Genes & Immunity

Background and objectivesMyasthenia gravis associated with antibodies against muscle-specific kinase (MuSK-MG) is a well-characterized IgG4-autoimmune disease, however, the mechanisms driving IgG4 predominance remain poorly understood. This study investigated whether promoter DNA methylation of cytokine genes involved in IgG4 class switching is associated with this immune response. MethodsPeripheral blood mononuclear cells were isolated from MuSK-MG patients (n=36), acetylcholine receptor myasthenia gravis (AChR-MG) patients as disease controls (n=7), and sex-matched healthy controls (n=12). Promoter DNA methylation of IL4, IL10, and IL13 was assessed by methylation-sensitive high-resolution melting and relative cytokine mRNA expression by qPCR. Associations with clinical variables, and antibody levels were subsequently evaluated. ResultsMuSK-MG patients showed lower median IL13 promoter methylation compared with healthy controls (p = 0.004). Median IL4 promoter methylation was also reduced in MuSK-MG compared with healthy controls (p < 0.001) and AChR-MG disease controls (p < 0.001), whereas no differences were observed for IL10 promoter methylation. Relative mRNA expression of IL4 (p = 0.0005), IL10 (p = 0.0462), and IL13 (p = 0.0002) was increased in MuSK-MG compared with AChR-MG. Compared with healthy controls, only IL4 expression remained significantly increased (p < 0.0001). Promoter methylation was inversely correlated with relative mRNA expression for IL4 (p < 0.0001), while IL13 showed a similar but non-significant trend (p = 0.054), no association was observed for IL10. Multivariable analysis demonstrated that treatment at sampling was independently associated with lower IL10 and IL13 promoter methylation, whereas no associations were observed with age, sex, disease phase, or disease duration. Promoter methylation did not correlate with total serum IgG4 or anti-MuSK IgG4 levels. DiscussionMuSK-MG is associated with selective hypomethylation of IL4 and IL13 promoters accompanied by increased cytokine gene expression, while IL10 promoter methylation remains unchanged. The association between treatment and IL10 and IL13 promoter methylation suggests that immunosuppressive therapy may influence epigenetic regulation in MuSK-MG. Together, these findings support a role for epigenetic dysregulation of Th2-associated cytokines in the immunological environment associated with IgG4 subclass switch. To our knowledge, this is the first study investigating IL4, IL10, and IL13 promoter DNA methylation in MuSK-MG.

Global incidence and outcomes of glioma have been found to vary significantly by region, however research into the disease continues to lack diversity. Here we investigated epigenetic patterns in glioma subtypes from cohorts collected from China and the USA. We retrospectively analysed the Chinese Glioma Genome Atlas (CGGA) and The Cancer Genome Atlas (TCGA) datasets following reclassification of glioma subtypes based on the WHO 2021 central nervous system (CNS) tumour classification. We used DNA methylation and transcriptomics data to identify methylation-driven cancer genes in the CGGA cohort, assessed their prognostic value and compared against the non-Hispanic White cohort in the TCGA database to consider ethnic influence. Furthermore, we used machine learning classification and clustering techniques to identify methylation patterns in glioma subgroups. Here, we showed that DNA methylation profiles of CGGA glioblastomas have a methylation signature more similar to TCGA high-grade astrocytomas: 58.1% of CGGA glioblastomas were identified as high-grade astrocytomas using classification modelling. Assessment of survival revealed that CGGA glioblastoma patients had a significantly better survival rate than non-Hispanic White glioblastoma patients (p = 0.037). Four key methylation-driven genes were identified in the CGGA glioblastoma samples: GLDN, PRKDC, S100A1 and NCAPH. Hypermethylation of GLDN significantly suppressed gene expression in all glioma subtypes in only the East Asian cohort; a gene that has not been previously described as a driver in gliomas. Together these data suggest alternative epigenetic mechanisms occurring in glioma subtypes of different ethnic populations, which is important for our understanding of glioma and strategies for personalized treatment.

Despite significant advancements in microsurgical techniques in recent years, the treatment and prognosis of craniopharyngiomas remain unsatisfactory. As a central nervous system tumor located adjacent to important brain structures such as the hypothalamus-pituitary axis and accompanied by a highly inflammatory microenvironment, the tumor heterogeneity and tumor microenvironment characteristics of papillary craniopharyngiomas (PCPs) remain unclear. In this study, we integrated multimodal single-cell and spatial profiling from PCP tissue and peripheral blood mononuclear cells (PBMCs) to elucidate the tumor heterogeneity and microenvironment characteristics of PCP. Our single-cell and spatial analyses defined four specific tumor cell states in PCP, representing specific transcriptional regulatory programs and spatial heterogeneity characteristics during tumor progression. By constructing a spatial niche composed of tumor, immune, and stromal cells, we analyzed the cellular and spatial ecosystem of PCP at multiple levels to further assess the communication relationships between different tumor cell states and microenvironment cells. This study established a multidimensional molecular atlas of PCP from the perspectives of cell state, spatial structure, and microenvironment interactions, providing a foundation for understanding its biological behavior and exploring new intervention strategies.

Group 2 innate lymphoid cells (ILC2s) regulate type 2 immune responses partly by recruiting eosinophils, but the mechanisms underlying this process remain incompletely understood. Although both ILC2s and type 2 T helper (Th2) cells are capable of expressing IL-5, a cytokine critical for recruiting eosinophils, ILC2s are more potent than Th2 cells in this process. Here, we show that the transcription factor Bhlhe40 promotes GM-CSF production in ILC2s, and Bhlhe40 expression in ILC2s is required for efficient eosinophil recruitment during both papain- and helminth-induced type 2 immune responses. However, Bhlhe40 deficiency in ILC2s had no effect on the production of classical type 2 cytokines, including IL-4, IL-5 and IL-13, despite Bhlhe40 being required for type 2 cytokine production by Th2 cells. Furthermore, in contrast to ILC2s, Th2 cells produced little GM-CSF and administration of GM-CSF rescued eosinophil recruitment in ILC2-specific Bhlhe40-deficient mice. In addition to promoting GM-CSF expression, Bhlhe40 repressed IL-10 production in ILC2s as it did in Th2 cells, particularly during chronic inflammation. Single-cell transcriptomic analyses further supported this regulatory network, and the ChIP-Seq data revealed direct binding of Bhlhe40 to the enhancer and promoter regions within the Il10 and Csf2 loci. Collectively, our findings show that Bhlhe40 exerts distinct gene regulatory functions in ILC2s and Th2 cells, and Bhlhe40 modulates the inflammatory and anti-inflammatory functions of ILC2s by promoting GM-CSF while suppressing IL-10 production.

The longstanding association between psychological trauma or stress and subsequent chronic inflammatory disorders is well-documented, but the mechanism by which psychopathology causes these immune changes has yet to be elucidated. We have previously reported that sympathetic innervation to lymphoid organs and beta adrenergic receptor signaling are essential for T-lymphocyte interleukin 17A (IL-17A) production and TH17 polarization, though the exact mechanistic contribution of this signaling to the development of TH17 cells remained unclear. Therefore, we hypothesized that norepinephrine (NE) is a novel and direct regulator of T-lymphocyte IL-17A expression. Herein, we indeed observed that NE regulates baseline IL-17A in vivo. We further identified a novel mechanism by which transforming growth factor beta (TGF{beta}) and NE together result in TH17 polarization and IL-17A production in CD4+ T-lymphocytes. Additionally, we found that cAMP, PKA, and CREB are induced by NE signaling, which ultimately increases CBP/p300 activity to initiate ROR{gamma}t transcription. Surprisingly, our data also demonstrate that STAT3, a transcription factor previously described as necessary for canonical TH17 polarization, is not involved in this novel pathway and may even be downregulated. Combined with bulk RNA sequencing data, our data highlight robust differences between the novel and canonical pathways to TH17 polarization. Altogether, our data reveal a novel, noncanonical mechanism that links sympathetic nervous system activity with IL-17A related inflammation, which may have significant relevance to sympathoexcitation-related disorders that stem from psychological trauma or stress.

Human populations have evolved distinct immune responses to local pathogens, and investigating signatures of natural selection across populations can reveal both shared and population-specific immune response mechanisms. We compared genomic signatures of natural selection in Senegalese, Thai, and Peruvian populations using two complementary methods, hypothesising that this tri-continental comparison would reveal population-specific adaptive variants in genes regulating immune pathways. Our findings confirm that genetic diversity among these populations is reflected in their immune responses to regionally endemic pathogens. Furthermore, candidate immune-related genomic regions identified through selection scanning provide insights for ancestry-informed vaccine development by directing antigen design for region-specific pathogens, incorporating population-specific adjuvants, and tailoring administration strategies.

Background Monogenic autoinflammatory disorders arise from genetic defects that pathologically activate innate immunity. IRAK4, a serine/threonine kinase in the Myddosome pathway, mediates IL 1 and Toll like receptor signaling, driving proinflammatory cytokine and type I interferon responses. While biallelic loss of function IRAK4 variants cause an immunodeficiency, recent reports implicate biallelic IRAK4 variants in severe neuro and systemic autoinflammation (NASA). We investigated a child with a similar phenotype and screened unsolved autoinflammatory leukoencephalopathies in the Myelin Disorders Biorepository Project (MDBP). Methods Individuals with unexplained autoinflammatory leukoencephalopathy and no unifying molecular diagnosis were identified in the Myelin Disorders Biorepository Project (MDBP), and genome sequencing was reanalyzed to prioritize rare, protein altering and splice affecting variants. Candidate variants and their splicing consequences were interrogated with short read and targeted long read RNA sequencing, benchmarked against control PBMC and normal tissue transcriptomes. Nonsense mediated decay of transcripts was also assessed. Clinical, genetic, and treatment data were extracted by standardized deep phenotyping, and brain MRI was reviewed in consensus by two pediatric neuroradiologists. Results We identified six patients from five unrelated families with biallelic, rare IRAK4 variants presenting with severe, persistent autoinflammation without immunodeficiency. Variants included two homozygous and three compound heterozygous changes. All patients had a concordant clinical and radiologic syndrome: episodic, waxing and waning encephalopathy with refractory seizures; neuroimaging showed transient white matter edema that evolved to gliosis, superimposed on marked calcifications and ensuing cerebral atrophy. Biomarkers indicated neuroinflammation and anemia in all cases. Median age at neurologic symptom onset was 12.96 years (IQR 9.44). Immune suppressive therapies achieved partial benefit, but most patients had ongoing seizures, persistent neuroinflammation, and progressive disease, and without treatment, loss of life. Conclusion In these six patients, a strongly concordant clinical and radiological phenotype emerges of IRAK4-mediated autoinflammation, expanding the phenotypic and mutational spectrum of IRAK4 related disease. Further studies are needed to define mechanisms and optimal treatments.

NKG2D (encoded by KLRK1 in humans and Klrk1 in mice) is an activating receptor expressed by cytotoxic lymphocytes. In humans, NKG2D signaling is regulated post-transcriptionally: activated T cells retain intron 4 of KLRK1 to generate NKG2D-TR, a truncated dominant-negative isoform that limits receptor signaling. Whether mice, the principal preclinical model for NKG2D-directed therapies, possess an analogous regulatory mechanism remains unknown. Across four murine RNA-seq datasets comprising 50 samples and spanning T-cell differentiation, graft-versus-host disease, and acute and chronic LCMV infection, we examined the retained-intron isoform Klrk1-203. The transcript retains the canonical start codon, while its predicted stop codon lies within the terminal exon downstream of the final exon-exon junction, suggesting that it may escape nonsense-mediated decay. If translated, Klrk1-203 is predicted to encode a truncated product that retains the cytoplasmic and transmembrane domains but lacks most of the ligand-binding ectodomain. This predicted architecture resembles human NKG2D-TR, although the murine product contains a short C-terminal sequence encoded by the retained intron. Klrk1-203 was below the detection limit in unchallenged naive and early-effector T cells but was induced in differentiated effector and memory populations, reaching approximately one-fifth of total Klrk1 transcripts in one effector-memory sample. Read-level analyses independently demonstrated increased intron 4 retention with differentiation; however, short-read sequencing cannot fully distinguish Klrk1-203 from the co-retained Klrk1-204 transcript, making isoform-specific abundance dependent on model-based quantification. An independent coding-potential algorithm classified Klrk1-203 as non-coding, providing an important counterpoint to the structural predictions. Together, these findings identify Klrk1-203 as a candidate NMD-resistant, differentiation-associated regulator of murine NKG2D and a potential counterpart of human NKG2D-TR that warrants experimental validation.

Plasmodium parasites develop in the liver and egress to infect red blood cells, causing malaria. Vaccines that generate hepatic CD8+ T cells eliminate liver-stage parasites and prevent disease, yet how these T cells are induced is incompletely understood. We report that in mice vaccinated with replication-competent genetically attenuated Plasmodium parasites, antagonism of {gamma}{delta} T cell function curtails protection. Vaccination expands hepatic IFN{gamma}+ {gamma}{delta} NKT cells, and depletion of these cells abrogates hepatic CD8+ T cell responses. IFN{gamma}+ {gamma}{delta} NKT cells are nearly undetectable in the blood at steady state but their frequencies in the periphery are significantly increased following vaccination, hinting at their utility as biomarkers of protection. To assess the relevance of these results in humans, we performed secondary analyses of peripheral blood samples from human clinical trial participants immunized with attenuated Plasmodium parasites (Trial registration: ClinicalTrials.gov NCT01994525). Flow cytometric and single cell transcriptomic characterization of {gamma}{delta} T cells in these samples unveil for the first time, increased frequency of activated V{delta}2- {gamma}{delta} T cells and gene expression in cytotoxic, tissue-homing V{delta}1+ {gamma}{delta} T cells as correlates of protection. Together, these data identify hepatic {gamma}{delta} T cells as targets for the improvement of tissue-resident CD8+ T cell responses against hepatotropic pathogens.

Epstein-Barr virus (EBV) reprograms B cells in autoimmune disease. Reprogrammed EBV+ B cells activate nearby B and CD4+ T cells, via upregulated antigen presentation and costimulatory machinery, to drive autoimmune pathology. EBV reactivation is a known correlate of long COVID, which is a heterogeneous condition that can bear similarities to autoimmune disease. However, the mechanisms underpinning this association remain unresolved. We report on EBV metabolically reprogrammed B cells in patients with COVID-19. We find EBV+ B cells provide stimulatory signals to bystander B and CD4+ T cells. SARS-CoV-2 infected participants exhibiting elevated fractions of EBV+ B cells present, at convalescence, with dysregulated lipid profiles, increased autoantibody titers, and post-acute symptomology likely reflective of this metabolic reprogramming and cell-cell interactions. Enrichment of our EBV+ B cell signatures seen in patients with COVID-19 is similar in patients with lupus and multiple sclerosis suggesting a potentially shared pathway of EBV-driven dysfunction across diseases.

The extent to which rare and common genetic variants jointly contribute to the risk of acute myeloid leukemia (AML) still remains relatively unexplored in large-scale biobank whole-genome sequencing cohorts. Here, we leverage the latest sequencing and phenotypic data from the All of Us Research Program to identify variants, genes, and gene-sets associated with AML. We performed set-based association tests for rare protein-coding variants (Ncases=265 and Ncontrols=169,706) and single-variant association tests for common variants (Ncases=265 and Ncontrols=169,705) utilizing the large European-like ancestry sample. For the rare-variant set-based tests conducted using SAIGE-GENE+, four genes were statistically significant: DNMT3A, TET2, SRSF2, and IDH2 (Bonferroni-corrected Cauchy p-value < 0.05). We also constructed multiple rare-variant burden risk scores using different gene-sets to identify those with a substantial rare-variant burden for AML. Gene-sets derived from Genomic Data Commons whole-genome sequencing data, comprising two distinct groups-genes observed to harbor somatic mutations in AML and genes observed to harbor somatic mutations across all cancer types-showed a statistically significant rare-variant burden (Bonferroni-corrected p-value < 0.05). Ultimately, these findings demonstrate that leveraging whole-genome sequencing in large-scale biobanks enables the identification of rare protein-coding variants, genes, and gene sets associated with AML.

Down syndrome, caused by trisomy 21, is characterized by chronic interferon-associated inflammation and immune dysregulation, yet the contribution of human secondary lymphoid organs to shaping this immune landscape remains unclear. Using multimodal single-cell and spatial profiling of human tonsils, we identify extensive remodeling of immune organization in trisomy 21. CD4 T cells are skewed away from canonical follicular helper (TFH) programs toward inflammatory TFH1-like and cytotoxic helper states enriched for interferon-responsive transcriptional programs. Tonsillar TFH cells exhibit increased interferon-{gamma} and interleukin-21 production, indicating inflammatory skewing toward type 1 helper immunity. These alterations are accompanied by changes in dendritic cell and CD8 T-cell compartments, reduced follicular size, increased extrafollicular TFH1-B-cell proximity and altered B-cell differentiation trajectories. Together, our findings identify trisomy 21 as a unique human context to investigate how chronic interferon-associated inflammation reshapes lymphoid tissue organization and adaptive immune cell fate decisions.

In TLR7-driven macrophage activation syndrome (MAS), inflammatory hemophagocytes (iHPCs) differentiate from Ly6CHI monocytes, phagocytose red blood cells and promote disease, including anemia and thrombocytopenia. We demonstrate here that IRF5 is required for iHPC differentiation and MAS in TLR7-overexpressing (TLR7.1) mice. Both constitutive and myeloid-specific Irf5 deletion reduced iHPCs and improved anemia, thrombocytopenia and survival. Furthermore, therapeutic inhibition of IRF5 ameliorated MAS features and reduced splenic and circulating iHPCs. While cell-intrinsic IRF5 expression was required for iHPC differentiation, it was not required for TLR7.1 Ly6CHI monocyte differentiation and monocyte transcriptional programs. We further show that the transcriptome and chromatin landscape changed dramatically as iHPCs differentiated from TLR7.1 Ly6CHI monocytes. Many transcriptional programs gained in iHPCs were enriched in genes associated with IRF5-binding accessible chromatin regions, including those associated with NF-kB signaling, cytokine and chemokine production, and complement activation. Our data suggest that IRF5 collaborates with other transcription factor families, including NF-kB, ETS and AP1 members, to regulate iHPC gene programs. Together, our findings demonstrate that expression of IRF5 in myeloid cells is critical for MAS, for iHPC differentiation, and acts broadly across iHPC-specific gene programs in TLR7-driven inflammation.

Background/Objectives: MS4A4A is associated with M2-like macrophage states, while the MS4A gene cluster modifies soluble TREM2 levels and Alzheimer's disease risk. We asked whether MS4A4A consistently marks the M2 side of human myeloid activation and whether AlphaFold supports a proposed MS4A4A-MS4A6A interaction. Methods: We reanalysed four public human datasets: bulk RNA-seq and ATAC-seq of primary monocyte-derived macrophages from independent three-donor cohorts, and single-cell RNA-seq atlases of healthy liver and severe COVID-19 blood. MS4A4A and an MS4A4A-MS4A6A complex were modelled with AlphaFold 3 and evaluated using pLDDT, predicted aligned error, and ipTM. Results: MS4A4A was higher in M2 (IL-4) than in M1 (IFN-gamma; + LPS) macrophages in all three donors (log2 fold change +2.68, adjusted P = 0.0013). Its promoter showed the highest mean accessibility in M2. MS4A4A was macrophage-enriched in liver and monocyte-enriched in blood, and was detected in 76.7% of M2-like versus 39.3% of M1-like liver macrophages, with the difference driven mainly by the proportion of positive cells. AlphaFold confidently modelled the four transmembrane helices (mean pLDDT 83.1), but the predicted MS4A4A-MS4A6A interface was not supported (ipTM 0.59). Conclusions: MS4A4A is consistently associated with the M2 side of human myeloid activation across independent transcriptomic, chromatin, and single-cell datasets. The findings are associative, and the proposed MS4A4A-MS4A6A interface remains an untested structural hypothesis.

Background: The gradual decline in the functionality of the immune system during aging is commonly referred to as immunosenescence. This study aims to investigate changes in the B-cell receptor immunoglobulin heavy chain (BCR IGH) gene repertoire during natural aging and evaluate the dynamics of emergent low-level BCR IGH clonality in the elderly. We conduct a longitudinal study nested within the Doetinchem Cohort study, comprising 98 participants aged between 31 and 59 years old at study entry who had repeated blood samples drawn at 5 year intervals over a 30 year period (n=548 samples). We sequenced the IGH gene repertoire and evaluated the impact of aging on IGH gene repertoire clonality and diversity using linear mixed effects modeling. Results: Participants older than 60 years exhibited increased BCR IGH clonality and reduced IGH gene repertoire diversity. In a multivariable model, IGH gene repertoire diversity was significantly decreased for individuals with a dominant clonotype ratio greater than 10 (Beta=-0.57, p < 0.001). Additionally, a trend toward reduced IGH gene repertoire diversity was observed in participants aged 60-70 years (Beta =-0.19, p = 0.1) and those aged 70 years or older (Beta =-0.20, p = 0.13). IGH gene repertoire diversity was determined primarily by the naive and transitional B-cell pool, while BCR IGH clonality was influenced by switched memory and age-associated B-cell counts. Conclusions: In summary, our study indicates that IGH gene repertoire diversity decreases significantly after age 60, which coincides with an increased incidence of low-level BCR IGH clonality. This clonality may be driven largely by switched memory and age-associated B-cells. By providing deep insights into age-related dynamic changes in the IGH gene repertoire, these findings lay the groundwork for the molecular assessment and monitoring of incident clonality by clinicians and researchers alike.

BackgroundPrenatal growth restriction has been associated with adverse neonatal and long- term health outcomes, yet the epigenetic mechanisms by which an adverse intrauterine environment shapes fetal immune development remain incompletely understood. Monozygotic dichorionic-diamniotic twins with selective fetal growth restriction (sFGR) provide a unique human model for investigating environmentally driven developmental programming independent of genetic variation and inter-twin placental vascular anastomoses. MethodsUmbilical cord blood buffy coat samples were collected from three sFGR and two gestational age-matched concordant control twin pairs. Bulk RNA sequencing and genome-wide DNA methylation analysis were performed, followed by differential expression, pathway enrichment, hematopoietic and immune module analyses, differential methylation, and integrative transcriptomic-epigenomic analyses. ResultsCompared with concordant control twin pairs, discordant twins exhibited broad attenuation of immune and inflammatory transcriptional programs alongside enrichment of erythroid- and hypoxia-related pathways, consistent with adaptive hematopoietic responses to intrauterine stress. Within discordant twin pairs, the growth-restricted co-twins displayed marked transcriptional asymmetry characterized by selective enrichment of cytotoxic lymphoid signatures despite global suppression of myeloid and antigen-presenting cell-associated programs. Integrated transcriptomic and epigenomic analyses further revealed coordinated epigenetic remodeling, with hypomethylated regions in growth-restricted twins enriched for immune regulatory pathways, including T cell differentiation and leukocyte activation. At selected loci, concordant hypomethylation and increased gene expression suggested a potential epigenetic basis for the observed immune remodeling. ConclusionsThese findings suggest that intrauterine growth restriction is associated with coordinated hematopoietic and immune reprogramming at birth, consistent with both compositional and cell-intrinsic alterations. In genetically identical twins, relative growth divergence was associated with polarized transcriptional states, highlighting how intrauterine environmental differences may shape early immune development independent of genetic background.

Maintaining brain homeostasis is crucial for proper function of the central nervous system and has traditionally been attributed to neuronal and glial interactions. However, recent research highlights the essential role of brain-resident immune cells in this process. Our study characterizes brain-specific CD8+ T cells and elucidates their significant contribution to brain homeostasis and behavior. We identified a distinct population of CD8+ T cells that infiltrates the brain during early development, undergoes clonal expansion, and acquires effector memory-like characteristics through interactions with microglia. Notably, the absence of these cells results in hyperactivation of neuronal activity and abnormal behaviors, due to loss of regulation of interferon-gamma (IFN-{gamma}) secreted by CD8+ T cells. Our findings demonstrate that IFN-{gamma} secreting brain-specific CD8+ T cells are crucial for maintaining the physiological level of neuronal excitability and normal behavioral patterns. This study provides novel insights into neuroimmune interactions, emphasizing the critical role of CD8+ T cells in sustaining brain function and behavior.

Human leukocyte antigen (HLA) class II variation is implicated in Alzheimer's disease (AD) and longevity, but its mechanisms within the major histocompatibility complex remain unclear. We fine-mapped seven independent HLA-II haplotypes in 6,053 individuals (443 cognitively healthy centenarians [CHCs], 3,219 population controls, 2,391 AD patients). Three haplotypes overlapped previous AD and lifespan signals. Hap-B (DRB1*04subtypes) was protective, enriched in CHCs and controls versus AD, with its neuroprotective association with tau pathology replicated in an independent Netherlands Brain Bank cohort. Hap-R (DRB1*01:01) increased AD risk and reduced healthy longevity, with reduced microglial HLA-II activation. Hap-Y (DRB1*15:01) showed increased microglial HLA-II activation in post-mortem brain tissue, independent of quantitative AD neuropathology. These findings indicate distinct HLA-II haplotypes shape AD susceptibility and healthy longevity through separate mechanisms, linking HLA architecture to brain immune states beyond classical neuropathology.

Vascular cognitive impairment and dementia (VCID) is increasingly recognized as a major contributor to cognitive decline; however, the mechanisms through which vascular dysfunction drives innate immune dysregulation remain poorly understood. In this study, we explore the impact of VCID on the cerebral innate immune landscape, focusing on innate lymphoid cells (ILCs) and neutrophils, two key players in neuroinflammation and brain immune homeostasis. Using a murine model of VCID induced by bilateral common carotid artery stenosis (BCAS) with modifications in C57BL/6 mice, we investigated innate immune cell distribution, polarization, and functional profiles using flow cytometry and immunofluorescence staining. Our findings reveal a compartment-specific shift in ILC populations, with a reduction of ILC2s in the meninges and concurrent expansion in the choroid plexus, accompanied by altered cytokine production. Furthermore, VCID drove a marked shift in neutrophil polarization toward a pro-inflammatory N1-like phenotype in both the meninges and choroid plexus. Critically, immunofluorescence staining of hippocampal brain sections confirmed that activated N1-like neutrophils, characterized by elevated IL-1{beta} and MPO and reduced IL-10, infiltrate the hippocampal parenchyma in VCID, suggesting a spatially progressive innate immune response spanning from CNS border compartments to brain tissue. These results identify a novel innate immune signature in VCID, compartment-specific ILC redistribution, pro-inflammatory neutrophil polarization at CNS borders, and parenchymal neutrophil infiltration in the hippocampus, which may collectively amplify neuroinflammation and accelerate cognitive decline, identifying potential therapeutic targets for vascular-related dementia.

Introduction: How much of the variable (V) and joining (J) gene identity of a T-cell receptor is recoverable from its third complementarity-determining region (CDR3) amino-acid sequence alone? Immune repertoire studies often report the CDR3 with V and J annotation that is missing, low-confidence, or inconsistent, so what the CDR3 alone can and cannot fix is both a basic question about the receptor and a practical one for reading those repertoires. Methods: For each of 118,096 pooled human rearrangements (37,687 and 80,409 {beta}) we computed the posterior distribution over candidate genes under a generative model of V(D)J recombination and under its post-selection counterpart, and measured recoverability by conditional entropy, the candidate-list size needed to contain the annotated gene, the fraction of sequences admitting a high-confidence single-gene call, and the structure of gene-by-gene confusion. Results: The J gene was nearly determined by the CDR3 in both chains. The V gene was only partially recoverable, and behaved as a group rather than a gene: junctional trimming and non-templated insertion, together with the loss of synonymous codon information in translation, leave sets of mutually confusable V genes whose grouping departs sharply from germline family nomenclature (adjusted Rand index 0.05 for and 0.21 for {beta}). Selection sharpened the V posterior modestly (usage-controlled entropy shift -0.06 nats for and -0.28 for {beta}) and redistributed which V gene was most probable, a locus-scale rewrite in {beta} against a mild reweight in . Both the recoverability measurements and the confusion grouping reproduced in two held-out tumor cohorts. Discussion: V identity is an emergent, system-level property of the repertoire, set jointly by recombination and selection and invisible in any single rearrangement, so it should be reported as a calibrated group rather than a single gene. We also release the pipeline with a computational tool which can output a set of candidate genes with confidence values given a CDR3 sequence.