Genes & Immunity

Introduction: Killer-cell immunoglobulin-like receptor (KIR) gene content shapes natural killer-cell responses and varies substantially among populations. We examined whether worldwide KIR diversity reflects regional structure, isolation by distance, serial founder effects, or latitudinal gradients. Data and methods: Carrier frequencies for 11 variable KIR genes were obtained from the Allele Frequency Net Database. The primary analysis included 189 locally sampled, non-diaspora, non-mixed populations from 70 countries, comprising 25,469 individuals; 161 populations had complete 11-gene profiles. Diversity indices, ordination, clustering, permutation-based variance decomposition, Mantel tests, and regression models were used to characterize geographic structure. Serial founder effects were evaluated using four distance measures from East Africa, both globally and within the Old World. Models of latitude incorporated spatial autocorrelation. Prespecified sensitivity analyses evaluated alternative population sets, gene panels, geographic classifications, weighting schemes, and multivariate outlier exclusion. Results: Geographic region explained 53.5% of variation in KIR profiles, substantially exceeding the permutation-null expectation of 6.9%, although multivariate dispersion differed among regions. Twenty-five of 28 pairwise regional comparisons remained significant after false-discovery-rate correction. Isolation by distance was modest (Mantel r=0.3003) and weakened after controlling for region (r=0.1557). KIR diversity did not decline with distance from East Africa globally but decreased strongly within the Old World (expected heterozygosity {beta}=-0.0066 and standardized gene content {beta}=-0.0789). B-content decreased nominally with absolute latitude, but latitude was collinear with region and the association survived neither spatial modelling nor sensitivity analyses. Regional differentiation remained robust across analytical specifications, whereas the Old World decline was carried by gene content once standard errors were clustered by country. Conclusion: Worldwide KIR gene-content variation shows pronounced regional differentiation, modest isolation by distance, and no independent latitudinal gradient. Diversity declines with distance from East Africa across the Old World, supporting serial founder effects, but not once the Americas and Oceania are included.

Genetic ancestry composition has been used extensively as a predictor of clinical outcomes, multiomic biomarkers, and endophenotypes, but the models have most often used untransformed ancestry fractions as explanatory variables. Under a simplex constraint results from this type of model can be uninterpretable and misleading. We demonstrate the use of multiple transformed log ratio coordinates of ancestral proportions as predictors in a study of excreted myeloperoxidase (MPO), a neutrophilic enzyme used as a fecal biomarker to measure intestinal inflammation and enteropathy. We show how to convert these difficult-to-interpret effects into association results for shifts between two ancestries under an isoancestry constraint (holding an ancestry fraction constant) using post-estimation average marginal effects and explain their geometric interpretation. We found that increasing proportion of African ancestry was associated with increased levels of excreted MPO in low-income household infants in three Northeastern Brazil studies, with a smaller negative secondary association of European ancestry, all under a tri-continental ancestry composition (African, European, Amerindian). While the maximum log(MPO) outcome variance explained by differences in genetic ancestry was modest at a few percent, we show evidence that these differences in heritability were context-dependent on measurement of MPO under active enteric infection. The results were attenuated by socio-economic status, but a signal remained. Overall, we found that African genomes carry additional alleles that enable a more intensive neutrophil response to enteric infection relative to European and Amerindian genomes, illuminating a possible host genetic background role in modulating immune response to enteric diseases and pathogens.

Background: More than five years after the COVID-19 outbreak, the infection by the SARS-CoV-2 virus should still be considered as a global threat with highly heterogeneous clinical outcomes from asymptomatic to fatal depending on existing genetic and phenotypic inter-individual and inter-population variability. Our objective is to identify risk loci associated with COVID-19 in an admixed Latin American population. Methods: We performed a genome-wide association study in the framework of the Chilean C19-GenoNet team, analyzing a cohort of 3,417 individuals recruited from the northernmost to the southernmost regions of the country, who presented variations in the severity of their COVID-19 clinical manifestations. Results: Our investigation replicated the extensively reported association of several variants at the 3p21.31 locus with COVID-19 severity and found a suggestive association for a variant within the FOXP4 gene at 6p21.1 with COVID-19 hospitalization. Both associations appear to be shared with other populations. Importantly, our study identified three previously unreported loci associated with COVID-19 severity or hospitalization at 7q21.11, 16p13.12 and 6p25.3, and one additional locus at 4p13 associated with SARS-CoV-2 positivity, a proxy for infection susceptibility. Conclusions: these new risk loci may represent population-specific effects in Chilean and, potentially, other Latin American admixed groups. Our study highlights the importance of expanding efforts to study underrepresented and genetically different populations, which may provide new clues on the genetic basis of human diseases and may help to anticipate global responses to emerging viral infections and future pandemics.

Multiple sclerosis (MS) is approximately three times more common in females than in males, but sex-linked epigenetic mechanisms remain incompletely understood. We tested whether X-chromosome DNA methylation differs in females with MS and whether associated sites preferentially map to genes normally subject to X-chromosome inactivation (XCI). An X-chromosome-focused epigenome-wide association study was performed in whole blood from three datasets comprising 496 females with MS and 509 female controls, with independent evaluation in isolated CD4+ T cells (80 cases, 76 controls). At FDR < 0.01, 3 182 X-chromosome CpGs were hypomethylated in MS (mean {Delta}{beta} = -0.035). Hypomethylated CpGs were strongly enriched in non-escape genes normally subject to XCI relative to escape genes (OR 6.77; p = 1.55x10-57) and mapped to immune and chromatin-related processes. Exploratory cis-mQTL analysis identified strong local genetic effects at a small subset of loci, including WAS, IRAK1 and TLR7. In CD4+ T cells, 2 080 of the 3,182 whole-blood hypomethylated CpGs (65.4%) were also significantly hypomethylated. These findings identify a reproducible X-chromosome hypomethylation signature in female MS and support direct investigation of inactive-X regulation, XCI escape and X-linked immune gene dosage.

Human immune responses remain poorly characterized across Indigenous South American (ISA) populations, limiting our understanding of human immune variation. Here, we generated a single-cell transcriptional atlas of 1.4 million peripheral blood mononuclear cells from 345 individuals representing 13 South American populations, profiled at baseline and following stimulation with lipopolysaccharide, influenza A virus, or Trypanosoma cruzi. Genetic ancestry was associated with the expression of a large fraction of the transcriptome, often only after stimulation, and explained more variation than age or sex. On average, cis-eQTLs accounted for one-quarter of these ancestry-associated differences. Thousands of regulatory variants were common in ISA populations but rare or absent in European reference datasets. Integrating eQTLs with GWAS revealed stimulation-specific disease-associated regulatory variants and an enrichment of ancestry-associated expression differences among genes with colocalizing signals. Our findings highlight the importance of studying diverse populations across immune contexts to understand the genetic architecture of human immune responses.

The non-canonical NF-kappa B pathway, in which NFKB2 plays a central role, is critical for lymphoid organ development and immune homeostasis. Pathogenic NFKB2 variants have been strongly associated with a broad spectrum of human pathologies, notably immunodysregulation syndromes, characterized by recurrent infections, autoantibody production and endocrine abnormalities. The mechanisms underlying the resulting immune defects remain incompletely understood. In the present study, we characterized the immune phenotype of a novel rat model harboring a Nfkb2 non-sense mutation located in the c-terminal region of the gene (c.2602T>A; p.Tyr867*, Nfkb2p.Tyr867*). This variant has been identified in patients with a familial form of common variable immunodeficiency (CVID) presenting with autoimmunity manifestations. Using this model, we demonstrate that mutated NFKB2 resulted in profound alterations of the thymic microenvironment, including reduced K5+ medullary thymic epithelial cells and decreased AIRE expression, accompanied by altered thymocyte development and impaired thymic regulatory T populations. Peripheral lymphoid organization was also profoundly affected, with absence of lymph nodes, defects in the splenic marginal zone, and alterations of CD4+ and CD8+ T-cell homeostasis, including impaired Treg populations and reduced ICOS expression on CD4+ T cells. The B-cell compartment was markedly altered, with impaired B-cell maturation, characterized by accumulation of IgM+IgD- transitional cells and a marked reduction of IgD+ mature B cells. These abnormalities were associated with impaired humoral immunity and complete absence of circulating immunoglobulins. Collectively, our findings define a systemic combined immunodeficiency phenotype in the Nfkb2-mutated rat, highlighting its utility for studying the role of non-canonical NF-kB signaling in immune system organization and adaptative immunity.

The transcriptional and cell repertoire changes of lymph node (LN) T cells following influenza vaccination have been under-investigated across different ethnicities. Draining (dLN) and non-draining (ndLN) axillary LN cells from 17 participants with genotypically varied African or Asian ancestry (ISRCTN13657999) were collected by fine needle aspiration (FNA) before, 5 days and 42 days after adjuvanted influenza vaccination and analysed by single-cell RNA-sequencing (scRNA-seq). The early dLN transcriptional profile and cellular dynamics were distinct from the ndLN; BACH2 expressing T cells were highly induced, exhibiting stem-like and unique quiescence signatures. Proliferating T follicular helper cells (Tfh) were enriched in dLN and Th1-like Tfh predominated with highly induced transcriptional changes. The BACH2+ T cell state and Th1-like Tfh cells, transcriptionally distinct from germinal centre (GC) T cells, were co-localised with LAMP3+ dendritic cells in the T cell zone of publicly available LN datasets, a region that was also distinct from GC Tfh niches. Together, these findings indicate that the induction of a robust, proliferative, and transcriptionally diverse Tfh response, alongside a discrete subset of BACH2+ T cells, represents a marked feature of the early T cell zone immune response to adjuvanted influenza vaccine in the dLN.

Systemic lupus erythematosus (SLE) is the prototypical systemic autoimmune disease defined by the production of autoantibodies directed against diverse self-antigens. Antinuclear antibodies (ANA) are central to SLE diagnosis, and anti-double-stranded DNA (anti-dsDNA) antibodies are clinically used to track disease activity. However, these biomarkers provide only partial insight into the full spectrum of autoimmune changes in patients. To expand the known landscape of SLE autoreactivity shared among patients and associated with disease activity, we performed an unbiased characterization of 1,268 SLE plasma samples from 695 SLE patients and 301 healthy controls using phage immunoprecipitation and sequencing (PhIP-seq). This technique preferentially displays linear epitopes, and thus provides a complementary set of autoreactivities to previously discovered autoreactive targets. Despite the marked clinical heterogeneity of SLE, machine learning applied to this data surfaced a shared, reproducible signature that robustly discriminates between SLE and healthy controls in two validation cohorts. Autoreactivities in SLE were significantly enriched for RNA-binding protein targets. Autoreactive proteins containing Basic Acidic Dipeptides (BAD) repeat domains, features associated with biomolecular condensate formation, distinguished patients with high disease activity (by SLEDAI score) from patients with no disease activity. Among all shared autoreactivities, a peptide derived from YTHDF2 emerged as the most prevalent target across SLE cohorts occurring in ~25% of SLE patients and displayed striking sequence similarity to a peptide derived from the Epstein Barr virus (EBV) lytic switch protein BZLF1. Competition assays demonstrated higher-affinity binding to the viral peptide, supporting a model in which antiviral humoral responses to EBV may drive secondary epitope spreading toward molecularly mimicked self-antigens. Remarkably, orthogonal validation using the Luminex bead platform containing a panel of only 10 peptides, including BZLF1, demonstrated strong discrimination between SLE and healthy controls (AUC = 0.95). Together, these findings identify a rich, greatly expanded landscape of autoreactivities in SLE, candidate biomarkers associated with high disease activity, and provide mechanistic insight linking EBV-driven immunity to epitope-specific autoimmunity in lupus.

Background: Early-life adversity (ELA) is one of the strongest predictors of poor mental and physical health later in life, increasing an individual's risk for disorders ranging from depression to metabolic syndrome. However, whether and how ELA shapes immune memory through adulthood, subsequently affecting susceptibility to immune-associated diseases such as autoimmunity, remains elusive. Methods: To address this question, we employed a translationally and ethologically relevant mouse model of resource deprivation, the limited bedding and nesting model, to study the long-term effects of ELA on the immune system. ELA was induced by limited bedding and nesting material in the cage during postnatal days (P)2-9, which provokes fragmented and unpredictable maternal behavior in the dams, and results in chronic stress in the pups. Nucleic acid Linked ImmunoSandwich Assay (NULISA) was used to survey the proteome of adult (~P90) mice of both sexes that experienced ELA vs. control conditions. Results: Using a novel proteomic method, we detected significant upregulation in the levels of IL-17A in the adult blood, primarily in females. Within females, ELA also upregulated IL-13 and CCL3. Three proteins, HGF, PDGFA, and WNT16, were significantly downregulated in ELA mice of both sexes. Conclusions: Being a hallmark proinflammatory cytokine, IL-17A is found to increase in patients with systemic lupus erythematosus (SLE), as well as in animals with lupus-like diseases in virtually all reports. Importantly, autoimmune diseases like SLE have a higher prevalence in women than men, and our data support this sex bias. Together, our data suggest that ELA shapes long-term immune function in a way that may increase risk for autoimmune diseases, with promise for the development of more targeted and personalized therapies for autoimmunity.

Pregnancy involves profound changes to maternal immunity throughout gestation to simultaneously tolerate the fetus and protect both mother and baby from infection. Dysregulation of this process can lead to pregnancy complications and adverse outcomes. However, how the maternal peripheral immune system adapts throughout an uncomplicated pregnancy remains poorly understood, limiting our ability to identify and interpret alterations associated with pregnancy complications. Here, we longitudinally profiled maternal whole-blood transcriptomes of 1,305 nulliparous women at 12, 20, 28 and 36 weeks of gestation (n=3,776 samples) from the Pregnancy Outcome Prediction Study 2 (POPs2). Differential expression analysis revealed that the maternal immune system underwent its most pronounced remodeling in early pregnancy (between 12 and 20 weeks gestation). Co-expressed gene modules demonstrated immune-dominant programs were highly active in early stages, shifting towards increased cellular and metabolic activity in later pregnancy, reflecting maternal adaptation to increasing physiological demands. Through cis-eQTL mapping we found that genetic regulatory effects increasingly diverged from the non-pregnant state as pregnancy advanced. Colocalising with GWAS revealed putative mechanisms underlying genetic predisposition to pregnancy complications, with 58% of these colocalizations detectable only in the context of pregnancy. Finally, we identified eQTL that exhibit significant interactions with gestational age, implicating dynamic regulation of innate immune and metabolic pathways. These findings show that pregnancy is not only a state of changing gene expression, but also a dynamic regulatory environment that reshapes the effects of genetic variation. By characterizing these adaptations across gestation, this work provides a reference for interpreting maternal immune variation and genetic risk across gestation.

Thrombotic thrombocytopenic purpura (TTP) is a rare, life-threatening thrombotic microangiopathy caused by a severe deficiency of the ADAMTS13 protease. We performed the first large-scale genome-wide association study (GWAS) of TTP in 1,344 individuals of Han Chinese ancestry, comprising a discovery cohort (n = 913) and a validation cohort (n = 431). We identified two independent susceptibility loci, including the known locus 6p21 and the novel locus 14q32. At the known locus 6p21, the lead signal rs2187668 is near HLA-DQA1 and strongly associated with TTP risk (P = 5.35e-10; Odds Ratio [OR] = 3.94). At the novel locus 14q32, the lead SNP rs1024350 (P = 1.01e-10; OR = 1.90) is located between LINC00221 and MIR5195. Fine-mapping prioritized rs2187668 as the leading signal at 6p21, whereas HLA imputation and stepwise conditional analysis further pinpointed amino acid position 74 of HLA-DRB1 as the primary driver of the broader MHC association (P = 2.28e-10), superseding classical allele-based models. Structural analysis revealed that position 74 lines pocket 4 of the HLA-DRB1 peptide-binding groove; the risk-conferring Leu/Arg residues at this position carried by HLA-DRB1*08:03 and DRB1*03 may favour presentation of ADAMTS13-derived autoantigenic peptides, whereas the common Ala residue is protective. In summary, we reconstructed the genetic architecture of TTP in East Asians and identified structural gatekeepers of autoimmunity, providing novel targets for precision medicine and ethnic-specific risk stratification.

Background: Preeclampsia (PE) is a hypertensive pregnancy disorder with contributions from both maternal and fetal genetic factors, but how both genomes regulate placental transcription remains incompletely understood. Results: We analyzed placental 5'-end RNA sequencing data from 59 pregnancies in the FINNPEC cohort and performed separate maternal and fetal cis-eQTL analyses using gene-level expression and promoter-level expression defined as Transcript Far 5' Ends (TFE). Genotype-by-PE interaction models were used to identify genetic effects that differ according to PE status. No gene-level interaction eQTLs remained significant after multiple-testing correction, although suggestive signals included LILRB2 in the maternal and LPCAT3 in the fetal analyses. In contrast, we identified two significant syntenic promoter-level interaction eQTLs: rs12504642-TFE61820 at the FHDC1 locus in the maternal analysis and rs1557150-TFE9032 at the PPIAP31 locus in the fetal analysis. Conclusion: These findings suggest that PE-dependent genetic interaction effects may be detectable at specific transcript promoter regions even when they are not captured at annotated gene levels.

Pathogenic T helper 17 (pTH17) cells are a subset of CD4+ T cells driving autoimmune diseases including multiple sclerosis (MS). Compared to homeostatic TH17 cells and other TH subsets, pTH17 have enhanced mitochondrial function and oxidative phosphorylation (OXPHOS) that supports their differentiation and pathogenic function. Here we identify Copper Transporter 1 (CTR1), encoded by Slc31a1, as essential for copper uptake in CD4+ T cells, OXPHOS and pTH17 cell differentiation and function. While copper levels are known to be higher in the cerebrospinal fluid of patients with MS compared to healthy individuals, and excess copper contributes to oligodendrocyte loss in murine models of MS, the effect of copper on T cell function and pathogenicity in MS are unclear. We demonstrate that deletion of Slc31a1 in CD4+ T cells decreased intracellular copper levels, disrupting mitochondrial respiration and rewiring metabolism. These changes altered the epigenetic landscape of pTH17 cells by impairing DNA demethylation capacity, leading to hypermethylated DNA and altered chromatin accessibility at key binding sites for AP-1 transcription factors essential for pTH17 differentiation. As a result, CTR1-deficient T cells showed defective differentiation into pTH17 cells, with decreased production of IL-17A and expression of TH17 signature genes, while the differentiation of other CD4+ T cell subsets remained largely unaffected. Moreover, T cell-specific deletion of Slc31a1 protected mice from central nervous system (CNS) inflammation in the experimental autoimmune encephalomyelitis (EAE) model of MS by suppressing clonal expansion of autoreactive CD4+ T cells. These findings establish copper as a critical regulator of pTH17 differentiation and function, revealing a previously unknown molecular link between copper homeostasis, metabolism and epigenetic regulation governing pTH17-mediated autoimmunity.

Type 1 diabetes (T1D) is a chronic autoimmune disease characterized by T-cell mediated destruction of pancreatic islet {beta}-cells with genetic, environmental, and molecular triggers involved in disease pathogenesis. Patients with T1D have elevated serum levels of microRNA146a (miR146a). Polymorphisms in the miR146a gene that result in reduced expression of miR146a are associated with protection from T1D. We studied physiological regulators of miR146a expression and found that both hyperglycemia and elevated O-GlcNAcylation increased miR146a expression in T cells. Peripheral blood mononuclear cells (PBMCs) from T1D patients showed increased miR146a and O-GlcNAc transferase (OGT) expression, suggesting increased O-GlcNAcylation may promote miR146a expression in T1D patients. To determine the genetic and developmental role of miR146a in T1D, we generated miR146a-knockout (KO) non-obese diabetic (NOD) mice and found that absence of miR146a significantly protected NOD mice from spontaneous autoimmune diabetes. While we found no impact of miR146a knockout on general hematopoietic parameters and immune cell populations, remarkably, immune cell infiltration into the pancreas was significantly attenuated. Protection from autoimmune diabetes in miR146a-KO NOD mice was associated with increased regulatory T (Treg) cells in the spleen and pancreatic lymph node. Mechanistically, absence of miR146a increased NF-{kappa}B c-Rel expression in Treg cells and enhanced c-Rel binding at the Forkhead box protein P3 (FOXP3) promoter, which positively regulated Treg cell development and suppressor function, offering protection from T1D in miR146a-KO NOD mice. Our findings reveal miR146a as a key regulator of Treg cell-mediated immune tolerance through controlling NF-{kappa}B c-Rel-dependent FOXP3 expression and suggest targeting miR146a as a potential strategy to restore peripheral tolerance in T1D.

Background: Giant cell arteritis (GCA), traditionally considered T cell-driven, exhibits vascular B/plasma-cell infiltrates and altered circulating B-cell homeostasis, suggesting a pathogenic role for B cells. Relapse is common in newly diagnosed GCA (nGCA), yet predictive biomarkers remain elusive. Objective: To characterize circulating B-cell subpopulations in nGCA and assess their association with 12-month relapse. Methods: Baseline multiparametric flow cytometry was performed on peripheral blood samples from consecutive patients with nGCA and sex/age-matched healthy controls (HC). Patients received standard treatment per 2018 EULAR recommendations and were followed longitudinally. Results: 102 patients with nGCA and 102 matched HC were included. One-year outcome data were available for 55 patients, of whom 34 relapsed and 21 remained relapse-free. Baseline B-cell homeostasis differed by disease course. Non-relapsers showed reduced total CD19+ B-cell counts and contraction of most B-cell subsets, while CD27-IgD-double-negative (DN) B-cell counts remained comparable to HC. Conversely, relapsers maintained total B-cell numbers above HC despite reduced memory compartments, driven by expanded naive and DN B cells, alongside preserved plasmablast and transitional B-cell counts. At 6 months, total B-cell counts increased only in non-relapsers. DN B cells showed the greatest divergence between groups and independently predicted relapse. DN B-cell counts also correlated with circulating T peripheral helper cell numbers, supporting extrafollicular immune pathway activation. Conclusion: nGCA is characterized by outcome-dependent disturbances in B-cell homeostasis. Expansion of the DN B-cell compartment identifies a relapse-prone immunophenotype and represents a clinically relevant biomarker for early risk stratification.

Type 1 diabetes (T1D) is a complex autoimmune disease characterized by the destruction of insulin-producing pancreatic {beta} cells. Both genetic susceptibility and epigenetic dysregulation contribute to T1D risk. Recent studies have reported {beta}-cell dysfunction before disease onset, suggesting that {beta}-cell-intrinsic mechanisms contribute to pathogenesis. However, the mechanistic link between disease-associated variants and {beta}-cell dysfunction remains poorly understood. We hypothesized that a subset of T1D-associated variants directly influences cell type-specific candidate cis-regulatory elements (cCREs) by disrupting transcription factor (TF) binding and altering gene expression. To define cell type-specific cCREs in human islets, we integrated publicly available epigenomic datasets, including bulk histone modification profiles and single-cell multiomic data from human pancreatic islets. We combined these data with T1D genome-wide association study (GWAS) variants to identify disease-associated SNPs located within enhancer regions. Using multiomic datasets from PANC-DB, we characterized cell type-specific chromatin accessibility in nondiabetic and T1D islets and identified regulatory regions that may control gene expression in {beta} cells and other islet cell types. We then applied ChromBPNet, a deep learning model that predicts base-pair-resolution chromatin accessibility from scATAC-seq data, to evaluate how specific variants may alter local regulatory activity. In parallel, we used TF footprinting to nominate TFs likely to bind these variant-containing regions. These analyses identified several T1D-associated SNPs predicted to alter chromatin accessibility at candidate TF binding sites, suggesting mechanisms by which noncoding variants may contribute to {beta}-cell dysfunction and T1D susceptibility. Our findings link T1D-associated variants to cell type-specific enhancer activity and regulatory pathways and provide candidates for future mechanistic studies.

INTRODUCTION: Throughout history, viruses have been infecting humans, leaving genomic traces called endogenous viral elements (EVEs). This study explores the infectious hypothesis for Alzheimer's disease (AD) that suggests that viral infections may contribute to AD by analyzing EVEs in genomes of AD patients and cognitively healthy centenarians (CHCs) measured by long-read sequencing. METHODS: We implemented an EVE detection pipeline that screened the genomes of 248 AD patients and 240 CHCs. EVEs were measured based on EVE count, length, and chromosome location. RESULTS: The genomes of AD patients contain significantly more EVEs than those of CHCs (p=3.2x10-4). Moreover, certain chromosomal regions in AD patients show a higher EVE count, particularly of the Orthoherpesviridae family, near genes differentially expressed in AD brains. DISCUSSION: These findings suggest that viral infections may increase susceptibility to AD, highlighting that preventive measures against infections potentially reduce AD risk.

Autoreactive B cells must escape immune tolerance mechanisms to drive autoimmune disease, potentially through alternative paths to memory and antibody-secreting cell formation. "Atypical" B cells represent one such alternative pathway and are expanded in several human autoimmune diseases. Atypical B cells display phenotypic heterogeneity, but how this connects with differences in transcriptional programming, isotype switching and somatic hypermutation is incompletely understood in type 1 diabetes (T1D). Screening efforts to detect T1D prior to clinical diabetes onset affords an opportunity to study B cells early in immunopathogenesis, in which they primarily function as antigen-presenting cells. Prior evidence points to atypical B cell populations as reservoirs for islet autoreactivity in human T1D. We therefore developed sorting strategies to enrich for atypical and other autoreactive-prone B cell populations from the peripheral blood of early-stage T1D individuals and performed single-cell RNA/BCR-sequencing. We identified four transcriptionally defined atypical B cell clusters, each showing differential upregulation of atypical B cell defining genes. Additional gene expression changes were noted in broadly transcriptionally similar, but phenotypically distinct atypical B cell populations, with differences noted in the average extent of isotype switching and somatic hypermutation. Some atypical B cell populations showed extensive clonal sharing with classical memory or plasmablast subsets, consistent with relationships amongst these subsets. B cells reactive against a key islet autoantigen, insulin, were enriched in select atypical B cell populations. These findings highlight specific atypical B cell populations and features with potential value as biomarkers of disease progression or response to immunotherapy in T1D, and potentially other autoimmune diseases.

V{delta}2+ {gamma}{delta} T cells contribute to antimalarial immunity via pro-inflammatory and cytotoxic mechanisms. Among children who have experienced repeated episodes of malaria, V{delta}2+ T cells develop reduced pro-inflammatory function through mechanisms that remain unknown. We hypothesized that recurrent malaria drives coordinated epigenetic and transcriptional remodeling of these semi-innate cells. Using PBMC from Ugandan children in cohorts spanning high and low transmission (10 children) and longitudinally across a marked decline in transmission (20 children, 3 timepoints), we profiled the epigenome and transcriptome of V{delta}2+ T cells by paired bulk ATAC-seq and RNA-seq and by CITE-seq. Higher malaria exposure was associated with reduced V{delta}2+ T cell TNF and IFN{gamma} production and with thousands of differentially accessible chromatin regions. Immunoregulatory genes including LYN, PLCG2, and HAVCR2 (Tim-3) showed increased chromatin accessibility and/or expression at high exposure, whereas pro-inflammatory gene (IFNG, GZMK, IL7R) and AP-1 (JUN/FOS) motif accessibility were increased at low exposure; linkage of regulatory elements with target genes corroborated these associations. Single-cell transcriptional analysis identified a cytotoxic CD8+CD16+CD57+ V{delta}2+ T cell subset. In our in vitro model, repeated stimulation with malaria-infected red blood cells or the phosphoantigen HMBPP was similarly associated with reduced V{delta}2+ T cell degranulation and cytokine production. Diminished responsiveness was predominantly TCR-dependent, accompanied by heightened p38 signaling, and was partially reversed by rest induced by the tyrosine kinase inhibitor dasatinib. Together these data reveal how repeated malaria may reshape cellular immunity by reprogramming V{delta}2+ T cells toward a reversible, hyporesponsive state and highlight targets for therapeutically restoring their function.

Sepsis causes approximately 11 million deaths globally each year. Whole-genome sequencing (WGS) of founder populations offers a unique opportunity for discovery of genes related to susceptibility of sepsis. We performed GWAS and EXWAS on WGS data for n=210 Arab ICU patients (n=68 sepsis cases, n=142 controls, other ICU-related disorders) and prioritized n=40 associated deleterious founder variants in n=31 genes (REGENIE Firth regression p < 0.05; CADD score > 20; enriched AAF vs AllofUs/gnomAD), including a novel start-loss variant in UBE2L3 (c.2T>G; p.Met1?; CADD = 25.6; SIFT = 0.001) in sepsis cases (3/68 vs 0/142 controls; Fisher's exact P = 0.026). In All of Us (AoU), UBE2L3 missense burden was associated with bacterial infection (n=26,939 cases; SKAT-O P = 2.38x10-3; OR=23.10; 95% CI = [0.63-845.27]). LLM AI models fine-tuned for drug development scored UBE2L3 a 7.8 of 10 as a drug target for sepsis, consistent with mouse UBE2L3 KO showing increased IL-1Beta mediated inflammation in sepsis.