ENAapplication/xmlftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/025/SRR29360025/SRR29360025_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/017/SRR29360017/SRR29360017_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/013/SRR29360013/SRR29360013_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/023/SRR29360023/SRR29360023_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/020/SRR29360020/SRR29360020_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/021/SRR29360021/SRR29360021_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/018/SRR29360018/SRR29360018_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/026/SRR29360026/SRR29360026_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/020/SRR29360020/SRR29360020_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/014/SRR29360014/SRR29360014_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/025/SRR29360025/SRR29360025_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/016/SRR29360016/SRR29360016_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/019/SRR29360019/SRR29360019_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/028/SRR29360028/SRR29360028_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/022/SRR29360022/SRR29360022_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/019/SRR29360019/SRR29360019_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/027/SRR29360027/SRR29360027_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/023/SRR29360023/SRR29360023_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/013/SRR29360013/SRR29360013_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/021/SRR29360021/SRR29360021_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/017/SRR29360017/SRR29360017_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/026/SRR29360026/SRR29360026_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/015/SRR29360015/SRR29360015_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/014/SRR29360014/SRR29360014_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/024/SRR29360024/SRR29360024_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/016/SRR29360016/SRR29360016_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/028/SRR29360028/SRR29360028_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/022/SRR29360022/SRR29360022_2.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/027/SRR29360027/SRR29360027_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/018/SRR29360018/SRR29360018_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/024/SRR29360024/SRR29360024_1.fastq.gzftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR293/015/SRR29360015/SRR29360015_1.fastq.gzprimaryOK200GenomicsSharpe, Immunology, Harvard Medical Schoolhttps://www.ebi.ac.uk/ena/browser/view/PRJNA1122563Mus musculusT cell exhaustion is a state of CD8+ T cell dysfunction elicited by chronic exposure to antigen and inflammation, arises in both cancer and chronic viral infection. The co-inhibitory receptor PD-1 plays a key role in mediating exhaustion, but complete ablation of PD-1 by gene knock-out leads to deeper functional deficits and poor T cell survival. We hypothesized that an intermediate level of PD-1 expression may confer an improved balance of exhausted CD8+ T cell functionality, so we deleted an exhaustion-associated enhancer of PD-1 which indeed resulted in a reduced expression level. We compared EnhDel, WT and PD-1 KO T cells using single-cell RNA-Seq and found that PD-1 KO but not EnhDel cells are strongly biased towards the terminally exhausted subset. EnhDel cells also uniquely enrich for effector-associated genes and gene signatures. However, all three genotypes (EnhDel, WT and PD-1 KO) exhibit a similar chromatin accessibility landscape by ATAC-Seq, controlling for exhausted subset. These data suggest that tuning of PD-1 expression may uniquely permit the maintenance of an “effector” transcriptional profile in exhausted CD8+ T cells. Overall design: Enhancer-deleted and WT P14+ CD8+ T cells were isolated from donor mice, mixed at a 50:50 ratio, and transferred to congenically-distinct recipient mice (n = 8). Recipients were infected with LCMV Clone 13. Transferred CD8+ T cells were isolated from spleens at day 9. Genotypes (Enhancer-deleted, WT) and cell types (progenitor exhausted SLAMF6+TIM3-, terminally exhausted SLAMF6-TIM3+CX3CR1-) were then isolated by sorting, pooled in pairs to create four samples, and processed for bulk RNA-seq. We then performed differential gene expression analysis using DESeq2 in R to compare the transcriptomic profiles of EnhDel and wild type CD8+ T cells at the D9 time point, controlling for exhausted subset.xref:PubMed:39289557ENAfalseDeletion of a state-specific PD-1 enhancer modulates exhausted T cell fate and function [RNA-Seq]Deletion of a state-specific PD-1 enhancer modulates exhausted T cell fate and function [RNA-Seq]2025-09-242024-07-31PRJNA1122563GSE2695801009039289557