The outer layer of the meninges, the dura mater, forms a critical interface at the border of the central nervous system (CNS). While historically the dura was viewed as a protective physical barrier for the brain and spinal cord, providing structural support for the venous sinuses, more recent research has shown that it is intimately connected to adjacent bones, CNS organs, the systemic circulation, and peripheral organs, particularly the gastrointestinal tract, via immune cell immigrants. In parallel, advances in immunophenotyping have revealed that the dura houses a plethora of immune cells, some within aggregates in dural-associated lymphoid tissue that can support the activation of adaptive immune cells, including germinal center responses. These dural immune cells can acquire immunological information from the network of dural blood and lymphatic vessels, as well as autonomic and sensory nerves, and newly discovered arachnoid cuff entry points provide a direct connection with the subarachnoid space. In this review, we will summarize recent evidence that highlights the dura as a hub for the detection, integration, and relay of immune signals from outside and inside the CNS.

Abstract The human kidney contains highly specialized cell populations. Despite numerous single-cell and single-nucleus transcriptomics studies, differences in cohorts, technologies, analytical pipelines, and annotation frameworks have limited the ability to define consensus kidney cell states, identify disease-associated populations and interpret kidney disease genetic susceptibility. Here, we assembled 18 human kidney single-cell and single-nucleus RNA-sequencing datasets spanning 232 donors and five major disease contexts into a uniformly processed and computationally integrated Human Kidney Cell Atlas (HKCA), comprising over one million high-quality cells (816,895) and nuclei (215,308). The HKCA resolves 63 cell types and 120 harmonized cell states, including rare epithelial and stromal populations associated with kidney diseases. Integration with spatial transcriptomics, intercellular communication networks, and human genetic association data further defined the anatomical context and disease relevance of these populations. The HKCA also provides a framework for automated annotation of independent kidney human and mouse datasets. Together, the HKCA establishes a comprehensive reference for human kidney biology, enabling disease interpretation and genetic risk localization at cellular resolution.

The meninges form the border between the brain and periphery and house a rich network of immune cells. Here we show that gastrointestinal challenges (intracellular or extracellular bacteria and parasites) reshape the nature of CD4+ T cells in the dura mater, the outer meningeal layer, changing the dominant polarization states to T helper (TH) 1, TH17 and TH2 cells, respectively, with differing cytokine profiles. This occurs via CXCR6-CXCL16-dependent migration of gut-activated CD4+ T cells to the central nervous system, where they establish long-lived memory populations around the dural venous sinuses, within dural lymphoid aggregates and in the brain. Functionally, these orally primed dural CD4+ T were capable of rapid, antigen-specific recall responses, proliferating and producing cytokines upon intravenous rechallenge. Our findings reveal a direct link between intestinal and dural immunity, enabling the central nervous system borders to acquire immunological memory of gut microorganisms, a major source of bloodborne pathogens capable of reaching the brain via fenestrated dural vasculature.

The iterative bleaching extends multiplexity (IBEX) Knowledge-Base is a central portal for researchers adopting IBEX and related 2D and 3D immunofluorescence imaging methods. The design of the Knowledge-Base is modeled after efforts in the open-source software community and includes three facets: a development platform (GitHub), static website, and service for data archiving. The Knowledge-Base facilitates the practice of open science throughout the research life cycle by providing validation data for recommended and non-recommended reagents, such as primary and secondary antibodies. In addition to reporting negative data, the Knowledge-Base empowers method adoption and evolution by providing a venue for sharing protocols, videos, datasets, software, and publications. A dedicated discussion forum fosters a sense of community among researchers while addressing questions not covered in published manuscripts. Together, scientists from around the world are advancing scientific discovery at a faster pace, reducing wasted time and effort, and instilling greater confidence in the resulting data.

Adaptive immunity is generated in lymphoid organs, but how these structures defend themselves during infection in humans is unknown. The nasal epithelium is a major site of viral entry, with adenoid nasal-associated lymphoid tissue (NALT) generating early adaptive responses. In the present study, using a nasopharyngeal biopsy technique, we investigated longitudinal immune responses in NALT after a viral challenge, using severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection as a natural experimental model. In acute infection, infiltrating monocytes formed a subepithelial and perifollicular shield, recruiting neutrophil extracellular trap-forming neutrophils, whereas tissue macrophages expressed pro-repair molecules during convalescence to promote the restoration of tissue integrity. Germinal center B cells expressed antiviral transcripts that inversely correlated with fate-defining transcription factors. Among T cells, tissue-resident memory CD8 T cells alone showed clonal expansion and maintained cytotoxic transcriptional programs into convalescence. Together, our study provides unique insights into how human nasal adaptive immune responses are generated and sustained in the face of viral challenge. Clatworthy and colleagues examine adult nasal lymphoid tissues in response to SARS-CoV-2 infection. Longitudinal profiling reveals changes in barrier tissue to block viral entry beyond the epithelial cell layer and how tissue repair occurred after viral infection.

Tumor-associated macrophages (TAM) are a universal feature of cancers but variably influence outcomes and treatment responses. In this study, we used a photoconvertible mouse to distinguish newly entering, monocyte-derived TAMs (mdTAM) that were enriched at the tumor core from resident-like TAMs that localized with fibroblasts at the tumor-normal interface. The mdTAM pool was highly dynamic and continually replenished by circulating monocytes. Upon tumor entry, these monocytes differentiated down two divergent fate trajectories distinguished by the expression of MHC class II. MHC-II+ mdTAMs were functionally distinct from MHC-II- mdTAMs, demonstrating increased capacity for endocytosis and Fc-gamma receptor-mediated phagocytosis, as well as proinflammatory cytokine production. Both mdTAM subsets showed reduced expression of inflammatory transcripts and increased expression of PD-L1 with increasing tumor dwell time. Treatment with anti-PD-L1 skewed mdTAM differentiation toward the MHC-II+ fate and attenuated the anti-inflammatory effects of the tumor environment. Anti-PD-L1 enhanced mdTAM-CD4+ T cell interactions, establishing an IFNγ-CXCL9/10-dependent positive feedback loop. Altogether, these data resolve distinct temporal, spatial, and functional properties of TAMs and provide evidence of subset-specific effects of PD-L1 blockade.

The meninges house several innate and adaptive immune cell populations[1][1]–[3][2]. These predominantly localise within the dura mater and include gut-derived IgA-secreting plasma cells[4][3]. Whether T cell adaptive memory in the dura is similarly linked to the gut is currently unknown. Here we show that dural CD4 T cell polarisation to a T helper (Th) 1, Th2 and Th17 state is determined by the nature of the immunological challenge encountered in the gastrointestinal tract. We find that intestinally polarised CD4 T cells seed to the dura in a CXCR6-CXCL16-dependent manner, express tissue-residency markers and are long-lived. Functionally, these orally-primed dural CD4 T are capable of a rapid antigen-specific recall response that limits pathogen spread into the brain following intravenous re-challenge. Our work reveals how linked intestinal and dural immunity enables the central nervous system to accrue immunological memory of gut microbes, the most likely source of life-threatening bloodborne pathogens. ### Competing Interest Statement The authors have declared no competing interest. Wellcome Trust, 102163/B/13/Z, 110199/Z/15/Z, 220268/Z/20/Z, 107057/Z/15/Z, 227890/Z/23/ Medical Research Council, MR/S035842/1 NIHR, RP-2017-08-ST2-002 [1]: #ref-1 [2]: #ref-3 [3]: #ref-4

Abstract Background and Aims There is growing evidence that B cells (memory and innate-like) reside in non-lymphoid organs where they play an important role for generating local immune responses or maintaining tolerance [1]. Several studies observed accumulation of innate-like self-reactive B cells in human kidneys following an injury or transplant rejection, associated with progressive organ dysfunction [2,3]. However, the origin of these B cells is unknown. Here, were investigated whether human kidneys house B cells in homeostasis and how they change with donor age. Method We examined the number, phenotype and clonality of B cells in human kidneys that were perfused to remove circulating cells, and in matched splenic tissue obtained from the same transplant donor (N = 19, median age 56 years (range: 18–80). Suspensions from homogenized organs were analyzed using a 35-marker mass cytometry panel and single-cell RNA sequencing. B cells were also sorted for bulk BCR-sequencing. Results At steady state, human kidneys house B cells enriched for non-naïve (CD27+IgD− and double-negative) subsets when compared to spleen or younger donors. The renal cortex harbours ten times more B cells per gram of tissue than medulla. In contrast to spleen, B cell count and B:T cell ratio in renal cortex significantly increase with age (Fig. A). Kidney B-cell immune repertoire is less diverse but also less mutated than spleen, suggesting the presence of innate-like B cells. Indeed, single-cell-RNA sequencing analysis reveals that large proportion of non-naïve kidney B cells belongs to IgM/IgA memory subset with transcriptomic similarity to murine B-1 cells (not marginal-zone B cells) (Fig. B). Conclusion Our study shows that under homeostatic conditions, human kidneys harbour a large proportion of IgM/IgA memory B cells with innate-like features that transcriptomically mirror murine B-1 cells and increase with age. This B cell subset might further expand following an injury and fuel local immunopathology and organ dysfunction as observed by previous studies [2,3]. Hence, selective targeting of these innate-like B cells could be an important therapeutic strategy.

Diabetic kidney disease (DKD), the most common cause of kidney failure, is a frequent complication of diabetes and obesity, and yet to date, treatments to halt its progression are lacking. We analyze kidney single -cell transcriptomic profiles from DKD patients and two DKD mouse models at multiple time points along disease progression-high-fat diet (HFD)-fed mice aged to 90-100 weeks and BTBR ob/ob mice (a genetic model)-and report an expanding population of macrophages with high expression of triggering receptor expressed on myeloid cells 2 ( TREM2 ) in HFD-fed mice. TREM2 `"'` macrophages are enriched in obese and diabetic patients, in contrast to hypertensive patients or healthy controls in an independent validation cohort. Trem2 knockout mice on an HFD have worsening kidney filter damage and increased tubular epithelial cell injury, all signs of worsening DKD. Together, our studies suggest that strategies to enhance kidney TREM2 `"'` macrophages may provide therapeutic benefits for DKD.

Lower urinary tract infection (UTI) is common but only rarely complicated by pyelonephritis. However, the mechanisms preventing extension to the kidney are unclear. Here, we identified neutrophil extracellular traps (NETs) in healthy human urine that provide an antibacterial defense strategy within the urinary tract. In both in vivo murine models of UTI where uropathogenic E. coli are inoculated into the bladder and ex vivo human urine models, NETs interacted with uromodulin to form large webs that entrapped the bacteria. Peptidyl arginine deiminase 4 (PADI4) inhibition in mice blocked NETosis and resulted in progression of cystitis into pyelonephritis, suggesting that NETosis of urinary neutrophils acts to prevent bacterial ascent into the kidney. Analysis of UK Biobank data revealed that genetic variants in PADI4 that associated with increased risk of rheumatoid arthritis in multiple genome-wide association studies were consistently associated with reduced susceptibility to UTI. Last, we showed that urine dipstick testing for leukocyte esterase was negative in the presence of intact blood neutrophils but became positive when neutrophils were stimulated to NET, and this could be prevented by selective PADI4 inhibition, demonstrating that this test does not detect absolute neutrophil count, as has long been assumed, but specifically detects neutrophils that have undergone NETosis. These findings highlight the role of NETosis in preventing ascending infections in the urinary tract and improve our understanding of one of the most common clinical tests in medicine.