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 initiation and progression and associate these changes with genetic modifications. We welcome both molecular biology and bioinformatics approaches.


Our research focus

Our group aims at addressing the following questions:
  1. Determine the role of epigenetic remodeling in oncogenic transformation for cancers with recurrent copy number changes
  2. Investigate the consequences of somatic genomic alterations on the epigenetic landscape in cancer in these cancers
  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.


Our methodological research is centered on data integration and the development of high throughput data analysis methods to study regulation in cancer with a special focus on epigenetic regulation. Methods we are specialists in include:

  • 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 cancer RNA-seq: detection of abnormal transcripts expressed in cancer cells


Check the whole list of the developed software.

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.

We are supported by:

WCR WCR WCR ARC