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BET inhibition reforms the immune microenvironment and alleviates T cell dysfunction in chronic lymphocytic leukemia
Audrey L. Smith, Sydney A. Skupa, Alexandria P. Eiken, Timothy E. Reznicek, Elizabeth Schmitz, Nolan Williams, Dalia Y. Moore, Christopher R. D’Angelo, Avyakta Kallam, Matthew A. Lunning, R. Gregory Bociek, Julie M. Vose, Eslam Mohamed, Anna R. Mahr, Paul W. Denton, Ben Powell, Gideon Bollag, M. Jordan Rowley, Dalia El-Gamal
Audrey L. Smith, Sydney A. Skupa, Alexandria P. Eiken, Timothy E. Reznicek, Elizabeth Schmitz, Nolan Williams, Dalia Y. Moore, Christopher R. D’Angelo, Avyakta Kallam, Matthew A. Lunning, R. Gregory Bociek, Julie M. Vose, Eslam Mohamed, Anna R. Mahr, Paul W. Denton, Ben Powell, Gideon Bollag, M. Jordan Rowley, Dalia El-Gamal
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Research Article Immunology Oncology

BET inhibition reforms the immune microenvironment and alleviates T cell dysfunction in chronic lymphocytic leukemia

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Abstract

Redundant tumor microenvironment (TME) immunosuppressive mechanisms and epigenetic maintenance of terminal T cell exhaustion greatly hinder functional antitumor immune responses in chronic lymphocytic leukemia (CLL). Bromodomain and extraterminal (BET) proteins regulate key pathways contributing to CLL pathogenesis and TME interactions, including T cell function and differentiation. Herein, we report that blocking BET protein function alleviates immunosuppressive networks in the CLL TME and repairs inherent CLL T cell defects. The pan-BET inhibitor OPN-51107 reduced exhaustion-associated cell signatures resulting in improved T cell proliferation and effector function in the Eμ-TCL1 splenic TME. Following BET inhibition (BET-i), TME T cells coexpressed significantly fewer inhibitory receptors (IRs) (e.g., PD-1, CD160, CD244, LAG3, VISTA). Complementary results were witnessed in primary CLL cultures, wherein OPN-51107 exerted proinflammatory effects on T cells, regardless of leukemic cell burden. BET-i additionally promotes a progenitor T cell phenotype through reduced expression of transcription factors that maintain terminal differentiation and increased expression of TCF-1, at least in part through altered chromatin accessibility. Moreover, direct T cell effects of BET-i were unmatched by common targeted therapies in CLL. This study demonstrates the immunomodulatory action of BET-i on CLL T cells and supports the inclusion of BET inhibitors in the management of CLL to alleviate terminal T cell dysfunction and potentially enhance tumoricidal T cell activity.

Authors

Audrey L. Smith, Sydney A. Skupa, Alexandria P. Eiken, Timothy E. Reznicek, Elizabeth Schmitz, Nolan Williams, Dalia Y. Moore, Christopher R. D’Angelo, Avyakta Kallam, Matthew A. Lunning, R. Gregory Bociek, Julie M. Vose, Eslam Mohamed, Anna R. Mahr, Paul W. Denton, Ben Powell, Gideon Bollag, M. Jordan Rowley, Dalia El-Gamal

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Figure 7

CD8+ T cell exhaustion–associated chromatin organization is altered with BET-i.

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CD8+ T cell exhaustion–associated chromatin organization is altered with...
(A–H) Bulk ATAC-Seq of CD8+ T cells isolated from CLL patient PBMCs (n = 4) that were treated with 0.5μM OPN-51107 (OPN5) or equivalent vehicle (VEH; DMSO) for 16 hours, in the presence of anti-CD3/anti-CD28 stimuli. (A) Principal component analysis (PCA) of BPM normalized signal at consensus peaks. (B) Differential peaks (P < 0.05) called in grouped OPN5 versus VEH analysis. Closing indicates peaks with decreased signal upon OPN5 treatment; opening indicates peaks with increased signal upon OPN5 treatment. Significant difference between groups was assessed using unpaired, 2-tailed Mann-Whitney U test. *P < 0.05. (C) Enrichment of T cell signatures based on ATAC-Seq data from Satpathy et al. (52). Data are represented as mean ± SEM. Significant difference between groups was assessed using unpaired Mann-Whitney U test or paired Student’s t test. **P < 0.01. (D and E) Overrepresentation analysis of gene ontology terms associated with genes near accessibility peaks that decreased (D) and increased (E) upon OPN5 treatment. (F) Differential promoter peaks identified in grouped OPN5 versus VEH analysis (volcano plot). Top heatmaps illustrate ATAC-Seq signal at consensus peaks between 3 or more patients for peaks decreased (left) and increased (right) upon OPN5 treatment. Bottom heatmaps display variation across CLL patient samples for differential promoter peaks identified in grouped analysis. (G) Chromatin accessibility derived from ATAC-Seq signal tracks at TCF7, CD101, SLAMF6, LAG3, and IFNG loci for grouped OPN5 and VEH samples. (H) Differentially accessible transcription factor binding motifs at increased (top) and decreased (bottom) peaks upon OPN5 treatment. Transcription factor families are annotated by color.

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