Dynamics of genome architecture and chromatin function during human B cell differentiation and neoplastic transformation

Abstract

Despite recent advances, the dynamics of genome architecture and chromatin function during human cell differentiation and its potential reorganization upon neoplastic transformation remains poorly characterized. Here, we integrate in situ Hi-C and nine additional omic layers to define and biologically characterize the dynamic changes in three-dimensional (3D) genome architecture across normal B cell differentiation and in neoplastic cells from different subtypes of chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) patients. Beyond conventional active (A) and inactive (B) compartments, an integrative analysis of Hi-C data reveals the presence of a highly-dynamic intermediate compartment enriched in poised and polycomb-repressed chromatin. During B cell development, we detect that 28% of the compartments change at defined maturation stages and mostly involve the intermediate compartment. The transition from naive to germinal center B cells is associated with widespread chromatin activation, which mostly reverts into the naive state upon further maturation of germinal center cells into memory B cells. The analysis of CLL and MCL neoplastic cells points both to entity and subtype-specific alterations in chromosome organization. Remarkably, we observe that large chromatin blocks containing key disease-specific genes alter their 3D genome organization. These include the inactivation of a 2Mb region containing the EBF1 gene in CLL and the activation of a 6.1Mb region containing the SOX11 gene in clinically aggressive MCL. This study indicates that 3D genome interactions are extensively modulated during normal B cell differentiation and that the genome of B cell neoplasias acquires a tumor-specific 3D genome architecture.

Integration of chromatin accessibility and gene expression data with cisREAD reveals a switch from PU.1/SPIB-driven to AP-1-driven gene regulation during B cell activation

“…Application of our method to a model system of human B cell differentiation has revealed how a core network of transcription factors exercise regulatory control over B cell differentiation, explicitly coupled to the CD40 and BCR activation stimuli administered to the in vitro cell system. In many cases, observed regulation downstream of CD40 and BCR signals is consistent with regulatory dynamics observed in ex vivo murine B cells stimulated by lipopolysaccharide (LPS) (5,39,40) as well as in primary human B cell populations (8,10). Findings reported in these studies, in conjunction with the analyses presented here, suggests that common mechanisms define genetic regulation during B cell activation and plasma cell differentiation; characterised by declining regulation at PU.1/SPIB associated motifs and increased regulation at motifs occupied by NF-κB, AP-1, IRF4, OCT2, E2A (E-Box) and MEF2 factors (MADs-Box).…”

“…B cell differentiation is driven through changes in genetic regulation, where regulatory circuits are rewired through dynamic shifts in epigenetic remodelling and transcription factor activity. Genome wide studies of epigenomic, transcriptomic and conformational datasets have been instrumental in uncovering how the chromatin environment shapes B cell populations, and responds to stimuli to determine cell fate (5,8,10,35,39,40). However, there are gaps in our understanding of the complex associations between cis and trans acting factors which fine-tune transcription to orchestrate B cell maturation.…”

“…Linking accessible regulatory elements to gene expression remains a challenge. Three dimensional chromatin conformation technologies like Hi-C have been used to determine regulatory chromatin domains in B cells (8)(9)(10). Yet tens of millions of cells are required for sufficient resolution to detect enhancer-promoter interactions, as opposed to tens of thousands for ATAC-seq, limiting their use (11,12).…”

Assessment of Expression of Homeobox A5 in Endometrial Cancer on the mRNA and Protein Level

“…It is therefore important to evaluate variances in HOXA5 expression in different grades of endometrial cancer. In addition, it should be remembered that the process of neoplastic transformation is extremely dynamic and varies to some extent in different types of cancer [ 23 ]. The study of Ordóñez-Morán et al using IHC staining in colorectal cancer showed a low level of HOXA5 in stem cells and high expression in differentiated villi, suggesting that HOXA5 is strongly associated with regulation of metastatic potential.…”

How chromosome topologies get their shape: views from proximity ligation and microscopy methods

“…Compartments become intensely rearranged during cellular differentiation and reprogramming [24–29]. For instance, as demonstrated by Hi‐C, along the in vitro differentiation path from human embryonic stem cell (ESC) to cardiomyocyte, nearly one‐fifth of the genome switches from the one compartment to the other [24].…”