Cytokine signaling, immunoregulation and autoimmune disease

细胞因子调节细胞生长和分化、造血、新陈代谢和组织修复。这些因素在包括病毒感染在内的宿主防御中也是至关重要的，但也是类风湿性关节炎、狼疮、IBD、斑秃和牛皮癣等自身免疫性疾病以及过敏和哮喘的主要致病因素。这强调了需要更好地了解细胞因子作用的分子基础和细胞因子表达的调节，以更好地了解各种疾病的机制和改进治疗。一个关键的细胞因子家族是那些使用JAK-STAT途径的人；该途径在细胞因子信号转导中的作用几十年来一直是实验室的中心兴趣。 我们今年取得的几项进展包括细胞因子对免疫代谢的调节。众所周知，激活的淋巴细胞调节其代谢以满足快速生长和增殖所施加的能量和生物合成需求，其中细胞因子IL-2在支持T细胞增殖中起核心作用。我们研究了IL-2-STAT5调节的T细胞的代谢组和转录组，以了解直接的分子网络来控制代谢。我们发现，IL-2-STAT5轴通过靶向必需的限速酶和转运蛋白，直接控制能量生产和氨基酸的合成。Stat5与MYC全基因组合作，在转录上编程T细胞新陈代谢，促进细胞生长和增殖。相反，IL-27是一种免疫抑制调节细胞因子，我们的工作揭示了一种胆固醇代谢酶CH25H，它是由IL-27和TGFb诱导的关键代谢开关，以抑制T细胞介导的皮肤炎症。CH25H产生25OHC(25OHC)，25OHC分泌到微环境中，抑制旁观者T细胞的增殖，抑制过度炎症，促进皮肤炎症消退。我们进一步扩展了我们的研究以评估NK细胞的新陈代谢，并发现NK细胞在发育、动态平衡和功能方面独特而特异地依赖于神经鞘糖脂(GSL)的合成(11)。GSL合成中的限速酶UGcg由NK细胞中一个延伸的超级增强子结构调控，并由一个长的非编码RNA并列，表明通常由lncRNAs代表的基因座的复杂和错综复杂的转录调控(7)。这些系列工作有助于扩大我们对支持细胞类型特异性免疫反应的代谢状态的看法。 我们还参与了一项研究记忆CD8反应的合作工作。我们研究了磷脂酰肌醇3激酶(PI3K)突变对CD8T细胞记忆性的影响。具有PI3K突变功能获得突变的患者会患上病毒感染。使用小鼠模型(Pik3cdE1020K/+小鼠)，我们发现激活的Pik3cdE1020K/+CD8+T细胞无法维持维持包括TCF1在内的长寿命记忆细胞的关键蛋白的表达，并在体内建立了不充分的记忆反应。 我们实验室之前的工作也确立了miR-221和miR-222在平衡肠道Th17细胞反应中的调节作用。利用基因缺失的小鼠模型，我们发现miR-221和miR-222作为负反馈回路的一部分抑制了促炎反应的幅度。今年，我们在一个合作项目中扩展了这项工作，研究了miR-221/222在B细胞中的作用。通过对成熟激活的B细胞中microRNAs的缺失和补救筛选，我们确定miR221/222是Ig类开关重组(CSR)的正调控因子。内源性miR-221/222调节B细胞CSR为IgE和IgG1，基因缺失的小鼠在过敏性呼吸道攻击中表现出Ig E产生缺陷。对mir221/222靶点的询问确定Foxp1和ARID1A是推测的直接靶点，它们在CSR对IgE和IgG1的反应中发挥关键作用。 今年我们扩展知识的另一个方向是解决三维染色质结构的问题，以及它与基因转录的关系。我们用HIC方法比较了先天T细胞(ILC2)和适应性T细胞(Th2)的2型细胞因子基因座的三维结构，并观察到ILC2和Th2之间信号诱导的染色质重塑。我们进一步确定了嵌入在2型细胞因子基因座上的细胞类型特定和上下文特定的调节元件，它们的不同使用有助于天然细胞和适应性细胞之间不同的3D形成。我们将把这种方法扩展到准备中的手稿中的1型细胞因子基因座，包括IFNG，IFNGAS1和IL22。 总体而言，我们继续追求基于多组学的方法，允许我们在单细胞水平上绘制免疫细胞中的转录组、表观基因组、因子结合和染色质构象，以回答起源于不同细胞外环境的细胞因子信号如何塑造免疫细胞反应的范围和程度的问题，以及在健康和疾病中的作用。

Cytokines regulate cellular growth and differentiation, hematopoiesis, metabolism, and tissue repair. These factors are also critical in host defense including viral infection but are also major contributors to the pathogenesis of autoimmune diseases such as rheumatoid arthritis, lupus, IBD, alopecia areata and psoriasis, as well as allergy and asthma. This underscores the need to better understand the molecular basis of cytokine action and the regulation of cytokine expression to better understand mechanisms of diverse diseases and improve treatment. A critical family of cytokines are those that use the JAK-STAT pathway; the role of this pathway in cytokine signaling has been a central interest of the lab for multiple decades. Several advances we made this year include regulation of immunometabolism by cytokines. It has been well known that activated lymphocytes adapt their metabolism to meet the energetic and biosynthetic demands imposed by rapid growth and proliferation in which a cytokine IL-2 plays a central role to support T cell proliferation. We investigated metabolome and transcriptome of IL-2-STAT5 modulated T cells to learn direct molecular network to control metabolism. We found that IL-2-STAT5 axis directly control energy production and amino acid synthesis by targeting essential, rate-limiting enzymes and transporters. STAT5 cooperates with MYC genome-wide to transcriptionally programming T cell metabolism, empowering cell growth and proliferation. In contrast, IL-27 is an immunosuppressive regulatory cytokine, and our work unveiled a cholesterol metabolizing enzyme, Ch25h, as a critical metabolic switch induced by IL-27 and TGFb to constrain T cell mediated skin inflammation. Ch25h generates 25-hydroxychoresterol (25OHC), and 25OHC is secreted into microenvironment and suppress proliferation of bystander T cells, dampening excess inflammation and promote resolution of skin inflammation. We further extended our study to evaluate metabolism in NK cells, and found that NK cells are uniquely and specifically dependent on glycosphingolipid (GSL) synthesis for development, homeostasis and function (11). A rate-limiting enzyme in GSL synthesis, Ugcg, is regulated by an extended super-enhancer structure in NK cells and juxtaposed by a long non-coding RNA, indicating complex and intricated transcriptional regulation of the locus often represented by lncRNAs (7). Those series of work contributed to expand our view on underpinning metabolic states supporting cell type specific immune response. We also contributed to a collaborative work investigating memory CD8 response. We studied the impact of mutations of phosphoinositide 3 kinase (PI3K) on memory CD8 T cells. Patients with gain-of-function mutations of PI3K mutations suffer from viral infections. Using a mouse model, (Pik3cdE1020K/+ mice), we showed that activated Pik3cdE1020K/+ CD8+ T cells failed to sustain expression of proteins critical for maintenance of long-lived memory cells, including TCF1, and mounted inadequate memory responses in vivo. Previous work from our lab also established modulatory roles of micro RNAs, miR-221 and miR-222, in balancing intestinal Th17 cell response. Using gene deleted mouse models, we showed that miR-221 and miR-222 constrained the magnitude of proinflammatory response as a part of negative feedback circuit. Extending this work in a collaborative project this year, we examined the role of miR-221/222 in B cells. Using deletion and rescue screening of microRNAs in mature activated B cells, we identified miR221/222 as a positive regulator of Ig class switch recombination (CSR). Endogenous miR-221/222 regulated B cell CSR to IgE and IgG1, and the gene deleted mice exhibited defective Ig E production in allergic airway challenge. Interrogation of mir221/222 targets identified Foxp1 and Arid1a as putative direct targets which play key roles in CSR to IgE and IgG1. Another direction we took this year to expand our knowledge is to address the question of 3 dimensional chromatin architecture and how it relates to gene transcription. Using HiC approach, we compared 3D structure of type 2 cytokine loci between innate (ILC2) and adaptive T cells (Th2), and observed signal inducible chromatin remodeling that differs between ILC2 and Th2. We further identified cell type specific- and context specific-regulatory elements embedded across type 2 cytokine loci whose differential usage contributes to distinct 3D formation between innate and adaptive cells. We will extend this approach to address type 1 cytokine loci including Ifng, Ifngas1 and Il22 in the manuscript in preparation. Overall, we continue to pursue multi-omics based approach that allows us mapping transcriptome, epigenome, factor binding and chromatin conformation in immune cells at single cell levels to answer the question of how cytokine signals originating in diverse extracellular milieu shape the scope and degree of immune cell responsesin health and diseases.