The research activities of the team aim to decipher the mechanisms involved in the repair of complex DNA lesions in order to better understand cancer development, particularly kidney cancer, and the mechanisms of chemoresistance in tumor cells, by leveraging the complementarity and expertise of the team members. The knowledge gained from mechanistic studies of alternative DNA repair pathways and post-replicative DNA modifications could lead to the development of new diagnostic and therapeutic targets, with the goal of designing DNA repair inhibitors to combat acquired resistance in cancers—particularly in renal carcinoma, which will be used as a model.
We investigate a novel post-replicative DNA modification catalyzed by poly(ADP-ribose) polymerases (PARPs) and its role in the repair of DNA strand breaks in both normal and cancer cells. PARP enzymes play a key role in the DNA damage response, and PARP1 hyperactivation is frequently linked to drug resistance in cancer. Notably, PARP1 interacts with the transcription factor HIF and regulates the hypoxia response in vivo. Our previous work showed that cisplatin-resistant cancer cells exhibit heightened PARP1 activity and are more sensitive to PARP inhibitors than cisplatin-sensitive cells. We also demonstrated that human PARP1, 2, and 3 can catalyze covalent attachments between DNA ends and poly-/mono-ADP-ribose chains in vitro—modifications that are reversible via PARG activity. These findings suggest that DNA ADP-ribosylation is a dynamic response to complex DNA damage and may help coordinate the repair of clustered strand breaks. Our current projects aim to characterize the mechanisms by which PARPs catalyze DNA ADP-ribosylation, identify the proteins that detect these modified DNA structures, and determine whether ADP-ribosylated DNA is present in cancer cells exposed to genotoxic treatments. We also seek to understand the role of this modification in the DNA damage response and its potential contribution to the coordination of DNA strand break repair and to acquired chemoresistance in cancer cells.
We study DNA damage-induced signaling pathways in kidney cancer, with a focus on their links to hereditary forms of the disease. While most renal cell carcinomas (RCC) are sporadic, about 3% have a hereditary basis. Four major susceptibility genes have been identified—three tumor suppressors (VHL, FLCN, FH) and one oncogene (MET)—alongside newer candidates like MITF, BAP1, and PBRM1. Identifying causal mutations enables genetic testing and surveillance of at-risk individuals, facilitating early diagnosis and improved outcomes. These hereditary genes are also frequently altered in sporadic RCCs, highlighting shared mechanisms in renal tumorigenesis. For instance, VHL inactivation is common in both hereditary and sporadic RCC, and its protein, pVHL, plays a key role in degrading HIF under normal oxygen levels. This discovery has led to targeted therapies that inhibit HIF-driven angiogenesis, reinforcing the idea that kidney cancer is a metabolic disease driven by HIF pathway dysregulation. Through the national reference network PREDIR, we access patient tumor and blood samples to explore genetic predispositions to RCC. Our work has revealed a gradient of pVHL dysfunction in hypoxia signaling and deregulated mRNA/miRNA profiles in VHL-associated tumors. Recently, we identified germline missense mutations in two families affecting a DNA repair protein involved in interstrand crosslink (ICL) repair, telomere maintenance, and the Fanconi anemia pathway. Our current research focuses on characterizing these mutations at the cellular and tissue levels (normal vs. tumor kidney) and assessing their functional impact after genotoxic stress. Using samples from hereditary RCC patients, we also search for novel mutations in DNA damage response genes to better understand the molecular mechanisms driving renal carcinogenesis and therapy resistance.
Role of the DNA glycosylase initiated repair of 5-hydroxymethylcytosine residues in occurrence of drug-tolerant cells in cancer. Post-replicative methylation of cytosine at the C5 position (5mC) together with its erasure are essential epigenetic processes in the course of organism development, cell differentiation, genomic imprinting and suppression of mobile elements. The methylation status of DNA is a result of balance between methylation and demethylation, which can undergo dramatic changes during organism development, cell differentiation and cancer. DNA demethylation can occur either in passive or by active process via direct enzymatic removal of 5-methylcytosine (5mC) residues from DNA. In latter, the TET family proteins (TET1, 2 and 3) catalyse the sequential conversion of 5mC in the DNA first to 5hmC and then further to 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC). Human mismatch-specific Thymine-DNA glycosylase (TDG) catalyses the removal of 5fC and 5caC residues in DNA and their replacement with regular cytosine via base excision repair (BER) pathway. The global levels of 5mC and 5hmC are significantly reduced in many cancer types, intriguingly decreased level of 5hmC correlated with tumor aggressiveness. Although, it was thought that 5hmC is resistant to DNA repair, recently we demonstrated that TDG exhibits slow excision kinetic towards 5hmC residues in duplex DNA. We suggest that DNA demethylation and regulation of gene expression may also proceed via DNA glycosylase-catalysed removal of 5hmC. Cancer recurrence is observed when a subset of tumor cells, referred to as drug-tolerant cells, which can enter to slow-proliferating or quiescent state to survive genotoxic stress. Most of drug-tolerant cells do not divide in the presence of anticancer drug, however a subpopulation of these cells can re-enter the cell cycle during treatment and start to proliferate. Recent data suggest that non-genetic mechanisms such as epigenetic changes in the chromatin might have an important role in the development of a drug-tolerant persistent state. Here, we propose that re-establishment of the pattern of DNA hydroxymethylation in cancer cells might be linked to metabolic reprogramming and drug tolerance. Our data suggest that 5hmC, similar to 5fC and 5caC residues, can be removed in the BER pathway albeit at low rate and this in turn may lead to metabolic heterogeneity among human tumors via epigenetic alterations of the expression of enzymes involved in cellular metabolism. The aim of the present study is to understand the role TDG-catalysed excision of 5hmC in cell differentiation, particular in adaptive changes of the patterns of gene expression in cancer cells exposed to DNA damage.
