SUMMARY Long recognized to be potent suppressors of immune responses, Foxp3+CD4+ regulatory T (Treg) cells are being rediscovered as regulators of nonimmunological processes. We describe a phenotypically and functionally distinct population of Treg cells that rapidly accumulated in the acutely injured skeletal muscle of mice, just as invading myeloidlineage cells switched from a proinflammatory to a proregenerative state. A Treg population of similar phenotype accumulated in muscles of genetically dystrophic mice. Punctual depletion of Treg cells during the repair process prolonged the proinflammatory infiltrate and impaired muscle repair, while treatments that increased or decreased Treg activities diminished or enhanced (respectively) muscle damage in a dystrophy model. Muscle Treg cells expressed the growth factor Amphiregulin, which acted directly on muscle satellite cells in vitro and improved muscle repair in vivo. Thus, Treg cells and their products may provide new therapeutic opportunities for wound repair and muscular dystrophies.

T regulatory cells that express the transcription factor Foxp3 (Foxp3+ Treg) promote tissue homeostasis in several settings. We now report that symbiotic members of the human gut microbiota induce a distinct Treg population in the mouse colon, which constrains immuno-inflammatory responses. This induction, which we find to map to a broad, but specific, array of individual bacterial species, requires the transcription factor Rorγ, paradoxically in that Rorγ is thought to antagonize FoxP3 and promote T helper 17 (Th17) cell differentiation. Rorγ's transcriptional footprint differs in colonic Tregs and Th17 cells, controlling important effector molecules. Rorγ, and the Tregs that express it, contribute substantially to regulating colonic Th1/Th17 inflammation. Thus, the marked context-specificity of Rorγ results in very different outcomes even in closely related cell-types.

Summary Foxp3+ T regulatory (Treg) cells regulate immune responses and maintain self-tolerance. Recent work shows that Treg cells are comprised of many subpopulations with specialized regulatory functions. Here we identified Foxp3+ T cells expressing the co-inhibitory molecule TIGIT as a distinct Treg cell subset that specifically suppresses pro-inflammatory T helper 1 (Th1) and Th17 cell, but not Th2 cell responses. Transcriptional profiling characterized TIGIT+ Treg cells as an activated Treg subset with high expression of Treg signature genes. Ligation of TIGIT on Treg cells induced expression of the effector molecule fibrinogen-like protein 2 (Fgl2), which promoted Treg cell-mediated suppression of T effector cell proliferation. In addition, Fgl2 was necessary to prevent suppression of Th2 cell cytokine production in a model of allergic airway inflammation. TIGIT expression therefore identifies a Treg cell subset that demonstrates selectivity for suppression of Th1 and Th17 cell but not Th2 cell responses.

Within the human gut reside diverse microbes coexisting with the host in a mutually advantageous relationship. Evidence has revealed the pivotal role of the gut microbiota in shaping the immune system. To date, only a few of these microbes have been shown to modulate specific immune parameters. Herein, we broadly identify the immunomodulatory effects of phylogenetically diverse human gut microbes. We monocolonized mice with each of 53 individual bacterial species and systematically analyzed host immunologic adaptation to colonization. Most microbes exerted several specialized, complementary, and redundant transcriptional and immunomodulatory effects. Surprisingly, these were independent of microbial phylogeny. Microbial diversity in the gut ensures robustness of the microbiota's ability to generate a consistent immunomodulatory impact, serving as a highly important epigenetic system. This study provides a foundation for investigation of gut microbiota-host mutualism, highlighting key players that could identify important therapeutics.

Severe COVID-19 is characterized by persistent lung inflammation, inflammatory cytokine production, viral RNA and a sustained interferon (IFN) response, all of which are recapitulated and required for pathology in the SARS-CoV-2-infected MISTRG6-hACE2 humanized mouse model of COVID-19, which has a human immune system [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17][18][19][20] . Blocking either viral replication with remdesivir 21-23 or the downstream IFN-stimulated cascade with anti-IFNAR2 antibodies in vivo in the chronic stages of disease attenuates the overactive immune inflammatory response, especially inflammatory macrophages. Here we show that SARS-CoV-2 infection and replication in lung-resident human macrophages is a critical driver of disease. In response to infection mediated by CD16 and ACE2 receptors, human macrophages activate inflammasomes, release interleukin 1 (IL-1) and IL-18, and undergo pyroptosis, thereby contributing to the hyperinflammatory state of the lungs. Inflammasome activation and the accompanying inflammatory response are necessary for lung inflammation, as inhibition of the NLRP3 inflammasome pathway reverses chronic lung pathology. Notably, this blockade of inflammasome activation leads to the release of infectious virus by the infected macrophages. Thus, inflammasomes oppose host infection by SARS-CoV-2 through the production of inflammatory cytokines and suicide by pyroptosis to prevent a productive viral cycle.Acute SARS-CoV-2 infection resolves in most patients but becomes chronic and sometimes deadly in about 10-20% of patients [1][2][3][4][5][6][7][14][15][16]20,[24][25][26][27] . Two hallmarks of severe COVID-19 are a sustained IFN response and viral RNA persisting for months [1][2][3][4][5][6][7][8][9][10][11][12][13][14][15][16][17]20,[24][25][26][27][28] . This chronicity is recapitulated in SARS-CoV-2-infected MISTRG6-hACE2 humanized mice 19 . High levels of IL-1β, IL-18 and lactate dehydrogenase (LDH) are correlated with COVID-19 severity in patients, suggesting a role for inflammasome activation and pyroptosis in pathology [5][6][7][14][15][16][17][18]29 . Here we show that human lung macrophages are infected by SARS-CoV-2. Replicating SARS-CoV-2 in these human macrophages activates inflammasomes and initiates an inflammatory cascade with a unique transcriptome, results in pyroptosis, and contributes to the downstream type-I IFN response. Blocking viral replication, the downstream IFN response or inflammasome activation in vivo during the chronic phase of the disease attenuates many aspects of the overactive immune inflammatory response (especially the inflammatory macrophage response) and disease. Viral replication and the IFN responseChronic interferon is associated with disease severity and impaired recovery in influenza infection 30 . To test whether a viral-RNAdependent type-I IFN response was a driver of chronic disease, we treated SARS-CoV-2-infected MISTRG6-hACE2 mice with remdesivir [21][22][23] and/or anti-IFNAR2 antibodies (Fig. 1a) to inhibit vi...