Regulatory T cells in the Tumor Microenvironment Display a Unique Chromatin Accessibility Profile (ATAC-Seq)

Regulatory T cells (Tregs) are a suppressive CD4+ T cell population that limit the anti-tumor immune response. In this study, we analyzed the chromatin accessibility of Tregs in the murine tumor microenvironment (TME) to identify tumor-specific accessible peaks and if these are altered over time in the tumor microenvironment, with or without anti-PD1 immunotherapy. We found that Tregs have a more distinct chromatin accessibility signature in the TME compared to Tregs in the periphery than within location over time in the models we accessed. This distinct tumor Treg chromatin accessibility profile highlights reduced accessibility at loci important for an CD4+ conventional T cell (CD4+ Foxp3—) effector phenotype and reinforcement of a suppressive phenotype. Analysis of chromatin accessibility in Tregs in B16 and MC38 tumor models indicated similar regulation independent of tumor type, indicating a tumor-derived Treg effector signature in the models we accessed. We also found that Tregs do not alter their transcriptome nor chromatin accessibility following immunotherapy. We conclude that chromatin accessibility in Tregs is altered in the TME, but is otherwise remarkably stable and appears unaltered by tumor type, over time, or following immunotherapy. Overall design: Regulatory T cells from the murine B16 and MC38 tumor microenvironment were accessed for chromatin accesibility by bulk ATAC-sequencing.

调节性T细胞（Regulatory T cells，Tregs）是一类抑制性CD4+ T细胞群，可抑制抗肿瘤免疫应答。本研究对小鼠肿瘤微环境（murine tumor microenvironment，TME）中的Tregs进行染色质开放性分析，旨在鉴定肿瘤特异性开放染色质峰，并探究在伴或不伴抗PD-1免疫治疗（anti-PD1 immunotherapy）的情况下，这些峰在肿瘤微环境中随时间的变化情况。
我们发现，在所研究的模型中，肿瘤微环境内的Tregs相较于外周Tregs，其染色质开放性特征的差异程度远高于同一部位Tregs随时间推移的变化程度，即该特征具有显著的组织特异性。这种独特的肿瘤Treg染色质开放性特征表现为：在对CD4+常规T细胞（CD4+ conventional T cell，CD4+ Foxp3⁻）效应表型至关重要的基因座上，染色质开放性降低，同时强化了其抑制性表型。对B16与MC38肿瘤模型中Tregs的染色质开放性分析显示，其调控模式相似且不受肿瘤类型影响，表明在所研究的模型中存在肿瘤来源的Treg效应特征。我们还发现，经免疫治疗后，Tregs的转录组与染色质开放性均未发生显著改变。
综上，肿瘤微环境中的Tregs染色质开放性确实发生了改变，但除此之外，其染色质开放性整体极为稳定，不受肿瘤类型、时间推移或免疫治疗的影响。
整体实验设计：通过批量ATAC测序（bulk ATAC-sequencing）检测小鼠B16与MC38肿瘤微环境中的调节性T细胞的染色质开放性。