EP2561088A1 - Composés et leurs utilisations pour induire la mort d'une cellule cancéreuse immunogène chez un sujet - Google Patents

Composés et leurs utilisations pour induire la mort d'une cellule cancéreuse immunogène chez un sujet

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Publication number
EP2561088A1
EP2561088A1 EP20110713731 EP11713731A EP2561088A1 EP 2561088 A1 EP2561088 A1 EP 2561088A1 EP 20110713731 EP20110713731 EP 20110713731 EP 11713731 A EP11713731 A EP 11713731A EP 2561088 A1 EP2561088 A1 EP 2561088A1
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EP
European Patent Office
Prior art keywords
seq
cells
subject
cancer
nonsyn
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EP20110713731
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German (de)
English (en)
Inventor
Laurence Zitvogel
Guido Kroemer
Nicolas Delahaye
Yuting Ma
Oliver Kepp
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Institut Gustave Roussy (IGR)
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Institut Gustave Roussy (IGR)
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Priority claimed from PCT/EP2010/055404 external-priority patent/WO2011131246A1/fr
Priority claimed from PCT/IB2010/002034 external-priority patent/WO2012007783A1/fr
Application filed by Institut Gustave Roussy (IGR) filed Critical Institut Gustave Roussy (IGR)
Priority to EP14165240.4A priority Critical patent/EP2806034B1/fr
Priority to EP20110713731 priority patent/EP2561088A1/fr
Priority claimed from PCT/EP2011/055134 external-priority patent/WO2011131472A1/fr
Publication of EP2561088A1 publication Critical patent/EP2561088A1/fr
Withdrawn legal-status Critical Current

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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
    • A61K31/70—Carbohydrates; Sugars; Derivatives thereof
    • A61K31/7042—Compounds having saccharide radicals and heterocyclic rings
    • A61K31/7048—Compounds having saccharide radicals and heterocyclic rings having oxygen as a ring hetero atom, e.g. leucoglucosan, hesperidin, erythromycin, nystatin, digitoxin or digoxin
    • 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
    • A61K31/045—Hydroxy compounds, e.g. alcohols; Salts thereof, e.g. alcoholates
    • A61K31/05—Phenols
    • 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
    • A61K31/13—Amines
    • A61K31/132—Amines having two or more amino groups, e.g. spermidine, putrescine
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/335—Heterocyclic compounds having oxygen as the only ring hetero atom, e.g. fungichromin
    • A61K31/365—Lactones
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/4353—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/436—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom ortho- or peri-condensed with heterocyclic ring systems the heterocyclic ring system containing a six-membered ring having oxygen as a ring hetero atom, e.g. rapamycin
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/395—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins
    • A61K31/435—Heterocyclic compounds having nitrogen as a ring hetero atom, e.g. guanethidine or rifamycins having six-membered rings with one nitrogen as the only ring hetero atom
    • A61K31/47—Quinolines; Isoquinolines
    • A61K31/4738—Quinolines; Isoquinolines ortho- or peri-condensed with heterocyclic ring systems
    • A61K31/4741—Quinolines; Isoquinolines ortho- or peri-condensed with heterocyclic ring systems condensed with ring systems having oxygen as a ring hetero atom, e.g. tubocuraran derivatives, noscapine, bicuculline
    • 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
    • A61K31/33—Heterocyclic compounds
    • A61K31/555—Heterocyclic compounds containing heavy metals, e.g. hemin, hematin, melarsoprol
    • 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
    • A61K31/7028—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages
    • A61K31/7034—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages attached to a carbocyclic compound, e.g. phloridzin
    • A61K31/704—Compounds having saccharide radicals attached to non-saccharide compounds by glycosidic linkages attached to a carbocyclic compound, e.g. phloridzin attached to a condensed carbocyclic ring system, e.g. sennosides, thiocolchicosides, escin, daunorubicin
    • 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
    • A61K31/715—Polysaccharides, i.e. having more than five saccharide radicals attached to each other by glycosidic linkages; Derivatives thereof, e.g. ethers, esters
    • A61K31/734—Alginic acid
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K45/00—Medicinal preparations containing active ingredients not provided for in groups A61K31/00 - A61K41/00
    • A61K45/06—Mixtures of active ingredients without chemical characterisation, e.g. antiphlogistics and cardiaca
    • 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
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/106—Pharmacogenomics, i.e. genetic variability in individual responses to drugs and drug metabolism
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    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/136—Screening for pharmacological compounds
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers
    • 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
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/172—Haplotypes

Definitions

  • the present disclosure generally relates to the fields of genetics, immunology and medicine.
  • the present invention more specifically relates to in vitro or ex vivo methods for determining the susceptibility to a cancer treatment of a subject having a tumour. These methods comprise a step of determining the ability of the treatment, of the subject and/or of the tumour to induce an anticancer immune response, the inability of at least one of the treatment, the subject and the tumor to induce an anticancer immune response being indicative of a resistance of the subject to the therapeutic treatment of cancer.
  • Inventors in particular identify genes specific of a human subject or of cancerous cells which can be used to predict or assess the sensitivity of a subject to a treatment of cancer.
  • the invention also relates to particular compounds capable of activating or enhancing the immune system of a particular subject, when the subject is exposed to a therapeutic treatment of cancer or before such an exposition. It further relates to uses of such compounds, in particular to prepare a pharmaceutical composition to allow or improve the efficiency of a therapy of cancer in a subject in need thereof.
  • the present invention in addition provides kits, methods for selecting a compound of interest, as well as pharmaceutical compositions and uses thereof.
  • anthracyclines such as daunorubicine, doxorubicin (DX), idarubicin and mitoxantrone (MTX), as well as oxali-platinum (oxaliplatin or OXP), cis-platinum (cisplatin or CDDP), and taxanes (paclitaxel or docetaxel) are considered as the most efficient cytotoxic agents of the oncologist armamentarium] and radiotherapy [XR] , the benefits of said treatments still tends to be insufficient. Cytotoxic agents are supposed to directly destroy cancer cells by stimulating diverse cell death pathways.
  • OXP and anthracyclines induce immunogenic cell death while other chemotherapeutic agents such as CDDP and alkylating agents tend to induce non- immunogenic cell death (Casares et al., 2005; Obeid et al., 2007). They have further observed that some patients were also resistant to treatments identified as inducing an immunogenic cell death. Solutions to detect dysfunctions responsible for an absent or reduced response to existing treatments as well as compounds usable to overcome said dysfunctions therefore appear critical for the patient and are herein advantageously provided by inventors.
  • the present invention is based on the observation by inventors that the cell death immunogenicity depends on the lethal stimulus, on the presence of specific signals produced by or exposed on tumor cells, as well as on the ability of the subject having the tumor, and in particular of the subject's immune system, to recognize said signals.
  • the present invention provides an in vitro or ex vivo method of assessing the sensitivity of a subject having a tumor to a treatment of cancer (in other words of determining susceptibility of a patient having a tumor to respond to a treatment of cancer), which method comprises a step of detecting the presence of an anticancer immune response of the subject undergoing the treatment of cancer, the absence of an anticancer immune response being indicative of a resistance of the subject to the treatment of cancer.
  • the method may be applied before and/or after exposition of the subject to the treatment of cancer.
  • the therapeutic treatment of cancer is a conventional immunogenic treatment of cancer selected from a chemotherapy using a drug selected from an anthracyclin, a platin, a taxane and an antimitotic agent, preferably from an anthracyclin, a platin, and an antimitotic agent; and radiotherapy.
  • the presence of cells selected from IL-17 producing ⁇ T lymphocytes, dendritic cells and cytotoxic T lymphocytes, in the tumor of the subject may in particular be indicative of an anticancer immune response and of a sensitivity of the subject to the treatment of cancer.
  • the appearance of anti-CRT antibodies in a sample typically a serum sample, of a subject after a first exposition of the subject to a treatment of cancer, and preferably an increase of said anti-CRT antibodies during said treatment, may be indicative of an anticancer immune response and of a sensitivity of the subject to said treatment of cancer.
  • In vitro or ex vivo methods of assessing the sensitivity of a subject having a tumor to a treatment of cancer comprise a step of determining the ability of the treatment, of the tumor and/or of the subject to induce an anticancer immune response, the inability of at least one of the treatment, the subject and the tumor to induce an anticancer immune response being indicative of a resistance of the subject to the treatment of cancer.
  • the presence, in the subject, of an alteration leading to the abnormal expression of an immune gene, as herein described, may in particular determine the inability of the subject to induce an anticancer immune response.
  • the alteration may be a single nucleotide polymorphism (SNP).
  • the step of determining the ability of the tumor to induce an anticancer immune response may in particular consist in verifying the expression by tumor cells of an immunogenic cell death marker selected from a protein allowing or enhancing CRT exposure at the surface of tumor cells, and a protein expressed during the endoplasmic reticulum (ER) stress response and/or during the macroautophagic response of the subject's immune system.
  • an immunogenic cell death marker selected from a protein allowing or enhancing CRT exposure at the surface of tumor cells, and a protein expressed during the endoplasmic reticulum (ER) stress response and/or during the macroautophagic response of the subject's immune system.
  • a method of selecting an optimal therapeutic treatment of cancer in a subject having a tumor comprises a step as previously described of assessing the sensitivity of the subject to a first treatment of cancer (herein also identified as “conventional treatment”) and, if the subject is resistant to said first treatment of cancer, a step of selecting a "compensatory molecule", to be used, alone or in combination with the first treatment of cancer as the optimal therapeutic treatment of cancer for the subject.
  • a particular method of selecting an optimal therapeutic treatment of cancer in a subject having a tumor is a method comprising a step of assessing the sensitivity of the subject to a first treatment of cancer with a method as herein described, and, if the subject is resistant to said first treatment of cancer, and a step of selecting (i) a product allowing or enhancing the secretion of ATP, HMGB 1 , LysRS and/or IL-8, and/or the exposure of CRT, ERp57, LysRS and/or KDEL receptor at the surface of a tumour cell, (ii) a product stimulating the autophagy machinery and/or an ER stress response, (iii) a product recruiting and/or activating IL-17 producing ⁇ T lymphocytes, cytotoxic T cells and/or dendritic cells, (iv) a product promoting activation of the TLR4/myd88 pathway, or able to bypass said pathway, (v) a product triggering the P2RX7 (P2X purino
  • compensatory molecules for use in the treatment of cancer, preferably in combination with a conventional treatment of cancer, in particular a chemotherapeutic treatment of cancer, in a subject identified, by a method as previously described, as resistant to a conventional treatment of cancer.
  • the present invention further encompasses the use of such a compensatory molecule to prepare a pharmaceutical composition for treating a cancer in a subject identified, by a method as previously described, as resistant to a conventional treatment of cancer, as well as the corresponding pharmaceutical composition.
  • the pharmaceutical composition further comprises, as a combined preparation, a drug used in a conventional treatment of cancer, for simultaneous, separate or sequential use in the treatment of said cancer.
  • the present invention in particular encompasses a drug selected from (i) a product allowing or enhancing the secretion of ATP, HMGB 1, LysRS and/or IL-8, and/or the exposure of CRT, ERp57, LysRS and/or KDEL receptor at the surface of a tumour cell, (ii) a product stimulating the autophagy machinery and/or an ER stress response, (iii) a product recruiting and/or activating IL- 17 producing ⁇ T lymphocytes, cytotoxic T cells and/or dendritic cells, (iv) a product promoting activation of the TLR4/myd88 pathway, or able to bypass said pathway, (v) a product triggering the P2RX7 (P2X purinoceptor 7) and/or the NALP3 inflammasome, (vi) a product allowing or enhancing the secretion of IL-lb, (vii) a product capable of stimulating intratumoral Vd2 T lymphocytes, and (viii
  • Induction of immunogenic cancer-cell death using a compensatory molecule as herein described, allows the subject's immune system, thanks to the present invention, to contribute, through a "bystander effect", to the eradication of cancer cells and cancer stem cells which are resistant to conventional therapeutic treatments.
  • a method of treating cancer comprising the administration to a subject in need thereof, as previously explained, of a compensatory molecule, preferably together with a drug used in a conventional treatment of cancer (as a combined preparation).
  • kits to detect the abnormal expression, in particular in a tumor biopsy, of a gene selected from CCR1, EIF2AK2, DNAJC10, PDIA3, EIF2A, PPP1CB, IKBKB, PPP1CC, BAX and combinations thereof, in a tumor sample of the subject comprising (i) at least one pair of primers and (ii) at least one fluorescent probe, for example two different probes, allowing the quantitative detection of the expression of a gene selected from CCR1, EIF2AK2, DNAJC10, PDIA3, EIF2A, PPP1CB, IKBKB, PPP1CC, BAX, and (iii) a leaflet providing the control quantitative expression values corresponding to at least one of said genes in a control population.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a gene selected from AHR and MTHFR for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene
  • the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from AHR and MTHFR.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a gene selected from FAT2 and MTHFR for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene
  • the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from FAT2 and MTHFR.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a gene selected from DDX58 (RIG-1) and CX3CR1 for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene, in a tumor or blood sample of the subject, the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from DDX58 and CX3CR1.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a NLRP4 gene for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene
  • the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of the NLRP4 gene.
  • kits comprising :
  • FIGURES Figure 1 Thl and Thl7 related genes expression in tumors post-chemotherapy.
  • A MCA205 tumors were treated with Doxorubicin (DX) or PBS. Tumor growth was monitored before and 8 days post-chemotherapy.
  • DX Doxorubicin
  • PBS PBS
  • CH223191 was dissolved with DMSO and diluted in Olive Oil. Mice treated with either PBS or DX received a daily i.p. injection of CH223191 (2 mM, 100 ⁇ ) for 4 days starting from the day of DX (or PBS) treatment.
  • Each graph depicts means ⁇ SEM of tumor sizes (A, D) or protein expression (C) or percentages of positive cells (E). *p ⁇ 0.05, **p ⁇ 0.01, ***p ⁇ 0.001.
  • CD8 + T cells and ⁇ T cells are the major sources of IFN- ⁇ and IL-17 respectively post-chemotherapy.
  • IL-17 contributes to prophylactic and therapeutic responses to immunogenic chemotherapy.
  • Established MCA205 were treated locally with DX in various genetic backgrounds (A, C) or in WT mice in addition to systemic administration of neutralizing antibodies anti-CCL20 (or isotype Ctrl Ab) (B).
  • A-B Cocultures of naive LNs derived ⁇ T (A-B) or TCR ⁇ T (A) cells in the presence of recombinant mouse cytokines (1 g/ml IL- ⁇ or/and IL-23, 5 g/ml TGF- ⁇ , 10 g/ml IL-6) (A) with or without TCR cross-linking with anti-CD38 mAb pre -coated plates (5 g/ml, Clone 145- 2C11) (B).
  • D DX-treated MCA205 loaded DC/ ⁇ T cell cross-talk was also performed in the presence of 20 ⁇ g/ml IL-1RA (Amgen) or anti-IL-23 or IL-23R neutralizing antibodies or 10 ⁇ g/ml IL-18BP or 20 ⁇ CH-223191. IL- ⁇ and IL-17A release was measured at 48 hrs in ELISA.
  • C-D The percentage of CD8 T cells among TILs and their IFN- ⁇ production (C) and the percentage of ⁇ T cells among TILs and their IL-17 production (D) were examined in PBS versus DX-treated tumors by flow cytometry. Means ⁇ SEM of percentages in 5 tumors/group are indicated.
  • SNP single-nucleotide polymorphism
  • rs2066853 Arg554Lys
  • the proportion of pathological complete responses was compared in wild-type and mutated groups of patients.
  • the Chi square test was used to test the genetic association between the primary endpoint and the AHR-R554Ks SNP.
  • U20S cells stably expressing CRT-GFP treated with 1 ⁇ mitoxantrone (MTX) 150 ⁇ cisplatin (CDDP) or 300 ⁇ oxaliplatin (OXP) for the indicated time have been analyzed by means of automated image acquisition and automated analysis.
  • Data is depicted as (A) representative images (B) and normalized CRT-GFP granularity values as well as percent of cells exhibiting nuclear shrinkage. The data is depicted as mean ⁇ s.e.m. of quadruplicates from a representative experiment.
  • C Immunofluorescene was conducted on CRT-GFP expressing cells by means of staining with anti-CRT antibody and subsequent confocal image acquisition.
  • FIG. 15 Mitochondrial cell death upon treatment with oxaliplatin and cisplatin.
  • U20S cells stably expressing CRT-GFP treated with 1 ⁇ mitoxantrone (MTX) 150 ⁇ cisplatin (CDDP) or 300 ⁇ oxaliplatin (OXP) have been acquired by means of an automated microscope and subsequently subjected to automated analysis. The data is depicted as representative images (A) and (B) normalized Bax-GFP granularity values.
  • the data represents mean ⁇ s.e.m. of quadruplicates from a representative experiment.
  • the data represents means ⁇ s.e.m. of triplicate determinations.
  • Figure 16 Oxaliplatin and cisplatin induced ATP release.
  • MTX mitoxantrone
  • OXP oxaliplatin
  • CDDP cisplatin
  • Results are means ⁇ SEM of triplicate determinations.
  • Cells stably expressing G3BP-GFP or GFP-LC3 were treated for 4 h with 1 mM sodium arsenate heptahydrate (NaHAs0 4 ) or 10 ⁇ rapamycin for 8 h as positive controls respectively.
  • the cells have been treated with 150 ⁇ cisplatin (CDDP) or 300 ⁇ oxaliplatin (OXP) for the indicated time to assess (A, B) the formation of stress granules and (C, D) the lipidation of LC3 as an indicator for autophagy. Representative images (A, C) and mean granularity values (B, D) of quadruplicates are shown.
  • A, B U20S or HaloTag ® -CRT stably expressing U20S cells were assessed after a treatment with mitoxantrone (MTX), oxaliplatin (OXP) , cisplatin (CDDP), thapsigargin (THAPS) or cisplatin combined with thapsigargin by immunofluorescence staining or incubation with impermeable fluorescent HaloTag ® ligand respectively followed by flow cytometric analysis.
  • CRT exposure upon combination of 150 ⁇ CDDP with 1 ⁇ THAPS was confirmed in (C) mouse lewis lung cell carcinoma, (D) CT26 and (E) MCA205 cells by means of immunostaining and following flow cytometric analysis.
  • the data represents means ⁇ s.e.m. of triplicate determinations.
  • Results are means ⁇ SEM of triplicate determinations.
  • SVM Support Vector Machine
  • the prediction accuracy of each molecular classifier was assessed by Fisher's exact test on the « pCR vs non pCR » contingency tables obtained from the LOOCV approach of SVM procedure.
  • the SVM training parameters used were a polynomial kernal matrix with a diagonal factor of 1.3.
  • the predictive value of the classifier was also evaluated by the sensibility (Se) and specificity (Spe) parameters.
  • the "calreticulin pathway” was represented by an initial set of 43 genes in the cohort HOUSTON FEC and 53 genes in the cohort IGGO FEC/TET. Figure 24.
  • Three genes based - « Calreticulin pathway* molecular classifiers are independant predictive factors in the two anthracyclines treated cohorts (FEC) but not in the taxane treated cohort (TET).
  • Figure 25 Search of a common « Calreticulin pathway* molecular classifier between the two anthracyclines treated cohorts (FEC).
  • FEC anthracyclines treated cohorts
  • the prediction accuracy of the common molecular classifier was assessed by Fisher's exact test on the « pCR vs non pCR » contingency tables obtained from the LOOCV approach of SVM procedure.
  • the SVM training parameters used were a polynomial kernal matrix with a diagonal factor of 2.
  • the predictive value of the classifier was also evaluated by the sensibility (Se), specificity (Spe), positive and negative predictive values (PPV and NPV) and accuracy parameters.
  • a molecular parameter signature (also herein identified as “algorithm”) that integrates the "CALR pathway” signature and a MTHFR SNP is particularly efficient to predict the ability of a given subject to respond to anthracyclines in the HOUSTON FEC cohort.
  • FIG. 28 Cardiac Glycosides emit immunogenic signals.
  • HMGB1 release was measured using HMGB1 ELISA 24 h after treatment in the supernatants of cells.
  • C MCA205 cells have been used for tumor vaccination in vivo.
  • Digoxin used as single treatment caused tumor growth on the vaccination side and did not preclude the living cells from forming a tumor after rechallenge.
  • Dl Overall survival of 150 breast cancer patients. 50 digoxin cotreated patients are opposed by 100 non digoxin treated controls.
  • Subgroup analysis depict anthracycline based chemotherapy with and without digoxin cotreatment and non anthracycline based therapy with and without digoxin cotreatment.
  • D2 Overall survival of 60 breast cancer patients anthracycline based chemotherapy. 20 digoxin cotreated patients are opposed by 40 non digoxin treated controls.
  • D3 Overall survival of 90 breast cancer patients non anthracycline based therapy. 30 digoxin cotreated patients are opposed by 60 non digoxin treated controls.
  • SNP single-nucleotide polymorphism
  • the NLRP4-rs302453 Gln925Leu polymorphism was genotyped in three cohorts (REMAGUS, Dijon, Houston).
  • SNP single-nucleotide polymorphism
  • Figure 32 Using a non strained selection of immune SNPs associated with shorter time to progression among a multiplex 356 SNP genotyping based on fluorescent PCR (Veracode Illumina) in a cohort of 280 N+ adjuvant BC patients and 360 neoadjuvant BC, inventors identified two additional SNPs (located in DDX58/RIG-I and CX3CR1 encoding a cytosolic receptor detecting viral nucleic acids, and fractalkine respectively) in adjuvant and two highly significant SNPs in neoadjuvant (MTHFR: rsl801133 and FAT2: rsl432862) in a multivariate Cox model (integrating proliferation index and HR status).
  • MTHFR rsl801133
  • FAT2 rsl432862
  • Figure 33 The single-nucleotide polymorphism (SNP) in DDX58, CX3CR1 and FAT2 affects the efficacy of conventional anti-cancer therapy.
  • SNP single-nucleotide polymorphism
  • AUC Cross-validated accuracy and AUC for the threee families of signatures, as a function of the number of factors in the signature, for the RCH endpoint
  • Figure 35 Genes regulated 2 and 8 days after doxorubicin treatment.
  • C CxcllO, Ccl2, Ccl3, Ccl4, Ccl7 and Cxcll genes are specifically up-regulated in the CD45+ fraction 2 days after doxorubicin treatment.
  • Figure 36 IgA and IgG dosage in sera from Healthy Volonteers (HV) and Breast Cancer Patients (BC). Cut-off values were calculated as 60 AU for IgA anti-CRT antibodies and 90 AU for IgG anti-CRT antibodies.
  • Figure 37 Percentage of positive samples for anti-Calreticulin IgA and IgG in Healthy Volonteers (HV) and Breast Cancer Patients (BC). Cut-off values were calculated as 60 AU for IgA anti- calreticulin antibodies and 90 AU for IgG anti-calreticulin antibodies.
  • Figure 38 The level of Ig anti-Calreticulin at the diagnosis and the capacity to develop a humoral response during chemotherapy treatment are associated to clinical response to anthracyclines and metastasis free survival.
  • pCR pathological Complete Response.
  • Figure 39 (A) Immunohistochemistry of ER stress response markers (eif2a phosphorylation, CRT, ERp57 and HMGB 1) in BC at diagnosis in FFPE (B) The panel is a graph summarizing scoring
  • Figure 40 The core machinery of autophagy is indispensable for ATP release during exposure with immunogenic chemotherapies.
  • Figure 40 upper panel.
  • the percentages of Quinacrine negative cells, assessed by immunofluorescence (GFP emission) represent the proportions of cells that have lost intracellular ATP.
  • the positive control for autophagy induction is starvation.
  • Figure 40 lower panel. ATP release is indirectly measured by the percentages of cancer cells that have lost quinacrine expression.
  • Figure 41 Induction of autophagy in vivo following chemotherapy of established tumors.
  • Figure 42 Prophylactic immunization with dying tumor cells is impaired when dying cells are autophagy-deficient.
  • Statistical analyses were performed with Anova test (Fisher's exact method) with significant results at p ⁇ 0.05.
  • Figure 44 Autophagy-deficient tumors failed to properly respond to chemotherapy unless apyrase inhibitors are coadministered along with chemotherapy.
  • TLR4 agonists potentiate the immunogenicity of anthracyclines and oxaliplatine PBS treated mice cannot control the tumor growth whereas chemotherapy-treated mice are able to do so.
  • Dendrophilin combined with Chemotherapy increases the control of the tumor growth, meaning that TLR4 agonists potentiate the immunogenicity of anthracyclines and oxaliplatin in 2 tumor models.
  • Figure 46 4- IBB agonists potentiate the immunogenicity of anthracyclines and oxaliplatine
  • This pathway may be interrupted at several levels, by the loss of a positive mediator or by the presence of an inhibitor of such a positive mediator.
  • the result of such an interruption will be the absence of reaction of the subject's immune system, in other words, the absence of "immunogenic cell death".
  • Inventors herein below identify particular products the detection of which can be used to determine if a subject will respond or not to a cancer treatment.
  • Inventors further herein below provide methods which can be used (i) to determine the presence of an immunogenic response in a subject having a tumor, (ii) to determine the presence or level of exposure of particular proteins on the surface of tumour cells or of immune cells (as herein defined), (iii) to determine the presence or level of expression of particular proteins secreted by tumor cells or immune cells, (iv) to determine the susceptibility of a tumour cell to a cancer treatment, and/or (v) to determine if a subject will respond to a cancer treatment or will be resistant to said treatment.
  • Immunogenic cell death is a subject will respond to a cancer treatment or will be resistant to said treatment.
  • Cell death can be classified according to the morphological appearance of the lethal process (that may be apoptotic, necrotic, autophagic or associated with mitosis), enzymological criteria (with and without the involvement of nucleases or distinct classes of proteases, like caspases), functional aspects (programmed or accidental, physiological or pathological) or immunological characteristics (immunogenic or non-immunogenic) (Kroemer et al , 2009).
  • Cell death is defined by Casares et al. (2005) as "immunogenic” if dying cells that express a specific antigen (such as the model antigen ovalbumin OVA or a tumor antigen), yet are uninfected (and hence lack pathogen-associated molecular patterns), and are injected subcutaneously into mice, in the absence of any adjuvant, cause a protective immune response against said specific antigen.
  • a protective immune response precludes the growth of living transformed cells expressing the specific antigen injected into mice.
  • the response from the immune system is herein called an "anti-cancer immune response" when it is directed against tumour cells, in particular cancerous cells.
  • the anticancer immune response is allowed by a reaction from the immune system of the subject to the presence of cells, preferably of tumor cells, dying from an immunogenic cell death (as defined previously).
  • the anti-cancer immune response allows, at least partly, the regression or destruction of the tumor.
  • the patient or subject is a mammal.
  • the mammal is a human being, whatever its age or sex.
  • the patient may have a tumor.
  • the tumor is a malignant tumor.
  • An in vitro or ex vivo method of assessing the sensitivity of a subject having a tumor to a treatment of cancer comprises a step of detecting the presence of an anticancer immune response of the subject, the absence of an anticancer immune response being indicative of a resistance of the subject to the treatment of cancer.
  • non-responder or “resistant” refers to the phenotype of a subject who does not respond to a treatment of cancer, in particular to a conventional treatment of cancer as previously defined, i.e. the volume of the tumor does not substantially decrease, or the symptoms of the cancer in the subject are not alleviated, or the cancer progresses, for example the volume of the tumor increases and/or the tumor generates local or distant metastasis.
  • non-responder or “resistant” also refer to the phenotype of a subject who will die from the cancer.
  • responder or “sensitive” refers to the phenotype of a patient who responds to a treatment of cancer, in particular to a conventional treatment of cancer as previously defined, i.e. the volume of the tumor is decreased, at least one of his symptoms is alleviated, or the development of the cancer is stopped, or slowed down.
  • a subject who responds to a cancer treatment is, in the sense of the present invention, a subject who typically has a much longer disease free survival chance than a patient who has been identified, with a method as herein described, as resistant to a treatment of cancer.
  • a subject who responds to a cancer treatment is a subject who will be completely treated (cured).
  • pathological complete response means that the tumor size dramatically decreases under chemotherapy, typically after a neoadjuvant chemotherapy, and then becomes operable or undetectable.
  • a subject who responds to a cancer treatment is a subject who will be completely treated (cured), i.e., a subject who will survive to the cancer [the detected or measured parameter (for example the expression product of gene as herein disclosed) has a beneficial impact on the "overall survival” (OS)].
  • the detected or measured parameter for example the expression product of gene as herein disclosed
  • a subject who responds to a cancer treatment is also, in the sense of the present invention, a subject who typically has a much longer disease free survival (DFS) or metastasis free survival chance than a patient who has been identified, with a method as herein described, as resistant to a treatment of cancer.
  • DFS disease free survival
  • the sensitivity or susceptibility of a subject to a treatment of cancer indicates whether the subject is "responder” or “non-responder”, in other words whether the subject will or will not, be at least partially treated (tumor growth retardation or regression), preferably be completely treated (cured), by said cancer treatment.
  • the subject is typically a subject undergoing a treatment of cancer, in particular a conventional treatment of cancer (preferably chemotherapy and/or radiotherapy).
  • a treatment of cancer preferably chemotherapy and/or radiotherapy.
  • the subject may have been exposed to part of a complete conventional treatment protocol, for example to at least one cycle of the all treatment protocol, for example two cycles of the all treatment protocol.
  • the method of assessing the sensitivity of a subject to a treatment of cancer is applied on a subject who has not been previously exposed to a treatment of cancer.
  • the serum of such a subject is free of anti-CRT antibodies.
  • Methods herein described are predictive methods, i.e., methods capable of assessing the ability of a subject to mount an immune response in the context of an anthracycline, oxaliplatine or X Rays treatment as herein defined and not only prognostic methods, only capable of indicating whether the subject will survive to the cancer or die from the cancer.
  • a "conventional treatment of cancer” may be selected from a chemotherapy, a radiotherapy, an hormonotherapy, an immunotherapy, a specific kinase inhibitor-based therapy, an antiangiogenic agent based-therapy, an antibody-based therapy, in particular a monoclonal antibody-based therapy, and surgery.
  • the term “conventionally” means that the therapy is applied or, if not routinely applied, is appropriate and at least recommended by health authorities.
  • the "conventional” treatment is selected by the cancerologist depending on the specific cancer to be prevented or treated.
  • the cancer is a cancer that is usually or conventionally treated with one of the following therapy: a chemotherapy, a radiotherapy, an hormonotherapy, an immunotherapy, a specific kinase inhibitor-based therapy, an antiangiogenic agent based-therapy, an antibody-based therapy and a surgery.
  • the cancer may be any kind of cancer or neoplasia.
  • the cancer is preferably selected from a breast cancer, a prostate cancer, an oesophagus cancer, a colon cancer, a rectal cancer, a kidney cancer, a lung cancer, in particular a non-small cell lung cancer (NSCLC), a thyroid cancer, an osteosarcoma, a gastrointestinal sarcoma (GIST), a melanoma, a leukaemia, in particular an acute lymphoid leukemia, an Hodgkin lymphoma, and a neuroblastoma.
  • the tumour cell mentioned in the present invention is a cell obtained from a tumor of a subject suffering from a cancer, in particular from at least one of the previously identified cancers.
  • the tumor cell is preferably selected from a carcinoma, a sarcoma, a lymphoma, a melanoma, a paediatric tumour and a leukaemia tumour.
  • tumor cells used to identify cells obtained from a tumor of a subject, is also used, in the present description, to identify circulating tumor cells (in the case of leukaemia for example), cells obtained from a tumor bed, or cells obtained from a metastase.
  • An hormonotherapy is a therapy leading to apoptosis or Fas ligands or soluble /membrane bound TRAIL (TNF-related-apoptosis-inducing-ligand) or soluble/membrane bound TNF (tumor necrosis factor) alpha (TNFa).
  • TRAIL tumor necrosis factor-related-apoptosis-inducing-ligand
  • TNFa tumor necrosis factor alpha
  • Cancers sensitive to an immunotherapy are conventionally treated using a compound selected for example from IL-2 (Interleukine-2), IFN (Interferon) alpha (IFNa), and a vaccine.
  • IL-2 Interleukine-2
  • IFN Interferon alpha
  • a vaccine a compound selected for example from IL-2 (Interleukine-2), IFN (Interferon) alpha (IFNa), and a vaccine.
  • Cancers sensitive to a specific kinase inhibitor-based therapy are conventionally treated using a compound selected for example from a tyrosine kinase inhibitor, a serine kinase inhibitor and a threonine kinase inhibitor.
  • Cancers sensitive to an antibody-based therapy are conventionally treated using a specific antibody such as for example anti-CD20 (pan B-Cell antigen) or anti-Her2/Neu (Human Epidermal Growth Factor Receptor-2/NEU).
  • a specific antibody such as for example anti-CD20 (pan B-Cell antigen) or anti-Her2/Neu (Human Epidermal Growth Factor Receptor-2/NEU).
  • the conventional treatment of cancer is a conventional chemotherapy or a conventional radiotherapy.
  • the treatment may consist in exposing the subject to an irradiation selected for example from XR, gamma irradiations and/or UVC irradiations.
  • the treatment may use a cytotoxic agent or cell death inducer (chemotherapeutic agent), in particular a genotoxic agent.
  • chemotherapeutic agent in particular a genotoxic agent.
  • the chemotherapeutic agent is an agent selected for example from an anthracyclin, an antimitotic agent (spindle poison such as vincristine or vinblastine), a DNA intercalating agent, a taxane (such as docetaxel, larotaxel, cabazitaxel, paclitaxel (PG-paclitaxel and DHA-paclitaxel), ortataxel, tesetaxel, and taxoprexin), gemcitabine, etoposide, mitomycine C, an alkylating agent, a platin based component such as CDDP and OXP, and a TLR (Toll-like receptor) -3 ligand.
  • an anthracyclin an antimitotic agent (spindle poison such as vincristine or vinblastine)
  • a DNA intercalating agent such as docetaxel, larotaxel, cabazitaxel, paclitaxel (PG-paclitaxel and DHA-paclit
  • the chemotherapeutic agent in particular when chemotherapy is administered to the subject before any surgical step, is not a taxan, and preferably also not an antimitotic agent.
  • Particular anthracyclins may be selected, in the context of the present invention, from DX, daunorubicin, idarubicin and MTX.
  • the antibody used in an antibody-based therapy is a cytotoxic antibody.
  • a particular breast cancer is a breast cancer conventionally treated with anthracyclins, taxanes, Herceptin, anti-PARP (Poly (ADP-ribose) polymerase), anti-PBK (Phosphoinositide 3-kinase), mTOR (mammalian Target of Rapamycin) inhibitors, navelbine, gemcitabine, antioestrogens, antiaromatases, and/or a TLR-3 ligand, before or after a surgical step to remove breast tumor, preferably before such a surgical step.
  • PARP Poly (ADP-ribose) polymerase
  • anti-PBK Phosphoinositide 3-kinase
  • mTOR mimmalian Target of Rapamycin
  • a particular thyroid cancer is a thyroid cancer treated with radioactive iodine or tyrosine kinase inhibitors, preferably RET inhibitors.
  • a particular Hodgkin lymphoma is a Hodgkin lymphoma conventionally treated with CHOP [Cyclophosphamide, Hydroxydaunorubicin, Oncovin (vincristine), and Prednisone and/or Prednisolone] or anthracyclines.
  • a particular prostate cancer is a prostate cancer conventionally treated with taxanes and XR.
  • a particular colon cancer is a colon cancer conventionally treated with OXP and/or the combination of 5-fluorouracil (5 FU) and folinic acid.
  • a particular metastatic colon cancer is a metastatic colon cancer conventionally treated with 5 FU and OXP or irinothecan.
  • a particular rectal cancer is a rectal cancer conventionally treated with radiotherapy, preferably local radiotherapy, preferably together with CDDP and/or 5 FU.
  • a particular oesophagus cancer is an oesophagus cancer treated with CDDP, before or after a surgical step to remove the oesophagus tumor, preferably before such a surgical step, the administration of CDDP being preferably combined to the administration to the patient of a radiotherapy, preferably a local radiotherapy.
  • kidney cancer is a kidney cancer conventionally treated with cytokines or anti- angiogenic drugs (sorafenib).
  • a particular lung cancer is a lung cancer conventionally treated with XR and platine or Permetrexed (Alimta®).
  • a particular early stage NSCLC is an NSCLC conventionally treated with CDDP and/or etoposide, or with taxanes and avastin [anti-VEGF (Vascular endothelial growth factor) antibody].
  • a particular osteosarcoma and a preferred GIST are respectively an osteosarcoma and a GIST conventionally treated with anthracyclins, imatinib (Gleevec®) and/or sunitinib.
  • a particular melanoma is a melanoma conventionally treated with dacarbazine (DTIC); B -Raf inhibitors (PLX4032); sorafenib and/or temozolomide; electrochemotherapy; or isolated limb perfusion of TNFalpha, in particular of high doses of TNFalpha.
  • DTIC dacarbazine
  • PLX4032 B -Raf inhibitors
  • sorafenib and/or temozolomide sorafenib and/or temozolomide
  • electrochemotherapy or isolated limb perfusion of TNFalpha, in particular of high doses of TNFalpha.
  • a particular neuroblastome is a neuroblastome conventionally treated with anthracyclines or alkylating agents, in particular in the context of autologous bone marrow transplantation or of stem cells transplantation.
  • a particular acute lymphoid leukemia is an acute lymphoid leukemia treated with anthracyclins, vinblastine and/or vincristine.
  • a particular multiple myeloma is a malignant hemopathy treated with anthracyclins, bortezomiv, revlimide, thalidomide and/or an alkylating agent, in particular in the context of autologous bone marrow or stem cell transplantation.
  • conventional immunogenic treatments As indicated previously, it is possible to distinguish between conventional treatments of cancer able to induce an immunogenic cell death, herein identified as “conventional immunogenic treatments", and conventional treatments of cancer which induce or tend to induce a non-immunogenic cell death, herein identified as “conventional non-immunogenic treatments”.
  • OXP and anthracyclines in particular induce immunogenic cell death, as do radiotherapy (ionizing radiations), while other agents such as CDDP and alkylating agents tend to induce a non- immunogenic cell death (Casares et al., 2005; Obeid et al., 2007), as do etoposide, 5-FU and mitomycin C.
  • a typical in vitro method used to assess the immunogenicity of a particular drug comprises the steps of:
  • mammalian cells for example cells from the CT26 or MCA205 mouse cell line
  • mammalian cells typically of mammalian cells capable of expressing calreticulin (CRT)
  • CRT calreticulin
  • step (b) inoculating (for example intradermally) the dying mammalian cells from step (a) in a particular area (for example a flank) of the mammal, typically a mouse, to induce an immune response in this area of the mammal;
  • step (c) inoculating (for example intradermally) the minimal tumorigenic dose of syngeneic live tumor cells in a distinct area (for example the opposite flank) from the same mammal, for example 7 days after step (b);
  • step (d) comparing the size of the tumor in the inoculated mammal with a control mammal also exposed to the minimal tumorigenic dose of syngeneic live tumor cells of step (c) [for example a mouse devoid of T lymphocyte], the stabilization or regression of the tumor in the inoculated mammal being indicative of the drug immunogenicity.
  • Inventors herein demonstrate that a subject having a tumor may however resist even to a conventional immunogenic treatment as previously identified and/or defined.
  • an in vitro or ex vivo method of assessing the sensitivity of a subject having a tumor, as previously defined, to a treatment of cancer, in particular to a conventional immunogenic treatment which method comprises a step of determining the ability of the subject and/or of the tumor to induce an anticancer immune response, the inability of at least one of the subject and of the tumor to induce an anticancer immune response being indicative of a resistance of the subject to the treatment of cancer.
  • immune cells which reveal the presence of an anticancer immune response from a subject having a tumor.
  • this subject has been exposed to a treatment of cancer, in particular to at least one conventional treatment of cancer.
  • a method of assessing the sensitivity of a subject having a tumor to a treatment of cancer comprises a step of detecting the presence of immune cells selected in particular from ⁇ T lymphocytes, dendritic cells and cytotoxic T lymphocytes, in a tumor sample of the subject.
  • the previously described method is applied on a subject who has not been exposed to a treatment of cancer.
  • This method may further be applied to the same subject after said subject has been exposed to a treatment of cancer, in particular to a chemotherapeutic treatment of cancer, preferably to several cycles, for example two, three or four cycles of a complete chemotherapeutic treatment.
  • the method may further comprise a step of comparing the presence of immune cells in a tumor sample of the subject before and after exposition of the subject to a treatment of cancer as explained previously.
  • This method may be applied in vitro or ex vivo on a biological sample or biopsy from the subject, in particular on a tumor sample or biopsy, on a biopsy of cells from the tumor bed, on cytospins, on cells from a metastase, or on circulating tumor cells.
  • the presence of immune cells in the tumor of a subject is indicative of the presence of an anticancer immune response in the subject who has been exposed to a treatment of cancer and reveals the sensitivity of the subject to the treatment of cancer (responder phenotype).
  • the absence of immune cells in the tumor of a subject is indicative of the absence of an anticancer immune response in the subject who has been exposed to a treatment of cancer and reveals a resistance of the subject to the treatment of cancer (non responder phenotype).
  • the ⁇ T lymphocytes are preferably selected from Vy4 + ⁇ T lymphocytes (mouse), in particular activated Vy4 + ⁇ T lymphocytes; V52 (or V5l in humans) T lymphocytes; Vy6 + ⁇ T lymphocytes, in particular activated Vy6 + ⁇ T lymphocytes; IL-17 producing ⁇ T lymphocytes (also herein called " ⁇ T17 cells"), in particular cells expressing RORyt (RAR-related orphan receptor), AHR (aryl hydrocarbone receptor), IL-23R, IL-17A and/or IL-22; ⁇ T lymphocytes expressing the IL-1 receptor (IL-1R or IL-1R1); and any combination of the previously mentioned ⁇ T lymphocytes such as, in particular IL-17 producing- Vy4 + and ⁇ 6 + ⁇ T lymphocytes, preferably expressing the IL-1R.
  • Vy4 + ⁇ T lymphocytes in particular activated Vy4 + ⁇ T lymphocytes
  • V52 or
  • ⁇ T lymphocytes populations identify populations of mammalian cells.
  • Human ⁇ T lymphocytes have ⁇ 2 (circulating) T lymphocytes but no Vd2 (mucosal) T lymphocytes, contrary to mouse ⁇ T lymphocytes. Both populations of ⁇ 2 and Vd2 T lymphocytes are however able to differentiate into VydT17 cells.
  • ⁇ T lymphocytes in particular those present in tumor beds, have the following phenotype: Ki67 + , GzB + , CD69 + and IL-17 + , when they are activated.
  • the dendritic cells are preferably selected from myeloid cells (such as monocytic cells and macrophages) expressing langerin, MHC (major histocompatibility complex) class II, CCR2 (chemokine (C-C motif) receptor 2), CX3CR1 and/or Grl molecules in mice; myeloid cells expressing CD14, CD16, HLA dR (human leukocyte antigen disease resistance) molecule, langerin, CCR2 and/or CX3CR1 in humans; dendritic cells expressing CDl lc, MHC class II molecules, and/or CCR7 molecules; and IL- ⁇ producing dendritic cells.
  • myeloid cells such as monocytic cells and macrophages
  • myeloid cells such as monocytic cells and macrophages
  • MHC major histocompatibility complex
  • CCR2 chemokine (C-C motif) receptor 2)
  • CX3CR1 and/or Grl molecules in mice
  • myeloid cells expressing CD14
  • the cytotoxic T lymphocytes are preferably selected from CD3+, CD4+ and/or CD8+ T lymphocytes, FOXP3 (forkhead box P3) T lymphocytes, Granzyme B/TIA (Tcell-restricted intracellular antigen) T lymphocytes, and Tel cells (IFN- ⁇ producing CD8+ T lymphocytes).
  • Other immune cells are cells expressing a CRT receptor.
  • Such immune cells may be selected from cells expressing at least one of the following proteins: LRP1 (Low density lipoprotein receptor-related protein 1, CD91), Ca ++ -binding proteins such as SCARF1 and SCARF2, MSR1 (Macrophage scavenger receptor 1), SRA, CD59 (protectin), CD207 (langerin), and THSDl (thrombospondin).
  • LRP1 Low density lipoprotein receptor-related protein 1, CD91
  • Ca ++ -binding proteins such as SCARF1 and SCARF2
  • MSR1 Macrophage scavenger receptor 1
  • SRA protectin
  • CD207 langerin
  • THSDl thrombospondin
  • the detection step of the previously identified immune cells can be easily performed according to methods known by the man of the art such as immunochemistry, immunophenotyping, flow cytometry, Elispots assays (Panaretakis T. et al., 2009), classical tetramer stainings (Ghiringhelli F, et al., 2009), intracellular cytokine stainings, (Conforti R et al, 2010).
  • the step of determining the presence of an anticancer immune response may consist in detecting and/or dosing, in a biological sample of the patient, for example in a blood or serum sample of the patient, the presence (or normal expression) of a particular cytokine, a particular chemokine, and/or of particular antibody, the absence or abnormal expression (in particular an insufficient amount), when compared to a standard expression (for example level of expression), of the particular cytokine, of the particular chemokine and/or of the particular antibody being indicative of an absent or insufficient anticancer immune response.
  • the cytokine the presence of which is to be determined according to the previously described method may be selected from IL-lb, IL-7, IL-10, IL-12a, IL-12b, IL-15, IL-17, IL-21, IL-23, IL- 27, IL-33, TNFa, LTbeta (lymphotoxin beta), IFNalpha, beta, lambda, gamma, and the following cytokine receptors [ST2/ILlrll, IL-1R1, IL-7r, IL-15Ra, IL-21R, IL-23R, LtbR, AHR, Flt3 (fms- like tyrosine kinase receptor-3, CD135)] and the following transcription factors (RORc, RORgt, FOXP3, Ikaros, Id2, PU-1).
  • the chemokine the presence of which is to be determined according to the previously described method may be selected from CCL2 (Chemokine (C-C motif) ligand), CCL20/MIP3A, CCL5/R ANTES, CCL7, CCL25, CXCL1, CXCL2, CXCL9/ITAC, CXCL10/IP10, CXCL12/SDF1, CXCL13, CXCL16/Bonzo, CX3CL1/Fractalkine, and their receptors (CXCR1, CXCR2, CXCR4, CXCR5, CXCR6, CCR2, CCR4, CCR5, CCR7, CX3CR1).
  • the antibody (Ab) the presence of which is to be determined according to the previously described method may be selected from anti-CRT Ab, anti-NY-ESOl Ab, anti-LAGEl Ab, anti-MICA/B Ab, anti-disulfide isomer ase ERp5 Ab, anti-PARPl Ab, anti-ZNF707 (zinc finger protein) Ab in combination with PTMA (prothymosin, alpha), anti-CEP78 (centrosomal protein) Ab, anti-ODF2 (outer dense fiber of sperm tail 2) Ab, anti-SDCCAGl (serologically defined colon cancer antigen 1) Ab, anti-endothelin 1 (ET-1) ligand Ab, anti-endothelin B receptor (ET B R) Ab and anti-Rgs5 (regulator of G protein signalling 5) Ab.
  • anti-CRT Ab anti-NY-ESOl Ab
  • anti-LAGEl Ab anti-MICA/B Ab
  • the step of determining the ability of the tumor to induce an anticancer immune response consists in verifying, in the tumor cells (in particular in dying tumor cells, for example cells which have been exposed to a treatment of cancer), the presence of specific features herein disclosed and identified as "immunogenic cell death-associated molecules or signals" or “danger signals”.
  • Inventors herein demonstrate that stressed and dying tumor cells emit a particular pattern of "danger signals". These immune cell death-associated molecules are either exposed on the surface of dying cells or secreted into the microenvironment. Thus, the combined action of 'find-me' signals (for the attraction of phagocytes) and 'eat-me' signals (for corps engulfment) together with the release of hidden molecules (which often signal danger and are usually secluded within live cells), influence the switch between silent corpse removal and inflammatory reactions that stimulate the cellular immune response.
  • immunogenic cell death-associated molecules are inherent to the tumor, i.e., independent from the subject having the tumor or from the treatment the subject may have been exposed to. Others only appear in or around the tumor (for example in a tumor bed) after an exposition of the subject having the tumor to a conventional treatment of cancer.
  • an additional treatment herein identified as "compensatory immunogenic treatment of cancer" should be administered to said patient, preferably in addition to a conventional treatment of cancer, to favour a reaction from the immune system against said tumour cells.
  • the exposure or secretion can be observed or determined before or after exposition of the subject to a conventional therapy as described previously, preferably after such an exposition, even more preferably before and after such an exposition.
  • the method of determining the ability of a tumor to induce an anticancer immune response comprises a step of comparing the expression by tumor cells of functional immunogenic cell death-associated molecules before and after exposition of said tumor cells to a treatment of cancer.
  • An absent or abnormal (for example insufficient) level of expression of an immunogenic cell death-associated molecule by the tumor cell in response to a cancer treatment indicates that the cell will not be, completely or partially, destroyed or eradicated by said cancer treatment.
  • EP2084531 inventors have shown that the pre-apoptotic translocation of intracellular CRT (endo-CRT) to the plasma membrane surface (ecto-CRT) is a key feature of "immunogenic cell death". They demonstrated that when CRT is exposed on the surface of dying cells, it promotes their destruction by phagocytes such as dendritic cells. Phagocytes then interact with the immune system which is, in turn, responsible for the immune response.
  • proteins whose expression level and post-transcriptional modification regulate CRT exposure comprise in particular:
  • ceramide synthase dihydroceramide desaturase, 3- ketosphingane reductase, serine palmitoyltransferase, sphingomyelin synthase, shingomyelinase, ceramidase, ceramide synthase, sphingosine kinase, sphingosine-1 -phosphate phosphatase ;
  • Bcl-2 proteins Bax, Bak, Bok, Bcl-2, Bcl-XL, Mcl-1 as well as all the other multidomain or BH3-only proteins from the Bcl-2 family
  • FADD Fluor necrosis factor receptor type 1 -associated DEATH domain
  • FLIP FLICE-inhibitory protein
  • RIP Receptor-interacting protein
  • TRADD Tumor necrosis factor receptor type 1 -associated DEATH domain
  • BAP31 B-cell receptor- associated protein 31
  • eIF2alpha eIF2A
  • phosphorylated eIF2alpha CRT, ERp57, GCN2, HRI, PERK, PKR, PP1, GADD34, IRE1, PERK, HMGB 1 and ATF6, BiP
  • eIF2alpha eIF2A
  • CRT CRT
  • ERp57 CRT
  • KARS lysyl-tRNA synthetase
  • LysRS lysyl-tRNA synthetase
  • KDEL receptor Li-Asp-Glu-Leu endoplasmic reticulum protein retention receptor
  • the step of determining the ability of the tumor to induce an anticancer immune response may for example consist in verifying the correct expression, by tumour cells, of a protein allowing or enhancing CRT exposure at the surface of the cells (herein considered as an immunogenic cell death-associated molecule or immunogenic cell death marker).
  • a protein may be anyone of the previously described proteins.
  • such a protein may be selected in particular from CRT, CCL3 (MIP-1 -alpha) (SEQ ID NO: 456); CCR1 (MlPlalpha receptor, RANTES-R) (SEQ ID NO: 457); CCR2 (MCP-1 receptor) (SEQ ID NO: 458); IL-8 (C-X-C motif chemokine 8) (SEQ ID NO: 459); CXCR1 (IL-8 Receptor type 1) (SEQ ID NO: 460); CXCR2 (IL-8 Receptor type 2) (SEQ ID NO: 461); TNFRSF10A or TRAIL-receptor 1 (SEQ ID NO: 462), TNFRSF10B or TRAIL-receptor 2 (SEQ ID NO: 463), TNFRSF10C or TRAIL-receptor 3 (SEQ ID NO: 464), TNFRSF10D or TRAIL- receptor 4 (SEQ ID NO: 465D), iNOS (Inducible NO syntha
  • the step of determining the ability of the tumor to induce an anticancer immune response may also for example consist in verifying the correct expression (as defined previously), by tumour cells, of a protein expressed during the ER stress response and/or during the macroautophagic response of the subject's immune system (identified by inventors as involved in the immunogenic tumor cell death and herein considered as an immunogenic cell death-associated molecules).
  • Such a protein may be selected for example from AMBRA1 (Activating Molecule in Beclin-1- Regulated Autophagy), AMPK (5' adenosine monophosphate-activated protein kinase), ATG1, ATG5, ATG7, ATG10, ATG12, ATG14L (BARKOR), BCLN1 (Beclin 1), BIF1, CaMKK3 ⁇ 4 (calcium/calmodulin-dependent protein kinase kinase), DAPK (death-associated protein kinase), DDIT3 (DNA damage inducible transcript 3) (CHOP, GADD153), DRAM (damage-regulated autophagy modulator), FIP200 (RB1CC1), Fox03 (forkhead box O transcription factor), GATE-16 (Golgi-associated ATPase enhancer of 16 kDa), HDAC6 (histone deacetylase 6), HSPA5 (BiP (Binding immunoglobulin protein), GFP78, GP96
  • the presence, in a tumor sample of the subject, of an abnormal expression of a gene selected from CCR1, EIF2AK2, DNAJC10, PDIA3, EIF2A, PPP1CB, IKBKB, PPP1CC, and BAX determines the inability of the subject to induce an anticancer immune response.
  • the expression is correct if the expressed protein is active or functional, i.e., in the context of the present invention, if the expressed protein is able to directly or indirectly induce a response from the immune system directed against the tumour cell.
  • the expression abnormality is a downregulation of the expression of CCRl, a downregulation of the expression of EIF2AK2, an upregulation of the expression of DNAJC10, and/or an upregulation of the expression of PDIA3.
  • the expression abnormality is a downregulation of the expression of CCRl, a downregulation of the expression of EIF2AK2, and an upregulation of the expression of DNAJC10.
  • the expression abnormality is a downregulation of the expression of CCRl, a downregulation of the expression of EIF2AK2, and an upregulation of the expression of PDIA3.
  • tumour cells do not express or abnormally express the previously mentioned proteins
  • inventors herein indicates that a "compensatory immunogenic treatment of cancer" has to be applied to the subject having a tumor to induce a reaction of the immune system directed against said tumor.
  • the present disclosure further relates to the abnormal expression of a gene which is specific to tumor cells.
  • the step of determining the ability of the tumor to induce an anticancer immune response may also consist in detecting the presence of an altered mutated nucleic acid, of an abnormal expression of the nucleic acid, or of an abnormal expression or activity of the protein encoded by the nucleic acid in a biological sample from the tumor's subject (as defined previously), the presence of said altered nucleic acid, abnormal expression of the nucleic acid, or abnormal expression or activity of the protein encoded by said nucleic acid being indicative of the inability for the tumor to induce an anticancer immune response, in particular when the subject having the tumor has been previously exposed to a treatment of cancer.
  • This detection step may indeed be performed before or after the administration to the subject having the tumor of at least part of a treatment of cancer, typically of at least part of a conventional treatment of cancer as previously explained.
  • the detection step is preferably performed after such an administration, for example after one or two cycles of a complete treatment protocol.
  • the nucleic acid may be a gene encoding a protein selected from Eomes (SEQ ID NO: 493), IFNg (SEQ ID NO: 494), Tbx21 (Tbet) (SEQ ID NO: 495), IL-1R1 (SEQ ID NO: 496), FOXP3 (SEQ ID NO: 497), Ltb (SEQ ID NO: 498), LtbR (SEQ ID NO: 499), CXCL12 (SEQ ID NO: 500), CXCL13 (SEQ ID NO: 522), IL-33 (SEQ ID NO: 501), IL1RL1 (ST2) (SEQ ID NO: 502), IL-7r (SEQ ID NO: 503), IL-7 (SEQ ID NO: 504), Ccl5 (SEQ ID NO: 505), IL-21 (SEQ ID NO: 493), IFNg (SEQ ID NO: 494), Tbx21 (Tbet) (SEQ ID NO: 495), IL-1R1 (S
  • the step of determining the ability of the tumor to induce an anticancer immune response may consist in determining alteration in a gene locus or in the expression of the protein encoded by said gene, in a biological sample of the patient, the presence of such an alteration being indicative of the inability of the tumor to induce an anticancer immune response.
  • a method of determining the ability of a tumor to induce an anticancer immune response may comprise the following steps of (a) obtaining from the subject a test sample of tumoral DNA, cDNA or RNA, (b) contacting the test sample with at least one nucleic acid probe, wherein said nucleic acid is complementary to and specifically hybridises with a targeted altered nucleic acid sequence (one of the previously identified sequence) preferably comprising at least one point mutation, in particular a single nucleotide polymorphism (SNP), to form a hybridization sample, (c) maintaining the hybridization sample under conditions sufficient for the specific hybridization of the targeted nucleic acid sequence with the nucleic acid probe to occur, and (d) detecting whether there is specific hybridization of the altered targeted nucleic acid sequence with the nucleic acid probe.
  • a targeted altered nucleic acid sequence one of the previously identified sequence
  • SNP single nucleotide polymorphism
  • the subject if the tumor of a subject is not able to induce an anticancer immune response, the subject will be identified as resistant to conventional treatments of cancer.
  • Inventors herein demonstrate that a "compensatory immunogenic treatment of cancer" as disclosed in the present description should be administered, preferably in addition to a conventional treatment of cancer, to such resistant subjects having a tumor which is not able to induce an efficient anticancer immune response, in order to allow such a response.
  • immunogenic cell death-associated products or signals specific to the mammal, in particular to the human, i.e., independent from the presence of a tumor in the mammal subject, and independent from any treatment a mammal subject having a tumor may have been exposed to.
  • the step of determining the ability of the subject to induce an anticancer immune response may consist in detecting, using one of the previously identified methods (well known by the man skilled in the art), the presence of a mutated nucleic acid, of an abnormal expression of the nucleic acid, or of an abnormal expression or activity of the protein encoded by the nucleic acid in a biological sample (as defined previously) from the subject, the presence of said mutated nucleic acid, abnormal expression of the nucleic acid, or abnormal expression or activity of the protein encoded by said nucleic acid, being indicative of the inability for the subject to induce an anticancer immune response.
  • a method of determining the ability of a subject to induce an anticancer immune response may comprise the following steps of (a) obtaining from the subject a test sample of DNA, preferably of genomic DNA, (b) contacting the test sample with at least one nucleic acid probe, wherein said nucleic acid is complementary to and specifically hybridises with a targeted mutated nucleic acid sequence (one of the below identified sequences) comprising a point mutation, preferably a single nucleotide polymorphism (SNP), to form a hybridization sample, (c) maintaining the hybridization sample under conditions sufficient for the specific hybridization of the targeted nucleic acid sequence with the nucleic acid probe to occur, and (d) detecting whether there is specific hybridization of the mutated targeted nucleic acid sequence with the nucleic acid probe.
  • a targeted mutated nucleic acid sequence one of the below identified sequences
  • SNP single nucleotide polymorphism
  • the previously described detection step may be performed before and/or after any conventional treatment of cancer.
  • the step of determining the ability of a subject to induce an anticancer immune response may consist in detecting an abnormal nucleic acid sequence in a biological sample from the subject, the detection of such an abnormal nucleic acid sequence determining the inability of the subject to induce an anticancer immune response.
  • the method may in particular consist in verifying the presence, in the genome of the subject, of a mutated nucleic acid sequence leading to the abnormal expression of a gene involved in the "anticancer immune response", the presence of such a mutated nucleic acid sequence determining the inability of the subject to induce an anticancer immune response.
  • the nucleic acid mentioned in the previously described methods, is typically located in an immune gene as defined previously and identified below.
  • immune genes may be selected from anyone of the genes identified below in Table 1.
  • Table 1 further identifies, for each immune gene, SNP(s) associated to a non-responder status of the subject (in other words, to the inability of the subject to induce an anticancer immune response).
  • HORMAD1 rsl 336900 A/G SEQ ID NO 157 NONSYN
  • FCAR rs 16986050 A/G SEQ ID NO 177 NONSYN
  • AKAP3 rs2072355 A/C/G/T SEQ ID NO: 224 NONSYN
  • VARS2 rs2074506 A/C SEQ ID NO: 228 NONSYN
  • CEBPZ rs2098386 A/C/G/T SEQ ID NO: 231 NONSYN
  • GZMB rs2236338 A/G SEQ ID NO: 239 NONSYN
  • MORC1 rs2593943 A/G SEQ ID NO: 286 NONSYN
  • CDSN rs3130981 C/T SEQ ID NO: 297 NONSYN
  • SIGIRR rs3210908 A/G SEQ ID NO: 303 NONSYN
  • NME1-NME2 rs3760468 A/T SEQ ID NO: 330 flanking_5UTR
  • CTLA4 rs4553808 A/G SEQ ID NO: 355 flanking_5UTR
  • EGF rs4698803 A/T SEQ ID NO: 359 NONSYN
  • CTLA4 rs5742909 C/T SEQ ID NO: 388 flanking_5UTR
  • IRAK2 rs708035 A/T SEQ ID NO: 414 NONSYN
  • CTLA4 rs733618 A/G SEQ ID NO: 420 flanking_5UTR
  • Immune genes are preferably selected the NLR family pyrin domain containing 4 (NLRP4I NALP4IPAN2ICT58) gene, DDX58 [DEAD (Asp-Glu-Ala-Asp) box polypeptide 58] or RIG1 gene, the chemokine (C-X3-C motif) receptor 1 (CX3CR1/Fractalkine receptor!
  • CMKBLR11 GPR13 IV28 gene
  • MTHFR methylene tetrahydrofolate reductase
  • FAT2 gene human fat homolog proto-cadherin Fat2 (of the fly fat gene which is a tumor suppressor gene controlling cell proliferation) localized in 5q33 region]
  • AHR BHLHE76
  • TNFRSF10A/TRAILR1/CD261 gene
  • the sialic acid binding Ig-like lectin 5 SIGLEC5/CD170/OBBP2/CD33L2
  • the CPX chromosome region candidate 1 CPXCR1/CT77
  • IFNGR1/CD119 IFNy receptor 1
  • myotubularin related protein 15 MTMR15/KIAA1018.
  • Table 2 identifies, for each identified immune gene, SNP(s) associated to a non-responder status of the subject (in other words, to the inability of
  • the method is typically performed on the nucleic acid obtained from cells of a biological sample (blood or serum for example) of the subject, for example on the genomic DNA obtained from blood or seric cells, in particular leukocytes, more preferably Peripheral Blood Mononuclear Cells (PBMC), which are non cancerous cells.
  • a biological sample blood or serum for example
  • PBMC Peripheral Blood Mononuclear Cells
  • the method may also be performed on tumoral cells of the subject whose normal cells (non cancerous cells) have an altered genotype.
  • Inventors herein demonstrate that a "compensatory immunogenic treatment of cancer", as disclosed in the present description, should be administered, preferably in addition to a conventional treatment of cancer, to such resistant subjects which are not able to induce an anticancer immune response, in order to allow such a response.
  • the alteration in a nucleic acid sequence may be determined at the level of the selected gene (immune gene, specific to the subject, or tumor gene, specific to the tumor), for example AHR DNA, cDNA, RNA or polypeptide.
  • the detection is performed by sequencing all or part of the gene locus or by selective hybridization or amplification of all or part of the gene locus. More preferably a gene locus specific amplification is carried out before the alteration identification step.
  • An alteration in the gene locus may be any form of mutation(s), deletion(s), rearrangement(s) and/or insertions in the coding and/or non-coding region of the locus, alone or in various combination(s). Mutations more specifically include point mutations.
  • Deletions may encompass any region of two or more residues in a coding or non-coding portion of the gene locus, such as from two residues up to the entire gene or locus. Typical deletions affect smaller regions, such as domains (introns) or repeated sequences or fragments of less than about 50 consecutive base pairs, although larger deletions may occur as well. Insertions may encompass the addition of one or several residues in a coding or non-coding portion of the gene locus. Insertions may typically comprise an addition of between 1 and 50 base pairs in the gene locus. Rearrangement includes inversion of sequences.
  • the gene locus alteration may result in the creation of stop codons, frameshift mutations, amino acid substitutions, particular RNA splicing or processing, product instability, truncated polypeptide production, etc.
  • the alteration may result in the production of a polypeptide or protein with altered function, stability, targeting or structure.
  • the alteration may also cause a reduction in protein expression or, alternatively, an increase in said production.
  • said alteration is a mutation, an insertion or a deletion of one or more bases.
  • the alteration in the gene locus is selected from a point mutation, a deletion and an insertion in the gene or corresponding expression product, more preferably a point mutation and a deletion.
  • the alteration may be determined at the level of the DNA, RNA or polypeptide.
  • the "gene locus”, for example "the AHR gene locus” designates all sequences or products in a cell or organism including, regarding AHR for example, the AHR coding sequences, AHR non-coding sequences (e.g., introns), AHR regulatory sequences controlling transcription and/or translation (e.g., promoter, enhancer/silencer regions, terminator, 5'UTR, 3'UTR, etc.), all corresponding expression products, such as AHR RNAs (e.g., mRNAs) and AHR polypeptides (e.g., a pre-protein and a mature protein); as well as surrounding sequences of 20 kb region, preferably 15.3 kb region, upstream the starting codon (flanking the 5'UTR region) of the AHR gene and 20 kb region, preferably 14.1 kb region, downstream the untranslated region (flanking the 3'UTR region).
  • AHR RNAs e.g., mRNAs
  • the step of determining the ability of the subject to induce an anticancer immune response may consist in determining alteration in a gene locus (in particular an immune gene locus) or in the expression of the protein encoded by said gene, in a biological sample of the patient, the presence of such an alteration being indicative of the inability of the subject to induce an anticancer immune response.
  • Alteration of a nucleic acid sequence herein described is preferably a mutation, an insertion or a deletion of one or more bases. More preferably said alteration is one or several single nucleotide polymorphism(s) (SNPs).
  • the altered nucleic acid is a wild-type nucleic acid comprising at least one point mutation, preferably a single nucleotide polymorphism (SNP), for example a loss-of- function SNP, i.e., a SNP responsible for the absent or abnormal (non-functional) expression of the protein encoded by the nucleic acid.
  • the wild-type nucleic acid may also comprise several single nucleotide polymorphism(s) (SNPs).
  • any SNP in linkage disequilibrium with a first SNP associated with non- responder phenotype will be associated with this trait. Therefore, once the association has been demonstrated between a given SNP and non-responder phenotype, the discovery of additional SNPs associated with this trait can be of great interest in order to increase the density of SNPs in this particular region.
  • Identification of additional SNPs in linkage disequilibrium with a given SNP involves: (a) amplifying a fragment from the genomic region comprising or surrounding a first SNP from a plurality of individuals; (b) identifying of second SNP in the genomic region harboring or surrounding said first SNP; (c) conducting a linkage disequilibrium analysis between said first SNP and second SNP; and (d) selecting said second SNP as being in linkage disequilibrium with said first marker. Sub-combinations comprising steps (b) and (c) are also contemplated. These SNPs in linkage disequilibrium can also be used in the methods according to the present invention, and more particularly in the methods to predict treatment response or ability to induce an anticancer immune response according to the present invention.
  • Mutations in a gene locus which are responsible for non-responder phenotype may be identified by comparing the sequences of the gene locus from patients presenting non-responder phenotype and responder phenotype. Based on the identified association of SNPs of the particular gene, the identified locus can be scanned for mutations. In a preferred embodiment, functional regions such as exons and splice sites, promoters and other regulatory regions of the gene locus are scanned for mutations.
  • patients presenting non-responder phenotype carry the mutation shown to be associated with non-responder phenotype and responder phenotype do not carry the mutation or mutated allele associated with reduced cancer treatment response.
  • the SNPs protect the host against relapse, i.e, is a protective SNP.
  • the method used to detect such mutations generally comprises the following steps: amplification of a region of the gene locus of interest comprising a SNP or a group of SNPs associated with non responder phenotype from DNA samples of the gene locus from patients presenting non responder phenotype and responder phenotype; sequencing of the amplified region; comparison of DNA sequences of the corresponding genes from patients presenting non responder phenotype and responder phenotype; determination of mutations specific to patients presenting non responder phenotype.
  • the SNP may be more particularly selected from rsl0250822 (SEQ ID NO: 3), rsl 1505406 (SEQ ID NO: 4), rsl476080 (SEQ ID NO: 5), rsl7779352 (SEQ ID NO: 6), rs2066853 (SEQ ID NO: 7), rs2074113 (SEQ ID NO: 8), rs2158041 (SEQ ID NO: 9), rs2282885 (SEQ ID NO: 10), rs34938955 (SEQ ID NO: 11), rs35225673 (SEQ ID NO: 12), rs4986826 (SEQ ID NO: 13), rs713150 (SEQ ID NO: 14), rs7796976 (SEQ ID NO: 15), and rs7811989 (SEQ ID NO: 16).
  • a typical SNP in the AHR gene is rs2066853 (SEQ ID NO: 7).
  • SNP AHR A/G R554K
  • the SNP is preferably rs302453 (SEQ ID NO: 60).
  • SNP NLRP4 A/T Gln925Leu
  • the SNP is preferably rsl7217280 (SEQ ID NO: 17).
  • Such a SNP DDX58/RIG-1 A/T is indicative of the inability of the subject to respond to conventional treatments of cancer.
  • the presence of a wild-type allele A in a subject is indicative of being able to induce a better anticancer immune response.
  • the SNP is preferably rs3732378 (SEQ ID NO: 39).
  • Such a SNP CX3CR1 A/G is indicative of the inability of the subject to respond to conventional treatments of cancer.
  • the presence of a wild-type allele A in a subject is indicative of being able to induce a better anticancer immune response.
  • the SNPs are preferably rsl432862 (SEQ ID NO: 162), rs2053028 (SEQ ID NO: 216), rs6650971 (SEQ ID NO: 403).
  • SNPs FAT2 C/T (Arg574Cys), T/C (Leu3514Ser), G/A (Met3631Ile) are indicative of a subject being able to induce a better anticancer immune response.
  • Such a subject is typically responder to conventional treatments of cancer. In other words, the presence of a mutated allele in a subject is indicative of being able to induce a better anticancer immune response.
  • the SNP is preferably rsl801133 (SEQ ID NO: 194).
  • SNP MTHFR C/T A222V
  • A222V A222V
  • the presence of a wild-type allele C in a subject is indicative of the inability of the subject to respond to conventional treatments of cancer.
  • a particular method herein described comprises, in addition to previously described steps, a step of controlling, in a tumor, blood or serum sample of the subject, the presence of a herein described single nucleotide polymorphism (SNP); the detection of at least one of:
  • the alteration is a single nucleotide polymorphism (SNP) corresponding to rsl 801133 (wild type allele C / mutated allele T) (SEQ ID NO: 194).
  • SNP single nucleotide polymorphism
  • the SNP may be more particularly selected from rs302453 (SEQ ID NO: 60), rsl7857373 (SEQ ID NO: 61), rsl7857374 (SEQ ID NO: 62), rs34627915 (SEQ ID NO: 63) and rsl7854614 (SEQ ID NO: 64).
  • the SNP may be more particularly selected from rsl7217280 (SEQ ID NO: 17), rs35253851 (SEQ ID NO: 18), rs951618 (SEQ ID NO: 19), rs35527044 (SEQ ID NO: 20), rsl l795404 (SEQ ID NO: 21), rsl0813831 (SEQ ID NO: 22), rsl l899 (SEQ ID NO: 23), rsl0363 (SEQ ID NO: 24), rsl0970987 (SEQ ID NO: 25), rs35050877 (SEQ ID NO: 26), rsl2236816 (SEQ ID NO: 27), and rsl2235719 (SEQ ID NO: 28).
  • the SNP may be more particularly selected from rs3732378 (SEQ ID NO: 39), rs3732380 (SEQ ID NO: 40), rs41535248 (SEQ ID NO: 41), rsl 1715522 (SEQ ID NO: 42), rs7636125 (SEQ ID NO: 43), rsl 1710546 (SEQ ID NO: 44), rsl7038674 (SEQ ID NO: 45), rsl050592 (SEQ ID NO: 46), rs4986872 (SEQ ID NO: 47), and rsl7038679 (SEQ ID NO: 48).
  • the SNP may be more particularly selected from rs2230229 (SEQ ID NO: 29), rsl7088980 (SEQ ID NO: 30), rs20576 (SEQ ID NO: 31), rs20575 (SEQ ID NO: 32), rsl 1986840 (SEQ ID NO: 33), rs20577 (SEQ ID NO: 34), rs34737614 (SEQ ID NO: 35), rs34127830 (SEQ ID NO: 36), rs2230230 (SEQ ID NO: 37) and rs3808537 (SEQ ID NO: 38).
  • the SNP may be more particularly selected from rs3829655 (SEQ ID NO: 49), rs8108074 (SEQ ID NO: 50), rs2278831 (SEQ ID NO: 51), rs34553740 (SEQ ID NO: 52), rsl973019 (SEQ ID NO: 53), rsl7740650 (SEQ ID NO: 54), and rs8107754 (SEQ ID NO: 55).
  • the SNP may be more particularly selected from rs5984611 (SEQ ID NO: 56), rs5940915 (SEQ ID NO: 57), rs41307393 (SEQ ID NO: 58), and rsl2556970 (SEQ ID NO: 59).
  • the SNP may be more particularly selected from rsl 327475 (SEQ ID NO: 65), rsl887415 (SEQ ID NO: 66), rsl7175350 (SEQ ID NO: 67), rsl7175322 (SEQ ID NO: 68), rsl 1575936 (SEQ ID NO: 69), rs7769141 (SEQ ID NO: 70), rsl7181562 (SEQ ID NO: 71), and rsl 1914 (SEQ ID NO: 72).
  • the SNP may be more particularly selected from rs4779794 (SEQ ID NO: 73), rsl7846417 (SEQ ID NO: 74), rs34722914 (SEQ ID NO: 75), and rs8023700 (SEQ ID NO: 76).
  • the SNP may be more particularly selected from rsl432862 (SEQ ID NO: 162), rs 2053028 (SEQ ID NO: 216), and rs6650971 (SEQ ID NO: 403).
  • the presence of an alteration in a nucleic acid may be easily detected by the man skilled in the art using methods of the art such as restriction digestion, sequencing, selective hybridisation (for example with a nucleic acid probe present on a nucleotide array), and/or selective amplification, as further explained below.
  • Alterations in a gene may also be detected by determining the presence of an altered RNA expression.
  • Altered RNA expression includes the presence of an altered RNA sequence, the presence of an altered RNA splicing or processing, the presence of an altered quantity of RNA, etc. These may be detected by various techniques known in the art, including by sequencing all or part of the RNA or by selective hybridisation or selective amplification of all or part of said RNA, for instance.
  • a target nucleic acid which may be a nucleic acid from the subject or from the tumor
  • qRT-PCR real time quantitative reverse transcription PCR
  • the method comprises detecting the presence of an altered expression of the polypeptide or protein encoded by the gene of interest.
  • Altered polypeptide expression includes the presence of an altered polypeptide sequence, the presence of an altered quantity of polypeptide, the presence of an altered tissue distribution, etc. These may be detected by various techniques known in the art, including by sequencing and/or binding to specific ligands (such as antibodies), for instance.
  • the detection of an abnormal protein expression may be easily performed, by the man skilled in the art, by measuring the cellular level of mRNA encoding a normal protein, a decreased level compared to a control or standard level being correlated to an abnormal protein expression.
  • Sequencing can be carried out using techniques well known in the art, using automatic sequencers.
  • the sequencing may be performed on the complete gene locus or, more preferably, on specific domains thereof, typically those known or suspected to carry deleterious mutations or other alterations.
  • Amplification is based on the formation of specific hybrids between complementary nucleic acid sequences that serve to initiate nucleic acid reproduction.
  • Amplification may be performed according to various techniques known in the art, such as by polymerase chain reaction (PCR), ligase chain reaction (LCR), strand displacement amplification (SDA) and nucleic acid sequence based amplification (NASBA). These techniques can be performed using commercially available reagents and protocols.
  • Preferred techniques use allele-specific PCR or PCR-SSCP.
  • Nucleic acid primers useful for amplifying sequences from the gene locus of interest are able to specifically hybridize with a portion of the gene locus that flank a target region of said locus, said target region being altered, for example in the case of the immune genes, in non responder patients.
  • nucleic acid primer useful for amplifying sequences from the gene or locus of interest including surrounding regions.
  • Such primers are preferably complementary to, and hybridize specifically to nucleic acid sequences in the gene locus.
  • Particular primers are able to specifically hybridize with a portion of the gene locus that flank a target region of said locus, said target region being altered, for example in the case of the immune genes, in non responders.
  • Primers that can be used to amplify target region comprising SNPs may be designed based on their sequence or on the genomic sequence of a particular gene.
  • the invention also relates to a nucleic acid primer, said primer being complementary to and hybridizing specifically to a portion of a gene locus coding sequence (e.g., gene or RNA) altered in certain non responders subjects.
  • a gene locus coding sequence e.g., gene or RNA
  • particular primers of this invention are specific for altered sequences in a gene locus or RNA.
  • the invention also concerns the use of a nucleic acid primer or a pair of nucleic acid primers as mentioned above in a method of determining the treatment response of a subject having a tumor or in a method of assessing the response of a subject to a treatment of cancer.
  • Hybridization detection methods are based on the formation of specific hybrids between complementary nucleic acid sequences that serve to detect nucleic acid sequence alteration(s).
  • a particular detection technique involves the use of a nucleic acid probe specific for wild- type or altered (immune or tumor) gene or corresponding RNA, followed by the detection of the presence of a hybrid.
  • the probe may be in suspension or immobilized on a substrate or support (as in nucleic acid array or chips technologies).
  • the probe is typically labeled to facilitate detection of hybrids.
  • a particular embodiment of this invention comprises contacting the sample from the subject with a nucleic acid probe specific for an altered immune gene locus, and assessing the formation of an hybrid.
  • the method comprises contacting simultaneously the sample with a set of probes that are specific, respectively, for wild type gene locus and for various altered forms thereof.
  • a probe refers to a polynucleotide sequence which is complementary to and capable of specific hybridization with a (target portion of) gene or RNA, and which is suitable for detecting polynucleotide polymorphisms associated with the gene alleles which predispose to or are associated with a reduced ability of the subject or of the tumor to induce an anticancer immune response ("mutated allele").
  • Probes are preferably perfectly complementary to the particular gene, RNA, or target portion thereof. Probes typically comprise single-stranded nucleic acids of between 8 to 1000 nucleotides in length, for instance of between 10 and 800, more preferably of between 15 and 700, typically of between 20 and 500. It should be understood that longer probes may be used as well.
  • a preferred probe of this invention is a single stranded nucleic acid molecule of between 8 to 500 nucleotides in length, which can specifically hybridize to a region of a gene locus or RNA that carries an alteration.
  • the method of the invention employs a nucleic acid probe specific for an altered (e.g., a mutated) gene or RNA, i.e., a nucleic acid probe that specifically hybridizes to said altered gene or RNA and essentially does not hybridize to a gene or RNA lacking said alteration.
  • a nucleic acid probe specific for an altered (e.g., a mutated) gene or RNA i.e., a nucleic acid probe that specifically hybridizes to said altered gene or RNA and essentially does not hybridize to a gene or RNA lacking said alteration.
  • the invention also concerns the use of a nucleic acid probe as described above in a method of determining cancer treatment response of a subject or in a method of assessing the response of a subject to a cancer treatment.
  • alteration in the (immune or tumor) gene locus may also be detected by screening for alteration(s) in polypeptide sequence or expression levels.
  • immunohistochemistry for example in a tumor bed
  • ELISA for example in a blood or serum sample
  • immunoblotting in particular Western blot
  • proteomics or antibody-based biosensors directed against the protein of interest, as well as any other method known from the man of the art, can be applied to a tumour specimen as previously defined (see Obeid et al., 2007 which provide examples of such techniques).
  • Imunofluorescence staining or FACS (Fluorescent Activated Cell Sorting) analyses is an example of an appropriate method to detect the translocation of a particular protein from the inside to the surface of a cell, in particular of a tumour cell that has been previously submitted to a treatment of cancer.
  • ligands may be used, such as specific antibodies.
  • the sample is contacted with an antibody specific for a polypeptide encoded by a particular gene and the formation of a complex is determined.
  • Various methods for detecting such a complex can be used, such as ELISA, radio-immunoassays (RIA) and immuno-enzymatic assays (IEMA).
  • an antibody designates a polyclonal antibody, a monoclonal antibody, as well as fragments or derivatives thereof having substantially the same antigen specificity. Fragments include Fab, Fab' 2, CDR regions, etc. Derivatives include single -chain antibodies, humanized antibodies, poly-functional antibodies, etc.
  • An antibody specific for a polypeptide encoded by a particular gene designates an antibody that selectively binds said polypeptide, i.e., an antibody raised against said polypeptide or an epitope-containing fragment thereof.
  • Immunoblotting can in particular be used to measure the degradation of BAP31, the phosphorylation of eIF2alpha, the presence of a protein selected for example from GCN2 and HRI or the activation of a protein selected for example from caspase 8, reticulon-3, PERK, PKR, Bax and Bak in a cell, in particular a tumor cell, more particularly in a tumor cell which has been previously exposed to a cancer treatment, in particular to a conventional cancer treatment.
  • kits to predict treatment response or to predict ability to induce an anticancer immune response comprising products and reagents for detecting in a sample from a subject the presence of an alteration in a gene locus or in the corresponding polypeptide or protein; in the gene or corresponding polypeptide or protein expression; and/or in the gene activity.
  • kits comprise any primer, any pair of primers, any nucleic acid probes (wild-type and mutant) and/or any ligand, preferably antibody, described in the present invention.
  • kits can further comprise reagents and/or protocols for performing a hybridization, amplification or antigen- antibody immune reaction.
  • Particular kits are the following kits:
  • kits to detect the abnormal expression of a gene selected from CCR1, EIF2Ak2, DNAJC10, PDIA3, EIF2A, PPPICB, IKBKB, PPPICC, BAX and combinations thereof, in a tumor sample of the subject comprising (i) at least one pair of primers, in particular two, three, four, five, six, seven, eight, nine pairs of primers corresponding to the previously mentioned genes, and (ii) at least one probe, preferably a fluorescent probe, allowing the quantitative detection of the expression of a gene selected from CCR1, EIF2Ak2, DNAJC10, PDIA3, EIF2A, PPPICB, IKBKB, PPPICC, BAX, preferably at least one fluorescent probe for each of the selected genes of the previously mentioned list of genes, and (iii) a leaflet providing the control quantitative expression values corresponding to at least one of said genes in a control population.
  • kits to detect an abnormal expression of a gene selected from AHR and MTHFR comprising (i) at least one pair of primers, preferably two pairs of primers corresponding respectively to the AHR and to the MTHFR gene, and (ii) at least two differently labelled probes, preferably two differently labelled fluorescent probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from AHR and MTHFR, preferably two differently labelled probes for each of said genes.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a gene selected from FAT2 and MTHFR for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene
  • the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from FAT2 and MTHFR.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a gene selected from DDX58 (RIG-1) and CX3CR1 for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene, in a tumor or blood sample of the subject, the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from DDX58 and CX3CR1.
  • kits to detect the presence of a polymorphism associated with an abnormal expression of a NLRP4 gene for example a kit to detect the presence of a polymorphism associated with an abnormal expression of such a gene
  • the kit comprising (i) at least one pair of primers, and (ii) at least two differently labelled probes, the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of the NLRP4 gene.
  • a) (i) at least one pair of primers, (ii) at least two distinct probes, preferably different fluorescent probes, allowing the quantitative detection of the expression of a gene selected from CCR1, EIF2Ak2, DNAJC10, PDIA3, EIF2A, PPP1CB, IKBKB, PPP1CC and BAX and (iii) a leaflet providing the control quantitative expression values corresponding to at least one of said genes in a control population; and
  • kits comprising :
  • the first probe recognizing the wild-type allele and the second probe recognizing the mutated allele of a gene selected from NLRP4, FAT2 and MTHFR (for neoadjuvant therapy) or TLR4, P2RX7, DDX58 (for adjuvant therapy).
  • kits may further comprise a micro-array or a 96-wells or 384-wells plate to be used for the herein described methods and read through quantitative PCR or multiplex technology.
  • Compensatory immunogenic treatment of cancer Inventors advantageously herein provide a new strategy for treating cancer which consists in administering to the subject in need thereof an additional treatment herein identified as "compensatory immunogenic treatment of cancer".
  • a typical subject is a subject resistant to a treatment of cancer, in particular to a conventional treatment of cancer.
  • This compensatory immunogenic treatment of cancer will allow a reaction from the immune system of the subject having a tumor directed against the tumour cells, or will stimulate such a reaction.
  • Inventors have in particular discovered that such a compensatory immunogenic treatment of cancer is able to allow or improve the efficiency of a conventional therapy as described above, in a subject in need thereof.
  • the compensatory immunogenic treatment of cancer typically involves the exogenous supply, administration for example, to the subject, of at least one compensatory product (molecule, compound, drug or therapeutic agent, cell), preferably together with a conventional therapeutic agent used in a treatment as described above (in order to obtain a therapeutic effect, preferably a synergistic effect), said conventional treatment being easily selected by the cancerologist, as exemplified previously, according to the nature of the cancer to be prevented or treated.
  • a compensatory product molecule, compound, drug or therapeutic agent, cell
  • a compensatory product in the context of the present invention, is to allow the immune system to generate a cancer immune response in a subject identified, with a method herein described, as resistant to a treatment of cancer.
  • a resistance may be due to the inability of the treatment of cancer the subject has been exposed to, to the inability of the subject and/or to the inability of the tumor, to induce an anticancer immune response.
  • the compensatory product may be selected from a protein, as previously herein identified, i) allowing or enhancing CRT, ERp57, LysRS (KARS) and/or KDEL receptor exposure at the surface of tumor cells, ii) allowing or enhancing the secretion of ATP, HMGB 1 (High-mobility group box 1), LysRS and/or IL-8, iii) stimulating the autophagy machinery, and/or an ER stress response, iv) recruiting and/or activating specific effectors in tumor beds, such as IL-17 producing ⁇ T lymphocytes, cytotoxic T cells and dendritic cells, v) promoting activation of the TLR4/myd88 pathway, vi) triggering the NALP3 (Nacht Domain-, Leucine-Rich Repeat-, and PYD-Containing Protein 3) inflammasome.
  • NALP3 Nacht Domain-, Leucine-Rich Repeat-, and PYD-Containing Protein 3 inflamm
  • the compensatory product may also be selected from (i) a product allowing or enhancing the secretion of ATP, HMGB l, LysRS and/or IL-8, and/or the exposure of CRT, ERp57, LysRS and/or KDEL receptor at the surface of a tumour cell, (ii) a product stimulating the autophagy machinery and/or an ER stress response, (iii) a product recruiting and/or activating IL-17 producing ⁇ T lymphocytes, cytotoxic T cells and/or dendritic cells, (iv) a product promoting activation of the TLR4/myd88 pathway, or able to bypass said pathway, (v) a product triggering the P2RX7 (P2X purinoreceptor 7) and/or the NALP3 inflammasome, (vi) a product allowing or enhancing the secretion of IL-lb, (vii) a product capable of stimulating intratumoral Vd2 T lymphocytes, and (viii)
  • the term "endogenous" means that a particular protein (for example IL-lb) is produced by the cell as a wild-type protein.
  • the wild-type protein has to be distinguished from the recombinant protein (for example rIL-lb), the recombinant protein whose activity, in particular regarding the immune system, is respectively substantially identical to that of the previously mentioned wild-type protein, but which need a human intervention to be produced by the cell.
  • the term "homologous variant” is used to designate any protein that comprises deleted or substituted amino acid(s), for example any wild-type or recombinant protein or protein fragment that exhibits the properties of the corresponding wild-type protein, in particular that is able to induce a response from the immune system, for example an immunogenic tumor cell death or apoptosis as previously defined.
  • a preferred "compensatory product" usable in the present invention that allows or enhances the secretion of ATP, HMGB l, LysRS and/or IL-8, and/or the exposure of CRT, ERp57, LysRS and/or KDEL receptor at the surface of a tumour cell, in particular of a dying tumor cell, can be selected from rCRT, rIL-8, inhibitors of PP1/GADD34, chloroquine, TLR7 agonists, antihistaminic drugs such as brompheniramine maleate, bumetanide, cyproheptadine, fenspiride, flunisolide, ketotifene, loratadine and/or cardiotrop drugs such as amlodipine besylate, atenolol, benazepril hydrochloride, nimodipine and/or antimicrobial such as cycloserine, diloxanide furoate, fluconazole, mebendazole,
  • a preferred "compensatory product" usable in the present invention for stimulating the autophagy machinery may be selected from an apyrase inhibitor such as ecto-nucleoside-triphosphate- diphosphohydrolase (CD39) inhibitor (polyoxometalate 1), 6-N,N-Diethyl-D-beta-gamma- dibromomethylene adenosine triphosphate (ARL 67156), 2'(3')-0-(4-benzoylbenzoyl)-adenosine triphosphate, an antibody inhibiting the ecto-apyrase activity of CD39 and an antibody inhibiting the ecto-5 '-nucleotidase activity; spermidin; resveratrol; rapamycin analogs; and/or an ER stress response may be selected from recombinant calreticulin, digoxin, digitoxin, ouabain, strophantin, proscillaridin, sanguina
  • a preferred "compensatory product" usable in the present invention for recruiting and/or activating specific effectors in tumor beds may be selected from rIL-lb, rIL-17, rIL-22, a phosphoantigen, a V52 T lymphocytes activator, a leukotrien, a prostaglandin, and a chemokine.
  • a preferred "compensatory product" usable in the present invention for promoting activation of the TLR4/myd88 pathway, or able to bypass said pathway may be selected from dendrophilin, a TLR3 ligand such as such as Poly I:C, poly A:U; a TLR9 ligand such as CpG ODN (CpG oligodeoxynucleotides); HMGBl ;and chloroquine.
  • a TLR3 ligand such as such as Poly I:C, poly A:U
  • a TLR9 ligand such as CpG ODN (CpG oligodeoxynucleotides); HMGBl ;and chloroquine.
  • a product capable of promoting activation of the TLR4/myd88 pathway is selected from dendrophilin and any TLR4/myd88 agonists.
  • a preferred "compensatory product" usable in the present invention for triggering the P2RX7 (P2X purinoceptor 7 ) and/or the NALP3 inflammasome may be selected from a TLR7 agonist such as synthetic oligoribonucleotides containing arabinonucleotides, imiquimod and resiquimod; a TLR8 agonist such as polyGlO; a recombinant cytokine such as rIL-lb and IL-12; and an inhibitor of apyrases such as ecto-nucleoside-triphosphate-diphosphohydrolase (CD39) inhibitor (polyoxometalate 1), 6-N,N-Diethyl-D-beta-gamma-dibromomethylene adenosine triphosphate (ARL 67156), 2'(3')-0-(4-benzoylbenzoyl)-adenosine triphosphate, an antibody inhibiting the
  • a preferred "compensatory product" usable in the present invention that allows or enhances the secretion of IL-lb, in particular by an immune cell can be selected from recombinant IL-12 (rIL-12) and/or recombinant IL-lb (rIL-lb).
  • a recombinant cytokine may advantageously be used in combination with a molecule selected from an anti-PDl (Programmed Death 1) molecule, a B7-DCFc molecule, an antibody directed against CTLA4 (anti-Cytotoxic T- Lymphocyte Antigen 4 Ab) or against 4-1BBL (anti-4-lBBL Ab), a metronomic cyclophosphamide and any combination thereof.
  • the compensatory molecule may also be a molecule capable of stimulating intratumoral Vd2 T lymphocytes such as a molecule selected from a phosphoantigen (such as bromohydrinpyrophosphate or BrHPP, phosphostim®) and a lipid.
  • a phosphoantigen such as bromohydrinpyrophosphate or BrHPP, phosphostim®
  • a lipid such as a lipid selected from a phosphoantigen (such as bromohydrinpyrophosphate or BrHPP, phosphostim®) and a lipid.
  • a compensatory molecule is preferably used in combination with a conventional chemotherapeutic agent in particular in patients who do not correctly express IL-17.
  • the compensatory molecule may also be a molecule capable of promoting activation of costimulatory receptors (such as agonists CD40 Ab, CD27 Ab, 4- IBB Ab) or a molecule (for example an antibody) capable of blocking inhibitory pathways such as CTLA4, LAG3, Tim-3, PD- 1, PDL1, BTLA4.
  • costimulatory receptors such as agonists CD40 Ab, CD27 Ab, 4- IBB Ab
  • a molecule for example an antibody capable of blocking inhibitory pathways such as CTLA4, LAG3, Tim-3, PD- 1, PDL1, BTLA4.
  • the compensatory molecule may more particularly be selected from an anti-allergic drug, in particular an anti-histaminic drug or an anti-inflammatory drug; a neurotropic drug, in particular an antidepressant drug, an antipsychotic drug, an antiparkinsonian drug, an anti-headache drug, an analgesic drug, an anticonvulsant drug and an immunosuppressive drug; an antihypertensive or cardiotropic drug such as a Na + K + ATPase inhibitor; a spindle poison drug such as an antineoplastic drug, an antimitotic drug and an antigout drug; an antimicrobial drug, in particular an anthelmintic drug, an amebicide drug, an antibacterial drug, an antifungal drug and an antimalarial drug; an anti- osteoclastic drug; a diuretic drug; an oestrogen; an apyrase inhibitor; and any combination thereof.
  • an anti-allergic drug in particular an anti-histaminic drug or an anti-inflammatory drug
  • the anti-histaminic drug may be selected from antazoline phosphate, azelastine hydrochloride, brompheniramine maleate, cyclizine, cyproheptadine, ketotifene, fenspiride, loratadine and terfenadine.
  • the anti-inflammatory drug may be flunisolide.
  • the antidepressant drug may be selected from sertraline hydrochloride, paroxetine hydrochloride, mianserin hydrochloride, trazodone and mirtazapine.
  • the antipsychotic drug may be selected from ketanserin tartrate, risperidone, olanzapine, quetiapine fumarate, ziprasidone, clozapine, aripiprazole, haloperidol and perphenazine.
  • the antigout drug may be colchicine.
  • the antiparkinsonian drug may be selected from procyclidine hydrochloride and bromocriptine mesylate.
  • the anti-headache drug may be selected from methylsergide maleate and pizotyline malate.
  • the analgesic drug may be carbamazepine.
  • the anticonvulsant drug may be carbamazepine.
  • the immunosuppressive drug may be rapamycin.
  • the antihypertensive or cardiotropic drug may be selected from atenolol, benazepril hydrochloride, amlodipine besylate and nimodipine.
  • the antineoplastic drug may be selected from MTX, DX, vinblastine sulphate and vincristine sulphate.
  • the antimitotic drug may be colchicine.
  • the amebicide drug may be diloxanide furoate.
  • the anthelmintic drug may be mebendazole.
  • the antibacterial drug may be selected from cycloserine
  • the antifungal drug may be fluconazole.
  • the antimalarial drug may be mefloquine.
  • the anti-osteoclastic drug may be etidronate disodium.
  • the diuretic drug may be bumetanide.
  • the oestrogen may be estrone.
  • the Na + K + ATPase inhibitor may be a cardiac glycoside such as digoxin, digitoxin, ouabain, proscillaridin, strophantin and sanguinarin.
  • the apyrase inhibitor may be a ecto-nucleoside-triphosphate-diphosphohydrolase (CD39) inhibitor (polyoxometalate 1), 6-N,N-Diethyl-D-beta-gamma-dibromomethylene adenosine triphosphate (ARL 67156), 2'(3')-0-(4-benzoylbenzoyl)-adenosine triphosphate, an antibody inhibiting the ecto- apyrase activity of CD39 and an antibody inhibiting the ecto-5 '-nucleotidase activity.
  • CD39 ecto-nucleoside-triphosphate-diphosphohydrolase
  • ARL 67156 6-N,N-Diethyl-D-beta-gamma-dibromomethylene adenosine triphosphate
  • ARL 67156 2'(3')-0-(4-benzoy
  • the compensatory molecule may further be selected from an histamine HI antagonist such as antazoline phosphate, azelastine hydrochloride, brompheniramine maleate, cyclizine, cyproheptadine, ketotifene, fenspiride, loratadine or terfenadine; a 5HT uptake inhibitor such as sertraline hydrochloride or paroxetine hydrochloride; a Ca channel blocker such as amlodipine besylate or nimodipine; a spindle poison such as colchicine, vinblastine sulphate or vincristine sulfate; a topoisomerase II inhibitor such as MTX or DX; a dopamine antagonist such as haloperidol; a dopamine and serotonin antagonist such as risperidone, olanzapine, or clozapine; a glucose uptake inhibitor such as mebendazole; an inhibitor
  • the compensatory molecule may further be selected from an acetamide, an alkaloid derived from periwinkle, an alkaloid derived from ergot, an anthracycline, a benzimidazole, a benzodiazepine, a butyrophenone, a dibenzoazepine, a dibenzocycloheptene, a dibenzodiazepine, a dihydropyridine, a diphosphonate, a phenylpiperidine, a propanol and a thiazole derivative.
  • a particular acetamide may be selected from for example acetaminosalol, acetanilide, aminitrozol, bufexamac, citiolone, clofexamide chlorhydrate, clofezone, fenoxedil chlorhydrate, guanfacine chlorhydrate, lidocaine, lidocaine chlorhydrate, mefexamide chlorhydrate, oxetacaine, salicylate de picolamine, thiamphenicol, thiamphenicol aminoacetate acetylcysteinate, thiamphenicol aminoacetate chlorhydrate and valpromide.
  • a particular alkaloid derived from periwinkle may be selected from for example vindesine sulphate and vinorelbine ditartrate.
  • a particular alkaloid derived from ergot may be selected from for example lisuride maleate acide, methylergometrine maleate, methysergide maleate acide and nicergoline.
  • a particular anthracycline may be selected from for example aclarubicine chlorhydrate, daunorubicine chlorhydrate, epirubicine chlorhydrate, idarubicine chlorhydrate, pirarubicine and zorubicine chlorhydrate.
  • a particular benzimidazole may be selected from for example albendazole, astemizole, bendazol, benperidol, candesartan cilexetil, chlormidazole chlorhydrate, clemizole hexachlorophenate, clemizole penicilline, clemizole undecylenate, domperidone, flubendazole, lansoprazole, mibefradil dichlorhydrate, mizolastine, omeprazole, oxatomide, pantoprazole sodique, pimozide, rabeprazole sodique, telmisartan and tiabendazol.
  • a particular benzodiazepine may be selected from for example alprazolam, bromazepam, brotizolam, chlordiazepoxide, clobazam, clonazepam, clorazepate dipotassique, clotiazepam, cloxazolam, delorazepam, diazepam, estazolam, flunitrazepam, ketazolam, loflazepate d'ethyle, loprazolam mesilate, lorazepam, lormetazepam, medazepam, midazolam chlorhydrate, nitrazepam, nordazepam, oxazepam, pirenzepine dichlorhydrate, prazepam, temazepam, tetrazepam, tofisopam and triazolam.
  • a particular butyrophenone may be selected from for example benperidol, buflomedil chlorhydrate, droperidol, fluanisone, haloperidol decanoate, moperone chlorhydrate, pipamperone dichlorhydrate, primaperone chlorhydrate and trifluperidol chlorhydrate
  • a particular dibenzoazepine may be selected from for example carpipramine dichlorhydrate, clomipramine chlorhydrate, desipramine chlorhydrate, imipramine chlorhydrate, metapramine fumarate, opipramol dichlorhydrate, prozapine chlorhydrate, quinupramine, trimipramine maleate and trimipramine mesilate.
  • a particular dibenzocycloheptene may be selected from for example amineptine chlorhydrate, amitriptyline, amitriptyline chlorhydrate, cyproheptadine chlorhydrate, demexiptiline chlorhydrate, nortriptyline chlorhydrate, noxiptiline chlorhydrate and protriptyline chlorhydrate.
  • a particular dibenzodiazepine may be selected from for example clozapine and dibenzepine chlorhydrate.
  • a particular dihydropyridine may be selected from for example felodipine, isradipine, lacidipine, nicardipine chlorhydrate, nifedipine and nitrendipine.
  • a particular diphosphonate may be selected from for example alendronate monosodique, clodronate disodique, ibandronate sodique, pamidronate disodique and tiludronate disodique.
  • a particular phenylpiperidine may be selected from for example remifentanil chlorhydrate and sufentanil.
  • a particular propanol may be selected from for example acranil, alprenolol chlorhydrate, bufeniode, buphenine chlorhydrate, bupranolol chlorhydrate, chlorobutanol, cimepanol, clofedanol, corbadrine chlorhydrate, cyclopentobarbital ephedrine, dimercaprol, dioxethedrine chlorhydrate, dioxyphedrine chlorhydrate, diphepanol, ephedrine, ephedrine chlorhydrate, ephedrine levulinate, ephedrine sulfate, fenalcomine chlorhydrate, ifenprodil tartrate, inosiplex, isoxsuprine chlorhydrate, metaraminol bitartrate, methoxamine chlorhydrate, metoprolol succinate, metoprolol tartrate, nadolol, ornidazole, oxprenolol chlorhydrate, penbut
  • a particular thiazole derivative may be selected from for example azathioprine, bifonazole, butoconazole nitrate, carbimazole, clotrimazole, dacarbazine, econazole nitrate, eprosartan mesilate, etomidate chlorhydrate, fenticonazole nitrate, histamine dichlorhydrate, imiquimod, isoconazole nitrate, ketoconazole, metronidazole, metronidazole benzoate, miconazole, miconazole nitrate, nimorazole, ondansetron chlorhydrate, ornidazole, oxiconazole nitrate, secnidazole, sertaconazole nitrate, sulconazole nitrate, thiamazole, tinidazole and tioconazole.
  • a further object of the present invention relates to the use of at least one compensatory molecule, from the molecules identified previously, to prepare a pharmaceutical composition that is preferably intended to be administered in combination with a distinct product, typically an agent used in a treatment of cancer, in particular in a conventional treatment of cancer as mentioned previously (for example a non immunogenic treatment), to prevent or treat a cancer as defined above, in a mammal, preferably a human.
  • a distinct product typically an agent used in a treatment of cancer, in particular in a conventional treatment of cancer as mentioned previously (for example a non immunogenic treatment), to prevent or treat a cancer as defined above, in a mammal, preferably a human.
  • the compensatory molecule can be considered as an adjuvant to the conventional therapeutic drug.
  • a compensatory product should be administered to the subject, preferably together with the first exposition, for example administration, of the immunogenic conventional cancer treatment (for example chemotherapeutic drug, ionizing radiation, etc.).
  • Such a compensatory product may be selected in particular from a recombinant CRT (rCRT) and a recombinant IL-8 (rIL-8).
  • rCRT recombinant CRT
  • rIL-8 recombinant IL-8
  • the compensatory product is preferably to be administered in the tumor or in the tumor bed.
  • an immunogenic conventional cancer treatment as previously defined, for example a chemotherapy using anthracyclines
  • the tumor for example a breast tumor
  • a method as herein described as able to induce an anticancer immune response
  • a compensatory product should be administered to the subject, preferably with a conventional treatment of cancer.
  • the conventional treatment of cancer is a chemotherapy and the compensatory product is administered after each cycle of the all chemotherapeutic treatment, preferably two, three, four or five days after the exposition of the subject to a cycle of the chemotherapeutic treatment.
  • Such a compensatory product may be selected for example from IL-17 producing ⁇ T cells, phosphantigens such as biphosphonates (zoledronate) and clodronate.
  • IL-17 producing ⁇ T lymphocytes in the tumor of a subject or the presence of SNP in the genomic DNA of the subject is indicative of the absence of an anticancer immune response in the subject who has been exposed to a conventional treatment of cancer, in particular to a chemotherapeutic treatment of cancer, and reveals a resistance of the subject to the treatment of cancer.
  • a compensatory product should thus be administered to this subject, preferably locally in the tumor, preferably together with the conventional treatment of cancer.
  • a compensatory product may be selected from IL-17 producing ⁇ T lymphocytes; recombinant IL-22 (rIL-22) and/or IL-17 (rIL-17); phosphoantigenic synthetic ligands of ⁇ T lymphocytes [preferably together with recombinant IL-lb (rIL-lb) and/or IL-23 (rIL-23)], such as bromohydrin pyrophosphate (BrHPP, active pharmaceutical ingredient in Phosphostim) and V52 T lymphocytes activators such as biphosphonates (zoledronate) and/or clodronate.
  • IL-17 producing ⁇ T lymphocytes recombinant IL-22 (rIL-22) and/or IL-17 (rIL-17); phosphoantigenic synthetic ligands of ⁇ T lymphocytes [preferably together with recombinant IL-lb (rIL-lb
  • the previously mentioned compensatory products are preferably injected locally into the tumor or in a tumor bed.
  • composition comprising such a drug or compensatory molecule or a combination of identical or different drugs or compensatory molecules, in association with a pharmaceutically acceptable excipient or diluent.
  • Appropriate excipient, diluant or carrier usable in the all present invention may be selected for example from saline, isotonic, sterile or buffered solutions, etc. They can further comprise stabilizing, sweetening and/or surface-active agents, etc. They can be formulated in the form of ampoules, flasks, tablets, or capsules, by using techniques of galenic known per se.
  • the pharmaceutical composition mentioned previously may be administered to the subject in need thereof, before, during and/or after any treatment of cancer described previously. It is preferably administered during or after said treatment, for example 24 hours, two days, three days or four days after the treatment.
  • the compensatory products are IL-17 producing ⁇ T lymphocytes which may be advantageously administered to a subject in need thereof, two days after exposition of said subject to a treatment of cancer using radiotherapy or a chemotherapy wherein, for example, DX is administered to the subject.
  • compensatory molecules for use in the treatment of cancer, preferably in combination with a conventional treatment of cancer, in particular a chemotherapeutic treatment of cancer, in a subject identified, by a method as herein described, as resistant to a conventional treatment of cancer.
  • Method to prevent or treat a disease preferably in combination with a conventional treatment of cancer, in particular a chemotherapeutic treatment of cancer, in a subject identified, by a method as herein described, as resistant to a conventional treatment of cancer.
  • the present invention also relates to a method for preventing or treating a cancer, as herein defined, comprising the administration to a mammal, in particular a human, in need thereof, of at least one compound selected from the previously described compensatory molecules, preferably together with (in combination with) a distinct therapeutic agent, typically an agent used in a conventional treatment of cancer as defined previously.
  • a subject in need of a compensatory molecule is subject that has been tested and identified as resistant to a treatment of cancer according to the method described above.
  • the previously described method for treating cancer is performed on a subject having a tumor before surgical resection thereof.
  • the previously described method for treating cancer is performed on a subject having a tumor after surgical resection thereof.
  • the above method to treat a disease may comprise a step of directly injecting at least one selected compensatory molecule in the tumour, or in the tumor bed, of the subject in need thereof.
  • the present invention also provides a method for screening or selecting a compound that is able to modify the activity of the immune system towards a tumor cell, in particular to trigger an immunogenic tumor cell death, the method comprising a step of detecting and/or measuring the level of expression, by a particular tumor cell, of a functional immunogenic cell death-associated molecule as herein described, in the presence of a test compound, wherein a modified expression in comparison with a control cell that has not been exposed to or contacted with the test compound, is indicative of the capacity of said compound to modify the activity of the immune system towards said cell.
  • the present invention further provides a method for screening a compound usable for treating a cancer, as a compensatory product according to the present invention, in a subject having an altered nucleic acid, an altered nucleic acid expression, or an abnormal expression or activity of the protein corresponding to said nucleic acid, said method comprising determining in vitro, in vivo or ex vivo the ability of a test compound to (i) restore a functional expression of said altered or abnormal protein (ii) modulate (i.e., induce, increase, or decrease) the expression or activity of said protein, or (iii) modulate the expression or activity of a ligand of said protein.
  • Example 1 IL-lB-dependent contribution of IL-17 producing ⁇ cells in the efficacy of cytotoxic anticancer therapies
  • anthracyclines By triggering an immunogenic cell death modality, some anticancer compounds including anthracyclines elicit tumor-specific IFN- ⁇ producing CD8 + T cells that are mandatory for therapeutic success.
  • This adaptive immune response depends on IL- ⁇ produced by DC confronted with or exposed to anthracycline treated tumor cells.
  • Inventors analyzed the influence of immunogenic chemotherapy on the tumor microenvironment to identify inflammatory components which link innate and cognate immune responses.
  • Inventors herein demonstrate that distinct subsets of ⁇ T lymphocytes (Vy4 + and Vy6 + ) colonized tumors, where they proliferate and become potent IL-17 producers upon chemotherapy.
  • IL-17A production by ⁇ T cells fully depended on the DC mediated IL- ⁇ production and aryl hydrocarbon receptors also contributed to this process.
  • IL-17R IL-17/IL-17 receptor
  • adoptive transfer of ⁇ T cells increased the efficacy of anthracycline-based chemotherapy, under the condition that these cells express the IL-1R1. Therefore, IL-17 producing ⁇ cells or lymphocytes ⁇ 17 cells) represent a novel link between cell death and cognate immunity during anticancer chemotherapy.
  • IL-17A/IL-17R signaling pathway While the contribution of IFN- ⁇ to tumor surveillance and anticancer immune responses is clearly established, that of the IL-17A/IL-17R signaling pathway remains controversial (Kryczek et al., 2009; Martin-Orozco et al., 2009; Wang et al., 2009). In tumor models where CD4 + T cells are the source of IL-17, this cytokine promotes IL-6-mediated Stat3 activation, acting as a pro- tumorigenic trigger (Kortylewski et al., 2009; Wang et al., 2009). Thus, inventors supposed that IL- 17 could be one of the factors that link chronic inflammation to cancer development.
  • IL-17-producing CD8 + T cells could reduce the volume of large established tumor, presumably by differentiation into long-lasting IFN- ⁇ producers (Hinrichs et al., 2009). Therefore, the source and/or the targets of IL-17 must determine whether this cytokine enhances or reduces tumorigenesis. Interestingly, it appears that the production of IL-17 is strongly dependent on signaling via aromatic AHR, a ligand-activated transcription factor widely expressed in many tissues including lymphoid organs. In particular, Thl7 cells and dendritic cells express high levels of AHR.
  • ⁇ 1 T cells have been shown to either mediate immunosuppressive activities (Peng et al., 2007) or to be associated with a reduced occurrence of cancers in transplanted patients bearing a CMV infection (Dechanet et al., 1999).
  • ⁇ 2 T cells can be activated by various synthetic ligands to produce Thl-like cytokines and exhibit cytotoxic functions against tumors (Kabelitz et al., 2007).
  • ⁇ T cell subsets have been reported to be able to produce IL-17 during microbial infection or autoimmune disorders of mice (O'Brien et al., 2009; Shibata et al., 2007), no data are available on the incidence and functional relevance of IL-17- producing ⁇ T cells in cancer.
  • ⁇ 17 cells have been reported to share most phenotypic markers with Thl7 (expression of CCR6, RORyt, AHR, IL-23R, IL-17A, IL-22) (Martin et al., 2009).
  • a therapy-induced immunogenic cancer cell death which stimulates a therapeutic anti-cancer immune response influences the composition and the architecture of the immune infiltrate present in tumors, which in turn contributes to the control of residual tumor cells.
  • Inventors herein show that, in response to an immunogenic chemotherapy with anthracyclines and OXP, an early infiltration by ⁇ T17 cells is a prerequisite for optimal colonization of tumor beds by CD8 + T lymphocytes, eventually leading to tumor growth retardation or regression.
  • Inventors demonstrate that DC producing IL- ⁇ in response to dying tumor cells and AHR signaling determine and optimize IL-17 release by ⁇ T cells.
  • mice Wild type C57bl/6 (H-2 b ) and BALB/c (H-2 d ) mice aged between 7-12 weeks were purchased from Harlan (Gannat, France). Nude mice were bred in the animal facility of IGR. TCR ⁇ 7 ⁇ (H-2 b ), IL-1R1 7 (H-2 b ) and IL-17Roc 7 ⁇ (H-2 b ) mice were bred at CDTA, Louis, France through BR and PP (as for TCR ⁇ 7 ⁇ ). ⁇ 4 ⁇ 6 7 ⁇ mice (H-2 b ) were kindly provided by GM and KI. IL-23pl9 7 ⁇ (H-2 b ) were kindly provided by FP.
  • CD Id 7" and CCR6 7" (H-2 b ) were bred at St Vincent de Paul Hospital AP-HP, Paris, France and provided by KB.
  • the experimental protocols were approved by the Animal Care and Use Committee in the animal facility of Institut Gustave Roussy.
  • CT26 (H-2 d ) colon cancer, MCA205 sarcoma (H-2 b ), TS/A mammalian cancer (H-2 d ) and EL-4 thymoma (H-2 b ) were cultured in RPMI1640 supplemented with 10% FBS, 2 mM L-glutamine, 100 IU/ml penicillin/streptomycin, 1 mM sodium pyruvate, 1 mM non- essential amino acids, and 10 mM HEPES at 37° C, 5% C0 2 . All media were purchased from GIBCO, France.
  • AHR antagonist CH223191 was from Calbiochem.
  • IL- ⁇ interleukin- ⁇
  • IL-23 Recombinant mouse interleukin- ⁇
  • IL-6 Recombinant mouse interleukin- ⁇
  • TGF- ⁇ Recombinant mouse interleukin- ⁇
  • IL-18 BPd/Fc
  • DX hydrochloride D1515)
  • MTX dihydrochloride M6545
  • Mouse IL- 17, IL- ⁇ ELISA kits were purchased from eBioscience.
  • Mouse IL-22, IL-23 ELISA kits were purchased from R&D system.
  • Antibodies for CD45.2 (clone 104), CD38 (clone 145-2C11), CD4 (clone GK1.5), CD8oc (clone 53-6.7), TCR ⁇ GL-3, CD69 (clone H1.2F3), IL-17A (clone TC11-18H10) or IFN- ⁇ (clone XMG1.2) for surface or intracellular staining were from BD bioscience or eBioscience.
  • Neutralizing antibodies for IL-17 (MAB421), IFN- ⁇ (XMG1.2), CCL20 (MAB760), IL-23 (AF1619), IL-23R (MAB 1686) and IL-6 (MAB406) were from R&D system.
  • LIVE/DEAD Fixable Dead Cell Stain Kit, DiOC6(3) and DAPI were purchased from Molecular Probes, Invitrogen.
  • CpG oligodeoxynucleotide (ODN) 1668 was from MWG Biotech AG.
  • MCA205 or CT26 or TS/A tumor cells were inoculated subcutaneously near the thigh into C57B1/6 (H-2 b ) or BALB/c (H-2 d ) mice.
  • Anthracyclines-based chemotherapy was performed in MCA205 and CT26 models by intratumoral injecting DX (2 mM, 50 ⁇ ) when tumors reached the size 25-40mm .
  • Radiotherapy was performed by local X-ray irradiation (10 Gy, RT250, Phillips) at the unshielded tumor area when TS/A tumor reached the size 40-60 mm 2 .
  • RNA expression assays Tumors from mice either treated with DX or PBS were removed 8 days after treatment. Whole RNA was extracted using RNeasy Mini Kit, QIAGEN from pieces of tumor homogenates. 5 ⁇ g of RNA from each sample were reverse-transcribed using Quantitect Reverse Transcription Kit (QIAGEN). Gene expression assays were performed with TaqMan® 96 well Plates customized to test cytokines, chemokines as well as transcription factors using StepOnePlusTM Real-Time PCR System. PPIA was chosen as the endogenous control to perform normalization between different samples.
  • Tumor dissection and flow cytometry Tumor burdens were carefully removed, cut into small pieces with scissors within digesting buffer (400 U/ml Collagenase IV and 150 U/ml DNase I in RPMI1640) and incubated for 30 min at 37° C. Single cell suspension was obtained by grinding the digested tissue and filtering through 70 ⁇ cell strainer. After washing with PBS, cells were resuspended at 2xl0 7 /ml, blocked with 10 g/ml anti-CD 16/CD32 (eBioscience) in PBS containing 2% mouse serum for 5min at 4° C. 2.5 ⁇ g/ml of antibodies were used for surface staining at 4°C, 30 min.
  • digesting buffer 400 U/ml Collagenase IV and 150 U/ml DNase I in RPMI1640
  • Single cell suspension was obtained by grinding the digested tissue and filtering through 70 ⁇ cell strainer. After washing with PBS, cells were resuspended at 2xl0 7 /
  • LIVE/DEAD Fixable Dead Cell Stain Kit was used to distinguish live and dead cells.
  • freshly isolated cells were treated with, 50 ng/ml PMA, ⁇ g/ml ionomycin and Golgi-stop (BD Pharmingen), 4hrs, 37°C in RPMI containing 2% mouse serum (Janvier, France). Cells were then washed with PBS and stainied with anti-IFN- ⁇ (PE-cy7) and anti-IL-17 (PE) using BD Cytofix/CytopermTM Kit following the instructions.
  • Tumors were mechanically dissociated with lysis buffer (T-PER Tissue Protein Extraction Reagent, PIERCE) containing protease inhibitor (complete Mini EDTA-free, Roche). Tumor lysate was then centrifuged at lOOOOxg, 5min, 4°C to obtain supernatant.
  • lysis buffer T-PER Tissue Protein Extraction Reagent, PIERCE
  • protease inhibitor Complete Mini EDTA-free, Roche
  • LNs skin-draining lymph nodes
  • inguinal, popliteal, superficial cervical, axillary and brachial LNs were collected.
  • LNs were squeezed with tweezers gently in digesting buffer, kept at 37° C for 20 min and then pass through 40 ⁇ cell strainer to get single cell suspension.
  • Dead cells were removed using Dead Cell Removal Kit (Miltenyi Biotec) before purifying ⁇ T cells with TCRy/5 + T Cell Isolation Kit (Miltenyi Biotec).
  • An autoMACSTM Separator was used with the recommended programs. Purity of this isolation normally reached 95%.
  • the TCR ⁇ CD3 + cells fraction was also collected from the final separation step and was called 'non ⁇ T' cells for some experiments.
  • Day 2 after DX or PBS treatment 2.5xl0 5 cells were injected directly into the tumor with insulin syringes in adoptive transfer setting. T cell priming and tumor vaccination.
  • EG7 cells were pretreated either with 5 g/ml OXP or left untreated for 24hrs, washed thoroughly and injected at 1 million/50 ⁇ into the syngeneic mice foodpad.
  • CpG/OVA CpG (5 ⁇ g/mouse), OVA (1 mg/mouse)
  • PBS injection were used as positive and negative controls.
  • neutralizing antibody 200 ⁇ g/mouse
  • isotype control antibody was injected i.p. 5 days later, the popliteal lymph node cells were harvested, seeded in 96 well plate at 3xl0 5 /well and restimulated with 1 mg/ml OVA protein.
  • IFN- ⁇ secretion was measured by OptEIATM Mouse IFN- ⁇ ELISA kit (BD Bioscience).
  • MCA205 cells were treated with 2 ⁇ MTX for 18hrs, washed thoroughly and injected into left flank subcutaneously at 0.3 million/mouse. PBS was used as control. Mice were rechallenged with 5xl0 4 live MCA205 cells in the right flank 7 days later. Tumor growth was monitored every 2-3 days.
  • DC-tumor mixed lymphocyte cultures DC were propagated in Iscoves's medium (Sigma Aldrich) supplemented with J558 supernatant, 100 Ul/ml Penicillin, 100 ⁇ g/ml Streptomycin, 2 mM L- glutamine, 50 ⁇ 2-mercaptoethanol (Sigma), 10% heat-inactivated and filtered, 10% FCS and 40ng/ml GM-CSF. DC were used between day 8 and 12 when the proportion of CDl lc/MHC class 11+ cells was > 80%. In mixed cocultures, DC were seeded at 10 5 /100 ⁇ /well in U bottom 96 well plates.
  • Tumor cells were treated with 25 ⁇ DX or 2 ⁇ MTX for 16hrs, washed in PBS and added into these wells at 7.5xl0 5 /100 ⁇ /well. 2xl0 4 /50 ⁇ ⁇ T cells were added into the wells 12 hrs later. Supernatant was collected 48 hrs later.
  • Anthracyclines induce immune responses that culminate in CD8 + T cell- and IFN-y/IFN-y R dependent antitumor effects (Ghiringhelli et al., 2009).
  • inventors performed quantitative RT-PCR to compare the transcription profile of 40 immune gene products expressed in MCA205 tumors which were regressing in response to chemotherapy with the anthracycline DX 8 days post-treatment, with that of progressing tumors due to the absence of treatment (PBS control) (Fig. 1A).
  • Thl-related gene products were specifically induced in regressing tumors (Fig. IB).
  • Thl transcription factors Eomes and Tbx21 also called T-bet
  • IFN- ⁇ the Thl transcription factors Eomes and Tbx21
  • DX doxorubicine
  • Fig. 8A Unsupervised hierarchical clustering indicates that IFN- ⁇ production correlates with that of the transcription factor Tbx21, which is the quintessential Thl transcription factor.
  • Fig. IB Other surrogate markers of Thl responses (lymphotoxin- ⁇ , Ccl5, CxcllO, Cxcl9, TNF-a) were also significantly induced at the mRNA level following anthracycline treatment (Fig. IB).
  • Fig. IB Another set of gene products were also overexpressed in the context of anthracycline-induced tumor regression.
  • These genes encoded IL-7R, IL-21, AHR, Cxcl2 and Foxp3, suggesting that inflammation and/or tissue repair took place in the tumor bed (Fig. IB, Fig. 8A). Indeed, on days 3 to day 8 post- chemotherapy, the protein levels of the inflammatory cytokine IL-17 were significantly increased within tumor homogenates (Fig. 1C, right panel).
  • CH -223191 is a pure antagonist of AHR since it does not have any agonist actions up to 100 ⁇ (Kim et al., 2006). Blocking AHR with CH-223191 markedly reduced the efficacy of DX on established cancers in vivo (Fig. ID) although CH-223191 had no cell-autonomous effects on the tumor cells, alone or in combination with anthracyclines (Fig. 8B).
  • TILs tumor infiltrating lymphocytes
  • Fig. IE flow cytometry
  • FIG. 2C A kinetic study indicated that ⁇ TILs invade MCA205 tumor beds at early time points (Fig. 2D), rapidly divide (as indicated by the expression of Ki67) (Fig. 2E) and produce IL-17 shortly after chemotherapy, with significant increases over the background 4 days after anthracyline injection (Fig. 2D, left panel). This early induction of IL- 17 contrasts with the comparatively late induction of IFN- ⁇ production by CD8 + T cells, which emerged 8 days after chemotherapy (Fig. 2D, right panel).
  • chemotherapy triggers the accumulation of cytokine producing TILs in the tumor bed.
  • IFN-y-producing CD8 + T cells which have previously been shown to contribute to the chemotherapy-induced anticancer immune response (Ghiringhelli et al., 2009), as well as to IL-17-producing ⁇ T cells, which inventors decided to characterize at the functional level.
  • ⁇ T17 TILs had an effector memory phenotype which was preponderantly CD44 + CD62L " CD69 + granzyme B + .
  • ⁇ T17 TILs did not express CD27, CD122, Scart 2 (a marker of ⁇ T17 cells residing in skin draining lymph nodes), CD24, c-kit or NKG2D (Fig. 10).
  • Flow cytometry indicated that around 60% of tumor filtrating ⁇ T17 utilized Vy4 chain (Fig. 10) but expression of Vyl and Vy7 chain was rarely found (data not shown).
  • ⁇ T cells accumulate in tumor beds and become ⁇ T17 cells, correlating with (and presumably preceding) the accumulation of Tel cells.
  • the IL-17/IL-17R pathway is involved in the immunogenicity of cell death
  • Inventors utilize this system to check whether IL-17 is involved in initiating the specific anti-tumor response, comparing normal wild type (WT) with IL-17R0C 7" mice.
  • WT normal wild type
  • IL-17R0C 7 mice.
  • the absence of IL-17R0C fully abolished antigen-specific T cell priming in response to dying cells, yet had no negative effect to T cell priming by OVA holoprotein admixed with CpG oligodeoxynucleotides (Fig. 4B).
  • a neutralizing anti-IL-17A antibody (but not the isotype control antibody) markedly impaired the OVA-specific T cell response to OXP-treated EG7 cells (Fig. 4C).
  • IL-17 was not significantly produced by CD4 + T cells, neither in the draining LN (not shown) nor in tumor beds during chemotherapy (Fig. 2A, 2B, Fig. 9B), they refrained from investigating Thl7 cells and rather focused on ⁇ T and NKT cells as potential IL-17 producers (Mills, 2008; Pichavant et al., 2008) that might contribute to the anticancer vaccination by dying tumor cells.
  • ⁇ T lymphocytes are indispensable for the efficacy of chemotherapy
  • mitoxanthrone on established MCA205 sarcomas
  • TCR ⁇ " ⁇ 4/6 "
  • systemic chemotherapy As compared to wild type controls, the absence of the TCR ⁇ chain, as well as Vy4 and Vy6 ⁇ T cells greatly reduced the efficacy of chemotherapy (Fig. 5A).
  • CCR6 is a hallmark of Thl7 cells at the phenotypic and functional (Reboldi et al., 2009) levels during some inflammatory processes. Inventors therefore analyzed the role of CCR6 in the efficacy of chemotherapy. Since CCL20 was abundant in tumor tissues post-chemotherapy (data not shown), they assessed whether ⁇ T17 cells could be recruited in a CCL20/CCR6- dependent manner. The tumoricidal activity of DX against CT26 was not affected by repetitive systemic injections of neutralizing anti-CCL20 mAb before and during anthracyclines treatment (Fig. 5B).
  • ⁇ T17 cell activation was sorted from the skin-draining lymph nodes (LNs) of naive mice (representing about 1 % of the T cell pool contained in LN).
  • LNs skin-draining lymph nodes
  • IL-17 but not IFN- ⁇
  • PMA/ionomycine data not shown
  • LN-resident ⁇ T cells potently secreted IL-17A (and IL-22, not shown) in response to the combined stimulation with IL- ⁇ plus IL-23 (Fig. 6A).
  • TCR engagement also synergized with IL- ⁇ ⁇ (and to a lesser extent with IL-23) to trigger IL-17 secretion by LN-resident ⁇ T cells (Fig. 6B). It is noteworthy that these stimuli specifically activated IL-17 (Fig. 6A, 6B) but not IFN- ⁇ production (data not shown) by ⁇ T cells.
  • Vy4 + and Vy6 + ⁇ T cells were activated (as indicated by their Ki67 + , GzB + , CD69 + , IL-17 + phenotype) within tumor beds after chemotherapy, inventors addressed the question as to whether dying tumor cells could directly or indirectly (through myeloid antigen presenting cells) promote the activation of Vy4 + and Vy6 + T cells.
  • doxorubicin-treated MCA205 cells failed to directly induce IL-17 (or IL-22, not shown) secretion by ⁇ T cells, they did so indirectly.
  • bone marrow-derived DC (DC) that had been loaded with doxorubicin- treated MCA205 cells (Fig.
  • Dying tumor cells (exposed to doxorubicin) but not live tumor cells could trigger IL- ⁇ production by DC (Fig. 6C and (Ghiringhelli et al., 2009)).
  • the IL-17 production by ⁇ T cells was dependent on IL- ⁇ since the IL-lRl/IL- ⁇ antagonist IL-1RA entirely abrogated the DC/ ⁇ T cell cross-talk in the presence of dying cells while IL- ⁇ production was not modified (Fig.6D). Blocking AHR could also hamper IL-17 production in this co-culture system.
  • Blocking AHR markedly attenuated IL-17 production by ⁇ T cells, both at the level of cytokine release (not shown) and on a per cell basis (Fig. 6E, left panel) in response to CD3 cross-linking and IL- ⁇ and/or IL-23, yet did not affect ⁇ T cell viability (not shown) or their activation pattern (Fig. 6E, right panel).
  • ⁇ T cells might be activated locally by this cytokine. Indeed, the adoptive transfer of ⁇ T cells (instead of the non ⁇ T cells purified from naive skin LNs) into tumor beds two days post-DX ameliorated the efficacy of chemotherapy (Fig. 7A) while infusion of ⁇ T cells into non-treated tumors (failing to release IL- ⁇ ) could not control tumor outgrowth (Fig. 7A).
  • ⁇ T cells were derived from IL-1R1 loss-of-function mice, the synergistic antitumor effects of doxorubicine and adoptively transferred ⁇ T cells were lost (Fig. 7B), demonstrating the key role of endogenous IL- ⁇ in driving the ⁇ T cell response.
  • ⁇ T cells can act as enhancers of the immunological component of anticancer immune therapies, provided that they express the IL-1R.
  • Example 1 demonstrate a critical role for a subset of ⁇ T cells, particularly the Vy4 and Vy6- expressing subsets, which produce the effector cytokine IL-17, in the adaptive immune response against dying tumor cells which contributes to the efficacy of anthracycline -based conventional anticancer chemotherapy.
  • Inventor demonstrate that the IL-17/IL-17R0C signalling pathway is required for the priming of IFN-y-secreting antigen-specific T cells by tumor cells exposed to chemotherapy (Fig. 4B, 4C).
  • This tumor-specific Tcl-mediated immune response is essential for the protective anticancer immunity that is triggered by immunization with dying tumor cells (Fig. 4D) because this protective immune response is lost in athymic nude mice (Fig.
  • ⁇ T cells were the quantitatively and functionally most important IL-17 producers, based on several observations.
  • ⁇ T17 cells accumulated within tumors (Fig. 2B, 2C, 3C, Fig. 9D). Indeed, most IL-17 producing cells were positive for ⁇ T markers (Fig. 2A, Fig. 9B).
  • antigen-specific CD4 + T cells in lymph nodes (LNs) draining the dying tumor cells are polarized to a Thl cytokine (IL-2 and IFN- ⁇ ) secretion pattern (Ghiringhelli et al., 2009) instead of a Thl7 pattern (data not shown).
  • Thl cytokine IL-2 and IFN- ⁇
  • IL-6 and TGF- ⁇ two key regulatory cytokines essential for the differentiation of Thl 7 cells (Ivanov et al., 2006) were dispensable for the efficacy of chemotherapy (Fig. 12A, 12B), suggesting that Thl7 cells are not required for the anticancer immune response that amplify the effect of chemotherapy.
  • IL- ⁇ an inflammatory cytokine that is produced by dendritic cells (DC) plays a major role in stimulating IL-17 production and the anticancer function of ⁇ T cells.
  • the key role of IL- ⁇ in regulating ⁇ T cells function was shown by using IL-1RA in cocultures of DC/ ⁇ T cells in the presence of dying tumor cells (Fig. 6D).
  • ⁇ T cells that lack IL-IR cannot amplify the tumoricidal action of anthracyclines as IL-IR expressing ⁇ T cells do (Fig. 7B).
  • Example 2 the single-nucleotide polymorphism R554K (rs2066853) in AHR gene affects the efficacy of conventional anti-cancer therapy in a neoadjuvant setting (before surgery) breast cancer patients
  • SNP single-nucleotide polymorphism
  • AHR polymorphisms have the same predictive value, in particular the following AHR SNPs: rsl0250822 (SEQ ID NO: 3), rsl 1505406 (SEQ ID NO: 4), rsl476080 (SEQ ID NO: 5), rsl7779352 (SEQ ID NO: 6), rs2074113 (SEQ ID NO: 8), rs2158041 (SEQ ID NO: 9), rs2282885 (SEQ ID NO: 10), rs34938955 (SEQ ID NO: 11), rs35225673 (SEQ ID NO: 12), rs4986826 (SEQ ID NO: 13), rs713150 (SEQ ID NO: 14), rs7796976 (SEQ ID NO: 15), and rs7811989 (SEQ ID NO: 16).
  • Genotyping assay ID: C 11170747_20 was used to genotype the AHR G/A polymorphism
  • rs2066853 10 ng of genomic DNA was mixed with 5 ⁇ ⁇ of 2X TaqMan Genotyping Master Mix (Applied Biosystems) and 0,25 ⁇ ⁇ of 40X genotyping assay in a final volume of 10 ⁇ ⁇ . Temperature cycling and real time fluorescence measurement were done using an StepOnePlus System (Applied Biosystems). The genotypes were assigned to each subject, by comparing the signals from the two fluorescent probes, FAM and VIC, and calculating the -log(F AM/VIC) ratio for each data point with the StepOne software v2.0(Applied Biosystems). The other AHR SNPs have been tested with the same procedure. Examples of the following TAQMAN Genotyping assays have been used : rsl0250822 (SEQ ID NO: 3) (TAQMAN Genotypin g assay ID
  • Example 3 Restoration of the immunogenicity of cisplatin-induced cancer cell death
  • inventors specifically addressed the question why CDDP - in contrast to the related compound OXP - fails to induce immunogenic cell death.
  • they designed a screening system allowing them to identify compounds that are inert with regard to apoptotic signalling, yet can restore CDDP's capacity to induce CRT exposure and to stimulate immunogenic cell death.
  • U20S, 293FT and HeLa were cultured in DMEM medium supplemented with 10% (v/v) fetal calf serum, 1 mM sodium pyruvate and 10 mM Hepes buffer.
  • CT26, Lewis lung cell carcinoma and MC205 cells were grown in RPMI supplemented with identical components.
  • U20S clones were selected with 1 mg/ml G418 (Gibco) or Zeocin or 5 ⁇ g/ml Blasticidine and stable clones were kept under 200 ⁇ g/ml or 1 ⁇ g/ml selection respectively.
  • Lenti viral particles for the transduction of cells with H2B-RFP have been produced in 293FT cells by means of the ViraPower lenti viral expression system (Invitrogen) following the manufacturer's instructions.
  • an H2B-RFP cDNA sequence has been cloned into the pLenti6 vector by means of the gateway system.
  • the HaloTag® sequence was amplified from a pHT2 plasmid (Promega) as NotI restriction fragment with the STOP codon removed from the Halotag sequence.
  • the following primers were used: Forward :5 ' -AAGCGGCCGCAATGGGATCCGAAATCGGTAC-3 ' (SEQ ID NO: 453); Reverse : 5'-AAGCGGCCGCGCCGGCCAGCCCGGGGAGCC-3' (SEQ ID NO: 454).
  • PCR products were isolated on agarose gel, purified using the QIAquick Gel Extraction kit (Qiagen), and digested with the restriction enzyme NotI (Biolabs).
  • the digested PCR product was ligated into the CRT-GFP plasmids at the NotI restriction site after removing the GFP sequence.
  • Transfection of U20S cells with the HaloTag®-CRT was carried out with Lipofectamine 2000 (Invitrogen) following the manufacturer's instructions. Stable clones stably were selected by means of Zeocin selection. CRT-GFP, Bax-GFP; G3BP-GFP; GFP-LC3 stably expressing U20S cells
  • U20S cells have been transfected by means of Lipofectamin 2000 following the manufacturers instruction with either CRT-GFP, Bax-GFP, G3BP-GFP or LC3-GFP cDNA. Subsequently the cells have been stably selected using G418 selection antibiotic (Gibco). Resistant cells have been single cell sorted with a FACSvantage cell sorter and GFP expressing clones have been selected. Some of the clones have further been stably transduced with lenti viral particles expressing H2B- RFP. These cells have again been single cell sorted to identify double fluorescent clones.
  • U20S cells were treated with the indicated cell death inducers for 16 h at the indicated concentrations. Subsequently, cells were labeled with quinacrine as described previously (Martins et al , 2009). In short, cells were labeled with 1 ⁇ quinacrine in Krebs-Ringer solution (125 mM NaCl, 5 mM KC1, 1 mM MgS0 4 , 0,7 mM KH 2 P0 4 , 2 mM CaCl 2 , 6 mM glucose and 25 mM Hepes, pH 7.4) for 30 min at 37°C.
  • quinacrine 1 ⁇ quinacrine in Krebs-Ringer solution (125 mM NaCl, 5 mM KC1, 1 mM MgS0 4 , 0,7 mM KH 2 P0 4 , 2 mM CaCl 2 , 6 mM glucose and 25 mM Hepes, pH 7.4) for 30 min at 37°C.
  • HaloTag ® staining cells were incubated for 30 min with HaloTag ® Alexa Fluor ® 488 Ligand, diluted in DMEM medium containing 10% of fetal bovine serum. Then cells were washed and incubated in DMEM medium for 30 min. Thereafter, cells were rinsed with PBS and stained with 1 g/ml PI (Invitrogen). For CRT immune staining, cells were washed twice with PBS and fixed in 0.25% paraformaldehyde in PBS for 5 min.
  • CRT calreticulin
  • the CRT -HaloTag ® fusion protein underwent a similar intracellular redistribution (detected by staining with HaloTag ® Alexa Fluor® 488) as did CRT-GFP when the cells were treated with MTX (not shown) or OXP. Moreover, U20S cells expressing the CRT- HaloTag” fusion protein did not stain with the cell-impermeable HaloTag” ligand, unless they were treated with immunogenic cell death inducers such as OXP (Fig. 14F). Again, CDDP failed to induce the surface exposure of CRT-HaloTag ® , as determined by fluorescence microscopy (Fig. 14F) or cytofluorometric analysis of HaloTag ® TMR Ligand-stained cells (Fig. 14G).
  • CDDP is unable to induce CRT exposure in conditions in which it does induce nuclear apoptosis.
  • CDDP and OXP When used at their IC 50 , CDDP and OXP had a comparable potency in inducing nuclear apoptosis (not shown). Moreover, both agents were able to induce mitochondrial perturbations that were assessed by two different methods. First, inventors determined the A ⁇ m dissipation by means of the A ⁇ IV-sensitive fluorochrome DiOC 6 (3) (Fig. 15A,B). Second, they measured the relocation of a Bax-GFP fusion protein (von Haefen et al , 2004) from a diffuse to a punctate (presumably mitochondrial) pattern (Fig. 15C,D). Both CDDP and OXP induced similar mitochondrial perturbations (Fig. 15).
  • both agents induced a similar release of ATP, which is one of the obligatory signals linked to immunogenic cell death (Ghiringhelli et al , 2009).
  • This result was obtained using two different methods, namely staining of the cells with the ATP-sensitive fluorochrome quinacrine (Fig. 15A,B), or by measuring the residual ATP content within the cells (Fig. 16C) or the ATP secreted into the supernatant by means of a luciferase-based assay (Fig. 16D).
  • both agents lead to similar perturbations in energy metabolism.
  • OXP and CDDP ware rather different in their capacity to elicit the redistribution of G3BP-GFP (Tourriere et al , 2003) or LC3-GFP (Kabeya et al , 2000) from a diffuse to a punctiform distribution, which indicates the formation of stress granules (Fig. 17A,B) or of autophagosomes (Fig. 17C,D), respectively.
  • This difference was particularly remarkable at early time points.
  • the formation of stress granules and autophagosomes is subordinated to the mandatory phosphorylation of eIF2oc, which is also required for the redistribution of CRT to the cell surface (Obeid et al , 2007b).
  • OXP was much more efficient than CDDP in inducing eIF2oc phosphorylation on serine 51 , as determined by means of a phospho-neoepitope-specific antibody (Fig. 17E). Accordingly, the activating phosphorylation of PERK, the principal eIF2oc kinase elicited by chemotherapeutic agents (Panaretakis et al , 2009), was detectable shortly after treatment with OXP but not CDDP (Fig.l7E). Altogether, these results suggest that CDDP is much less efficient in inducing an ER stress response than OXP. Identification of thapsigargin as an agent that reestablishes CRT relocalization in response to cisplatin.
  • THAPS was capable of inducing the redistribution of CRT-HaloTag ® (Fig. 19A), as well as that of endogenous CRT (Fig. 19B), as determined using the cell-impermeable CRT-HaloTag ® ligand or antibodies recognizing CRT, respectively. While THAPS alone (in the absence of CDDP) was comparably inefficient in inducing CRT-GFP granularity (Fig. 18D), CRT-HaloTag ® exposure (Fig. 19A) or native CRT exposure (Fig. 19B), it was highly efficient in the presence of CDDP.
  • THAPS exhibited no major cytotoxic effects and did not increase the toxicity of CDDP in any of these cellular models, as exemplified for U20S cells in which inventors monitored A ⁇ m (Fig. 20A), intracellular ATP content (Fig. 20B,C,D) and extracellular ATP release (Fig. 20E).
  • CDDP-treated MCA204 cells were inefficient in inducing a protective anticancer immune response when injected subcutaneously into immunocompetent B6B157 mice one week before rechallenge with live tumor cells, in conditions in which OXP-treated MCA205 cells readily induce such a tumor-protective response (which precludes the growth of live MCA205 cells).
  • the vaccine of dying cells generated in the presence of CDDP combined with THAPS, elicited an effective anticancer immune response in vivo (Fig. 19F).
  • THAPS can reestablish the defective CRT exposure and associated immunogenicity of CDDP-induced cell death.
  • CDDP fails to induce immunogenic tumor cell death that would allow the stimulation of an anticancer immune reponse and hence amplify its therapeutic efficacy. This failure to induce immunogenic cell death can be attributed to CDDP' s incapacity to elicit the translocation of CRT from the lumen of the ER to the cell surface.
  • the previous results show that, in contrast to OXP, CDDP is unable to activate the protein kinase-like ER kinase (PERK)-dependent phosphorylation of the eukaryotic translation initiation factor 2a (eIF2a).
  • PERK protein kinase-like ER kinase
  • CDDP also failed to stimulate the formation of stress granules and macroautophagy, two processes that only occur after eIF2oc phosphorylation.
  • THAPS an inhibitor of the sarco/endoplasmic reticulum Ca(2+) ATPase (SERCA) as a molecule that on its own does not stimulate CRT exposure, yet endows CDDP with the capacity to do so.
  • SERCA sarco/endoplasmic reticulum Ca(2+) ATPase
  • Such a molecule is identified, in the context of the present invention, as a compensatory molecule.
  • This experiment also allowed the identification of other compensatory molecules (in particular microtubules destabilizers), identified in the description part, which are also able to induce an immunogenic cell death.
  • Example 4 Restoration of the immunogenicity of conventional treatment-induced cancer cell death
  • the protocol described in example 3 has been applied in example 4 to screen other compounds (Fig. 21) from the US drug collection library from MS discovery (US 090917 A). These compounds have been screened at ⁇ .
  • Inventors analyzed the capacity of the drugs to induce immunogenic cell death or to render the per se non immunogenic anticancer agent mitomycin C immunogenic. To address this question, they generated several cell lines that express a series of cell death- or cell stress-relevant biomarkers. This screening system enabled the identification of compounds that can restore or confer the capacity to induce ER stress-dependent CRT exposure, autophagy-dependent ATP release as well as cell death-dependent HMGB 1 release and thereby stimulate immunogenic cell death. Materials and Methods Reagents and materials
  • U20S and 293FT were cultured in DMEM medium supplemented with 10% (v/v) fetal calf serum, 1 mM sodium pyruvate and 10 mM Hepes buffer.
  • MCA205 cells were grown in RPMI supplemented with identical components.
  • U20S clones were selected with 1 mg/ml G418 (Gibco) or Zeocin or 5 ⁇ g/ml Blasticidine and stable clones were kept under 200 ⁇ g/ml or 1 ⁇ g/ml selection respectively.
  • Lenti viral particles for the transduction of cells with H2B-RFP have been produced in 293FT cells by means of the ViraPower lenti viral expression system (Invitrogen) following the manufacturer's instructions.
  • an H2B-RFP cDNA sequence has been cloned into the pLenti6 vector by means of the gateway system.
  • U20S cells have been transfected by means of Lipofectamin 2000 following the manufacturers instruction with either HMGB 1-GFP cDNA. Subsequently the cells have been stably selected using G418 selection antibiotic (Gibco). Resistant cells have been single cell sorted with a FACSvantage cell sorter and GFP expressing clones have been selected. The clones have further been stably transduced with lenti viral particles expressing H2B-RFP. These cells have again been single cell sorted to identify double fluorescent clones.
  • the images were segmented and analyzed for GFP-granularity and nuclear shape area using the BD Atto Vision software version 1.6 before data mining.
  • the data was statistically evaluated using graph pad. To avoid inter plate variations the data has been intra plate normalized by calculating the ratio to untreated controls for each datapoint. CRT- exposition inducing, and ATP-, HMGB1- releasing drugs death assays
  • WT cells were incubate for 16 h before staining with quinacrine (see below). After washing with PBS 4 viewfields per well were acquired by means of a BD pathway 855 automated microscope. The images were segmented and analyzed for GFP-granularity, HMGB1- GFP nuclear intensity and quinacrine cytoplasmic granularity in addition the nuclear shape area was analyzed as a marker for apoptosis using the BD AttoVision software version 1.6 before data mining. The data was statistically evaluated using graph pad. To avoid inter plate variations the data has been intra plate normalized by calculating the ratio to untreated controls for each datapoint.
  • U20S cells were treated with the indicated cell death inducers or compound library for 16h at the indicated concentrations. Subsequently, cells were labeled with quinacrine as described previously (Martins et al , 2009). In short, cells were labeled with 1 ⁇ quinacrine in Krebs-Ringer solution (125 mM NaCl, 5 mM KC1, 1 mM MgS0 4 , 0,7 mM KH 2 P0 4 , 2 mM CaCl 2 , 6 mM glucose and 25 mM Hepes, pH 7.4) for 30 min at 37°C.
  • Krebs-Ringer solution 125 mM NaCl, 5 mM KC1, 1 mM MgS0 4 , 0,7 mM KH 2 P0 4 , 2 mM CaCl 2 , 6 mM glucose and 25 mM Hepes, pH 7.4
  • CRT immune staining cells were washed twice with PBS and fixed in 0.25% paraformaldehyde in PBS for 5 min. After washing again twice in cold PBS, cells were incubated for 30 min with primary antibody, diluted in cold blocking buffer (2% fetal bovine serum in PBS), followed by washing and incubation with the Alexa488-conjugated monoclonal secondary antibody in a blocking buffer (for 30 min). Each sample was then analyzed by FACScan (Bee ton-Dickinson) to identify cell surface CRT. Isotype-matched IgG antibodies were used as controls, and the fluorescent intensity of stained cells was gated on Pi-negative cells.
  • FACScan Bee ton-Dickinson
  • U20S cells were seeded in 6 well plates 24 h before the experiment. The medium was changed to fresh DMEM before the treatment was applied. Supernatants were collected at 24 h post treatment, dying tumor cells were removed by centrifugation and supernatants were collected and shock frozen in liquid nitrogen. Quantification of HMGB 1 in the collected supernatants was performed by enzyme -linked immunosorbent assay according to the manufacturer's instructions. Retrospective clinical study
  • CRT-GFP redistribution as a surrogate marker for CRT-exposure was validated by means of a cluster analysis in which untreated control, MTX or CG treated CRT-GFP cells were additionally stained with anti-CRT and secondary Alexa546-labeld antibody. A minimum of 500 cells was analysed and increased CRT-GFP redistribution and CRT surface staining was scored. In most of all cases the treated cells displayed the phenotype of CRT-GFP redistribution together with CRT exposure (Fig. 28 B and C) validating the chosen screening model. The exposure of CRT was strongly dependent of reactive oxygen species as the antioxidants NAC and GSH significantly diminished CRT exposure upon Digoxin and Digitoxin treatment (Fig.
  • CGs most widely used in clinics are digoxin and digitoxin, with the first being the most favoured. Focussing on these two inventors could show that both of them induce CRT exposure (Fig. 28F), HMGB1 release (Fig. 28G) and ATP release (Fig 28H) in a dose dependent fashion but still within the therapeutic window for human application in the nanomolar range thereby validating the findings of the initial HTS approach.
  • MCA cells cotreated with digoxin and MitoC inocculated into immunocompetent mice kept living cell of the same kind from forming a tumor as compared to MitoC alone that failed to confer any vaccinating effect (Fig. 29C). Due to its incapacity to induce cell death at the concentrations used digoxin treated cells used for the same studies led to tumor formation at the vaccination side and were therefore not further evaluated.
  • HTS designed for monitoring immunogenic signals induced by cytotoxic treatment enabled the screening of a huge number of drugs for their potential to cause or restore immunogenic cell death.
  • Cardiac glycosides and in particular digoxin and digitoxin induced all features of immunogenic cell death.
  • MitoC fails to induce immunogenic tumor cell death that would allow the stimulation of an anticancer immune response and hence amplify its therapeutic efficacy.
  • Digoxin with MitoC effectively induced immunogenic cell death, while each agent alone was inefficient.
  • clinical data underline the importance of this finding as CG co- treated patients depict an increased overall survival. Altogether, these results indicate again the contribution of ion fluxes especially Ca 2+ for the translocation of CRT to the cell surface.
  • Example 5 a single-nucleotide polymorphism in anyone of CCR1, EIF2AK2, DNA.TC10 genes affects the efficacy of conventional anti-cancer therapy in a neoadjuvant setting (before surgery) breast cancer patients
  • Inventors attempted to generate a molecular parameter signature of a pathological complete response (pCR) from two datasets of gene -expression arrays in neoadjuvant (before any surgery step) anthracycline treated-breast cancer patient cohorts (cohorts respectively herein identified HOUSTON FEC and IGGO FEC).
  • pCR pathological complete response
  • One dataset of gene-expression arrays in neoadjuvant taxane treated-breast cancer patients was used as negative control (cohort IGGO TET).
  • Inventors extracted a set of 43 genes from cohort HOUSTON FEC and 53 genes from cohort IGGO FEC/TET implicated in the "calreticulin" pathway from the global sets of genes identified previously in the description (using respectively 22 283 probes and 61 359 probes) to construct the molecular parameter signature.
  • Inventors performed a molecular classifier development analysis based on a supervised learning classification technique (Support Vector Machines - SVM) (Fig. 22). Leave -one-out cross- validation (LOOCV) was used to estimate the prediction accuracy of the rule determined on the training set (the previously mentioned 43 and 53 genes). One sample is left out, and the remaining samples are used to build the prediction rule, which is then used to classify the left-out sample. Then, they performed, in one hand, univariate analyses with contingency tables: the statistical significance of the discrimination between pCR and non-pCR patients was assessed by Fisher's exact test.
  • LOOCV Leave -one-out cross- validation
  • multivariate methods such as logistic regression and ROC analyses, were performed to validate the independency of the molecular parameter signature as compared to classical clinical factors [age at diagnosis, hormone receptors, tumor grade, tumor size (pT), node status (pN)] (Fig. 22).
  • the classifier was constructed with the 3 candidate genes located in the grey areas (Fig. 25). Univariate analyses based on non-pCR vs pCR contingency tables and multivariate analyses revealed that the common classifier based on the CCRl, EIF2AK2 and DNAJC10 gene expressions ("CALR pathway" signature) was able to predict accurately the response of a human subject having a tumor to anthracyclines (Fig. 26).
  • tumour parameters such as gene expression signatures
  • host the subject having a tumor
  • genetic parameters such as SNPs
  • microarray analyses such as SVMs (Brown et al., 2000) and non parametric Mann-Whitney test, were performed with the MEV software version 4.5 (Saeed et al., 2006; Saeed et al., 2003).
  • MEV software version 4.5 For multivariate logistic regression and ROC (Receiver operating characteristic) analyses, the SPSS 18.0 software was used. The Fisher's exact test was performed with the StatEL software (ad Science, France).
  • Example 6 a single-nucleotide polymorphism in anyone of NLRP4, DDX58, CX3CR1, FAT2, MTHFR genes affects the efficacy of conventional anti-cancer therapy in a neoadjuvant setting (before surgery) breast cancer patients
  • SNP single-nucleotide polymorphism
  • pCR pathological complete response

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Abstract

La présente invention concerne le domaine de la génétique, de l'immunologie et de la médecine. De manière plus spécifique, la présente invention concerne des procédés in vitro et in vivo permettant la détermination de la susceptibilité à un traitement du cancer d'un sujet atteint d'une tumeur. Ces procédés comprennent une étape de détermination de la capacité du traitement, du sujet et/ou de la tumeur d'induire une réponse immunitaire anti-cancéreuse, l'incapacité d'au moins un parmi le traitement, le sujet et la tumeur d'induire une réponse immunitaire anti-cancéreuse indiquant une résistance du sujet au traitement thérapeutique du cancer. En particulier, les inventeurs identifient des gènes spécifiques d'un sujet humain ou de cellules cancéreuses qui peuvent être utilisés pour prédire ou évaluer la sensibilité d'un sujet à un traitement du cancer. L'invention concerne également des composés particuliers capables d'activer ou d'améliorer le système immunitaire d'un sujet particulier, lorsque le sujet est exposé à un traitement thérapeutique du cancer ou avant une telle exposition. L'invention concerne en outre les utilisations de tels composés, notamment pour préparer une composition pharmaceutique pour permettre ou améliorer l'efficacité d'une thérapie du cancer chez un sujet qui en a besoin. Enfin, la présente invention concerne des trousses, des procédés pour la sélection d'un composé d'intérêt, ainsi que des compositions pharmaceutiques et leurs utilisations.
EP20110713731 2010-04-22 2011-04-01 Composés et leurs utilisations pour induire la mort d'une cellule cancéreuse immunogène chez un sujet Withdrawn EP2561088A1 (fr)

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PCT/IB2010/002034 WO2012007783A1 (fr) 2010-07-13 2010-07-13 Trousses et procédés de détection de la capacité à induire une mort cellulaire cancéreuse immunogène chez un patient
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US9605080B2 (en) 2014-11-21 2017-03-28 Bristol-Myers Squibb Company Antibodies against CD73
US10653791B2 (en) 2014-11-21 2020-05-19 Bristol-Myers Squibb Company Antibodies comprising modified heavy constant regions
CN112641783A (zh) * 2021-01-05 2021-04-13 福建中医药大学 乙氧基血根碱的用途及相关产品

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EP3153591A1 (fr) * 2015-10-06 2017-04-12 Eberhard Karls Universität Tübingen Détermination du risque de cancer colorectal et de la probabilité de survie
KR102431703B1 (ko) * 2017-01-23 2022-08-11 인스티튜트 구스타브 루시 방사선요법에 대해 종양을 민감화하기 위해 사용하기 위한 세포 상호포식의 인핸서

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US90917A (en) 1869-06-08 Improved mode of forming the connections of gas-purifiers
US20080027010A1 (en) * 2004-09-02 2008-01-31 Bionaut Pharmaceuticals, Inc. Treatment of refractory cancers using Na+/K+-ATPase inhibitors
EP2084531B1 (fr) 2006-09-08 2013-11-06 Institut Gustave Roussy Composés régulateurs de l'exposition de la calreticuline ou des récepteurs kdel et utilisation pour évaluer l'efficacité d'un traitement anticancéreux

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Cited By (7)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US9605080B2 (en) 2014-11-21 2017-03-28 Bristol-Myers Squibb Company Antibodies against CD73
US10100129B2 (en) 2014-11-21 2018-10-16 Bristol-Myers Squibb Company Antibodies against CD73 and uses thereof
US10167343B2 (en) 2014-11-21 2019-01-01 Bristol-Myers Squibb Company Antibodies against CD73
US10653791B2 (en) 2014-11-21 2020-05-19 Bristol-Myers Squibb Company Antibodies comprising modified heavy constant regions
US11352440B2 (en) 2014-11-21 2022-06-07 Bristol-Myers Squibb Company Antibodies against CD73 and uses thereof
CN112641783A (zh) * 2021-01-05 2021-04-13 福建中医药大学 乙氧基血根碱的用途及相关产品
CN112641783B (zh) * 2021-01-05 2022-01-28 福建中医药大学 乙氧基血根碱的用途及相关产品

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