Leukemia, Lymphocytic, Chronic, B-Cell study with ATAC-seq, SRA Metadata data on dbGaP (5 participants)

phs003613 — Chromatin Landscape of BET Inhibitor-Treated CD8+ T-cells from Chronic    Lymphocytic Leukemia Patients

The pan-BET (bromodomain and extra-terminal) inhibitor, OPN-51107 (OPN5) was found to alleviate features of T-cell exhaustion in models of chronic lymphocytic leukemia (CLL). To evaluate if OPN5 treatment could relieve fixed chromatin states associated with terminal T-cell dysfunction, ATAC-sequencing was performed on CLL patient T-cells. Peripheral blood mononuclear cells (PBMCs) from 4 treatment-naïve CLL patients were treated ex vivo with 0.5 μM OPN5 or equivalent vehicle (DMSO) in the presence of T-cell activating stimuli (10 μg/mL anti-CD3 and 5 μg/mL anti-CD28) for 16 hours. Live CD8+ T-cells were then isolated via fluorescence-activated cell sorting, and approximately 100,000 viable CD8+ T-cells were subjected to ATAC-sequencing. Libraries were prepared using the Active Motif ATAC-seq kit and underwent paired-end sequencing (2 x 50 bp, 100 cycles) on an Illumina NovaSeq 6000 SP sequencer. Analysis of this data revealed that OPN5 treatment induces a unique chromatin landscape in CLL patient T-cells that is less like that of terminally exhausted T-cells and more like that of effector and memory T-cells. In particular, OPN5 treatment reduced chromatin accessibility at promoter regions of terminal exhaustion-associated genes (e.g., <a href="https://www.ncbi.nlm.nih.gov/gene/9398">CD101</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/1234">CCR5</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/3902">LAG3</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/55509">BATF3</a>) and increased chromatin accessibility at promoter regions of genes associated with progenitor T-cell function (e.g., <a href="https://www.ncbi.nlm.nih.gov/gene/6932">TCF7</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/3558">IL2</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/643">CXCR5</a>, <a href="https://www.ncbi.nlm.nih.gov/gene/3458">IFNG</a>). Individual raw sequencing (fastq) files and processed bigwig files (aligned to the hg38 human reference genome), as well as bigwig files for grouped OPN5- and vehicle-treated samples (aggregate of all 4 patient samples per treatment group) are available via authorized access request through dbGaP.