Our newly created ATIP-Avenir group of Institut Cochin focuses on cancer epigenomics with the aim to understand the role of epigenetic changes in cancer development and progression and associate these changes with genetics modifications.


We aim at addressing the following questions:

  1. Determine the role of epigenetic remodeling in oncogenic transformation for tumors with recurrent copy number changes
  2. Investigate the consequences of somatic genomic alterations on the epigenetic landscape in cancer
  3. Adjust methodology for studying genetic and epigenetic changes in cancer
Methods and techniques we develop for the analysis of cancer genomes and epigenomes can be applied to most of the cancer types. Currently, we are interested in understanding the oncogenic processes related to two cancer types: neuroblastoma and adrenocortical carcinoma. But we are open to collaborations with research groups studying other types of cancer.


Methodogological development by the members of the lab includes methods for:

  • ChIP-seq data analysis: transcription factors, histone modifications in normal and cancer cells
  • Analysis of whole genome / whole exome / target sequencing data: detection of copy number alterations and structural variants
  • Analysis of clonal heterogeneity in cancer
  • Analysis of cancer RNA-seq: detection of abnormal transcripts expressed in cancer cells


Check the whole list of the developed software.

Complete list of publications: Link

Projects

Institut Curie

The role of chromatin remodeling in neuroblastoma

Several collaborative projects with Institut Curie focus on studying aspects of neuroblastoma development and progression. The main interest of our lab is the role of epigenetic modifications in these events. This project is based on the analysis of histone modifications profiles in neuroblastoma cell lines and primary tumors coupled with the analysis of genetic events (mutations and amplifications in cancer pathways). It will implicate production and analysis of several types of high-throughput data including targeted sequencing, ChIP-seq, and RNA-seq data. This project will involve development of computational methodology, data mining and tests of drug sensitivity on neuroblastoma cells lines.


Institut Cochin

The role of chromatin remodeling in adrenocortical carcinomas

In collaboration with the National Centre for Rare Adrenal Diseases at Institut Cochin, we are going to discover the role of chromatin remodelling in the formation of the agressive subtype of adrenocortical carcinomas characterized by the extensive hyper-methylation of promoters of about 500 genes. We are going to determine specific genetic and epigenetic events associated with this phenotype using high-throughput sequencing techniques.