Individual projects

Research project

DC12 Decoding the role of the noncoding genome in diffuse large B cell lymphoma


In this project we will decipher how non-coding mutations and epigenetic alterations drive lymphomagenesis by altering the transcriptional programs of cancer cells and fibroblast of the tumor microenvironment to ultimately identify new drug targets and biomarkers to improve patient survival.

Keywords: DLBCL, non-coding (epi)mutations, 3D epigenome organization, enhancer-promoter loop

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Diffuse Large B Cell Lymphomas (DLBCLs) arise from antigen-exposed mature B-cells during the germinal center (GC) reaction, but the mechanisms underlying this transformation are not fully understood. Genome-wide association studies (GWAS), whole genome sequencing (WGS) and whole genome bisulphite sequencing (WGBS) of DLBCL samples have identified many mutations and epimutations ((epi)mutations) that may be implicated in disease development. However, these often occur in noncoding regions, frequently at enhancers, and elucidating the mechanisms through which they may drive DLBCL development is still a challenge. One likely pathogenic mechanism of these noncoding alterations is their possible ability to alter the function of enhancers (e.g., by disrupting transcription factor binding), leading to gene deregulation of distal targe genes that ultimately boosts disease. However, the cell-type specific repertoire of genes controlled by each enhancer remain uncharted. Enhancers cannot simply be assigned to the nearest gene because their target genes can be up to a few megabases away, often jumping over several intervening genes.

Enhancers function through spatial proximity to the genes they regulate, and this proximity is facilitated by chromatin loops. Thus, the three-dimensional genome organization, unique to each cell type, plays a fundamental role in regulating gene expression in both physiological and disease conditions, and its study can help us to understand the contribution of non-coding alterations to disease. Following this reasoning, the team led by Dr. Javierre has developed the low input capture Hi-C method named liCHi-C method (Tomás-Daza et al., Nat Commun 2023). liCHi-C enables the identification of disease-relevant cell types, genes and pathways potentially deregulated by non-coding alterations at distal regulatory elements, and uncovers genome-wide structural variants, resolve their breakpoints, and infer their pathogenic effects.

Based on this methodology, in combinations with epigenomics and functional validation, this proposal is to decipher the role of noncoding (epi)mutations affecting enhancers controlling normal and malignant B cell differentiation, as well as tumour microenvironment polarization, to: i) unravel the oncogenic role of these alterations during the DLBC lymphomagenesis, including its effect in supporting an pro-tumoral microenvironment; ii) discover new biomarkers and therapeutic targets to ultimately improve patient survival. To this end we propose the following objectives: i) Identify the repertoire key enhancers that may be targets of noncoding (epi)mutations associated with DLBC, which control tumoral cells but also cancer associated fibroblast; ii) Discover new noncoding (epi)mutations at enhancers underlying DLBCL development and relapse.



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NeoVirTech (Toulouse, France)