Genomic and transcriptomic instabilities in human diseases

  • We are developing genomic biomarkers for Homologous recombination deficiency (HRD) in breast in ovarian cancers, essential now for clinical choice of treatment by PARP inhibitors. HRD (or BRCAness) was initially connected to the tumors developed in patients with deleterious germline mutations of the two major breast cancer susceptibility genes BRCA1 or BRCA2, which play a major role in Homologous recombination pathway. However, HRD phenotype expands much beyond germline mutations in BRCA1/2 and includes more genes (PALB2, RAD51C) and somatic inactivation either by mutations or promoter methylation. HRD was detected in approximately half of high grade so called triple negative (hormone receptors negative, HER2 not amplified) breast carcinoma and in approximately half of high-grade ovarian carcinoma. We have developed a signature of genomic instability related to the HRD (1); published patents: 123056483 and 61913637; exclusive licensing with Myriad Genetics, USA). This signature measures Large Scale State Transition (LST), the large number of which sign HRD. We have shown that LSTs correspond to inter-chromosomal translocations, developed a predictive signature of BRCA2 mutations, and confirmed the diagnostic interest of the LST signature in independent series of breast and ovarian cancers  ADDIN EN.CITE.DATA (2-14). Recent developments include adapting the LST signature from shallow Whole Genome Sequencing, for affordable and robust clinical diagnosis (15).
  • The unusual genomic profiles found in ovarian carcinoma led us to identify a new genomic instability and to associate it with CDK12 inactivation (16). This instability is characterized by numerous giant tandem duplications distributed over the tumor genome. CDK12 encodes a Cyclin K dependent kinase that activates RNA polymerase II. Its inactivation has for main effect to allow intronic premature polyadenylation, downregulating the expression of large genes, including DNA repair genes. However, contrary to many DNA repair genes, we exclude a role of CDK12 germline mutations as predisposing factors for breast and ovary carcinomas (17).
  • Within a framework of genetic investigation of breast cancer prone families, we characterized in depth a family with an unusual predisposition to breast and kidney cancers. This led us to identify BAP1 as a new predisposing gene for clear cell renal cell carcinoma, while its role in breast cancer predisposition was excluded (18). We sought to understand the functions of BAP1 in cellular models and showed profound metabolic and cellular changes related to BAP1 expression (19). BAP1 is a deubiquitinase, mainly of histone H2A (H2AK119ub1), antagonizing the Polycomb Repressive Complex 1 (PRC1). We are presently involved in international studies on BAP1 germline mutations (20).
  • We are investigating DNA repair related diseases, which include rare pediatric complex syndromes, often associating immuno-deficiency and cancer proneness. We characterized unusual forms of such diseases, including ataxia telangiectasia, Nijmegen disease and ATLD, sometimes discovered in adults, and we developed assays to assist diagnosis and to understand the consequences of gene mutations on DNA repair (21-27).
  • Uveal melanoma (UM) is one of the major interests of the lab. We collected a large cohort of uveal melanoma patients and conducting now several projects to decipher oncogenic transformation and genetic background of UM. Exploring a metastatic uveal melanoma patient with an outlier response to immune checkpoint inhibitors, we discovered the role of MBD4 inactivation in a new genetic instability (28). We further showed the continuous acquisition of mutations in the course of the disease and used this biological clock to reconstruct the natural history of the disease (29). We recently demonstrated the predisposing role of germline MBD4 mutations in uveal melanoma (30). We are presently coordinating the INCa PRT-K19 TREAT-MBD4 project for better defining the spectrum of this novel cancer predisposition syndrome, including in gliomas, to develop diagnostic tools and to take advantage of MBD4 deficiency for targeted therapies.
  • Our discovery of SF3B1 mutations in UM (31) led us to explore transcriptional instability, and more precisely the splicing consequences of SF3B1 mutations (32-34). Pan-cancers analysis by cloud computing (in collaboration with Seven Bridges, USA) allowed us to identify SUGP1 mutations as genocopies of SF3B1 (35). Oncogenic consequences of these mutations are actively searched for in collaboration with the translational research group led by S. Alsafadi.
  • We explored and proved splicing abnormalities to be a possible source of neoantigens. We developed a pipeline for neoantgen prediction and performed their validated in collaboration with O. Lantz’s team, Inserm U932 (36). Patent : 20305477.



1.    Popova T, Manie E, Rieunier G, et al. Ploidy and large-scale genomic instability consistently identify basal-like breast carcinomas with BRCA1/2 inactivation. Cancer Res 2012;72(21):5454-62.

2.    Jdey W, Thierry S, Popova T, et al. Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA. Cancer Res 2017;77(16):4207-4216.

3.    Manie E, Popova T, Battistella A, et al. Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas. Int J Cancer 2016;138(4):891-900.

4.    Weigelt B, Ng CK, Shen R, et al. Corrigendum: metastatic breast carcinomas display genomic and transcriptomic heterogeneity. Mod Pathol 2015;28(4):607.

5.    Goundiam O, Gestraud P, Popova T, et al. Histo-genomic stratification reveals the frequent amplification/overexpression of CCNE1 and BRD4 genes in non-BRCAness high grade ovarian carcinoma. Int J Cancer 2015;137(8):1890-900.

6.    Curtit E, Benhamo V, Gruel N, et al. First description of a sporadic breast cancer in a woman with BRCA1 germline mutation. Oncotarget 2015;6(34):35616-24.

7.    Gruel N, Benhamo V, Bhalshankar J, et al. Polarity gene alterations in pure invasive micropapillary carcinomas of the breast. Breast Cancer Res 2014;16(3):R46.

8.    Pecuchet N, Popova T, Manie E, et al. Loss of heterozygosity at 13q13 and 14q32 predicts BRCA2 inactivation in luminal breast carcinomas. Int J Cancer 2013;133(12):2834-42.

9.    Natrajan R, Mackay A, Lambros MB, et al. A whole-genome massively parallel sequencing analysis of BRCA1 mutant oestrogen receptor-negative and -positive breast cancers. J Pathol 2012;227(1):29-41.

10.  Gentric G, Kieffer Y, Mieulet V, et al. PML-Regulated Mitochondrial Metabolism Enhances Chemosensitivity in Human Ovarian Cancers. Cell Metab 2019;29(1):156-173 e10.

11.  Golmard L, Castera L, Krieger S, et al. Contribution of germline deleterious variants in the RAD51 paralogs to breast and ovarian cancers. Eur J Hum Genet 2017;25(12):1345-1353.

12.  Coussy F, El-Botty R, Chateau-Joubert S, et al. BRCAness, SLFN11, and RB1 loss predict response to topoisomerase I inhibitors in triple-negative breast cancers. Sci Transl Med 2020;12(531).

13.  Labidi-Galy SI, Olivier T, Rodrigues M, et al. Location of Mutation in BRCA2 Gene and Survival in Patients with Ovarian Cancer. Clin Cancer Res 2018;24(2):326-333.

14.  Golmard L, Delnatte C, Lauge A, et al. Breast and ovarian cancer predisposition due to de novo BRCA1 and BRCA2 mutations. Oncogene 2016;35(10):1324-7.

15.  Eeckhoutte A, Houy A, Manie E, et al. ShallowHRD: detection of homologous recombination deficiency from shallow whole genome sequencing. Bioinformatics 2020;36(12):3888-3889.

16.  Popova T, Manie E, Boeva V, et al. Ovarian Cancers Harboring Inactivating Mutations in CDK12 Display a Distinct Genomic Instability Pattern Characterized by Large Tandem Duplications. Cancer Res 2016;76(7):1882-91.

17.  Eeckhoutte A, Saint-Ghislain M, Reverdy M, et al. Lack of evidence for CDK12 as an ovarian cancer predisposing gene. Fam Cancer 2020;19(3):203-209.

18.  Popova T, Hebert L, Jacquemin V, et al. Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet 2013;92(6):974-80.

19.  Hebert L, Bellanger D, Guillas C, et al. Modulating BAP1 expression affects ROS homeostasis, cell motility and mitochondrial function. Oncotarget 2017;8(42):72513-72527.

20.  Walpole S, Pritchard AL, Cebulla CM, et al. Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide. J Natl Cancer Inst 2018;110(12):1328-1341.

21.  Fievet A, Bellanger D, Rieunier G, et al. Functional classification of ATM variants in ataxia-telangiectasia patients. Hum Mutat 2019;40(10):1713-1730.

22.  Fievet A, Bellanger D, Valence S, et al. Three new cases of ataxia-telangiectasia-like disorder: No impairment of the ATM pathway, but S-phase checkpoint defect. Hum Mutat 2019;40(10):1690-1699.

23.  Fievet A, Bellanger D, Zahed L, et al. DNA repair functional analyses of NBN hypomorphic variants associated with NBN-related infertility. Hum Mutat 2020;41(3):608-618.

24.  Jacquemin V, Rieunier G, Jacob S, et al. Underexpression and abnormal localization of ATM products in ataxia telangiectasia patients bearing ATM missense mutations. Eur J Hum Genet 2012;20(3):305-12.

25.  Meneret A, Ahmar-Beaugendre Y, Rieunier G, et al. The pleiotropic movement disorders phenotype of adult ataxia-telangiectasia. Neurology 2014;83(12):1087-95.

26.  Rieunier G, D'Enghien CD, Fievet A, et al. ATM Gene Mutation Detection Techniques and Functional Analysis. Methods Mol Biol 2017;1599:25-42.

27.  Schrader A, Crispatzu G, Oberbeck S, et al. Actionable perturbations of damage responses by TCL1/ATM and epigenetic lesions form the basis of T-PLL. Nat Commun 2018;9(1):697.

28.  Rodrigues M, Mobuchon L, Houy A, et al. Outlier response to anti-PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors. Nat Commun 2018;9(1):1866.

29.  Rodrigues M, Mobuchon L, Houy A, et al. Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations. Clin Cancer Res 2019;25(18):5513-5524.

30.  Derrien AC, Rodrigues M, Eeckhoutte A, et al. Germline MBD4 Mutations and Predisposition to Uveal Melanoma. J Natl Cancer Inst 2021;113(1):80-87.

31.  Furney SJ, Pedersen M, Gentien D, et al. SF3B1 mutations are associated with alternative splicing in uveal melanoma. Cancer Discov 2013;3(10):1122-1129.

32.  Gentien D, Kosmider O, Nguyen-Khac F, et al. A common alternative splicing signature is associated with SF3B1 mutations in malignancies from different cell lineages. Leukemia 2014;28(6):1355-7.

33.  Alsafadi S, Houy A, Battistella A, et al. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat Commun 2016;7:10615.

34.  Canbezdi C, Tarin M, Houy A, et al. Functional and conformational impact of cancer-associated SF3B1 mutations depends on the position and the charge of amino acid substitution. Comput Struct Biotechnol J 2021;19:1361-1370.

35.  Alsafadi S, Dayot S, Tarin M, et al. Genetic alterations of SUGP1 mimic mutant-SF3B1 splice pattern in lung adenocarcinoma and other cancers. Oncogene 2021;40(1):85-96.

36.  Bigot J, Lalanne AI, Lucibello F, et al. Splicing patterns in SF3B1 mutated uveal melanoma generate shared immunogenic tumor-specific neo-epitopes. Cancer Discov 2021; 10.1158/2159-8290.CD-20-0555.