Probes for TNF

Microglial-derived inflammation has been linked to a broad range of neurodegenerative and neuropsychiatric conditions, including amyotrophic lateral sclerosis (ALS). Using single-cell RNA sequencing, a class of Disease-Associated Microglia (DAMs) have been characterized in neurodegeneration. However, the DAM phenotype alone is insufficient to explain the functional complexity of microglia, particularly with regard to regulating inflammation that is a hallmark of many neurodegenerative diseases. Here, we identify a subclass of microglia in mouse models of ALS which we term RIPK1-Regulated Inflammatory Microglia (RRIMs). RRIMs show significant up-regulation of classical proinflammatory pathways, including increased levels of Tnf and Il1b RNA and protein. We find that RRIMs are highly regulated by TNFα signaling and that the prevalence of these microglia can be suppressed by inhibiting receptor-interacting protein kinase 1 (RIPK1) activity downstream of the TNF receptor 1. These findings help to elucidate a mechanism by which RIPK1 kinase inhibition has been shown to provide therapeutic benefit in mouse models of ALS and may provide an additional biomarker for analysis in ongoing phase 2 clinical trials of RIPK1 inhibitors in ALS.

Tumor-elicited inflammation confers tumorigenic properties, including cell death resistance, proliferation, or immune evasion. To focus on inflammatory signaling in tumors, we investigated linear ubiquitination, which enhances the nuclear factor-κB signaling pathway and prevents extrinsic programmed cell death under inflammatory environments. Here, we showed that linear ubiquitination was augmented especially in tumor cells around a necrotic core. Linear ubiquitination allowed melanomas to tolerate the hostile tumor microenvironment and to extend a necrosis-containing morphology. Loss of linear ubiquitination resulted in few necrotic lesions and growth regression, further leading to repression of innate anti-PD-1 therapy resistance signatures in melanoma as well as activation of interferon responses and antigen presentation that promote immune-mediated tumor eradication. Collectively, linear ubiquitination promotes tumor-specific tissue remodeling and the ensuing immune evasion.

Immune checkpoint blockade is therapeutically successful for many patients across multiple cancer types. However, immune-related adverse events (irAE) frequently occur and can sometimes be life threatening. It is critical to understand the immunologic mechanisms of irAEs with the goal of finding novel treatment targets. Herein, we report our analysis of tissues from patients with irAE dermatitis using multiparameter immunofluorescence (IF), spatial transcriptomics, and RNA in situ hybridization (RISH). Skin psoriasis cases were studied as a comparison, as a known Th17-driven disease, and colitis was investigated as a comparison. IF analysis revealed that CD4+ and CD8+ tissue-resident memory T (TRM) cells were preferentially expanded in the inflamed portion of skin in cutaneous irAEs compared with healthy skin controls. Spatial transcriptomics allowed us to focus on areas containing TRM cells to discern functional phenotype and revealed expression of Th1-associated genes in irAEs, compared with Th17-asociated genes in psoriasis. Expression of PD-1, CTLA-4, LAG-3, and other inhibitory receptors was observed in irAE cases. RISH technology combined with IF confirmed expression of IFNγ, CXCL9, CXCL10, and TNFα in irAE dermatitis, as well as IFNγ within TRM cells specifically. The Th1-skewed phenotype was confirmed in irAE colitis cases compared with healthy colon.

The pattern-recognition receptor NOD2 senses bacterial muropeptides to regulate host immunity and maintain homeostasis. Loss-of-function mutations in NOD2 are associated with Crohn's disease (CD), but how the variations in microbial factors influence NOD2 signaling and host pathology is elusive. We demonstrate that the Firmicutes peptidoglycan remodeling enzyme, DL-endopeptidase, increased the NOD2 ligand level in the gut and impacted colitis outcomes. Metagenomic analyses of global cohorts (n = 857) revealed that DL-endopeptidase gene abundance decreased globally in CD patients and negatively correlated with colitis. Fecal microbiota from CD patients with low DL-endopeptidase activity predisposed mice to colitis. Administering DL-endopeptidase, but not an active site mutant, alleviated colitis via the NOD2 pathway. Therapeutically restoring NOD2 ligands with a DL-endopeptidase-producing Lactobacillus salivarius strain or mifamurtide, a clinical analog of muramyl dipeptide, exerted potent anti-colitis effects. Our study suggests that the depletion of DL-endopeptidase contributes to CD pathogenesis through NOD2 signaling, providing a therapeutically modifiable target.

Chemotherapy resistance is a critical contributor to cancer mortality and thus an urgent unmet challenge in oncology. To characterize chemotherapy resistance processes in high-grade serous ovarian cancer, we prospectively collected tissue samples before and after chemotherapy and analyzed their transcriptomic profiles at a single-cell resolution. After removing patient-specific signals by a novel analysis approach, PRIMUS, we found a consistent increase in stress-associated cell state during chemotherapy, which was validated by RNA in situ hybridization and bulk RNA sequencing. The stress-associated state exists before chemotherapy, is subclonally enriched during the treatment, and associates with poor progression-free survival. Co-occurrence with an inflammatory cancer-associated fibroblast subtype in tumors implies that chemotherapy is associated with stress response in both cancer cells and stroma, driving a paracrine feed-forward loop. In summary, we have found a resistant state that integrates stromal signaling and subclonal evolution and offers targets to overcome chemotherapy resistance.

Neuropathic pain is a leading cause of high impact pain, is often disabling and is poorly managed by current therapeutics. Here we focused on a unique group of neuropathic pain patients undergoing thoracic vertebrectomy where the dorsal root ganglia is removed as part of the surgery allowing for molecular characterization and identification of mechanistic drivers of neuropathic pain independently of preclinical models. Our goal was to quantify whole transcriptome RNA abundances using RNA-seq in pain-associated human dorsal root ganglia from these patients, allowing comprehensive identification of molecular changes in these samples by contrasting them with non-pain associated dorsal root ganglia. We sequenced 70 human dorsal root ganglia, and among these 50 met inclusion criteria for sufficient neuronal mRNA signal for downstream analysis. Our expression analysis revealed profound sex differences in differentially expressed genes including increase of IL1B, TNF, CXCL14, and OSM in male and including CCL1, CCL21, PENK and TLR3 in female dorsal root ganglia associated with neuropathic pain. Co-expression modules revealed enrichment in members of JUN-FOS signalling in males, and centromere protein coding genes in females. Neuro-immune signalling pathways revealed distinct cytokine signalling pathways associated with neuropathic pain in males (OSM, LIF, SOCS1) and females (CCL1, CCL19, CCL21). We validated cellular expression profiles of a subset of these findings using RNAscope in situ hybridization. Our findings give direct support for sex differences in underlying mechanisms of neuropathic pain in patient populations.

Background & Aims TNF superfamily member TL1A has been associated with susceptibility and severity of inflammatory bowel diseases. However, the function of TL1A and its receptor DR3 in the development of intestinal inflammation is incompletely understood. We investigated the role of DR3 expressed by intestinal epithelial cells (IEC) during intestinal homeostasis, tissue injury, and regeneration. Methods Clinical phenotype and histological inflammation were assessed in C57BL/6 (WT), Tl1a-/-, and Dr3-/- mice in dextran sulfate sodium (DSS)-induced colitis. We generated mice with an IEC-specific deletion of DR3 (Dr3ΔIEC) and assessed intestinal inflammation and epithelial barrier repair. In vivo intestinal permeability was assessed by Fluorescein isothiocyanate dextran uptake. Proliferation of IEC was analyzed by Bromodeoxyuridine incorporation. Expression of DR3 mRNA was assessed by fluorescent in situ hybridization. Small intestinal organoids were used to determine ex vivo regenerative potential. Results Dr3-/- mice developed more severe colonic inflammation than WT mice in DSS-induced colitis with significantly impaired IEC regeneration. Homeostatic proliferation of IEC was increased in Dr3-/- mice but blunted during regeneration. Cellular localization and expression of the tight junction proteins Claudin-1 and zonula occudens-1 (ZO-1) was altered leading to increased homeostatic intestinal permeability. Dr3ΔIEC mice recapitulated the phenotype observed in Dr3-/- mice with increased intestinal permeability and IEC proliferation under homeostatic condition and impaired tissue repair and increased bacterial translocation during DSS-induced colitis. Impaired regenerative potential and altered ZO-1 localization was also observed in Dr3ΔIEC enteroids. Conclusions Our findings establish a novel function of DR3 in IEC homeostasis and post-injury regeneration independent of its established role in innate lymphoid cells and T helper cells.

Immunological characterization of the Fiebig-equivalent stages of SHIVAD8-EO infection showed that, despite the observed differences in progression of infection between the challenge groups, the timing of virus-specific CD8+ T cell responses, as well as the viral load and virus distribution in the LNs, was concordant between the groups when assessed by Fiebig-equivalent staging. LN SHIVAD8-EO RNA+ cells were initially detected in both follicular and extrafollicular areas and mostly preceding peak plasma viremia at Fiebig-equivalent stage II, in agreement with previous studies (31, 41-44). Their levels increased proportionally to viral load in plasma, and seemed to decrease at Fiebig-equivalent stage VI when strong LN SIV-specific CD8+ T cell responses were detected. These responses, which appeared to develop at later stages than in the peripheral blood of acutely HIV-1-infected subjects (45), were predominantly characterized by production of the highly proinflammatory cytokine TNF and expression of CD107a, indicative of degranulation. In addition, levels of fCD8+ T cells, previously shown to be highly cytolytic ex vivo and able to mediate killing of HIV-infected target cells in vitro (31, 46), were higher at Fiebig-equivalent stage VI than stage V. LN NK cell levels also transiently increased at Fiebig-equivalent stage V. Thus, our data are consistent with the notion that, after peak plasma viremia during Fiebig-equivalent stages V and VI of SHIVAD8-EO infection, cytotoxic immune responses develop in the LNs and may lead to lysis of virus-infected cells and release of virions. In fact, LN SHIVAD8-EO RNA+ virions were almost absent at Fiebig-equivalent stage II when SHIVAD8-EO RNA+ cells, likely producing virions (47), were already present but CD8+ T cell responses were undetectable. However, virions were highly abundant in the follicles during Fiebig-equivalent stage VI when CD8+ T cell responses were stronger. Although there was no significant correlation between the levels of LN SHIVAD8-EO RNA+ cells and the virus-specific function of LN CD8+ T cells in our study, possibly because of limited sample size and data variation between animals, previous studies reported in situ observation of CD8+ T cells expressing T cell intracellular antigen-1 (TIA-1) or perforin (48, 49) and increased activation of cytotoxic cells (50) in the LNs of HIV-1-infected subjects. Furthermore, CD8+ T cells with HIV- or SIV-specific killing activity in vitro were detected in the LNs, splenic white pulp, and tonsil GCs of HIV-1-infected subjects (46, 51), and in the LNs of SIV-infected NHPs (31, 52, 53). Also, NK cells were shown to accumulate in the LNs of African green monkeys during nonpathogenic SIV infection, where they played an important role in the control of viral replication (54).