal Care and Use Committee protocol number 00308. [00284] In vivo treatments [00285] About 2-4 weeks post initial transplant, tumor burden in the bone marrow was determined to be above 5% in sentinel mice. Mice were then treated with various in vivo regimens as follows.
  • Venetoclax was given at 100mg/kg via oral gavage, five days/week for two weeks; Azacitidine was given at 3mg/kg via intraperitoneal injection, three days/week for two weeks; Cladribine was given at 10mg/kg via intraperitoneal injection, three days/week for two weeks. All treatments were given in the same two-week time window when stated together. [00286] CITE-seq sample preparation and library construction [00287] Mononuclear cell suspensions were prepared from freshly thawed primary AML specimens cryopreserved in liquid nitrogen.
  • cells were processed with the 10x Genomics 3’ dual index v3.1 library kit with feature barcoding technology for cell surface proteins. Briefly 10,000 cells were targeted from stock suspension of 1000 cells/ ⁇ l. Cells were processed following the protocol to generate 3’ gene expression libraries as well as Feature Barcode cell surface libraries. Both libraries were dual indexed, and samples were quantified by Qubit (Life Technologies) and assessed for size and quality by Tapestation (Agilent). Libraries were normalized and pooled for sequencing on a Novaseq 6000 (Illumina) for paired-end 2x150 bp sequencing. Targeted read depth for gene expression libraries was 100,000 reads/cell or ⁇ 500 million paired-end reads/library.
  • Targeted read depth for cell surface libraries was 40,000 reads/cell or 200 million paired end reads/library.
  • CITE-seq data pre-processing [00289] Raw sequencing data for gene expression, antibody derived tag (ADT; surface protein), and hashing libraries were processed using STARsolo 2.7.8a with the 10X Genomics GRCh38/GENCODE v32 genome and transcriptome reference (version GRCh38_2020A) or a TotalSeq barcode reference, as appropriate. Hashed samples were demultiplexed using GMM-Demux.
  • Scanpy and Seurat 4.1.1 were then used to generate uniform manifold approximation and projections from the TotalVI embeddings and perform exploratory analysis, data visualization, etc.
  • the myeloid subpopulation in the CITE-seq data was reannotated using scArches 0.5.7 and a leukemia reference dataset (see Zeng et al. Nat Med 2022;28: 1212–23).
  • the reference model was trained for 400 epochs based on the 3,000 most highly variable genes determined by scanpys’ pp.highly_variable_ genes() function.
  • CD34+_LSCs and KMT2A-r_LSCs were identified through scoring each individual cell using the AddModuleScore() function of the Seurat software and custom-generated candidate CD34+_LSC and KMT2A-r_LSC gene expression signatures, as stated in the main text.
  • WES Analysis [00293] WES libraries were generated using the Agilent SureSelect XT exome prep kit with 200 ng of input as per protocol (Agilent).
  • the probe used was SureSelect XT Human All Exon Attorney Docket No.: UNCO-049/001WO (300978-2220) V7 (Agilent). Libraries were normalized by Qubit (Invitrogen) and Tapestation (Agilent), and 2 ⁇ 150 bp reads were sequenced on a Novaseq 6000 (Illumina) to obtain 400 ⁇ coverage. Fastqc v0.11.9 was used to assess overall sequencing quality, and reads were trimmed using cutadapt (cutadapt, RRID:SCR_011841) v2.9 to remove the Illumina universal adapters, bases of poor quality (phred ⁇ 30), and any reads in which the minimum read length was ⁇ 10 base pairs in length.
  • Trimmed fastq files were then aligned to the GRCh38 p.13 genome using BWA v0.7.17 (BWA, RRID:SCR_010910).
  • Stringent quality control of alignments and read duplicate removal were performed using the Picard suite of tools v2.21.1 (Picard, RRID:SCR_006525) and samtools v1.8 (samtools, RRID:SCR_002105).
  • Variants were called on alignments using DeepVariant v1.0.0, followed by BCFtools (BCFtools, RRID:SCR_005227) v1.11 to filter variants of low quality. SNPs were removed if the raw unfiltered read depth was ⁇ 20 reads and the mapping quality ⁇ 30.
  • Pathway enrichment analysis was performed on metabolites that were ⁇ 1.2-fold higher in population D compared with E and with a P value of less than 0.1. All analyses were performed using the MetaboAnalyst 5.0 software (MetaboAnalyst, RRID:SCR_015539). [00296] Statistical Analysis [00297] Statistical analyses were performed in GraphPad Prism 9.3.1 (GraphPad Prism, RRID:SCR_002798). Median ⁇ interquartile range was used to describe summary statistics. One-tailed or two-tailed Mann–Whitney tests were used to compare two groups when applicable.
  • FIG.10A sows the percentage of total blast cells in each AML sample that were CD70+ (left side of graph) as well as the percentage of m-LSCs in each AML Sample that were CD70+ (right side of graph).
  • the results shown in FIG.10A demonstrate that CD70 is expressed on m-LSCs, with some samples exhibiting more than 50% m-LSCs that are CD70 positive.
  • FIG.10A shows the results from the analysis shown in FIG.10A based on whether the AML samples were obtained from patients that were sensitive to treatment with a combination of venetoclax and azacitidine or resistant to treatment with a combination of venetoclax and azacitidine.
  • FIG.10B shows the percentage of total blast cells and m-LSCs that were CD70+ in AML samples derived from Ven+Aza resistant samples and Ven+Aza sensitive samples. As shown in FIG.10B, patients who were sensitive to Ven+Aza treatment had a lower percentage of m-LSCs that were CD70+ as compared to patients that were Ven+Aza resistant. That is, the m-LSC populations of Ven+Aza resistant patients exhibited a higher percentage of cells that were CD70+.
  • these results indicate that patients who exhibit higher levels of CD70+ m-LSCs may be more resistant to treatment with Ven+Aza, and therefore would be benefit from alternative treatments, including those that incorporate the use of a CD70-targeting agent. Moreover, these results indicate that a patient’s response to treatment with a combination of venetoclax and azacitidine can be predicted by determining the number of CD70+ m-LSCs (thus, CD34-, CD4+, CD11b-, CD14-, CD36-, and CD70+ cells) in biological sample obtained from the patient.

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Abstract

La présente divulgation concerne des méthodes de traitement de la leucémie myéloïde aiguë (LMA) et des méthodes de détermination répondant à des régimes de traitement de LMA, les méthodes comprenant l'identification de la présence ou de l'absence de cellules souches de leucémie monocytique (m-LSC), comprenant des m-LSC CD70+, dans un échantillon provenant d'un sujet.
PCT/US2023/082102 2022-12-01 2023-12-01 Méthodes de traitement de la leucémie myéloïde aiguë WO2024119090A2 (fr)

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Non-Patent Citations (8)

* Cited by examiner, † Cited by third party
Title
EPPERT ET AL., NAT MED, vol. 17, 2011, pages 1086 - 93
HESS ET AL., BLOOD, vol. 108, 2006, pages 297 - 304
LOTFOLLAHI ET AL., NAT BIOTECHNOL, vol. 40, 2022, pages 121 - 30
NG ET AL., NATURE, vol. 540, 2016, pages 433 - 7
SOMERVAILEE ET AL., CANCER CELL, vol. 10, 2006, pages 257 - 68
SOMERVAILLE ET AL., CELL STEM CELL, vol. 4, 2009, pages 129 - 40
TRIANA ET AL., NAT IMMUNOL, vol. 22, 2021, pages 1577 - 89
ZENG ET AL., NAT MED, vol. 28, no. 1257044-40-8, 2022, pages 1212 - 23

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