Aggressive B-cell lymphomas retain ATR-dependent determinants of T-cell exclusion from the Germinal Center Dark Zone

Abstract

The germinal center (GC) dark zone (DZ) and light zone (LZ) represent distinct anatomical regions in lymphoid tissue where B-cell proliferation, immunoglobulin diversification, and selection are coordinated. Diffuse Large B-cell Lymphomas (DLBCL) with DZ-like gene expression profiles exhibit poor outcomes, though reasons are unclear and are not directly related to proliferation. Physiological DZs exhibit an exclusion of T-cells, prompting exploration for whether T-cell paucity contributes to DZ-like DLBCL. We used spatial transcriptomic approaches to achieve higher resolution of T-cell spatial heterogeneity in the GC and to derive potential pathways that underlie T-cell exclusion. We showed that T-cell exclusion from the DZ was linked to DNA damage response (DDR) and chromatin compaction molecular features characterizing the spatial DZ signature, and that these programs were independent of AID deaminase activity. As ATR is a key regulator of DDR, we tested its role in the T-cell inhibitory DZ transcriptional imprint. ATR inhibition reversed not only the DZ transcriptional signature but also DZ T-cell exclusion in DZ-like DLBCL in vitro microfluidic models and in in vivo samples of murine lymphoid tissue. These findings highlight that ATR activity underpins a physiological scenario of immune silencing. ATR inhibition may reverse the immune silent state and enhance T-cell based immunotherapy in aggressive lymphomas with GC DZ-like characteristics.

Keywords: Cell biology; Immunology; Lymphomas; Molecular pathology; Oncology; T cells.