An integrated transcription factor framework for Treg identity and diversity

• 成果类型: Article
• 署名作者: Chowdhary, Kaitavjeet; Leon, Juliette; Mathis, Diane; Benoist, Christophe
• 署名单位: Harvard University; Harvard Medical School; Universite Paris Cite; Institut National de la Sante et de la Recherche Medicale (Inserm)
• 刊物名称: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
• ISSN/ISSBN: 0027-11834
• DOI: 10.1073/pnas.2411301121
• 发表日期: 2024-09-03
• 关键词: regulatory t-cells; natural genetic-variation; factor foxp3; baf complex; reveals; program; differentiation; accessibility; population; expression

摘要

Vertebrate cell identity depends on the combined activity of scores of transcription factors (TF). While TFs have often been studied in isolation, a systematic perspective on their integration has been missing. Focusing on FoxP3+ regulatory T cells (Tregs), key guardians of immune tolerance, we combined single- cell chromatin accessibility, machine learning, and high- density genetic variation, to resolve a validated framework of diverse Treg chromatin programs, each shaped by multi-TF inputs. This framework identified previously unrecognized Treg controllers ( Smarcc1 ) and illuminated the mechanism of action of FoxP3, which amplified a pre- existing Treg identity, diversely activating or repressing distinct programs, dependent on different regulatory partners. Treg subpopulations in the colon relied variably on FoxP3, Helios+ Tregs being completely dependent, but ROR gamma+ Tregs largely independent. These differences were rooted in intrinsic biases decoded by the integrated framework. Moving beyond master regulators, this work unravels how overlapping TF activities coalesce into Treg identity and diversity.