Our team DNA Repair and Uveal Melanoma (D.R.U.M.) is mainly interested (i) in genomic instabilities in breast/ovarian cancers and uveal melanoma and (ii) in genetics and genomics of uveal melanoma, using innovative bioinformatics and data mining approaches.
1- Genomic characterization of breast and ovarian carcinoma.
- Deleterious germline mutations of the two major susceptibility genes BRCA1 or BRCA2 lead to an increased risk of developing breast and ovarian carcinomas. BRCA1 and BRCA2 encode key actors of the DNA repair by homologous recombination (HR) pathway and behave like classical tumor suppressor genes in approximately half of high grade so called triple negative (hormone receptors negative, HER2 not amplified) breast carcinoma and high grade ovarian carcinoma. We have identified a signature of genomic instability related to the inactivation of HR (HR deficiency or HRD, also known as BRCAness), most often by inactivation of BRCA1 or BRCA2 (1); published patents: US20150140122A1, US20170260588A1; 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 (2-10). Recent developments include adapting the LST signature from shallow Whole Genome Sequencing, for affordable and robust clinical diagnosis (Eeckhoutte, in preparation).
- However, the identification of unusual genomic patterns in ovarian carcinoma led us to identify a new genomic instability related to inactivation of CDK12 (11). 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 stimulate intronic premature polyadenylation, downregulating the expression of large genes, including DNA repair genes.
- As many breast cancer prone families are not explained by germline mutations of BRCA1, BRCA2 or other HR genes, 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 (12). We sought to understand the functions of BAP1 in cellular models and showed profound metabolic and cellular changes related to BAP1 expression (13). BAP1 is a deubiquitinase, mainly of histone H2A (H2AK119ub1), antagonizing the Polycomb Repressive Complex 1 (PRC1). We are now involved in international studies on BAP1 germline mutations (14).
- DNA repair related diseases 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 (15-18).
2- Genetic and genomic characterization of uveal melanoma (UM).
Choroidal UM is the most common form of intraocular primary malignancies in adults, but is a rare tumor with an incidence rate of 5.6 cases per million person-years (~500 new cases a year in France). Prognosis is dismal when the disease spreads, frequently to the liver. A better understanding of the disease is an urgent need, considering the rapidly unfavorable evolution and lack of effective chemotherapy in its metastatic form.
- In collaboration with R. Marais (Cancer Research UK), we have shown the low mutational burden and lack of ultra-violet radiation signature in UM, in contrast to cutaneous melanoma. We also described recurrent mutations of the splicing gene SF3B1 (19).
- We then deciphered the consequences of SF3B1 mutations on splicing (20-22). More recently, a pan-cancer analysis using cloud computing (in collaboration with Seven Bridges, USA) allowed us to identify SUGP1 mutations as a genocopy of SF3B1 (Alsafadi, submitted); the analysis of the oncogenic consequences of these SF3B1 mutations; and the exploitation of splicing abnormalities as a potential source of tumor immunogenicity (collaboration with O. Lantz).
- UM has an unusual epidemiology, as the disease occurs mostly in individuals of European ancestry. In the hypothesis of predisposing alleles in this population, we initiated the first pan-genomic association study (GWAS) for uveal melanoma. We identified risk variants in the TERT/CLPTM1L region, and the HERC2 pigmentation gene region (23). This study is currently being expanded to search for new risk loci (collaboration with CeRePP, CNG, IARC and CLB (Mobuchon et al, in preparation).
- We participated in the TCGA project to describe primary UM at the –omics level (24) and we are key players in the Horizon2020 project aiming to better understand and target metastatic UM (25). We analyzed the mechanisms of metastatic progression and resistance to chemotherapy of these metastases, and showed that mutational heterogeneity is very limited and does not explain the therapeutic resistance, whereas metastatic progression is mainly associated with the acquisition of recurrent genomic gains and losses (26).
3- DNA repair and uveal melanoma.
- Exploring a UM metastatic patient with an outlier response to immune checkpoint inhibitors, we discovered the role of MBD4 inactivation in a new genetic instability (27). We further explored UM progression in MBD4 deficient tumors, 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 (26).
- Most MBD4deficient UM cases are associated with deleterious germline MBD4 mutations, and we recently demonstrated the predisposing role of this gene in UM (Derrien, submitted).
4- Other translational activities.
In collaboration with O. Lantz, we initiated the analysis of tumor DNA circulating in UM. We developed several methods in different cancers (28-37), and 3 patents: US20190256921A1, WO2019011971A1, WO2019175323A12017,).
1. Popova T, Manie E, Rieunier G, Caux-Moncoutier V, Tirapo C, Dubois T, 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 doi 10.1158/0008-5472.can-12-1470.
2. Natrajan R, Mackay A, Lambros MB, Weigelt B, Wilkerson PM, Manie E, 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 doi 10.1002/path.4003.
3. Pecuchet N, Popova T, Manie E, Lucchesi C, Battistella A, Vincent-Salomon A, et al. Loss of heterozygosity at 13q13 and 14q32 predicts BRCA2 inactivation in luminal breast carcinomas. Int J Cancer 2013;133(12):2834-42 doi 10.1002/ijc.28315.
4. Gruel N, Benhamo V, Bhalshankar J, Popova T, Freneaux P, Arnould L, et al. Polarity gene alterations in pure invasive micropapillary carcinomas of the breast. Breast Cancer Res 2014;16(3):R46 doi 10.1186/bcr3653.
5. Goundiam O, Gestraud P, Popova T, De la Motte Rouge T, Fourchotte V, Gentien D, 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 doi 10.1002/ijc.29568.
6. Curtit E, Benhamo V, Gruel N, Popova T, Manie E, Cottu P, et al. First description of a sporadic breast cancer in a woman with BRCA1 germline mutation. Oncotarget 2015;6(34):35616-24 doi 10.18632/oncotarget.5348.
7. Manie E, Popova T, Battistella A, Tarabeux J, Caux-Moncoutier V, Golmard L, et al. Genomic hallmarks of homologous recombination deficiency in invasive breast carcinomas. Int J Cancer 2016;138(4):891-900 doi 10.1002/ijc.29829.
8. Weigelt B, Ng CKY, Shen R, Popova T, Schizas M, Natrajan R, et al. Erratum: Metastatic breast carcinomas display genomic and transcriptomic heterogeneity. Modern Pathology 2015;28(4):607- doi 10.1038/modpathol.2014.163.
9. Jdey W, Thierry S, Popova T, Stern MH, Dutreix M. Micronuclei Frequency in Tumors Is a Predictive Biomarker for Genetic Instability and Sensitivity to the DNA Repair Inhibitor AsiDNA. Cancer Res 2017;77(16):4207-16 doi 10.1158/0008-5472.CAN-16-2693.
10. Gentric G, Kieffer Y, Mieulet V, Goundiam O, Bonneau C, Nemati F, et al. PML-Regulated Mitochondrial Metabolism Enhances Chemosensitivity in Human Ovarian Cancers. Cell Metab 2019;29(1):156-73 e10 doi 10.1016/j.cmet.2018.09.002.
11. Popova T, Manie E, Boeva V, Battistella A, Goundiam O, Smith NK, 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 doi 10.1158/0008-5472.CAN-15-2128.
12. Popova T, Hebert L, Jacquemin V, Gad S, Caux-Moncoutier V, Dubois-d’Enghien C, et al. Germline BAP1 mutations predispose to renal cell carcinomas. Am J Hum Genet 2013;92(6):974-80 doi 10.1016/j.ajhg.2013.04.012.
13. Hebert L, Bellanger D, Guillas C, Campagne A, Dingli F, Loew D, et al. Modulating BAP1 expression affects ROS homeostasis, cell motility and mitochondrial function. Oncotarget 2017;8(42):72513-27 doi 10.18632/oncotarget.19872.
14. Walpole S, Pritchard AL, Cebulla CM, Pilarski R, Stautberg M, Davidorf FH, et al. Comprehensive Study of the Clinical Phenotype of Germline BAP1 Variant-Carrying Families Worldwide. J Natl Cancer Inst 2018;110(12):1328-41 doi 10.1093/jnci/djy171.
15. Meneret A, Ahmar-Beaugendre Y, Rieunier G, Mahlaoui N, Gaymard B, Apartis E, et al. The pleiotropic movement disorders phenotype of adult ataxia-telangiectasia. Neurology 2014;83(12):1087-95 doi 10.1212/WNL.0000000000000794.
16. Rieunier G, D’Enghien CD, Fievet A, Bellanger D, Stoppa-Lyonnet D, Stern M-H. ATM Gene Mutation Detection Techniques and Functional Analysis. Methods Mol Biol 2017;1599:25-42 doi 10.1007/978-1-4939-6955-5_3.
17. Fievet A, Bellanger D, Valence S, Mobuchon L, Afenjar A, Giuliano F, 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):1690-9 doi 10.1002/humu.23773.
18. Fievet A, Bellanger D, Rieunier G, Dubois d’Enghien C, Sophie J, Calvas P, et al. Functional classification of ATM variants in ataxia-telangiectasia patients. Hum Mutat 2019;40(10):1713-30 doi 10.1002/humu.23778.
19. Furney SJ, Pedersen M, Gentien D, Dumont AG, Rapinat A, Desjardins L, et al. SF3B1 mutations are associated with alternative splicing in uveal melanoma. Cancer Discov 2013;3(10):1122-9 doi 10.1158/2159-8290.CD-13-0330.
20. Alsafadi S, Houy A, Battistella A, Popova T, Wassef M, Henry E, et al. Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage. Nat Commun 2016;7:10615 doi 10.1038/ncomms10615.
21. Gentien D, Kosmider O, Nguyen-Khac F, Albaud B, Rapinat A, Dumont AG, et al. A common alternative splicing signature is associated with SF3B1 mutations in malignancies from different cell lineages. Leukemia 2014;28(6):1355-7 doi 10.1038/leu.2014.28.
22. Bondu S, Alary AS, Lefevre C, Houy A, Jung G, Lefebvre T, et al. A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome. Sci Transl Med 2019;11(500) doi 10.1126/scitranslmed.aav5467.
23. Mobuchon L, Battistella A, Bardel C, Scelo G, Renoud A, Houy A, et al. A GWAS in uveal melanoma identifies risk polymorphisms in the CLPTM1L locus. NPJ Genom Med 2017;2(1) doi 10.1038/s41525-017-0008-5.
24. Robertson AG, Shih J, Yau C, Gibb EA, Oba J, Mungall KL, et al. Integrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma. Cancer Cell 2017;32(2):204-20.e15 doi 10.1016/j.ccell.2017.07.003.
25. Rodrigues M, Koning L, Coupland SE, Jochemsen AG, Marais R, Stern MH, et al. So Close, yet so Far: Discrepancies between Uveal and Other Melanomas. A Position Paper from UM Cure 2020. Cancers (Basel) 2019;11(7):1032 doi 10.3390/cancers11071032.
26. Rodrigues M, Mobuchon L, Houy A, Alsafadi S, Baulande S, Mariani O, et al. Evolutionary Routes in Metastatic Uveal Melanomas Depend on MBD4 Alterations. Clin Cancer Res 2019;25(18):5513-24 doi 10.1158/1078-0432.CCR-19-1215.
27. Rodrigues M, Mobuchon L, Houy A, Fievet A, Gardrat S, Barnhill RL, et al. Outlier response to anti-PD1 in uveal melanoma reveals germline MBD4 mutations in hypermutated tumors. Nat Commun 2018;9(1):1866 doi 10.1038/s41467-018-04322-5.
28. Bidard FC, Kiavue N, Ychou M, Cabel L, Stern MH, Madic J, et al. Circulating Tumor Cells and Circulating Tumor DNA Detection in Potentially Resectable Metastatic Colorectal Cancer: A Prospective Ancillary Study to the Unicancer Prodige-14 Trial. Cells 2019;8(6) doi 10.3390/cells8060516.
29. Decraene C, Silveira AB, Bidard FC, Vallee A, Michel M, Melaabi S, et al. Multiple Hotspot Mutations Scanning by Single Droplet Digital PCR. Clin Chem 2018;64(2):317-28 doi 10.1373/clinchem.2017.272518.
30. Cabel L, Proudhon C, Romano E, Girard N, Lantz O, Stern MH, et al. Clinical potential of circulating tumour DNA in patients receiving anticancer immunotherapy. Nat Rev Clin Oncol 2018;15(10):639-50 doi 10.1038/s41571-018-0074-3.
31. Riva F, Bidard F-C, Houy A, Saliou A, Madic J, Rampanou A, et al. Patient-Specific Circulating Tumor DNA Detection during Neoadjuvant Chemotherapy in Triple-Negative Breast Cancer. Clinical Chemistry 2017;63(3):691-9 doi 10.1373/clinchem.2016.262337.
32. Riva F, Dronov OI, Khomenko DI, Huguet F, Louvet C, Mariani P, et al. Clinical applications of circulating tumor DNA and circulating tumor cells in pancreatic cancer. Molecular Oncology 2016;10(3):481-93 doi 10.1016/j.molonc.2016.01.006.
33. Saliou A, Bidard F-C, Lantz O, Stern M-H, Vincent-Salomon A, Proudhon C, et al. Circulating tumor DNA for triple-negative breast cancer diagnosis and treatment decisions. Expert Review of Molecular Diagnostics 2015;16(1):39-50 doi 10.1586/14737159.2016.1121100.
34. Madic J, Kiialainen A, Bidard FC, Birzele F, Ramey G, Leroy Q, et al. Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients. Int J Cancer 2015;136(9):2158-65 doi 10.1002/ijc.29265.
35. Lebofsky R, Decraene C, Bernard V, Kamal M, Blin A, Leroy Q, et al. Circulating tumor DNA as a non-invasive substitute to metastasis biopsy for tumor genotyping and personalized medicine in a prospective trial across all tumor types. Molecular Oncology 2015;9(4):783-90 doi 10.1016/j.molonc.2014.12.003.
36. Bidard FC, Madic J, Mariani P, Piperno-Neumann S, Rampanou A, Servois V, et al. Detection rate and prognostic value of circulating tumor cells and circulating tumor DNA in metastatic uveal melanoma. Int J Cancer 2014;134(5):1207-13 doi 10.1002/ijc.28436.
37. Madic J, Piperno-Neumann S, Servois V, Rampanou A, Milder M, Trouiller B, et al. Pyrophosphorolysis-activated polymerization detects circulating tumor DNA in metastatic uveal melanoma. Clin Cancer Res 2012;18(14):3934-41 doi 10.1158/1078-0432.CCR-12-0309.