Link to the Doctoral School website

Keywords

B lymphocyte, nuclear organization, Immunoglobulin genes, DNA damage

Profile and skills required

– Motivated student Master II Biology – Health
– Familiarity (theory +/- practice) with molecular biology techniques (amplification, sequencing) and cell biology (line culture)
– Interest in nuclear organization at different scales (nuclear, supranucleosomal and nucleosomal)
– Knowledge of basic immunology and B cell biology

Project description

Once activated, B lymphocytes undergo programmed DNA damage within the genes encoding immunoglobulins (Ig), with the aim of improving the quality of antibodies (Ig in soluble form) produced in response to an antigen (Ag). These events, known as somatic hypermutation (SHM) and class switching (CSR), are triggered by the LB-Ag encounter. SHM consists in introducing mutations that lead to an increase in Ig affinity, and CSR consists in changing the antibody class for a more effective response to the Ag. Both SHM and CSR are initiated by deamination of DNA cytidines to uracil by the AID enzyme; the resulting base mismatch leads either to the introduction of mutations (for SHM), or to the introduction of DNA double-strand breaks (for CSR). Although essential for improving antibody affinity when targeting Ig genes, such rearrangements represent a threat to the overall integrity of the LB genome, as they can unexpectedly affect other genes known as illegitimate AID targets (or AID off-target genes). AID collateral damage in these off-target genes can promote the formation of B-cell cancers, as evidenced by mutations and translocations frequently involving oncogenes of this lineage (e.g. mutations of Bcl6 in diffuse large-cell B-cell lymphomas). Studies from our laboratory have clarified the role of cis-regulatory regions present at the IgH locus (Ig heavy chains): these regions locally control SHM and CSR events [1-3]. However, these rearrangements take place in the three-dimensional space of the B cell nucleus, whose organization, evolution and regulation rememain little explored. Several studies show that the non-random organization of the nucleus into different compartments is a player in its own right, influencing in particular the handling of certain types of DNA damage. For example, DSBs artificially induced via the nucleases I-SceI or Cas9 at the periphery of the nucleus in regions known as LADs (Lamina Associated Domains) are preferentially repaired by the MMEJ (Microhomology Mediated End Joining) pathway [4, 5]. Another study analyzing mutations on a genome-wide scale shows that mutation frequency is higher at LADs in different types of cancer, including B-cell cancers (diffuse large B-cell lymphoma and chronic lymphocytic leukemia) [6].
The aim of the proposed thesis project is (i) to explore on a large scale the nuclear organization of resting and stimulated B cells in a cellular model (CH12 model) and (ii) to determine how this nuclear organization influences off-target gene rearrangements.
It is particularly important to study the organization of the nucleus (i.e. gene position) in the regulation of SHM and CSR events, as any deregulation of these events can lead to the appearance of illegitimate rearrangements at the origin of cancer.

Further information and application form : https://adum.fr/as/ed/voirproposition.pl?langue=&site=unilimBCS&matricule_prop=64271#version

Link to the Doctoral School website

Keywords

B cell, MYC, lymphoma, chromatin

Profile and skills required

We are looking for a motivated and rigorous PhD candidate with a strong interest in molecular and cellular biology, gene expression regulation, and epigenetic mechanisms associated with cancer.

Prior knowledge of normal B cell development is appreciated but not a prerequisite.

Required Skills:
Scientific autonomy and rigor: Ability to design and conduct experiments independently.

Teamwork: Collaboration with researchers and bioinformaticians.

Communication skills: Ability to present findings at conferences and seminars.

Proficiency in scientific English (written and spoken).

Required Education & Experience:
Master’s degree (M2) in molecular biology, biotechnology, bioinformatics, or a related field.

Hands-on experience in molecular biology and/or genomics.

Familiarity with high-throughput sequencing approaches.

Preferred but Not Required Skills:
Processing and analysis of high-throughput sequencing data, including:

Familiarity with bioinformatics tools for RNA-seq and Hi-C analysis (e.g., HiCExplorer, DESeq2, EdgeR).

Basic knowledge of R or Python for transcriptomic and epigenetic data analysis.

Experience using public databases (e.g., TCGA, ENCODE) to compare gene expression profiles.

Project description

Terminal maturation of B lymphocytes (B cells) following antigenic activation leads to transcriptional reprogramming. The three-dimensional (3D) organization of chromatin plays a crucial role in orchestrating gene expression essential for the immune response and may also be involved in B cell tumorigenesis, as demonstrated by several studies on B cell lymphomas.

The MYC oncogene plays a key role in these processes by influencing chromatin decompaction and chromatin loop formation, thereby facilitating long-range interactions that modulate gene expression. Its involvement in aggressive lymphomas, particularly Burkitt lymphoma (BL) and certain subtypes of diffuse large B-cell lymphoma (DLBCL), is well documented. In chronic lymphocytic leukemia (CLL), MYC overexpression is also associated with poor prognosis and genetic alterations.

This project aims to explore how MYC overexpression alters the 3D genome organization of B cells, contributing to genomic instability and transcriptional reprogramming. Specifically, we seek to establish a link between elevated MYC levels, chromatin interaction alterations, and genetic rearrangements that promote tumor progression.

Project Objectives:
Analyze the impact of MYC on chromatin architecture by studying changes in the 3D conformation of DNA in B cells.

Assess MYC’s influence on genomic instability, particularly in relation to specific rearrangements found in lymphomas.

Investigate MYC-induced transcriptional reprogramming to better understand the mechanisms driving B-cell cancer aggressiveness.

By combining chromosome conformation capture approaches (3C/Hi-C), transcriptional profiling, and DNA damage analysis, this project provides an innovative perspective on MYC’s role in B-cell lymphomas. It may pave the way for new therapeutic strategies targeting nuclear organization alterations to combat aggressive forms of these cancers.

Further information and application form : https://adum.fr/as/ed/voirproposition.pl?langue=&site=unilimBCS&matricule_prop=64070#version