The role of genome architecture in normal and neoplastic B cells: a multi-omics approach

Abstract

[eng] Nuclear organization and its impact on gene regulation have started to be elucidated thanks to the development of chromosomal conformation capture techniques. In this doctoral thesis, in situ Hi-C data and nine additional omic layers have been integrated to define and biologically characterize the dynamic changes in three-dimensional (3D) genome architecture across normal B-cell differentiation and in neoplastic cells from chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) patients. Beyond the classical genome organization into active and inactive compartments, a third intermediate 3D compartment enriched in poised and polycomb-repressed chromatin has been identified (Study 1). It has been observed that during B-cell differentiation, a 28% of the 3D genome structure changed, being an extensive activation from naive to germinal center B cells and a reversal into a naive-like 3D genome upon further maturation into memory B cells the most remarkable features. In case of neoplastic B cells, both CLL and MCL displayed entity and subtype-specific alterations in chromosome organization. Those alterations comprised large chromatin blocks containing key disease-specific genes such as EBF1 in CLL or SOX11 in MCL. Chromosomal conformation maps were also assessed to define structural variants in neoplastic cells (Study 2). The t(11;14) translocation in MCL cases leading to CCND1 deregulation was associated with a breakpoint-dependent 3D chromatin reconfiguration creating new topologically associating domain (TAD) borders.

Moreover, additional rearrangements have been identified by Hi-C in MCL and have been confirmed by standard methods such as cytogenetic analyses and next generation sequencing. An integrative multi-omics approach combining 3D genome architecture with histone modifications and DNA methylation allowed the identification of candidate epigenetic drivers in MCL (Study 3). In aggressive, conventional MCLs with overexpression of the SOX11 oncogene, a distant regulatory region looping to the SOX11 promoter was uncovered promoting oncogene deregulation in a biallelic fashion. Additional experiments revealed that the PAX5 transcription factor may play a role in activating the distant SOX11 enhancer (Study 4). This doctoral thesis highlights the role of the chromatin architecture as a key epigenomic player associated with the normal differentiation and neoplastic transformation of B cells.