Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
Immunology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
RNA. 2020 Oct;26(10):1320-1333. doi: 10.1261/rna.075929.120. Epub 2020 Jun 17.
Human CD4 T cells are often subdivided into distinct subtypes, including Th1, Th2, Th17, and Treg cells, that are thought to carry out distinct functions in the body. Typically, these T-cell subpopulations are defined by the expression of distinct gene repertoires; however, there is variability between studies regarding the methods used for isolation and the markers used to define each T-cell subtype. Therefore, how reliably studies can be compared to one another remains an open question. Moreover, previous analysis of gene expression in CD4 T-cell subsets has largely focused on gene expression rather than alternative splicing. Here we take a meta-analysis approach, comparing eleven independent RNA-seq studies of human Th1, Th2, Th17, and/or Treg cells to determine the consistency in gene expression and splicing within each subtype across studies. We find that known master-regulators are consistently enriched in the appropriate subtype; however, cytokines and other genes often used as markers are more variable. Importantly, we also identify previously unknown transcriptomic markers that appear to consistently differentiate between subsets, including a few Treg-specific splicing patterns. Together this work highlights the heterogeneity in gene expression between samples designated as the same subtype, but also suggests additional markers that can be used to define functional groupings.
人类 CD4 T 细胞通常被细分为不同的亚型，包括 Th1、Th2、Th17 和 Treg 细胞，这些细胞被认为在体内发挥不同的功能。通常，这些 T 细胞亚群是通过表达不同的基因谱来定义的；然而，关于分离方法和用于定义每种 T 细胞亚型的标记物，研究之间存在差异。因此，研究之间的可比性仍然是一个悬而未决的问题。此外，以前对 CD4 T 细胞亚群中的基因表达的分析主要集中在基因表达上，而不是选择性剪接上。在这里，我们采用荟萃分析方法，比较了十一项关于人类 Th1、Th2、Th17 和/或 Treg 细胞的独立 RNA-seq 研究，以确定每个亚群在研究之间的基因表达和剪接的一致性。我们发现，已知的主调控因子在适当的亚型中始终被富集；然而，细胞因子和其他常用作标记物的基因通常更具可变性。重要的是，我们还鉴定了以前未知的转录组标记物，这些标记物似乎能够始终如一地区分不同的亚群，包括一些 Treg 特异性的剪接模式。这项工作共同强调了指定为同一亚型的样本之间基因表达的异质性，但也提出了可用于定义功能分组的其他标记物。
