Cytokine signaling, immunoregulation and autoimmune disease

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Cytokines regulate cellular growth and differentiation, hematopoiesis metabolism, and tissue repair. These factors are also critical in host defense but are also major contributors to the pathogenesis of autoimmune diseases such as rheumatoid arthritis, lupus, IBD, and psoriasis, as well as allergy and asthma, underscoring the need to better understand the molecular basis of cytokine action and their regulation of expression. A critical family of cytokines are those that use the JAK-STAT pathway (1-5). This year we made efforts to better understand the control of interferon-gamma (IFN-g), a cytokine that is the canonical mediator of type 1 responses. Downstream of the IFN-g gene is a long noncoding RNA (lncRNA) designated IFN-g-AS1(6). DNA deletion within the IFN-g-AS1 locus disrupted chromatin organization of the extended Ifng locus, impaired IFN-g response, and compromised host defense. Insertion of a polyA signal ablated the IFN-g-AS1 full-length transcript and impaired host defense, while allowing proper chromatin structure. These results establish IFN-g-AS1 as an important regulator of IFN-g expression that potential contributes to immune memory. Type 2 responses encompass production of cytokines including interleukin (IL)-4, IL-5 and IL-13, which are important for elimination of helminths as well as the immunopathology of allergy and asthma. Innate lymphocytes maintain tissue homeostasis at mucosal barriers, with group 2 innate lymphoid cells (ILC2s) producing type 2 cytokines to control helminth infection. We used single-cell analysis to explore the diversity of gene expression among lung lymphocytes during helminth infection and identified a subset of ILC2s that preferentially expressed IL-5, together with the neuropeptide Calca-encoding calcitonin gene-related peptide (CGRP) (7). In the absence of CGRP signaling, ILC2 responses and worm expulsion were enhanced. We interpret these data to show that CGRP shapes innate lymphocyte responses to interleukins, alarmins and other neuropeptides during type 2 innate immune responses. JAKs propagate cytokine signals by activating members of a family of transcription factors called STATs (signal transducers and activators of transcription). One important action of cytokines in which STATs play a key role is the differentiation and activation of different subsets of lymphocytes to attain distinct fates, as well as the induction of other cytokines. Our previous work has documented critical functions of STAT5 in CD4+ helper T cells, ranging from suppression of follicular helper T cell function to promotion of regulatory T cells. Using an influenza infection model, we found that that, while germinal center follicular helper T cells secrete large amounts of IL-2, they respond poorly to this cytokine. We found that this feature was mediated by IL-6, which inhibited induction of IL-2Rb (CD122) by antagonizing STAT5 binding to the Il2rb locus (8). Retinoic acid (RA) is an important regulator of immune responses (9). We found that RA directly targeted the extended Il9 locus, antagonizing the action of STAT5 and broadly modifying the Th9 epigenome through RAR. RA-RAR activity limited murine Th9-associated pulmonary inflammation. Human allergic inflammation was associated with reduced expression of RA target genes. Extending our studies of T cell memory, we compared single-cell transcriptomes and epigenetic profiles of CD8 T cells responding to acute and chronic viral infections (10). We found that progenitor-like CD8 T cells became distinct from memory precursor cells before the peak of the T cell response. We also found that the presence of the Tox transcription factor in progenitor-like cells promoted the persistence of antiviral CD8 T cells. In related work, 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. In collaborative work, we showed that skin commensals such as S. epidermidis elicit IL-17- (Tc17) and IFN-g-(Tc1) producing CD8 T cells. Analysis of the transcriptomes of these cells revealed evidence of tissue repair function beyond typical effector functions. We also found that skin-resident commensal-specific T cells harbor a paradoxical program characterized by a type 17, associated with a poised type 2 state (11). Following injury or exposure to inflammatory mediators such as interleukin-18, these cells rapidly release type 2 cytokines, which promotes tissue repair. These data indicate that commensal-specific T cells co-opt tissue residency and cell-intrinsic flexibility as a means to promote both local immunity and tissue adaptation to injury. In comparing responses of adaptive lymphocytes and innate lymphocytes (ILCs), we previously showed that the accessibility of ILCs was acquired in a developmental manner. Studying the impact of acute activation of ILCs we found that rapid, high level gene induction was regulated by de novo chromatin accessibility and enhancer activation. Activation resulted in redeployment of a lineage-specific transcription factor to de novo enhancers, independent of their DNA sequence-specific motif recognition. Another important class of regulators of gene expression is microRNAs. We identified a microRNA cluster, mir221/222, which is differentially expressed among different subsets of CD4 T cells. Molecular targets of miR-221/222 included Maf and Il23r, and loss of miR-221/222 shifted the transcriptomic spectrum of intestinal Th17 cells to proinflammatory signature. Th17 cells lacking miR-221/222 expanded more efficiently in response to IL-23. Both global and T cell-specific deletion of miR221/222 rendered mice prone to mucosal barrier damage. Based on our success in using genomic approaches to gain insight into lymphocytes, we also contributed to work with collaborators on myeloid cells. Myeloid cells can contribute to cardiac repair during myocardial infarction. We identified a specialized macrophage population with a distinct transcriptomic program, the loss of which enhanced interstitial fibrosis after ischemic injury (7). These findings reveal an immune cardioprotective role for the pericardial tissue compartment and suggest that removal of the pericardium may need to be reconsidered. In another collaborative study, we examined the role of autophagy in macrophages (12). We identified a macrophage-specific isoform of the vacuolar ATPase protein ATP6V0D2 that promotes autophagosome-lysosome fusion. We generated Atp6v0d2 mice and showed that deficiency of the gene resulted in mitochondrial damage in macrophages, enhanced inflammasome activation and reduced clearance of Salmonella.