Epigenetic reprogramming leads to down regulation of CD4 and functional changes in African green monkey memory CD4+ T cells

African green monkeys (AGMs) are a natural host for a lentivirus related to human immunodeficiency virus, simian immunodeficiency virus. SIV-infected AGM rarely progress to AIDS despite robust viral replication. Though multiple mechanisms are involved, a primary component is their ability to downregulate CD4 expression on mature helper CD4+ T cells, rendering these cells resistant to infection by SIV. These CD8aa+ T cells retain functional characteristics of helper CD4+ T cells while simultaneously aquiring abilities of cytoxic CD8ab+ T cells. To determine mechanisms underlying functional differences between T cell subsets in AGMs, chromatin accessibility in purified populations was determined by ATACseq. Differences in chromatin accessibility alone were sufficient to cluster cells by subtype, and acceesibility at the CD4 locus reflected changes in CD4 expression. DNA methylation at the CD4 locus also correlated with inaccessible chromatin. By associating accessible regions with nearby genes, gene expression was found to correlate with accessibility changes. T cell and immune system activation pathways were identified when comparing regions that changed accessibility from CD4+ T cells to CD8aa+ T cells. Different transcription factor binding sites are revealed as chromatin accessibility changes, and these differences may elicit downstream changes in differentiation. This comprehensive description of the epigenetic landscape of AGM T cells identified genes and pathways that could have translational value in therapeutic approaches recapitulating the protective effects CD4 downregulation. This study involves ATAC-seq in 5 T cells populations from 10 separate african green monkeys, totalling 50 samples. Half of the monkeys have SIV and the other half do not.

非洲绿猴（African green monkeys, AGMs）是一类与人类免疫缺陷病毒（human immunodeficiency virus, HIV）亲缘相近的慢病毒——猴免疫缺陷病毒（simian immunodeficiency virus, SIV）的天然宿主。尽管感染SIV的非洲绿猴会出现活跃的病毒复制，但极少进展为艾滋病。尽管存在多种调控机制，但其核心特征之一是能够下调成熟辅助性CD4+ T细胞表面的CD4表达，使这些细胞对SIV感染产生抗性。这类CD8aa+ T细胞不仅保留了辅助性CD4+ T细胞的功能特性，同时还获得了细胞毒性CD8ab+ T细胞的功能。为解析非洲绿猴T细胞亚群功能差异的潜在机制，研究人员通过转座酶可及性测序（ATAC-seq）检测了纯化细胞群的染色质可及性。仅依靠染色质可及性的差异，即可根据细胞亚群对细胞进行聚类，且CD4基因座的染色质可及性变化与CD4表达水平的改变相一致。CD4基因座的DNA甲基化水平同样与染色质不可及状态呈显著相关。通过将可及染色质区域与邻近基因进行关联，研究发现基因表达水平与染色质可及性变化呈正相关。对比CD4+ T细胞向CD8aa+ T细胞转化过程中染色质可及性发生改变的区域，可鉴定出T细胞及免疫系统激活相关通路。染色质可及性的变化揭示了不同转录因子结合位点的差异，这些差异或可引发下游分化进程的改变。本研究对非洲绿猴T细胞的表观遗传景观进行了全面解析，鉴定出具备转化应用价值的基因与通路，可为通过模拟CD4下调的保护效应开发治疗策略提供理论依据。本研究共纳入10只独立来源的非洲绿猴的5种T细胞群，总计50个样本；其中半数猴子感染SIV，另一半未感染。