Deregulated CD8+ T cell cytotoxicity plays a central role in enhancing disease severity in several conditions. However, we have little understanding of the mechanisms by which immunopathology develops as a consequence of cytotoxicity. Using murine models of inflammation induced by the protozoan parasite leishmania, and data obtained from patients with cutaneous leishmaniasis, we uncovered a previously unrecognized role for NLRP3 inflammasome activation and IL-1β release as a detrimental consequence of CD8+ T cell-mediated cytotoxicity, ultimately resulting in chronic inflammation. Critically, pharmacological blockade of NLRP3 or IL-1β significantly ameliorated the CD8+ T cell-driven immunopathology in leishmania-infected mice. Confirming the relevance of these findings to human leishmaniasis, blockade of the NLRP3 inflammasome in skin biopsies from leishmania-infected patients prevented IL-1β release. Thus, these studies link CD8+ T cell cytotoxicity with inflammasome activation and reveal novel avenues of treatment for cutaneous leishmaniasis, as well as other of diseases where CD8+ T cell-mediated cytotoxicity induces pathology.

The gut microbiota is a key environmental determinant of mammalian metabolism. Regulation of white adipose tissue (WAT) by the gut microbiota is a process critical to maintaining metabolic fitness, and gut dysbiosis can contribute to the development of obesity and insulin resistance (IR). However, how the gut microbiota regulates WAT function remains largely unknown. Here, we show that tryptophan-derived metabolites produced by the gut microbiota controlled the expression of the miR-181 family in white adipocytes in mice to regulate energy expenditure and insulin sensitivity. Moreover, dysregulation of the gut microbiota–miR-181 axis was required for the development of obesity, IR, and WAT inflammation in mice. Our results indicate that regulation of miR-181 in WAT by gut microbiota–derived metabolites is a central mechanism by which host metabolism is tuned in response to dietary and environmental changes. As we also found that MIR-181 expression in WAT and the plasma abundance of tryptophan-derived metabolites were dysregulated in a cohort of obese human children, the MIR-181 family may represent a potential therapeutic target to modulate WAT function in the context of obesity.

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Leishmaniasis is a significant neglected tropical disease that is associated with a wide range of clinical presentations and a life long persistent infection. Due to the chronic nature of the disease there is a high risk of co-infection occurring in patients, and how co-infections influence the outcome of leishmaniasis is poorly understood. To address this issue, we infected mice with Leishmania major and two weeks later with lymphocytic choriomeningitis virus (LCMV), and monitored the course of infection. Leishmania parasites are controlled by production of IFN-γ, which leads to macrophage mediated parasite killing. Thus, one might predict that co-infection with LCMV, which induces a strong systemic type 1 response, would accelerate disease resolution. However, we found that infection with LCMV led to significantly enhanced disease in L. major infected animals. This increased disease correlated with an infiltration into the leishmanial lesions of NKG2D+ CD8+ T cells producing granzyme B, but surprisingly little IFN-γ. We found that depletion of CD8 T cells after viral clearance, as well as blockade of NKG2D, reversed the increased pathology seen in co-infected mice. Thus, this work highlights the impact a secondary infection can have on leishmaniasis, and demonstrates that even pathogens known to promote a type 1 response may exacerbate leishmanial infections.

The transcriptional programs that regulate CD8 T-cell differentiation and function in the context of viral infections or tumor immune surveillance have been extensively studied; yet how long noncoding RNAs (lncRNAs) and the loci that transcribe them contribute to the regulation of CD8 T cells during viral infections remains largely unexplored. Here, we report that transcription of the lncRNA Morrbid is specifically induced by T-cell receptor (TCR) and type I IFN stimulation during the early stages of acute and chronic lymphocytic choriomeningitis virus (LCMV) infection. In response to type I IFN, the Morrbid RNA and its locus control CD8 T cell expansion, survival, and effector function by regulating the expression of the proapoptotic factor, Bcl2l11, and by modulating the strength of the PI3K–AKT signaling pathway. Thus, our results demonstrate that inflammatory cue-responsive lncRNA loci represent fundamental mechanisms by which CD8 T cells are regulated in response to pathogens and potentially cancer.

Vaccination remains one of the greatest medical breakthroughs in human history and has resulted in the near eradication of many formerly lethal diseases in many countries, including the complete eradication of smallpox. However, there remain a number of diseases for which there are no or only partially effective vaccines. There are numerous hurdles in vaccine development, of which knowing the appropriate immune response to target is one of them. Recently, tissue-resident T cells have been shown to mediate high levels of protection for several infections, although the best way to induce these cells is still unclear. Here we compare the ability to generate skin-resident T cells in sites distant from the immunization site following intramuscular and intradermal injection using optimized synthetic DNA vaccines. We found that mice immunized intradermally with a synthetic consensus DNA HIV envelope vaccine by electroporation (EP) are better able to maintain durable antigen-specific cellular responses in the skin than mice immunized by the intramuscular route. We extended these studies by delivering a synthetic DNA vaccine encoding Leishmania glycosomal phosphoenolpyruvate carboxykinase (PEPCK) by EP and again found that the intradermal route was superior to the intramuscular route for generating skin-resident PEPCK-specific T cells. We observed that when challenged with Leishmania major parasites, mice immunized intradermally exhibited significant protection, while mice immunized intramuscularly did not. The protection seen in intradermally vaccinated mice supports the viability of this platform not only to generate skin-resident T cells but also to promote durable protective immune responses at relevant tissue sites.

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Metastatic cancer remains largely incurable due to an incomplete understanding of how cancer cells disseminate throughout the body. However, tools for probing metastatic dissemination and associated molecular changes at high resolution are lacking. Here we present multiplexed, activatable, clonal, and subclonal GESTALT (macsGESTALT), an inducible lineage recorder with concurrent single cell readout of transcriptional and phylogenetic information. By integrating multiple copies of combined static barcodes and evolving CRISPR/Cas9 barcodes, macsGESTALT enables clonal tracing and subclonal phylogenetic reconstruction, respectively. High barcode editing and recovery rates produce deep lineage reconstructions, densely annotated with transcriptomic information. Applying macsGESTALT to a mouse model of metastatic pancreatic cancer, we reconstruct dissemination of tens-of-thousands of single cancer cells representing 95 clones and over 6,000 unique subclones across multiple distant sites, e.g. liver and lung metastases. Transcriptionally, cells exist along a continuum of epithelial-to-mesenchymal transition (EMT) in vivo with graded changes in associated signaling, metabolic, and regulatory processes. Lineage analysis reveals that from a majority of non-metastatic, highly epithelial clones, a single dominant clone that has progressed along EMT drives the majority of metastasis. Within this dominant clone a parallel process occurs, where a small number of aggressive subclones drive clonal outgrowth. By precisely mapping subclones along the EMT continuum, we find that size and dissemination gradually increase, peaking at late-hybrid EMT states but precipitously falling once subclones are highly mesenchymal. Late-hybrid EMT states are selected from a predominately epithelial ancestral pool, enabling rapid metastasis but also forcing extensive and continuous population bottlenecking. Notably, late-hybrid gene signatures are associated with decreased survival in human pancreatic cancer, while epithelial, early-hybrid, and highly mesenchymal states are not. Our findings illuminate features of metastasis and EMT with the potential for therapeutic exploitation. Ultimately, macsGESTALT provides a powerful, accessible tool for probing cancer and stem cell biology in vivo.