Deciphering the Complexity of 3D Chromatin Organization Driving Lymphopoiesis and Lymphoid Malignancies

Abstract

Proper lymphopoiesis and immune responses depend on the spatiotemporal control of multiple processes, including gene expression, DNA recombination and cell fate decisions. High-order 3D chromatin organization is increasingly appreciated as an important regulator of these processes and dysregulation of genomic architecture has been linked to various immune disorders, including lymphoid malignancies. In this review, we present the general principles of the 3D chromatin topology and its dynamic reorganization during various steps of B and T lymphocyte development and activation. We also discuss functional interconnections between architectural, epigenetic and transcriptional changes and introduce major key players of genomic organization in B/T lymphocytes. Finally, we present how alterations in architectural factors and/or 3D genome organization are linked to dysregulation of the lymphopoietic transcriptional program and ultimately to hematological malignancies.

Keywords: 3D chromatin organization; B cells; T cells; activation; lymphoid malignancies; lymphopoiesis.

Figure 1

Major stages during B and T lymphocyte specification and differentiation and key transcription factors that control each transition. B and T cell development and differentiation is a stepwise process that involves multiple specification steps, cell fate bifurcations and cell migration. Multiple TFs, including but not limited to those acting at the chromatin level, have been extensively documented in HSC. Within the bone marrow, the transition of CLP towards pro-B cells is mediated through EBF1 and E2A, while the further maturation of the pre-B cells is under the control of EBF1 and PAX5. Upon BCR activation, BCL6 and OCA-B are controlling the differentiation of naive to GC cells, while the latest developmental stages are mediated through BACH2 for memory B cells and PRDM1 and XBP1 for plasma cells. Similarly, T cell development is also regulated by a strong network of TF, cytokines and genome organizers that control chromatin dynamics and T cell lineage specification. Upon thymocyte migration, the early steps of the thymocyte development are mediated through the genome organizers SATB1 and BCL11B while TF such as PU.1, TCF1 and GATA3 mediate the generation of the DN1 cells. The transition from the DN2 to DN3 is mediated by the STAT5, GATA3 and BCL11B, while RUNX, GATA3, HEB and E2A mediate the DN3 and DN4 transition. TCF-1 is also the major TF driving the DN4 to DP transition. The last steps of the intrathymic development are mediated through the expression of ThPOK and GATA3 for the CD4⁺ cells and NOTCH and RUNX for the CD8⁺ cells. Upon TCR activation, expression of the master regulator T-bet via STAT4 signaling leads to TH1 differentiation, while STAT6 and GATA3 regulate the TH2 differentiation. Activation of STAT3 and RORγ leads to TH17 cells, while IRF4 and PU-1 induce the differentiation towards TH9 cells. Activation of Bcl-6 induces the differentiation of naive CD4⁺ T cells into TfH. Differentiation of the Tregs is controlled by the transcription factor Foxp3 and STAT5. Generation of Tcr/Ig receptor diversity through VDJ recombination takes place at various stages during B/T lymphocyte development as depicted (red).

Figure 2

Global genome organization in mammalian nuclei from the megabase scale to the E-P level. Mammalian nuclei are organized into chromosomes with non-random distribution in the nucleoplasm. Each chromosome is further composed of chromosome territories (CT) further subdivided into A/B/I compartments. Within these compartments, TADs allow for interactions between regulatory elements (RE) that modulate gene expression. The cis/trans interactions take place between promoters (P-P), enhancers (E-E) or both (E-P).

Figure 3

Dynamic 3D chromatin changes during lymphocyte development and differentiation. B lineage: Upon commitment to the B-cell lineage, minor changes are documented for A/B compartments and TADs at the pro-B stage. Nonetheless, major changes in intra-TAD activity are associated with B-cell specific genes. Upon activation, GC B-cells are uniquely characterized by an increase in the weak Intermediate (I) compartments, which are maintained during plasma cells transition. TAD boundaries tend to be lost in GC B cells, leading to “gene cities” specific organization. While E-P loops tends to be increased in both GC and plasma cells, the latter subpopulation is characterized by a shift from long to short-range interactions. T lineage: During T lymphocyte development, the earliest global changes in A/B compartment, intra-TAD connectivity and loop formation take place at the T cell commitment step upon the transition of DN2 to DN3 cells but also in the DN4 to SP transition. Conversely, TCR activation does not cause changes in A/B compartments but results in TAD partitioning due to de novo and stronger TAD boundaries. A high proportion of both intra- and interchromosomal interactions are found for these 3 stages of T-cells development and differentiation for which the high E-P loop formation ensures T helper lineage specific gene expression.