Mots-Clés

CUT&Tag, RNA-seq, hematopoietic stem cells, transposable elements, clonal hematopoiesis, leukemia

Description

Clonal hematopoiesis of indeterminate potential (CHIP) is characterized by the overproduction of blood cells derived from a single hematopoietic stem cell (HSC) harboring somatic mutation(s) that confer a selective clonal advantage. CHIP is associated with increased all-cause mortality, risk of cardio-metabolic disease and an increased risk of myeloid malignancies.

CHIP is mainly driven by mutations in DNMT3A and TET2 epigenetic factors. However, the molecular mechanisms by which these variants confer a fitness advantage to HSCs and imbalance myeloid / lymphoid differentiation remain largely unknown. Notably, DNMT3A and TET2 have antagonistic biochemical activities, promoting DNA methylation and demethylation respectively, yet both mutations paradoxically result in similar functional alterations in HSCs.

The repressive histone mark H3K9me3 plays a crucial role in the maintenance of HSC identity. H3K9me3 controls transposable element (TEs) expression. TEs are repeated sequences that make out half of the human and mouse genome. They can spread in the genome through a copy/paste mechanism, constituting a great source of genomic instability. TEs have also been recently recognized as major contributors of gene regulatory networks. We previously showed that H3K9me3 enrichment at intronic L1 is crucial for HSC gene expression and function1. Interestingly, TET2 and DNMT3A have been linked to TE repression, through DNA methylation and/or H3K9me3, in different cell types.

We aim to test the hypothesis that the paradoxical similar consequences of TET2 and DNMT3A mutations on HSC functional changes and the establishment of a preleukemic state could involve changes in H3K9me3 and the derepression of common TEs, that will deregulate genes involved in HSC identity and myeloid differentiation.

To that end, we have already generated several sets of CUT&Tag (H3K9me3; H3K4me1; H3K27ac) and RNA-seq data from Tet2-/- and Dnmt3a-mut HSCs.

The successful candidate will be in charge of the bioinformatics part of the project. She/He will characterize the modifications to these different histone modifications at TEs in mutant HSCs, and identify common modifications in both mutants that could explain the similar functional alterations in HSCs. She/He will also characterize the common transcriptomic changes in both mutants. She/He will finally search for TF binding sites enriched in derepressed TE that could explain the common transcriptomic changes.

The internship will take place at Gustave Roussy in Villejuif, within an interdisciplinary environment. A knowledge of NGS data processing and basic bioinformatic skills (R, Bash…etc) is required. Good communication and presentation skills are necessary.

The candidate will work in close collaboration with a bioinformatic engineer in the group.

1.      Pelinski, Y. et al. NF-κB signaling controls H3K9me3 levels at intronic LINE-1 and hematopoietic stem cell genes in cis. J. Exp. Med. 219, e20211356 (2022).