Mitochondrial genotype score: a prognostic marker for chemotherapy-sensitive cancers

Abstract

A prognostic risk score for chemotherapy-sensitive cancers, particularly acute myeloid leukemia (AML), is based on somatic genetic abnormalities affecting specific genes in the mitochondrial genome.

Description

[Technical field]

[0001] The present invention relates to a prognostic risk score for chemotherapy-sensitive cancers, in particular acute myeloid leukemia (AML), based on somatic genetic abnormalities affecting specific genes in the mitochondrial genome. [Background technology]

[0002] In the following description, references in brackets [ ] refer to the literature list at the end of this document.

[0003] Acute myeloid leukemia (AML) is an uncontrollable malignant proliferation of immature myeloid precursor cells, called leukemic cells, that remain at an early stage of differentiation and accumulate in the bone marrow and eventually in other organs. Despite advances in treatment methods, the prognosis is very poor, with only 35-40% of adult patients under 60 years of age and 5-15% of adult patients over 60 years of age being cured. Currently, prognostic factors used in practice are based on age, level of circulating leukocytes, and the European LeukemiaNet (ELN) 2017 prognostic classification (Dohner et al., 2017) [1]. The ELN 2017 classification is based on cytogenetic and / or molecular alterations and defines three statuses: good, intermediate, and poor. However, this prognostic classification has room for improvement. For example, in the good group, the 5-year survival rate for patients under 60 years of age is only 64% (35% for patients over 60 years of age) [2]. The European LeukemiaNet prognostic classification has a recent update, the ELN 2022 (Dohner et al., 2017)[3].

[0004] Mitochondria are bacterial organelles present in all eukaryotic cells (except red blood cells). They play important roles in regulating cellular metabolism, energy supply (Krebs cycle, β-oxidation of fatty acids, etc.), as well as calcium homeostasis, generation of reactive oxygen species (ROS), and initiation of apoptosis. Somatic mutations in isocitrate dehydrogenase (IDH1, IDH2), a mitochondrial enzyme present on the nuclear genome, cause deregulation of the Krebs cycle with accumulation of 2-hydroxyglutarate, a neometabolite that causes leukemia.

[0005] In AML, the activity of oxidative phosphorylation (OXPHOS) levels directly correlates with the resistance of leukemic cells (Farge et al., 2017) [4]. Moreover, mitochondrial transfer between stromal cells and leukemic cells has been explained as the cause of leukemic cell resistance to chemotherapy. A prospective study (DRCI LAM38RC13-209) showed that deregulation of mitochondrial reactive oxygen species (ROS) production in leukemic cells is associated with poor prognosis (reduced overall survival), independent of the usual AML prognostic factors (age, WBC / l, ELN2017, transplant) (Mondet et al., 2019) [5]. Thus, several measures converge on the role of mitochondria in AML resistance to chemotherapy.

[0006] Some publications even suggest the use of mitochondrial targeting drugs in AML or other cancers to suppress resistance and increase sensitivity to chemotherapy (Bosc et al., 2021; Neuzil et al., 2013) [6, 7]. However, at present, there are no specific companion tests for these new therapeutic strategies that will benefit only certain patients. A companion test is a diagnostic test that allows the selection of only those patients diagnosed with a particular disease who are likely to benefit from the treatment based on the status of predictive markers identified by the test.

[0007] Venetoclax is an inhibitor of the anti-apoptotic protein BCL-2, a protein that localizes to the mitochondrial membrane. Venetoclax directly binds to the binding groove in the BH3 domain of BCL-2 by displacing pro-apoptotic proteins that contain a BH3 motif, such as BIM, and initiates mitochondrial outer membrane permeabilization (MOMP), caspase activation, and apoptosis. This therapy is currently approved for use in patients with chronic lymphocytic leukemia, lymphoma, and recently acute myeloid leukemia who are "unfit," i.e., unable to tolerate standard chemotherapy. Response to venetoclax treatment is related to mitochondrial status. However, no association with mitochondrial genome mutations has been reported to date.

[0008] In fact, regarding the mitochondrial genome, few studies have analyzed the impact of mitochondrial genome mutations as a prognostic marker for AML. Mutations in ND4, which encodes a subunit of complex I, were analyzed in 452 patients through targeted sequencing (different from high-throughput sequencing techniques) in AML and were associated with increased overall survival in univariate analysis (Damm et al., 2012) [8]. However, multivariate analysis did not provide significant support for this result (p=0.089). The article even concluded that this result should be confirmed by other studies. Another study investigated the prognostic impact of ND4 mutations in 121 AML patients (Chun et al., 2014) [9]. However, this study did not show any difference in overall survival or relapse-free survival. Therefore, the prognostic impact of ND4 is not a definite data for those skilled in the art.

[0009] Mutations affecting the COX1 and COX2 genes were analyzed by high-throughput sequencing (Silkjaer et al., 2013)

[13] and Sanger sequencing in acute myeloid leukemia (Silkjaer et al., 2013)

[14] . In the high-throughput sequencing study, COX1 and COX2 mutations were associated with decreased overall survival in univariate analysis. However, multivariate analysis did not significantly confirm this result

[13] . A subsequent Sanger sequencing study showed no prognostic impact of the presence of mutations in COX1 or COX2 in the entire group of 165 affected patients treated with curative chemotherapy

[14] . Thus, the prognostic impact of COX1 and COX2 mutations is not conclusive data for those skilled in the art. Furthermore, the sensitivity threshold of the techniques used in Sanger-type sequencing is 20% (see Materials and Methods in Ref.

[14] ), which underestimates the detection of variants in the patient cohort (16% variants in COX1 and COX2 genes, compared to 30-35% in high-throughput sequencing considering a heteroplasmy threshold of ≥2%). Finally, high-throughput sequencing studies did not take haplogroups into account in variant selection.

[0010] Nevertheless, the mitochondrial genome is 16 kB, with 37 genes encoding 13 proteins involved in the respiratory chain, 22 tRNAs, and 2 rRNAs. Another study based on publicly available somatic cell genetic data obtained from the cbioportal site (https: / / www.cbioportal.org / ) analyzed the effect of mutations on acute myeloid leukemia (Wu et al., 2018)

[10] . Nevertheless, this study has several biases. One of them is related to the use of bioinformatics analysis specific to genomic DNA, not limited to mitochondrial DNA. In this study, only 8% of AML patients have mutations in genes (ND1, ND2, ND3, ND4, ND4L, ND5, ND6, CYB, COX1, COX2, COX3, ATP6, ATP8). Errors in the analysis of genetic data can lead to an underestimation of the number of variants, distorting the final results. In comparison, a study of the ND4 gene alone (Damm et al., 2012)[8] found a mutation frequency of 6.4% (29 / 452). Because mitochondrial DNA has its own genetic code, using a common bioinformatics analysis between nuclear genomic and mitochondrial mutations leads to misinterpretation of the obtained variants (Caudron-Herger and Diederichs, 2018)

[11] . The same analytical bias exists in other pathologies (e.g., cbioportal site dated August 10, 2021, Study of Diffuse Large B-Cell Lymphoma, Duke 2017, 0% of mutations are present in the ND1, ND2, ND3, ND4, and ND4L genes, compared to 35% in the study by Zeng et al., 2018).

[0011] Other than the studies by Damm et al. and Chun et al., analyzing only the ND4 gene, Silkjaer et al., analyzing the COX1 and COX2 genes [13-14], and the study by WU et al., which used inadequate bioinformatics analysis, no studies have demonstrated the contribution of mitogenome alterations in the stratification of AML patients. Summary of the Invention [Problem to be solved by the invention]

[0012] Therefore, the study of the mitochondrial genome and the identification of possible new prognostic markers remain a challenge to better stratify AML patients in terms of overall survival and to adapt therapeutic management according to survival prognosis. [Means for solving the problem]

[0013] The present inventors have demonstrated, for the very first time, a score based on the combined presence and absence of mutations in specific genes of the mitochondrial genome as a prognostic marker for acute myeloid leukemia (AML).

[0014] Therefore, the inventors have developed a score (hereinafter referred to as Mitoscore) for predicting the response to chemotherapy treatment and survival of patients suffering from AML. Mitoscore is based on mitochondrial genome sequencing techniques (e.g. NGS techniques, etc.). Based on molecular abnormalities, particularly of the genes ND1, ND2, ND3, ND4, ND5, CYTB, ATP6, ATP8, COX1, COX2, COX3, 12S (also known as MT-ND1, MT-ND2, MT-ND3, MT-ND4, MT-ND5, MT-CYB, MT-ATP6, MT-ATP8, MT-CO1, MT-CO2, MT-CO3, MT-RNR1, respectively. Table 1 below shows the official nomenclature of the mitochondrial genes used in the prognostic score of the present invention), Mitoscore stratifies patients suffering from AML at the time of diagnosis into three respective prognostic groups: good, intermediate, and poor. This is in terms of overall survival based on the combination of variants of the above genes.

[0015] [Table 1]

[0016] Mitoscore allows improved prognostic stratification to distinguish good from bad responders and adapt therapeutic management compared to the currently used prognostic score European LeukemiaNet 2017 (ELN2017) for patients with AML. Mitoscore also allows improved prognostic stratification compared to the recently published prognostic score European LeukemiaNet 2022 (ELN 2022). Mitoscore is valid independently of the usual prognostic factors (age, WBC count, ELN, transplant) and can be combined with the prognostic scores European LeukemiaNet 2017 (ELN2017) or European LeukemiaNet 2022 (ELN 2022), collectively referred to as the ELN prognostic score, in the following score format referred to as Mitoscore+.

[0017] Mitoscore improves the prognostic stratification of AML patients at the time of diagnosis. Moreover, compared to ELN classification, which requires the culture of leukemic cells to obtain a karyotype and then sequence analysis of molecular abnormalities, for example by NGS techniques (panel of about 100 kb, depending on the center), Mitoscore, performed by sequence analysis of the mitochondrial genome (16 kb), has proven to be simple. Moreover, a significant number of leukemic cells is required for karyotype, which is not always available from poor bone marrow. Thus, Mitoscore shortens time, reduces costs, facilitates reproducibility (no culture, no interpretation difficulties) and requires less biological material.

[0018] Thus, a subject of the present invention is an in vitro method for establishing a survival prognostic Mitoscore in patients with chemotherapy-sensitive cancer, comprising the following steps: detecting the presence and / or absence of at least one mutation in the following nine genes of the mitochondrial genome in a biological sample from said patient: ND1, ND2, ND3, ND4, ND5, CYTB, ATP8, ATP6, COX1, COX2, COX3, and 12S. The detection results are compared to a reference biological sample, a reference sequence, or a reference haplogroup / haplotype. Establishing the survival prognosis of said patient.

[0019] In the sense of the present invention, the term "chemosensitive cancer" refers to a pathology treatable by chemotherapy (e.g. anthracyclines, antimetabolites, alkaloids or topoisomerase inhibitors, alone or in combination with other treatments) and selected from the group including, for example, acute myeloid leukemia (AML), sarcoma, testicular cancer (germ cell cancer in general), choriocarcinoma, hematological disorders, gynecological cancers such as ovarian cancer, breast cancer, lung cancer, neuroblastoma, malignant brain tumors, gastrointestinal cancers, pancreatic cancer, bladder cancer, prostate cancer, thyroid cancer, liver cancer, head and neck cancer. Preferably, acute myeloid leukemia (ALM).

[0020] In the sense of the present invention, the term "reference biological sample" refers to a biological sample from a healthy subject, such as DNA sample from bone marrow, blood or tissue.

[0021] In the sense of the present invention, the term "reference sequence" refers to a reference mitochondrial DNA sequence, such as the rCRS sequence (revised Cambridge Reference Sequence NC_012920.1) or a sequence present in the Mitomap / Mitomaster database, gnomAD.

[0022] The term "reference haplogroup / haplotype" in the present invention means the compositional diversity relative to a reference sequence (CRS or rCRS) that identifies a haplogroup or haplotype based on the 1998 Richards and Macaulay classification and can be determined using several tools (MitoTool, HaploFind, PhyloTree mt, Mitomap, ...).

[0023] According to a particular embodiment of the in vitro method for establishing a Mitocore survival prognosis in a patient suffering from a chemotherapy-sensitive cancer according to the invention, The presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, or ND4 genes, and the absence of mutations in the COX1, COX2, COX3, or 12S genes, is an indicator of a good prognosis for survival. The presence of at least one mutation in one of the COX1, COX2, COX3, and 12S genes, and the absence of mutations in the ND2, ND3, ATP8, CYTB, and ND4 genes, is an indicator of poor prognosis for survival; and The absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, and 12S genes (patients called "mitonaive A", approximately 30% of AML patients) or the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, and ND4 genes and at least one mutation in one of the COX1, COX2, COX3, and 12S genes is an indicator of an intermediate survival prognosis.

[0024] According to a particular embodiment of the in vitro method for establishing a Mitocore survival prognosis in a patient suffering from a chemotherapy-sensitive cancer according to the invention, The presence of at least one mutation in one of the ND2, ND3, ATP8, or CYTB genes, and the absence of mutations in the COX1, COX2, COX3, or 12S genes, is an indicator of a good prognosis for survival. The presence of at least one mutation in one of the COX1, COX2, COX3, and 12S genes, and the absence of mutations in the ND2, ND3, ATP8, CYTB, and ND4 genes, is an indicator of poor prognosis for survival; and The absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, and 12S genes (patients called "mitonaive A", approximately 30% of AML patients) or the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, and ND4 genes and at least one mutation in one of the COX1, COX2, COX, and 12S genes is an indicator of an intermediate survival prognosis.

[0025] According to a particular embodiment of the in vitro method for establishing a survival prognostic Mitoscore B in a patient suffering from a chemotherapy-sensitive cancer according to the invention, The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of mutations in the following genes ND1 / COX3 / 12S is an indicator of a good survival prognosis. The presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of mutations in the following genes ND2 / ND5 / ATP6 / CYTB / ND4 is an indicator of poor survival prognosis; and The absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 genes (patients called "mitonaive B", about 40% of AML patients) or the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes (patients called "intermediate mutations") is indicative of an intermediate survival prognosis.

[0026] In the sense of the present invention, the terms "good", "intermediate" and "poor" survival prognosis refer to stages (in terms of chances of survival, risk of complications and / or death) in the hypotheses made about the evolution of mitochondrial variant-based pathology.

[0027] The present invention also relates to an in vitro method for establishing a survival prognostic Mitoscore+ in patients with chemotherapy-sensitive cancers that do not have any mutations in the "ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S" or "ND2, ND5, ATP6, CYTB, ND4, ND1, COX3, 12S" genes (i.e. patients of the subgroups called Mitonaive A and Mitonaive B, respectively), which comprises establishing a survival prognostic Mitoscore as defined above in said patients and determining an ELN survival prognostic score. In the subgroups of patients called Mitonaive A or Mitonaive B, with an "intermediate" Mitoscore, an ELN stratification can be applied to determine the Mitoscore+ and to reclassify these AML patients into three prognostic groups in terms of overall survival.

[0028] According to a particular embodiment of the in vitro method for establishing a survival prognosis Mitoscore+ in patients suffering from chemotherapy-sensitive cancer according to the invention, The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and the absence of mutations in the COX1 / COX2 / COX3 / 12S genes, or the presence or absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and a “good” classification by the ELN score, are indicators of a good survival prognosis. The presence of at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 genes, or the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and a classification of “poor” by the ELN score, are indicators of poor survival prognosis. The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes, or the absence of mutations in ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and an "intermediate" classification by the ELN score, are indicators of an intermediate survival prognosis.

[0029] According to a particular embodiment of the in vitro method for establishing a survival prognosis Mitoscore+ in patients suffering from chemotherapy-sensitive cancer according to the invention, The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB genes and the absence of mutations in the COX1 / COX2 / COX3 / 12S genes, or the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and a “good” classification by the ELN score, are indicators of a good survival prognosis. The presence of at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 genes, or the absence of mutations in the ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and a classification of “poor” by the ELN score, are indicators of poor survival prognosis. The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes, or the absence of mutations in ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and an "intermediate" classification by the ELN score, are indicators of an intermediate survival prognosis.

[0030] According to a particular embodiment of the in vitro method for establishing a survival prognosis Mitoscore B+ in patients suffering from chemotherapy-sensitive cancer according to the invention, The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of mutations in the following genes ND1 / COX3 / 12S, or the absence of mutations in the ND2, ND5, ATP6, CYTB, ND4, ND1, COX3, 12S genes and a "good" classification by the ELN score are indicators of a good survival prognosis. The presence of at least one mutation in the ND1 / COX3 / 12S genes and the absence of mutations in the following genes ND2 / ND5 / ATP6 / CYTB / ND4, or the absence of mutations in the ND2, ND5, ATP6, CYTB, ND4, ND1, COX3, 12S genes and a classification of “poor” by the ELN score are indicators of poor survival prognosis. The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes, or the absence of mutations in the ND2, ND5, ATP6, CYTB, ND4, ND1, COX3, 12S genes and an "intermediate" classification by the ELN score, are indicators of an intermediate survival prognosis.

[0031] The present invention also relates to an in vitro method for establishing a survival prognostic Mitoscore B / A in patients suffering from chemotherapy-sensitive cancer, in particular acute myeloid leukemia (AML), according to the present invention, comprising: A good prognosis for survival is indicated by the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of mutations in the following genes: ND1 / COX3 / 12S, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and the presence of at least one mutation in one of the ND3, ATP8 genes and the absence of mutations in the COX1, COX2 genes. A poor prognosis for survival is indicated by the presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of mutations in the following genes: ND2 / ND5 / ATP6 / CYTB / ND4, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and the presence of at least one mutation in one of the "COX1, COX2" genes and the absence of mutations in one of the "ND3, ATP8" genes. Intermediate survival prognostic indicators correspond to the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and at least one mutation in one of the "COX1, COX2" genes and at least one mutation in one of the "ND3, ATP8" genes, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S / COX1 / COX2 / ND3 / ATP8 genes (patients called mitonaive B / A, which account for approximately 25% of AML patients).

[0032] The present invention also relates to an in vitro method for establishing a survival prognosis Mitoscore B / A+ in patients suffering from chemotherapy-sensitive cancer, in particular acute myeloid leukemia (AML), according to the present invention, comprising: Indicators of favorable prognosis for survival correspond to either the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of mutations in the following genes ND1 / COX3 / 12S, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and the presence of at least one mutation in one of the ND3, ATP8 genes and the absence of mutations in the COX1, COX2 genes, or the presence of mitogen-naive B / A patients classified as favorable by the ELN classification. Indicators of poor survival prognosis correspond to either the presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of mutations in the following genes ND2 / ND5 / ATP6 / CYTB / ND4, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and the presence of at least one mutation in one of the "COX1, COX2" genes and the absence of mutations in the "ND3, ATP8" genes, or the presence of mitogen-naive B / A patients classified as poor by the ELN classification. Intermediate survival prognostic indicators correspond to the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and at least one mutation in one of the "COX1, COX2" genes and the presence of mutations in the "ND3, ATP8" genes, or miton-naive B / A patients classified as intermediate by the ELN classification.

[0033] The present invention also relates to an in vitro method for establishing a survival prognostic Mitoscore A / B in a patient suffering from a chemotherapy-sensitive cancer, in particular acute myeloid leukemia (AML), according to the present invention, comprising: A good prognosis for survival is indicated by either the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, ND4 genes and the absence of mutations in the COX1, COX2, COX3, 12S genes, or the absence of mutations in the COX1, COX2, COX3, 12S, ND2, ND3, ATP8, CYTB, ND4 genes but the presence of at least one mutation in one of the ATP6, ND5 genes and the absence of mutations in the ND1 gene. A poor prognostic indicator of survival corresponds to either the presence of at least one mutation in one of the COX1, COX2, COX3, 12S genes and the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4 genes, or the absence of mutations in the COX1, COX2, COX3, 12S, ND2, ND3, ATP8, CYTB, ND4 genes, but the presence of at least one mutation in the ND1 gene and the absence of mutations in one of the ATP6, ND5 genes. Intermediate survival prognostic indicators correspond to either the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, ND4 genes and at least one mutation in one of the COX1, COX2, COX3, 12S genes, or the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and at least one mutation in one of the ND5 / ATP6 genes and at least one mutation in one of the ND5 / ATP6 genes and at least one mutation in the ND1 gene, or the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S, ND5, ATP6, ND1 genes (patients called mitonaive A / B, which represent approximately 25% of AML patients).

[0034] The present invention also relates to an in vitro method for establishing a survival prognosis Mitoscore A / B+ in patients suffering from chemotherapy-sensitive cancer, in particular acute myeloid leukemia (AML), according to the present invention, comprising: Good prognostic indicators of survival correspond to either the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, ND4 genes and the absence of mutations in the COX1, COX2, COX3, 12S genes, or the absence of mutations in the COX1, COX2, COX3, 12S, ND2, ND3, ATP8, CYTB, ND4 genes but the presence of at least one mutation in one of the ATP6, ND5 genes and the absence of mutations in the ND1 gene, or the presence of miton-naive A / B patients classified as good according to the ELN classification. Poor prognostic indicators of survival correspond to either the presence of at least one mutation in one of the COX1, COX2, COX3, 12S genes and the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4 genes, or the absence of mutations in the COX1, COX2, COX3, 12S, ND2, ND3, ATP8, CYTB, ND4 genes but the presence of at least one mutation in the ND1 gene and at least one mutation in one of the ATP6, ND5 genes, or the presence of miton-naive A / B patients classified as poor by the ELN classification. Intermediate survival prognostic indicator corresponds to the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, ND4 genes and at least one mutation in one of the COX1, COX2, COX3, 12S genes, or the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, 12S genes and at least one mutation in one of the ND5 / ATP6 genes and at least one mutation in the ND1 gene, or miton-naive A / B patients classified as intermediate according to the ELN classification.

[0035] In the sense of the present invention, a "good", "intermediate" or "poor" survival prognosis refers to a stage (in terms of chance of survival, risk of complications and / or death) in the hypotheses made about the development of a mitochondrial variant-based pathology.

[0036] According to a particular embodiment of the invention, the detection step is carried out by high-throughput sequencing (NGS) of the mitochondrial genome.

[0037] The present invention also relates to an in vitro method for predicting or assessing the efficacy and / or benefit of a treatment of a chemotherapy sensitive cancer, in particular acute myeloid leukemia (AML), in a patient suffering from said cancer, comprising the following steps: -Determining survival prognosis Mitoscore, Mitoscore+, Mitoscore B, Mitoscore B+, Mitoscore A / B, Mitoscore A / B+, Mitoscore B / A or Mitoscore B / A+ from a biological sample derived from a patient before treatment by the method of the present invention. From a biological sample derived from a patient after treatment, the survival prognosis Mitoscore, Mitoscore+, Mitoscore B, Mitoscore B+, Mitoscore A / B, Mitoscore A / B+, Mitoscore B / A or Mitoscore B / A+ is determined by the method of the present invention. Compare survival prognosis before and after treatment with Mitoscore, Mitoscore+, Mitoscore B, Mitoscore B+, Mitoscore A / B, Mitoscore A / B+, Mitoscore B / A or Mitoscore B / A+ - determining whether the patient is resistant to treatment, in which case the patient's survival prognosis after treatment is the same as or worse than the patient's survival prognosis before treatment, or whether the patient is sensitive to treatment, in which case the patient's survival prognosis after treatment is better than the patient's survival prognosis before treatment.

[0038] In the sense of the present invention, the term "chemosensitive cancer" refers to a pathology treatable by chemotherapy (e.g. anthracyclines, antimetabolites, alkaloids or topoisomerase inhibitors, alone or in combination with other treatments) and selected from the group including, for example, acute myeloid leukemia (AML), sarcoma, testicular cancer (germ cell cancer in general), choriocarcinoma, hematological disorders, gynecological cancers such as ovarian cancer, breast cancer, lung cancer, neuroblastoma, malignant brain tumors, gastrointestinal cancers, pancreatic cancer, bladder cancer, prostate cancer, thyroid cancer, liver cancer, head and neck cancer. Preferably, acute myeloid leukemia (ALM).

[0039] In the sense of the present invention, "the survival prognosis is the same before and after treatment" means that a good, intermediate or poor survival prognosis before treatment is maintained as a good, intermediate or poor survival prognosis, respectively, after treatment.

[0040] In the sense of the present invention, "worse survival prognosis after treatment than before treatment" means, for example, that a good or intermediate survival prognosis before use becomes an intermediate or poor survival prognosis, respectively, after treatment.

[0041] In certain embodiments of the methods of the present invention, the treatment of chemotherapy-sensitive cancer, in particular acute myeloid leukemia, comprises the administration of venetoclax, optionally in combination with other molecules (e.g., azacytidine).

[0042] A computer program was created to carry out the above method. It analyzes variants from the source data of the sequencer used, filters based on quality criteria and the location of the variants in the coding region, heteroplasmy rate and silent mutations. The program then applies the Mitoscore of the present invention (Mitoscore / Mitoscore+ / MitoscoreB / MitoscoreB+, MitoscoreB / A, MitoscoreB / A+, MitoscoreA / B, MitoscoreA / B+).

[0043] The invention therefore also relates to a program comprising instructions which, when executed by a computer, lead to the execution of the method described above.

[0044] The implementation of MitoCORE is therefore carried out with the benefit of computer programs developed to analyze the sequences of mitochondrial genomes.

[0045] The invention also relates to a computer readable data carrier comprising instructions which, when executed by a computer, cause the computer to carry out the above method. In one embodiment, said data carrier is non-transitory.

[0046] The present invention also relates to a method that allows the selection of only those patients diagnosed with a particular disease who are likely to benefit from treatment based on the status of predictive markers identified by this test, thereby predicting the addition of molecules / drugs targeting mitochondria in chemotherapy-sensitive cancers, particularly acute myeloid leukemia. For example, patients in the poor or intermediate mitocore group, who have a mutation in the 12S gene, can be treated with MOTS-c peptide to improve their sensitivity to standard treatment. Patients in the poor or intermediate mitocore group, who have a mutation in the COX1, COX2 or COX3 gene, can be treated with quercetin or drugs acting on complex IV to improve their sensitivity to standard treatment. Patients in the intermediate or poor mitocore group may benefit from treatments targeting complex I or III of the respiratory chain (e.g., olaparib, mubilitinib, trimetazidine dihydrochloride) in addition to standard treatment.

[0047] The present invention therefore relates to the use of the method according to the invention for establishing a Mitoscore in patients suffering from chemotherapy-sensitive cancer as a companion test, in particular as a companion test for the addition of a molecule that targets mitochondria. [Brief description of the drawings]

[0048] [Figure 1] FIG. 1 represents the technical workflow carried out to apply Mitoscore and Mitoscore+, and in particular defines the criteria used for manifold selection. [Figure 2A] FIG. 2A depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients according to Mitoscore. [Figure 2B] FIG. 2B depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients according to Mitoscore+. [Diagram 3]Figure 3 shows the hazard ratios (HR) (95%CI) for the risk of death according to Mitoscore and Mitoscore+ calculated according to the Cox model by univariate (UV) or multivariate (MV) analysis. Covariates used in the MV analysis were age at diagnosis, white blood cell (WBC) count by G / l, ELN2017 classification, and / or bone marrow transplantation. [Figure 4A] FIG. 4A depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients according to Mitoscore B, which includes the ND2 / ND5 / CYTB / ND4 / ATP6 / ND1 / CO3 / 12S genes. [Figure 4B] FIG. 4B depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time in AML patients with Mitoscore B+ including ND2 / ND5 / CYTB / ND4 / ATP6 / ND1 / CO3 / 12S genes in combination with ELN2017 in Mitonaive patients for the previously cited genes. [Diagram 5] Figure 5 shows the hazard ratios (HR) (95%CI) of the risk of death based on Mitoscore B and Mitoscore B+ calculated according to the Cox model by univariate (UV) or multivariate (MV) analysis. Covariates used in the MV analysis were age at diagnosis, white blood cell (WBC) count by G / l, ELN2017 classification, and / or bone marrow transplantation. [Figure 6] FIG. 6 is a block diagram showing a computer for implementing the prognostic probability method according to the present invention. [Figure 7A] FIG. 7A depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients with Mitoscore B / A in combination with ELN2017 in Mitonaive B / A patients. [Figure 7B] FIG. 7B depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients with Mitoscore B / A+ in combination with ELN2017 in Mitonaive B / A patients. [Figure 8A]FIG. 8A depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients with Mitoscore A / B in combination with ELN2017 in Mitonaive A / B patients. [Figure 8B] FIG. 8B depicts Kaplan-Meier survival curves (log-rank test p<0.05) showing overall survival as a function of time for AML patients with Mitoscore A / B+ in combination with ELN2017 in Mitonaive A / B patients. DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0049] <Example 1: Development of a mitochondrial genotype score considering the prognosis of acute myeloid leukemia (AML)> Abstract: We sequenced the entire mitochondrial genome from patients with AML using high-throughput mitochondrial sequencing (NGS) technology. From this sequence analysis, we defined a score, called Mitoscore, which can predict patient survival. The benefit of Mitoscore was confirmed by multivariate analysis independent of the usual prognostic factors for AML (i.e., age, circulating white blood cell (WBC) count, cytogenetic and molecular abnormalities, transplantation). Furthermore, Mitoscore was functionally characterized by comparison with ROS luminescence data with and without mitochondrial complex inhibitors (antimycin A, Rotenone).

[0050] (Definition of the preserved manifold) The sequencing of the mitochondrial genome was performed using the instrument S5 (Ion Torrent) after PCR amplification of the mitochondrial genome (two fragments of 8 kDa). The mitochondrial genome can be generated using other techniques for library synthesis, such as PCR amplification of the mitochondrial genome with two or more fragments, or recovery of the sequencing product by capture. In addition, sequencing can be performed with a sequencer of the Illumina technology type. The variant analysis was performed by Mitomaster. Variants affecting non-coding regions (D-loop, etc.), heteroplasmy rates strictly less than 2%, and silent mutations were excluded. The Mitomaster website defines the mitochondrial haplogroups. Variants showing a frequency of 0.5% or less in the haplogroups or variants described in cancer were retained. Any sequencing errors were confirmed by IGV or automatically filtered by a bioinformatics program. For haplogroups numbering less than 100, variant frequencies were ascertained with gnomAD v3 and were retained if they were less than 0.5% or had been described in cancer (Figure 1).

[0051] (Development of Mitoscore) Based on survival curves performed individually for genes of the mitochondrial genome in the 64 patients in the study who received induction chemotherapy, certain genes were determined to be "good prognosis" (ND2 / ND3 / ND4 / ATP8 / CYTB / ND5 / ATP6) or "poor prognosis" (COX1 / COX2 / COX3 / 12S / ND1).

[0052] Despite the good separation of survival curves, no significant differences were observed in univariate analysis of these genes taken individually.

[0053] Therefore, a “MitoScore” was created to stratify patients into three groups: good prognosis, intermediate prognosis, and poor prognosis (Figure 2A / Figure 4A).

[0054] This prognostic classification based on the "Mitoscore" is independent of the usual prognostic factors for AML (age, WBC / l, ELN 2017, bone marrow transplantation).

[0055] However, 30% of patients without mutations in all genes in the Mitoscore, i.e., a subgroup of patients called Mitonaive A, require reclassification. Therefore, by combining the ELN 2017 prognostic classification with the Mitoscore for mitonaive patients, the Mitoscore+ was created (Figure 2B). This allows a reduction in the use of the ELN 2017 prognostic classification by 70%. 40% of patients without mutations in all genes in the Mitoscore B, i.e., a subgroup of patients called Mitonaive B, require reclassification. Therefore, the Mitoscore B+ was created by combining the ELN 2017 prognostic classification with the Mitoscore for mitonaive patients (Figure 4B). This allows a reduction in the use of the ELN 2017 prognostic classification by 60%.

[0056] The advantage of Mitoscore and Mitoscore+ was confirmed by the Cox model in univariate (UV) and multivariate (MV) analyses, independent of the usual prognostic factors for AML (Figure 3). Covariates used in the MV analysis were age, number of circulating white blood cells (WBC) by G / l, ELN 2017 classification, and / or bone marrow transplantation. Similarly, Mitoscore B / B+ was significant in the multivariate analysis (Figure 5).

[0057] Furthermore, the mitocores were functionally characterized by comparison with ROS emission data. Interestingly, leukemia cells from patients in the "bad" mitocore subgroup released significantly less ROS under antimycin / rotenone-stimulated conditions (targeting mitochondrial ROS) compared to "good" and "intermediate" mitocore leukemia cells harboring COX1 / COX2 / COX3 / 12S and ND2 / ND3 / ATP8 / CYTB / ND4 mutations.

[0058] Within mitochondria, complexes I and III of the respiratory chain are the main sources of reactive oxygen species. Genes implicated in a "good" mitochondrial core affect subunits of complexes I (ND2 / ND3 / ND4 / ND5) and III (CYTB), as well as ATP synthase (ATP8 / ATP6). Thus, the hypothesis of a "good" mitochondrial core function is supported by ROS data, especially when mutations affect the release of ROS under chemotherapy-induced stimulatory conditions. Thus, a strong release of ROS triggers the apoptotic threshold, resulting in cell death in leukemic cells.

[0059] In the "bad" mitochondrial core subgroup, less ROS are released. Indeed, complex IV of the respiratory chain, encoded by the COX1 / COX2 / COX3 genes, is not the site that releases superoxide ions. Furthermore, the mitochondrial-derived peptide MOTS-c, encoded by the 12S gene, plays a role in metabolic adaptation to stress.

[0060] Mitoscore+ was also functionally characterized in the same way as Mitoscore: a subgroup of patients called mitonaive, whose leukemia cells are able to produce more ROS in the presence of antimycin / rotenone and diphenyleneiodonium (DPI), had significantly better overall survival than patients whose leukemia cells produced less ROS.

[0061] (Definition of Mitoscore and Mitoscore B) The MitoScore allowed stratifying 64 AML patients into three prognostic groups in terms of overall survival based on the following variant combinations:

[0062] A "good" MitoScore corresponds to the presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes or at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB genes and the absence of mutations in the following COX1 / COX2 / COX3 / 12S genes:

[0063] A "poor" mitoscore corresponds to the presence of at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and the absence of mutations in the following ND2 / ND3 / ATP8 / CYTB / ND4 genes.

[0064] An "intermediate" Mitoscore corresponds to either: At least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes AND at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes. This is a subgroup of patients called "mutation intermediate." or the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 / COX1 / COX2 / COX3 / 12S genes. This is a subgroup of patients called "mitonaive A" and represents approximately 30% of AML patients.

[0065] [Table 2]

[0066] Mitoscore B also allowed the stratification of 64 AML patients into three prognostic groups in terms of overall survival, based on the following combinations of variants:

[0067] A "good" MitoScore also corresponds to the presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and the absence of mutations in the following COX1 / COX2 / COX3 / 12S genes.

[0068] A "poor" mitoscore also corresponds to the presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of mutations in the following ND2 / ND5 / ATP6 / CYTB / ND4 genes.

[0069] An "intermediate" Mitoscore corresponds to either: The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes AND at least one mutation in one of the ND1 / COX3 / 12S genes. This subgroup of patients is called "intermediate mutations." Absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes. This is a subgroup of patients called "mitonaive B".

[0070] [Table 3]

[0071] (Definition of Mitoscore+ and Mitoscore B+) In the subgroup of patients with an "intermediate" mitoscore, termed mitonaive A, we applied the ELN stratification to determine the mitoscore+, which allows us to reclassify these 30% of AML patients into three prognostic groups in terms of overall survival, based on the following variant combinations:

[0072] A "good" Mitoscore+ corresponds to either: The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes, or the presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB genes and the absence of mutations in the COX1 / COX2 / COX3 / 12S genes. - Patients with mitogen-naive A disease classified as "good" by ELN.

[0073] A "poor" Mitoscore+ corresponds to any of the following: -At least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and no mutations in the following ND2 / ND3 / ATP8 / CYTB / ND4 genes. Patients with mitogen-naive A disease classified as “poor” by ELN.

[0074] An "intermediate" Mitoscore+ corresponds to either: At least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes. Patients must be mitogen-naive A and classified as "intermediate" by ELN.

[0075] [Table 4]

[0076] Even in the subgroup of patients with an "intermediate" mitoscore, called mitonaive B, the ELN stratification was applied to determine a mitoscore B+, which allows us to reclassify these 40% of AML patients into three prognostic groups in terms of overall survival, based on the following variant combinations:

[0077] A "good" Mitoscore of B+ corresponds to either: -At least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and no mutations in the following ND1 / COX3 / 12S genes. Patients with mitogen-naive B disease classified as "good" by ELN.

[0078] A "poor" Mitoscore of B+ corresponds to any of the following: -At least one mutation in one of the ND1 / COX3 / 12S genes and no mutations in the following ND2 / ND5 / ATP6 / CYTB / ND4 genes. Patients with mitogen-naive B disease classified as “poor” by ELN.

[0079] An "intermediate" Mitoscore of B+ corresponds to either: At least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes. Patients must be mitogen-naive B, classified as "intermediate" by ELN.

[0080] [Table 5]

[0081] (Definition of Mitoscore B / A) Mitoscore B / A also allowed stratifying 64 AML patients into three prognostic groups in terms of overall survival based on the following variant combinations:

[0082] A "good" Mitoscore B / A corresponds to either: The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of variants in the ND1 / COX3 / 12S genes. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / COX1 / COX2 genes and presence of at least one mutation in the ATP8 / ND3 gene.

[0083] A "poor" Mitoscore B / A corresponds to either: The presence of at least one mutation in the ND1 / COX3 / 12S gene and the absence of variants in the ND2 / ND5 / ATP6 / CYTB / ND4 genes. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / ATP8 / ND3 genes and presence of at least one mutation in COX1 / COX2 genes.

[0084] "Intermediate" Mitoscore B / A corresponds to either At least one mutation in the ND1 / COX3 / 12S gene and at least one mutation in the ND2 / ND5 / ATP6 / CYTB / ND4 gene. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 genes AND presence of at least one mutation in COX1 or COX2 genes AND presence of at least one mutation in ATP8 and ND3 genes. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / COX1 / COX2 / ATP8 / ND3 genes.

[0085] [Table 6]

[0086] (Definition of Mitoscore A / B) Mitoscore A / B allows stratification of 64 AML patients into three prognostic groups in terms of overall survival based on the following variant combinations:

[0087] A "good" Mitoscore A / B corresponds to either: The presence of at least one mutation in the ND2 / ND3 / ATP8 / CYTB / ND4 gene and the absence of variants in the COX1 / COX2 / COX3 / 12S gene. Absence of variants in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ND1 genes and presence of at least one mutation in the ATP6 / ND5 gene.

[0088] A "poor" Mitoscore A / B corresponds to either: The presence of at least one mutation in COX1 / COX2 / COX3 / 12S and the absence of variants in ND2 / ND3 / ATP8 / CYTB / ND4 genes. Absence of variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ATP6 / ND5 genes and presence of at least one mutation in the ND1 gene.

[0089] An "intermediate" Mitoscore A / B corresponds to either: At least one mutation in the COX1 / COX2 / COX3 / 12S gene and at least one mutation in the ND2 / ND3 / ATP8 / CYTB / ND4 gene. Absence of variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 genes AND presence of at least one mutation in ATP6 / ND5 gene AND presence of at least one mutation in ND1 gene. Absence of variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ATP6 / ND5 / ND1 genes.

[0090] [Table 7]

[0091] (Definition of Mitoscore B / A+) The Mitoscore B / A+ also allowed stratification of 64 AML patients into three prognostic groups in terms of overall survival, based on the following variant combinations:

[0092] A "good" Mitoscore B / A+ corresponds to either: The presence of at least one variant in the ND2 / ND5 / ATP6 / CYTB / ND4 gene and the absence of variants in the ND1 / COX3 / 12S gene. Absence of variants in the ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / COX1 / COX2 genes and presence of at least one variant in the ATP8 / ND3 gene. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / COX1 / COX2 / ATP8 / ND3 genes and favorable ELN.

[0093] A "poor" Mitoscore B / A+ corresponds to either: The presence of at least one variant in the ND1 / COX3 / 12S gene and the absence of variants in the ND2 / ND5 / ATP6 / CYTB / ND4 genes. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / ATP8 / ND3 genes and presence of at least one variant in COX1 / COX2 genes. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / COX1 / COX2 / ATP8 / ND3 genes and poor ELN.

[0094] An "intermediate" Mitoscore B / A+ corresponds to either: At least one variant in the ND1 / COX3 / 12S gene and at least one variant in the ND2 / ND5 / ATP6 / CYTB / ND4 gene. Absence of variants in the ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 genes, presence of at least one variant in the COX1 / COX2 gene, and presence of at least one variant in the ATP8 / ND3 gene. Absence of variants in ND1 / COX3 / 12S / ND2 / ND5 / ATP6 / CYTB / ND4 / COX1 / COX2 / ATP8 / ND3 genes and intermediate ELN.

[0095] [Table 8]

[0096] (Definition of Mitoscore A / B+) Mitoscore A / B+ allowed the stratification of 64 AML patients into three prognostic groups in terms of overall survival, based on the following variant combinations:

[0097] A "good" Mitoscore A / B+ corresponds to either: The presence of at least one variant in the ND2 / ND3 / ATP8 / CYTB / ND4 gene and the absence of variants in the COX1 / COX2 / COX3 / 12S gene. Absence of variants in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ND1 genes and presence of at least one variant in the ATP6 / ND5 gene. No variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ATP6 / ND5 / ND1 genes and good ELN.

[0098] A "poor" Mitoscore A / B+ corresponds to any of the following: The presence of at least one variant in the COX1 / COX2 / COX3 / 12S gene and the absence of variants in the ND2 / ND3 / ATP8 / CYTB / ND4 genes. Absence of variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ATP6 / ND5 genes and presence of at least one variant in the ND1 gene. Absence of variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ATP6 / ND5 / ND1 genes and poor ELN.

[0099] An "intermediate" Mitoscore A / B+ corresponds to either: At least one variant in the COX1 / COX2 / COX3 / 12S gene and at least one variant in the ND2 / ND3 / ATP8 / CYTB / ND4 gene. Absence of variants in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 genes AND presence of at least one variant in the ATP6 / ND5 gene AND presence of at least one variant in the ND1 gene. Absence of variants in COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 / ATP6 / ND5 / ND1 genes and intermediate ELN.

[0100] [Table 9]

[0101] The different Mitoscores according to the invention can be used to predict response to chemotherapy-sensitive cancer treatment, such as the use of venetoclax, and thus can define sensitivity to treatment (e.g., venetoclax) in acute myeloid leukemia indications and other indications where such treatments are used.

[0102] (Definition of Mitoscore as a companion test) In patients with intermediate and poor Mitoscores, the Mitoscore of the present invention allows modifying treatment in combination with chemotherapy using drugs capable of: Targeting the communication between mitochondria and leukemia cell nuclei by administering MOTS-c peptide in intermediate or poor disease patients with mutations in the 12S gene. Targeting mitochondrial complex IV, for example with quercetin or other drugs, in intermediate or poor disease patients with mutations in one of the COX1, COX2 or COX3 genes. In patients with intermediate or poor disease, mitochondrial targeted drugs, such as olaparib, mubritinib, trimetazidine dihydrochloride, and myxothiazol, target complexes I or III of the mitochondrial respiratory chain.

[0103] Thus, the Mitoscore of the present invention may serve as a companion test to improve patient treatment and define possible indications for the addition of complementary mitochondrial-targeted therapies / products.

[0104] (Computer program for performing mitochondrial genotype scoring) To be able to evaluate the effectiveness of therapeutic treatment, such as venetoclax, against chemotherapy-sensitive cancers, especially AML, a computer program was created to implement the above score.The program analyzes variants from the source data of the sequencer used and filters them according to quality criteria and the location of variants in coding regions, heteroplasmy rate and silent mutations.The program then applies a Mitoscore (Mitoscore / Mitoscore+, MitoscoreB / MitoscoreB+, MitoscoreB / A, MitoscoreB / A+, MitoscoreA / B, MitoscoreA / B+).

[0105] Fig. 6 is a block diagram of a device 600 for implementing the steps of the method for establishing a survival prognosis in a patient suffering from a chemotherapy-sensitive cancer as described above. The device comprises a processor 601, a volatile memory 602 and a non-volatile memory 603. The non-volatile memory contains instructions 604 which, when executed by the processor 601, cause the device 600 to implement the steps of establishing a survival prognosis in a patient suffering from a chemotherapy-sensitive cancer as described above. The different components are connected by a communication bus 605. The device may include other components or interfaces 606 to other components depending on the implementation, in particular a user interface. The processor 601 may be in any suitable form and may be one or more microprocessors, one or more microcontrollers or a combination of these. The volatile memory 602 is used for temporary data storage. The non-volatile memory 603 may comprise a hard drive, a static memory or other long-term storage device. The non-volatile memory stores the implementation instructions and may also store the operating system and / or applications. The device 600 may be, for example, a computer having a program loaded or downloaded thereon, the program including the instructions 604 .

[0106] The different Mitoscores according to the invention may prove useful for predicting response to treatment with venetoclax, for example allowing to define sensitivity to venetoclax in acute myeloid leukemia indications and other indications where such treatment is used.

[0107] (References) 1. Dohner et al., Blood, 129(4):424-447, 2017 2. Herold et al, Leukemia., 34(12):3161-3172, 2020 3. Dohner et al., Blood, 140(12): 1345-1377, 2022 4. Farge et al., Cancer discov., 7(7):716-735, 2017 5. Mondet et al, Hematologica, 104(9):e393-e397, 2019 6. Bosc et al., Nat. Cancer., 2(11): 1204-1223, 2021 7. Neuzil et al., Mitochondrion, 13(3): 199-208, 2013 8. Damm et al., Leukemia, 26: 289-295, 2012 9. Chun et al., Chin. J. Hematol., 35(8): 708-712, 2014 10. Wu et al., Scientific reports, 8: 13301, 2018 11. Caudron-Herger and Diederichs, Biology, 15: 62-69, 2018 12. Zeng et al., Scientific reports, 8: 3623, 2018 13. Silkjaer et al., Eur. J. Haematol., 90(5): 385-396, 2013 14. Silkjaer et al., Eur. J. Haematol., 91(4): 295-303, 2013

Claims

1. 1. An in vitro method for establishing a survival prognosis in a patient suffering from chemotherapy-sensitive cancer, comprising the steps of: - detecting in the patient's biological sample the presence and / or absence of at least one mutation in one of the following nine genes in the mitochondrial genome: ND1, ND2, ND3, ND4, ND5, CYTB, ATP8, ATP6, COX1, COX2, COX3 and 12S; - comparing the detection results to a reference biological sample, a reference sequence or a reference haplogroup / haplotype; - establishing a survival prognosis for said patient; A method comprising:

2. 10. The method of claim 1, The presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, or ND4 genes, and the absence of mutations in the COX1, COX2, COX3, or 12S genes, is an indicator of a favorable prognosis for survival; The presence of at least one mutation in one of the OX1, COX2, COX3, and 12S genes, and the absence of mutations in the ND2, ND3, ATP8, CYTB, and ND4 genes, is an indicator of poor prognosis for survival; The absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, and 12S genes (mitonaive A patients) or the presence of at least one mutation in one of the ND2, ND3, ATP8, CYTB, and ND4 genes and at least one mutation in one of the COX1, COX2, COX3, and 12S genes is an indicator of an intermediate survival prognosis. method.

3. 10. The method of claim 1, The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of mutations in the following ND1 / COX3 / 12S genes is an indicator of a good prognosis for survival; the presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 genes is an indicator of a poor prognosis for survival; The absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes (mitonaive B patients) or the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes is an indicator of an intermediate survival prognosis. method.

4. 4. The method according to claim 2 or 3, The method further comprises determining an ELN prognostic score in a subgroup of mitonaive A or mitonaive B patients.

5. 5. The method of claim 4, - The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and the absence of a mutation in the COX1 / COX2 / COX3 / 12S gene, or the absence of a mutation in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, or 12S gene and a "good" classification by the ELN score, are indicators of a good survival prognosis, The presence of at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and the absence of a mutation in the ND2 / ND3 / ATP8 / CYTB / ND4 genes, or the absence of a mutation in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, or 12S genes and a classification of "poor" by the ELN score, are indicators of a poor survival prognosis, The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes, or the absence of mutations in the ND2, ND3, ATP8, CYTB, ND4, COX1, COX2, COX3, or 12S genes and an "intermediate" classification by the ELN score, are indicators of an intermediate survival prognosis. method.

6. 5. The method of claim 4, - The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of a mutation in the following ND1 / COX3 / 12S gene, or the absence of a mutation in the ND1 / COX3 / 12S gene and a "good" classification by the ELN score, are indicators of a good survival prognosis, The presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of mutations in the following ND2 / ND5 / ATP6 / CYTB / ND4 genes, or the absence of mutations in the ND2, ND5, ATP6, CYTB, ND4, ND1, COX3, and 12S genes and a classification of "poor" by the ELN score, are indicators of poor survival prognosis. The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes, or the absence of mutations in the ND2, ND5, ATP6, CYTB, ND4, ND1, COX3, and 12S genes and an "intermediate" classification by the ELN score, are indicators of an intermediate survival prognosis. method.

7. 10. The method of claim 1, - the presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of a mutation in the ND1 / COX3 / 12S gene, or the absence of a mutation in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S gene and the presence of at least one mutation in one of the ND3 / ATP8 genes and the absence of a mutation in the COX1 / COX2 gene, is an indicator of a good prognosis for survival; - the presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of a mutation in the following ND2 / ND5 / ATP6 / CYTB / ND4 genes, or the absence of a mutation in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and the presence of at least one mutation in one of the COX1 / COX2 genes and the absence of a mutation in the ND3 / ATP8 gene, are indicators of a poor prognosis for survival; The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and at least one mutation in one of the COX1 / COX2 genes and at least one mutation in one of the ND3 / ATP8 genes, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S / COX1 / COX2 / ND3 / ATP8 genes (mitonaive B / A patients) is an indicator of an intermediate survival prognosis. method.

8. 10. The method of claim 1, - the presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and the absence of a mutation in the COX1 / COX2 / COX3 / 12S gene, or the absence of a mutation in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 genes but the presence of at least one mutation in one of the ATP6 / ND5 genes and the absence of a mutation in the ND1 gene, are indicators of a good prognosis for survival; the presence of at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 genes, or the absence of mutations in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 genes but the presence of at least one mutation in ND1 and the absence of mutations in the ATP6 / ND5 gene, are indicators of a poor prognosis for survival; The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes, or the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 / COX1 / COX2 / COX3 / 12S genes and at least one mutation in the ND5 / ATP6 gene and at least one mutation in the ND1 gene, or the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 / COX1 / COX2 / COX3 / 12S / ND5 / ATP6 / ND1 genes (mitonaive A / B patients) is an indicator of an intermediate survival prognosis. method.

9. 9. The method according to claim 7 or 8, The method further comprises determining an ELN prognostic score in a subgroup of mitonaive B / A or mitonaive A / B patients.

10. 10. The method of claim 9, - The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and the absence of a mutation in the ND1 / COX3 / 12S gene, or the absence of a mutation in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S gene and the presence of at least one mutation in one of the ND3 / ATP8 genes and the absence of a mutation in the COX1 / COX2 gene, or being a mitonaive B / A patient who is well classified in the ELN classification, are indicators of a good prognosis for survival; - the presence of at least one mutation in one of the ND1 / COX3 / 12S genes and the absence of a mutation in the ND2 / ND5 / ATP6 / CYTB / ND4 genes, or the absence of a mutation in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes, the presence of at least one mutation in one of the COX1 / COX2 genes and the absence of a mutation in the ND3 / ATP8 gene, or being a mitonaive B / A patient classified as poor in the ELN classification, are indicators of poor survival prognosis; The presence of at least one mutation in one of the ND2 / ND5 / ATP6 / CYTB / ND4 genes and at least one mutation in one of the ND1 / COX3 / 12S genes, or the absence of mutations in the ND2 / ND5 / ATP6 / CYTB / ND4 / ND1 / COX3 / 12S genes and the presence of at least one mutation in one of the COX1 / COX2 genes and at least one mutation in one of the ND3 / ATP8 genes, or being a mitonaive B / A patient classified as intermediate in the ELN classification, are indicators of an intermediate survival prognosis. method.

11. 10. The method of claim 9, - The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and the absence of a mutation in the COX1 / COX2 / COX3 / 12S gene, or the absence of a mutation in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 gene but the presence of at least one mutation in the ATP6 / ND5 gene and the absence of a mutation in the ND1 gene, or being a mitona-ve A / B patient who is well classified in the ELN classification, are indicators of a good prognosis for survival; - The presence of at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes and the absence of a mutation in the ND2 / ND3 / ATP8 / CYTB / ND4 genes, or the absence of a mutation in the COX1 / COX2 / COX3 / 12S / ND2 / ND3 / ATP8 / CYTB / ND4 genes but the presence of at least one mutation in the ND1 gene and the absence of a mutation in the ATP6 / ND5 gene, or being a mitonaive A / B patient classified as poor in the ELN classification, are indicators of poor survival prognosis, The presence of at least one mutation in one of the ND2 / ND3 / ATP8 / CYTB / ND4 genes and at least one mutation in one of the COX1 / COX2 / COX3 / 12S genes, or the absence of mutations in the ND2 / ND3 / ATP8 / CYTB / ND4 / COX1 / COX2 / COX3 / 12S genes, the presence of at least one mutation in the ND5 / ATP6 gene, and the presence of at least one mutation in the ND1 gene, or being a mitonaive A / B patient classified as intermediate in the ELN classification, are indicators of an intermediate survival prognosis. method.

12. 10. The method of claim 1, A method wherein the step of detecting is carried out by high-throughput sequencing of the mitochondrial genome.

13. 1. An in vitro method for predicting or assessing the efficacy and / or benefit of a treatment for a chemotherapy-sensitive cancer in a patient suffering from said cancer, comprising the steps of: - determining a survival prognosis from a biological sample derived from said patient before treatment by the method defined by claim 1; - determining a survival prognosis from a biological sample derived from said patient after treatment by the method defined by claim 1; -Compare survival prognosis before and after treatment, - determining whether the patient is resistant to treatment, in which case the patient's survival prognosis after treatment is the same as or worse than the patient's survival prognosis before treatment, or whether the patient is sensitive to treatment, in which case the patient's survival prognosis after treatment is better than the patient's survival prognosis before treatment; A method comprising:

14. 14. The method of claim 13, The method, wherein the treatment of the chemotherapy-sensitive cancer is treatment with venetoclax.

15. 10. The method of claim 1, The chemotherapy-sensitive cancer is selected from the group including acute myeloid leukemia (AML), sarcoma, testicular cancer, choriocarcinoma, hematological disorders, gynecological cancer, lung cancer, neuroblastoma, malignant brain tumor, gastrointestinal cancer, pancreatic cancer, bladder cancer, prostate cancer, thyroid cancer, liver cancer, and head and neck cancer.

16. A program, A program comprising instructions for performing the method of claim 1 when said program is executed by a computer.

17. A computer-readable data medium, comprising: A data medium containing instructions which, when executed by a computer, perform the method of claim 1.

18. 10. Use of the method of claim 1 as a companion test.

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