Central control of dynamic gene circuits governs T cell rest and activation

• 成果类型: Article
• 署名作者: Arce, Maya M.; Umhoefer, Jennifer M.; Arang, Nadia; Kasinathan, Sivakanthan; Freimer, Jacob W.; Steinhart, Zachary; Shen, Haolin; Pham, Minh T. N.; Ota, Mineto; Wadhera, Anika; Dajani, Rama; Dorovskyi, Dmytro; Chen, Yan Yi; Liu, Qi; Zhou, Yuan; Swaney, Danielle L.; Obernier, Kirsten; Shy, Brian R.; Carnevale, Julia; Satpathy, Ansuman T.; Krogan, Nevan J.; Pritchard, Jonathan K.; Marson, Alexander
• 署名单位: University of California System; University of California San Francisco; University of California System; University of California San Francisco; University of California System; University of California San Francisco; Stanford University; Stanford University; Stanford University; University of California System; University of California San Francisco; The J David Gladstone Institutes; University of California System; University of California San Francisco; University of California System; University of California San Francisco; University of California System; University of California San Francisco; UCSF Medical Center; UCSF Helen Diller Family Comprehensive Cancer Center; University of California System; University of California San Francisco; Stanford University; University of California System; University of California Berkeley; University of California System; University of California San Francisco; University of California System; University of California San Francisco
• 刊物名称: Nature
• ISSN/ISSBN: 0028-2212
• DOI: 10.1038/s41586-024-08314-y
• 发表日期: 2025-01-23
• 关键词: r package; read alignment; enhancers; tools; irf4; batf; car

摘要

The ability of cells to maintain distinct identities and respond to transient environmental signals requires tightly controlled regulation of gene networks1, 2-3. These dynamic regulatory circuits that respond to extracellular cues in primary human cells remain poorly defined. The need for context-dependent regulation is prominent in T cells, where distinct lineages must respond to diverse signals to mount effective immune responses and maintain homeostasis4, 5, 6, 7-8. Here we performed CRISPR screens in multiple primary human CD4+ T cell contexts to identify regulators that control expression of IL-2R alpha, a canonical marker of T cell activation transiently expressed by pro-inflammatory effector T cells and constitutively expressed by anti-inflammatory regulatory T cells where it is required for fitness9, 10-11. Approximately 90% of identified regulators of IL-2R alpha had effects that varied across cell types and/or stimulation states, including a subset that even had opposite effects across conditions. Using single-cell transcriptomics after pooled perturbation of context-specific screen hits, we characterized specific factors as regulators of overall rest or activation and constructed state-specific regulatory networks. MED12 - a component of the Mediator complex - serves as a dynamic orchestrator of key regulators, controlling expression of distinct sets of regulators in different T cell contexts. Immunoprecipitation-mass spectrometry revealed that MED12 interacts with the histone methylating COMPASS complex. MED12 was required for histone methylation and expression of genes encoding key context-specific regulators, including the rest maintenance factor KLF2 and the versatile regulator MYC. CRISPR ablation of MED12 blunted the cell-state transitions between rest and activation and protected from activation-induced cell death. Overall, this work leverages CRISPR screens performed across conditions to define dynamic gene circuits required to establish resting and activated T cell states.