Umhoefer Jennifer M, Arce Maya M, Whalen Sean, Dajani Rama, Goudy Laine, Kasinathan Sivakanthan, Belk Julia A, Zhang Wenxi, Zhou Royce, Subramanya Sanjana, Hernandez Rosmely, Tran Carinna, Kirthivasan Nikhita, Freimer Jacob W, Mowery Cody T, Nguyen Vinh, Ota Mineto, Gowen Benjamin G, Simeonov Dimitre R, Curie Gemma L, Li Zhongmei, Corn Jacob E, Chang Howard Y, Gilbert Luke A, Satpathy Ansuman T, Pollard Katherine S, Marson Alexander
Gladstone-UCSF Institute of Genomic Immunology, San Francisco, CA, USA.
Department of Medicine, University of California, San Francisco, CA, USA.
bioRxiv. 2025 Jan 14:2024.08.30.610436. doi: 10.1101/2024.08.30.610436.
FOXP3 is a lineage-defining transcription factor (TF) for immune-suppressive regulatory T cells (Tregs). While mice exclusively express FOXP3 in Tregs, humans also transiently express FOXP3 in stimulated conventional CD4+ T cells (Tconvs). Mechanisms governing these distinct expression patterns remain unknown. Here, we performed CRISPR screens tiling the locus and targeting TFs in human Tregs and Tconvs to discover cis-regulatory elements (CREs) and trans-regulators of FOXP3. Tconv FOXP3 expression depended on a subset of Treg CREs and Tconv-selective positive (TcNS+) and negative (TcNS-) CREs. The CREs are occupied and regulated by TFs we identified as critical regulators of FOXP3. Finally, mutagenesis of murine TcNS- revealed that it is critical for restriction of FOXP3 expression to Tregs. We discover CRE and TF circuitry controlling FOXP3 expression and reveal evolution of mechanisms regulating a gene indispensable to immune homeostasis.
FOXP3是免疫抑制性调节性T细胞（Tregs）的谱系决定性转录因子（TF）。虽然小鼠仅在Tregs中表达FOXP3，但人类在受刺激的常规CD4+ T细胞（Tconvs）中也会短暂表达FOXP3。控制这些不同表达模式的机制尚不清楚。在这里，我们进行了CRISPR筛选，覆盖该基因座并靶向人类Tregs和Tconvs中的转录因子，以发现FOXP3的顺式调节元件（CREs）和反式调节因子。Tconv FOXP3的表达依赖于Treg CREs的一个子集以及Tconv选择性阳性（TcNS+）和阴性（TcNS-）CREs。这些CREs被我们鉴定为FOXP3关键调节因子的转录因子占据并调控。最后，对小鼠TcNS-进行诱变表明，它对于将FOXP3表达限制在Tregs中至关重要。我们发现了控制FOXP3表达的CRE和转录因子调控网络，并揭示了调节免疫稳态不可或缺基因的机制的演变。
