Computational Epi- Genetics of Cancer
Understand cancer today to treat it tomorrow
Our research focusOur group aims at addressing the following questions:
- Determine the role of epigenetic remodeling in oncogenic transformation for cancers with recurrent copy number changes
- Investigate the consequences of somatic genomic alterations on the epigenetic landscape in cancer in these cancers
- Adjust methodology for studying genetic and epigenetic changes in 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.
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.
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.