SEARCH · bioRxiv Science

Results for “immunology”

Search indexed bioRxiv preprints in genomics, neuroscience, cell biology and bioinformatics. Read source abstracts and check manuscript versions; preprints are not peer reviewed.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 469 records · Page 26Linked to original sources

bioRxiv2019

Expression profiling of single cells and patient cohorts identifies multiple immunosuppressive pathways and an altered natural killer cell phenotype in glioblastoma

Glioblastoma (GBM) is an aggressive cancer with a very poor prognosis. Generally viewed as weakly immunogenic, GBM responds poorly to current immunotherapies. To better understand this problem we used a combination of NK cell functional assays together with gene and protein expression profiling to define the NK cell response to GBM and explore immunosuppression in the GBM microenvironment. In addition, we used transcriptome data from patient cohorts to classify GBM according to immunological profiles. We show that glioma stem-like cells, a source of post-treatment tumour recurrence, express multiple immunomodulatory cell surface molecules and are targeted in preference to normal neural progenitor cells by natural killer (NK) cells ex vivo. In contrast, GBM-infiltrating NK cells express reduced levels of activation receptors within the tumour microenvironment, with hallmarks of TGF-{beta} mediated inhibition. This NK cell inhibition is accompanied by expression of mutiple immune checkpoint molecules on T cells. Single cell transcriptomics demonstrated that both tumour and haematopoietic-derived cells in GBM express multiple, diverse mediators of immune evasion. Despite this, immunome analysis across a patient cohort identifies a spectrum of immunological activity in GBM, with active immunity marked by co-expression of immune effector molecules and feedback inhibitory mechanisms. Our data show that GBM is recognised by the immune system but that anti-tumour immunity is restrained by multiple immunosuppressive pathways, some of which operate in the healthy brain. The presence of immune activity in a subset of patients suggests that these patients will more likely benefit from combination immunotherapies directed against multiple immunosuppressive pathways.

immunology↗

bioRxiv2019

Leukocyte-derived High-mobility group box 1 controls innate immune responses against Listeria monocytogenes.

High-mobility group box 1 (HMGB1) is a damage-associated molecular pattern with key proinflammatory functions following tissue injury. Moreover, HMGB1 neutralization was shown to alleviate LPS-induced shock, suggesting a role for the protein as a master therapeutic target for inflammatory and infectious diseases. Here, we report that HMGB1 neutralization impedes immune responses to Listeria monocytogenes, a wide-spread bacterium with pathogenic relevance for humans and rodents. Using genetic deletion strategies and neutralizing antibodies, we demonstrate that hepatocyte HMGB1, a major driver of post-necrotic inflammation in the liver, is dispensable for pathogen defense during moderately severe infection with listeria. In contrast, antibody-mediated HMGB1 neutralization and HMGB1 deficiency in myeloid cells effectuate rapid and uncontrolled bacterial dissemination in mice despite preserved basic leukocyte functionality and autophagy induction. During overwhelming infection, hepatocyte injury may contribute to increased HMGB1 serum levels and excessive inflammation in the liver, supporting context-dependent roles for HMGB1 from different cellular compartments during infection. We provide mechanistic evidence that HMGB1 from circulating immune cells contributes to the timely induction of hepatic immune regulatory gene networks, early inflammatory monocyte recruitment to the liver and promotion of neutrophil survival, which are mandatory for pathogen control. In summary, our data establish HMGB1 as a critical co-factor in the immunological clearance of listeria, and argue against HMGB1 neutralization as a universal therapeutic strategy for sepsis.\n\nAuthor summaryHigh-mobility group box 1 (HMGB1) is an abundantly expressed nucleoprotein with signaling properties following secretion or release into the extracellular space. Given its central immune-regulatory roles during tissue injury and LPS-induced septic shock, interventions aimed at HMGB1 signaling have been advocated as therapeutic options for various disease conditions. Here, we show that antibody-mediated HMGB1 neutralization interferes with immunological defense against Listeria monocytogenes, a gram-positive bacterium with high pathogenic relevance for rodents and humans, effectuating uncontrolled bacterial growth and inflammation. Using conditional knockout animals, we demonstrate that while leukocyte functionality is preserved in HMGB1-deficient myeloid cells, HMGB1 released in response to Listeria triggers hepatic inflammatory monocyte recruitment and activation of transcriptional immune networks required for the early control of bacterial dissemination. Hepatocyte HMGB1, a key driver of post-necrotic inflammation in the liver, is dispensable for the immune response during moderately severe infection, but likely contributes to excessive hepatitis when infection is uncontrolled and cellular injury is high. We demonstrate a critical and non-redundant role for HMGB1 in the immune-mediated clearance of listeriosis and argue against HMGB1 neutralization as a universal therapeutic option in the context of infection.

immunology↗

bioRxiv2019

Anatomically remote education of B cells is required for colonic health

Mucosa-associated lymphoid tissues contain roughly 80% of all immune cells and produce virtually all of the bodys IgA1-3. Although the majority of IgA-secreting cells educated within a mucosal site home back to the same anatomic region, some cells are also found in distant mucosal tissues2-6. These observations underlie the notion of a common mucosal immune system, which holds that anatomically unrelated mucosal sites are functionally connected by a shared immune system2,3. However, the ontological basis of this separation between site of immune education and functionality has remained elusive. Here we show that mice lacking Peyers patches (PPs)--small-intestinal lymphoid tissue covered by antigen-sampling M cells--have no immunologic defect in the small-intestinal lamina propria. Surprisingly, the primary immunological abnormality in PP-deficient mice was a reduction in colonic B cells, including plasmablasts but not plasma cells. Adoptive transfer experiments conclusively demonstrated that PP-derived cells preferentially give rise to colonic--but not small-intestinal--B cells and plasmablasts. Finally, these PP-derived colonic B cells were critical for restraining colonic inflammation. Thus, PPs bridge the small-intestinal and colonic immune systems and provide a clear example of immune education being required in an anatomic compartment distinct from the effector site. Our findings, which highlight that the majority of fecal IgA is produced by colonic plasmablasts that originate from PPs, will help inform design of mucosal vaccines.

immunology↗

bioRxiv2019

An activity-guided map of electrophile-cysteine interactions in primary human immune cells

Electrophilic compounds originating from nature or chemical synthesis have profound effects on immune cells. These compounds are thought to act by cysteine modification to alter the functions of immune-relevant proteins; however, our understanding of electrophile-sensitive cysteines in the human immune proteome remains limited. Here, we present a global map of cysteines in primary human T cells that are susceptible to covalent modification by electrophilic small molecules. More than 3000 covalently liganded cysteines were found on functionally and structurally diverse proteins, including many that play fundamental roles in immunology. We further show that electrophilic compounds can impair T cell activation by distinct mechanisms involving direct functional perturbation and/or ligand-induced degradation of proteins. Our findings reveal a rich content of ligandable cysteines in human T cells, underscoring the potential of electrophilic small molecules as a fertile source for chemical probes and ultimately therapeutics that modulate immunological processes and their associated disorders.

immunology↗

bioRxiv2019

Serum proteomics expands on identifying more high-affinity antibodies in immunized rabbits than deep B-cell repertoire sequencing alone

AO_SCPLOWBSTRACTC_SCPLOWRabbits are a model for immunology studies, and monoclonal antibodies developed from rabbits have been sought after to empower immunoassays in a variety of applications. High-throughput characterization of circulating serum antibodies in response to specific antigens is highly impactful for both humoral immunology studies and antibody development. A combination of high throughput sequencing of antibody transcripts from B cells and proteomic analysis of serum antibodies, an approach referred to as immunoproteogenomics, is applied to profile the immune response of rabbits to {beta}-galactosidase (Beta-gal) in both recombinant antigen and peptide antigen immunization formats. The use of intact protein antigen resulted in observing 56.3% more heavy chains CDR3s in serum than immunization with peptide antigens. Additionally, sampling peripheral blood mononuclear cells (PBMCs) for B-cell repertoire sequencing at different time points throughout the immunization was found to capture 47.8%-72.8% of total proteomically observed heavy chain CDR3s, and would serve well in replacing sequencing the B cell rich, but more difficult to access spleen or bone marrow compartments. Despite B-cell repertoire sequencing to depths of 2M to 10M reads, we found proteomic evidence supporting at least 10% of serum antibodies are still missed. Further improvements to proteomic analysis techniques would enable more precise characterization of antibodies circulating in serum and determine antibody protein sequences missed by repertoire sequencing.

immunology↗

bioRxiv2025

Tissue-specific tolerance mechanisms and lymph node co-drainage converge to shape T cell immunity in the upper digestive system and regulate pancreatic cancer progression

The liver, pancreas, and duodenum share lymph nodes (LNs), providing a unique system to examine how tissue origin of self-antigens shapes T cell fate. Comparing mice expressing ovalbumin (OVA) from distinct subcellular compartments, we found that cytosolic OVA from liver or pancreas, but not gut, was immunologically ignored. High-dose hepatic secreted OVA triggered antigen-specific T cell deletion, whereas secreted pancreatic and intestinal OVA induced regulatory T (Treg) cells, revealing immunological ignorance, clonal deletion and Treg cell generation as tissue-specific tolerance mechanisms. Of these, LN co-drainage only influenced Treg cell induction, establishing gut-pancreas-liver axes: Intestinal viral infection rendered hepatocyte- and exocrine pancreas-specific T cells inflammatory; liver injury promoted pancreas- and gut-directed responses. These self-reactive T cells caused tissue destruction but enhanced pancreatic tumor control when neoantigen OVA was secreted but not cytosolic. Thus, LN co-drainage and tissue-specific tolerance mechanisms jointly shape immune homeostasis and disease susceptibility in the upper digestive system.

immunology↗

bioRxiv2025

Innate antiviral readiness drives the expansion of protective T stem cell memory against influenza

The development of T-cell-based influenza vaccines relies on eliciting broad CD8+ T-cell immunity, wherein T stem cell-like memory (TSCM) cells serve as the ultimate long-lived reservoir for immune memory, thereby unlocking the potential for durable protection against viral drift and shift. However, the specific immunological cues that drive the robust expansion and functional preservation of this self-renewing, multipotent subset remain unknown. Here, utilizing multi-omic systems immunology in a pediatric cohort immunized with live attenuated influenza vaccine, we identified the determinants governing the expansion of influenza virus-reactive TSCM cells. We show that a pre-existing state of innate antiviral readiness, defined by a plasmacytoid dendritic cell-associated type I interferon signature, is the requisite condition for a robust TSCM expansion. Mechanistically, this baseline innate state enhances antigen priming and enforces a qualitative divergence in T-cell fate, driving responders toward a functionally poised, Th1-dominant phenotype while non-responders default to a dysfunctional, hyper-proliferative state. To determine the clinical relevance of this cellular subset, we analyzed an independent controlled human influenza challenge study. This validation revealed a critical functional division of labor in host defense: whereas pre-existing antibodies primarily mitigated symptom severity, the baseline frequency of influenza virus-reactive TSCM cells was the strongest predictor of rapid viral load clearance. These findings establish that the expansion of durable cellular memory is not stochastic but is predetermined by the innate cytokine environment, providing a predictive biomarker for patient stratification and a validated target for adjuvants designed to expand the TSCM reservoir deliberately.

immunology↗

bioRxiv2025

Inhibitory potential of autologous neutralizing antibodies sets quantitative limits on the rebound-competent HIV-1 reservoir

HIV-1 cure requires preventing viral rebound after treatment interruption, but quantitative criteria defining the rebound-competent reservoir are lacking. We studied individuals undergoing observational treatment interruption without confounding interventions to identify virologic and immunologic determinants of rebound. In 9 of 13 participants, rebound viruses were genetically identical or similar to proviruses in circulating resting CD4+ T-cells. We found no evidence of recombination among rebound sequences. Instead, resistance to autologous neutralizing antibodies (aNAbs) was a critical determinant of viral rebound. Increased suppression of viral outgrowth by contemporaneous IgG isolated from plasma was correlated with longer time to rebound. Using inhibitory potential (IP), the log reduction in single-round infection at physiologic IgG concentrations, we defined quantitative limits governing rebound-competency with respect to contemporaneous aNAbs. Contemporaneous IgG antibodies inhibited different reservoir variants with a wide range of IP values (0.4-8.2 logs), whereas rebound viruses were minimally inhibited (0.5-2.8 logs), indicating that inhibition by even up to 2.8 logs (631-fold) cannot prevent rebound. Longitudinal analyses revealed that waning aNAb potency over time on ART allows previously neutralized variants to gain rebound potential, consistent with the finding that rebound can come from variants deposited in the reservoir at different pre-ART time points. Thus, rebound competency is a dynamic, immune-governed property defined by quantitative immunologic constraints, including those exerted by aNAbs. SIGNIFICANCE STATEMENTPreventing viral rebound after treatment interruption is the goal of HIV-1 cure research, but the latent proviruses responsible remain undefined. Although rebound is initiated in lymphoid tissues, we found rebound viruses are genetically similar to proviruses in circulating resting CD4+ T-cells. Rebound is not explained by recombination and is not solely from proviruses seeded at treatment initiation. Instead, rebound potential is governed by autologous neutralizing antibodies (aNAbs). We define a quantitative threshold of aNAb-mediated inhibition identifying reservoir variants with rebound potential. During treatment, waning aNAb levels allow previously neutralized variants to become rebound-competent. Thus rebound-competency is not a static property, but a dynamic immune-governed feature. Durable aNAb responses against all rebound-competent reservoir variants may be required for functional HIV-1 cure.

immunology↗

bioRxiv2026

Beyond the skin barrier: commensal S. epidermidis imprint systemic immunity to invasive biofilm infection

Staphylococcus epidermidis, a dominant human skin commensal from early life, can transition to an opportunistic pathogen, including invasive, biofilm-associated infections linked to medical devices. Neonatal exposure to skin commensals induces a lifelong immunological imprint in the skin, characterized by immunoregulatory responses. We therefore hypothesized that early life exposure to S. epidermidis influences immune responses to invasive biofilm-associated infections later in life. Using a mouse model of biofilm-related S. epidermidis bone infection, we show that neonatal and adult skin colonization altered the immune response to the subsequent infection in adulthood. Neonatal colonization led to increased NK cells and neutrophils compared to no colonization, along with reduced Tregs and Th1 cells, and consistent increase in immune checkpoint receptor PD-1+ Tregs, T effector, Th1 and Th2 cells across infected bone marrow, blood and spleen. These PD-1-related immune modulations were absent in the adult-colonized group, which had the highest numbers of Tregs, Th1 and Th2 cells of all groups. These findings reveal that early exposure to commensal bacteria strongly impacts the response to invasive infection later in life. Notably, the response depends on the timing of previous exposure. Neonatal colonization drives T cell modulation, resembling neonatal immunity, while adult-colonization increases specific T cell abundance. These differences highlight the essential role of skin colonization in shaping the quality of pathogen immunity to protect against invasive, biofilm-associated infection later in life, emphasizing that immunological studies using uncolonized animal models may not fully capture human immune dynamics.

immunology↗

bioRxiv2026

Myeloid CD209 impairs T-cell activation by inducing ICAM-2-ERM-dependent cortical stiffening

Resistance to PD-1-based immunotherapy remains a major challenge in cancer treatment, especially in immunologically "cold" tumors characterized by T-cell exclusion and impaired effector function. Tumor-associated myeloid cells are important mediators of this resistance, but whether they directly suppress T-cell immunity through mechanical regulation remains unclear. Here, we identify DC-SIGN (CD209), a myeloid-expressed C-type lectin receptor, as a mechanosuppressive regulator of antitumor T-cell immunity. DC-SIGN is selectively enriched in tumor-infiltrating M2-like macrophages and monocytes, and its expression is associated with poor clinical response to PD-1 blockade and elevated TIDE scores across multiple cancer types. Mechanistically, DC-SIGN directly engages ICAM-2 on T cells and activates ROCK1-ERM signaling. This interaction increases T-cell cortical stiffness, destabilizes T cell-antigen-presenting cell interactions, and attenuates T-cell receptor signaling. Blocking the DC-SIGN-ICAM-2-ERM pathway restores T-cell activation and promotes CD8+ T-cell infiltration and effector function in mouse, humanized, and ex vivo human tumor systems. Importantly, DC-SIGN blockade overcomes resistance to PD-1-based immunotherapy in refractory and immunologically "cold" tumor models, and further enhances the response to PD-1 inhibition. Together, our findings define a myeloid-derived mechanical immune checkpoint and reveal T-cell mechanosuppression as a targetable mechanism of tumor immune evasion and immunotherapy resistance.

immunology↗

bioRxiv2026

Single-Cell RNA Sequencing Reveals Commensal Microbes Amplify Sex-Specific Immune Programming in the Murine Lung

Sex-based differences in respiratory disease outcomes are well recognized. However, the underlying immunological mechanisms driving this dimorphism remain incompletely understood. While sex hormones influence immune cell development and function, the role of commensal microbes in shaping sex-specific lung immunity has not been explored. Here, we used single-cell RNA sequencing (scRNAseq) and flow cytometry to profile lung immune cells in male and female mice housed under specific pathogen-free (SPF) or germ-free (GF) conditions. Under SPF conditions, males exhibited a striking myeloid bias, with increased monocytes and macrophages, along with broad upregulation of inflammatory mediators, including S100a8, S100a9, and Il1b, across multiple cell types, and enrichment of TNF and interferon (IFN) signaling pathways. In contrast, females displayed lymphocyte-skewed profiles, with higher frequencies of T cells and natural killer (NK) cells. Interestingly, these sex-based differences in immune composition and inflammatory programs were largely absent in GF mice, indicating that microbial exposure amplifies baseline immunological dimorphism between males and females. Notably, select sex-associated features, including female-biased NK cell enrichment, persisted irrespective of microbial status, suggesting intrinsic, microbiota-independent programming. Together, these findings indicate that commensal microbes modulate sex-specific lung immunity by amplifying pre-existing intrinsic differences, highlighting the intersection of extrinsic (microbial) and intrinsic (sex-linked) factors in shaping baseline mucosal immunity.

immunology↗

bioRxiv2026

immgenT: A Comprehensive Reference of Convergent T-cell States in the Mouse

The immgenT collaborative project generated a comprehensive molecular atlas of T cells spanning virtually all mouse organs and disease states, profiling ~800,000 cells from 750 samples with RNA, 128-plex surface protein, and {beta}TCR sequence. Applying a deep generative model to joint RNA and protein data defined the landscape of T-cell states organized into eight lineages and 107 robust clusters, integrating similar cells from different contexts, and resolving prior nomenclatures. Analysis of effector molecules, transcription factors and modules showed that both immunological functions and regulatory programs are shared across cell states. This framework provides a stable, reusable reference, demonstrated by computationally integrating 16 external datasets from diverse biological contexts. A set of public web tools supports browsing of these data and mapping of any dataset onto the immgenT framework. These results propose a molecular classification of T cells organized around a set of shared states reused across immunological contexts.

immunology↗

bioRxiv2026

A comparative analysis of the immunotranscriptomic features of DENV-1, -3, and -4 human challenge models

BackgroundDengue virus (DENV) infections cause a range of clinical symptoms, from a mild febrile illness to severe disease. Higher levels of DENV RNAemia are associated with severe dengue, although this relationship is incompletely understood. Dengue Human Infection Models (DHIMs), in which volunteers are experimentally infected with underattenuated DENV strains, provide an invaluable tool for studying early virologic, transcriptional, and immunologic features of infection. DHIM studies using DENV-1, DENV-3, and DENV-4 have demonstrated qualitatively distinct clinical features, however, the contribution of RNAemia and serotype to divergent transcriptional and clinical profiles in these challenge models remains unclear. MethodsWe performed a comparative analysis of DHIM-1, DHIM-3, and DHIM-4 studies to determine shared and unique features of the transcriptional response to infection and their associations with RNAemia and clinical symptoms. We then exposed primary human PBMC in vitro to DENV-1 or DENV-3 at varying titers and performed bulk RNA sequencing. FindingsAcross DHIMs, we identified a set of conserved, upregulated genes at day of peak RNAemia, representing a core antiviral response independent of serotype. Further, a unique gene signature indicating downregulated cytoplasmic translation emerged in a subset of DHIM-3 participants with elevated RNAemia and symptomatology. In vitro PBMC exposure to DENV demonstrated that conserved and unique gene expression signatures varied as a function of viral dose rather than serotype. InterpretationThese data show that viral burden correlates with transcriptional responses and clinical symptomatology following experimental DENV infection, contributing to our understanding of dengue pathogenesis and immunity. Research in ContextO_ST_ABSEvidence for this studyC_ST_ABSDengue virus (DENV) infections are known to elicit a range of clinical symptoms. Previous studies have demonstrated the association of higher DENV RNAemia with more pronounced symptoms and elevated risk for severe disease. Understanding the molecular features associated with RNAemia kinetics may provide insight into disease immunologic and clinical pathogenesis. Three live virus human challenge model studies employing underattenuated DENV-1, DENV-3, and DENV-4 have been conducted which demonstrate variance in clinical and virologic features. These experimental DENV infections serve as a valuable model to study early kinetics of infection and immunotranscriptomic features associated with RNAemia irrespective of serotype. Added value of this studyThis study is the first to conduct a head-to-head comparison of the transcriptional features of DHIM-1, -3 and -4 models, and to provide an in-depth analysis of these signatures with respect to RNAemia kinetics. These unique datasets provide a rare opportunity to investigate the longitudinal transcriptional signatures associated with peak symptomatology, serotype and RNAemia kinetics. Implications of all the available evidenceThese data support the existence of conserved gene expression features of DENV infection, irrespective of serotype and dependent on RNAemia levels. These transcriptional signatures are relevant for our understanding of early events after DENV infection and their relationship to RNAemia as a correlate of disease severity.

immunology↗

bioRxiv2026

Integrated Modeling of BCR/TCR Repertoire Diversity Reveals the Mechanistic Basis of Immune Imprinting and Chronic Infection Control

The adaptive immune system orchestrates a complex interplay between humoral and cellular responses to resolve pathogen invasion and suppress tumorigenesis [1,91]. However, a unified quantitative framework integrating lymphocyte repertoire diversity with system-level kinetics remains elusive. Here, we present a multi-scale mathematical model that explicitly incorporates B-cell receptor (BCR) and T-cell receptor (TCR) clonotypic diversity into a discrete agent-based simulation. This framework mechanistically elucidates pivotal immunological phenomena, including the affinity-dependent selection in germinal centers [25], the kinetic constraints of immune imprinting ("original antigenic sin") [54], and the bifurcation between acute and chronic infection trajectories [15,59]. We identify that chronic infections are sustained by specific kinetic thresholds of viral replication relative to antibody affinity maturation. Furthermore, our simulations of cancer-immune interactions demonstrate that therapeutic efficacy is non-linearly dependent on neoantigen presentation [78] and T-cell exhaustion thresholds [79]. This work bridges the gap between reductionist data and systems biology, providing a "quantitative immunology" platform to optimize vaccine dosing schedules and design precision immunotherapies.

immunology↗

bioRxiv2026

Longitudinal and stability-aware analysis reveals treatment-specific microRNA response signatures following immune-reconstitution and B-cell-targeted therapies in multiple sclerosis

Disease-modifying therapies (DMT)s) for relapsing-remitting multiple sclerosis (RRMS) act through distinct immunological mechanisms, yet the within-patient molecular response programs associated with these therapies remain incompletely defined. Here, we reanalysed publicly available PBMC miRNA microarray data (GSE230064) using a longitudinal, robustness-focused framework to compare therapy-associated miRNA response patterns following cladribine versus ocrelizumab treatment. Baseline (t0) and 6-month post-treatment (t1) samples were paired within individuals and technical replicates consolidated prior to analysis, yielding a final paired cohort of 4 cladribine-treated and 6 ocrelizumab-treated patients. Within each treatment arm, we quantified per-patient {Delta}-miRNA (t1-t0) values and prioritized therapy-associated response features using a multi-evidence framework integrating effect direction, magnitude, directional consistency across individuals, and leave-one-out sensitivity. Cladribine treatment was associated with a highly coordinated, directionally concordant upregulation of five miRNAs including hsa-miR-27a-3p, hsa-miR-27b-3p, hsa-miR-503-5p, hsa-miR-148a-3p, and hsa-miR-26a-5p, all exhibiting 100% directional stability across patients and mean {Delta}-expression values ranging from +0.77 to +1.38. These miRNAs target pathways relevant to MS pathophysiology, including Th17/Treg balance, Wnt-{beta}-catenin signaling, macrophage polarization, and epigenetic immune regulation. In contrast, ocrelizumab elicited a more selective response pattern, with five miRNAs including hsa-miR-100-5p, hsa-miR-410-3p, hsa-miR-432-5p, hsa-miR-296-5p, and hsa-miR-485-3p showing moderate directional stability (83%) and greater inter-individual heterogeneity, consistent with the more targeted mechanism of CD20+ B-cell depletion. Notably, the two treatment-associated signatures were non-overlapping, with hsa-miR-27b-3p representing the only miRNA shared with prior cross-sectional analyses of this dataset. The identified ocrelizumab-associated miRNAs implicate pathways including mTOR/IGF1R signaling, NF-{kappa}B regulation, RNA editing, and mitochondrial biogenesis, several of which are dysregulated in progressive MS. Together, these findings demonstrate that cladribine and ocrelizumab induce distinct, treatment-specific miRNA response architectures that reflect their divergent immunological mechanisms. This work establishes a stability-aware analytic template for extracting reproducible longitudinal miRNA signals from small paired RRMS cohorts and provides a ranked set of biologically plausible candidate miRNAs for prospective validation and mechanistic investigation.

immunology↗

bioRxiv2026

Epigenetic signature at FOXP3 distal enhancer affects regulatory T cell development in Kabuki syndrome

Kabuki syndrome (KS) is a congenital developmental disorder caused by germinal pathogenic variants in the lysine methyltransferase 2D (KMT2D, KS1) or lysine demethylase 6A (KDM6A, KS2) genes. Kabuki patients display mental retardation, multiorgan malformations and immune dysregulation - ranging from immunodeficiency to autoimmunity - which strongly compromises their life expectancy. We explored whether the complex immunological scenario of Kabuki syndrome 1 subjects (Ks) could be ascribed to an altered generation of CD4+FOXP3+ regulatory T cells (Tregs). We report that pediatric Ks carrying KMT2D pathogenic variants show a significant reduction of Tregs. DNA methylation analysis reveals a specific methylation pattern at the FOXP3 distal enhancer that correlates with decreased FOXP3 transcription early during Treg cell induction and promotes T helper (Th)-2 lineage differentiation. Finally, in vitro T cell demethylation rescues FOXP3 expression and Treg induction in Ks, offering a novel potential therapeutic perspective. Our findings connect KMT2D loss-of-function to the inhibition of human FOXP3 gene transcription and provide novel molecular insights to explain the immunological phenotype in Ks, thus pinpointing this syndrome as a novel Tregopathy.

immunology↗

bioRxiv2026

TIGIT-NECTIN2/3 signaling preserves ignorant CD8⁺ T cells for favorable immune checkpoint outcomes in HBV-related hepatocellular carcinoma

BackgroundImmune checkpoint inhibitors (ICIs) have revolutionized cancer therapy by restoring anti-tumor immunity. However, persistent antigen exposure drives T cell exhaustion, limiting the effectiveness of ICIs. Ignorant T cells are antigen-specific T cells that maintain a naive state by regaining stem-like properties, allowing them to remain fully responsive to subsequent immunization. Virus-related hepatocellular carcinoma (HCC) demonstrates superior responses to ICIs compared to non-viral HCC, prompting us to investigate whether immunologically ignorant T cells exist in HBV-associated HCC and represent a promising target for improving immunotherapy outcomes. MethodsSingle-cell RNA sequencing (scRNA-seq) was performed on tumor tissues from patients with HBV-associated HCC. For validation, immunostaining was conducted on the discovery cohort and an independent cohort of 16 non-B non-C HCC and 22 HBV HCC. The enrichment of TIGIT and NECTIN3 in the proposed ignorant T cell was further validated using the TCGA database. ResultsscRNA-seq identified distinct HBV-infected HCC populations and revealed NECTIN3 upregulation in HBV-enriched subsets. CellChat analysis uncovered a novel NECTIN3-TIGIT tumor-immune interaction in HBV-enriched subsets, which shifted toward TIGIT-NECTIN2 as viral transcription declines. Trajectory analysis revealed the emergence of ignorant CD8 T cells following T cell exhaustion. TIGIT-NECTIN2/3 interactions deliver a weak exhaustion signal. This allows T cells to survive and regain naive-like properties as ignorant cells. Integration of bulk RNA-seq data identified CD24, STMN1, and EZH2 as potential biomarkers of ignorant CD8 T cells. ConclusionsTIGIT-NECTIN2/3 interactions present a promising axis for preserving immunologically ignorant T cells and sustaining ICI responsiveness in HBV-associated HCC.

immunology↗

bioRxiv2026

Obesity selectively disrupts long-lasting type 2 immune cell depots in white adipose tissue

White adipose tissue (WAT) has emerged as a tissue-resident niche for immunological memory, but whether this depot function extends to type 2 immune memory and how it is modulated by metabolic disease remains incompletely understood. Here, we show that Nippostrongylus brasiliensis infection, in which the parasite transits and damages the lung, establishes a long-lasting immune cell depot in distal abdominal WAT comprising eosinophils, group 2 innate lymphoid cells (ILC2s), and memory T cells that persists after parasite clearance. Intranasal papain administration recapitulates this depot phenotype, demonstrating that depot formation is a general feature of pulmonary type 2 inflammation rather than a response restricted to live infection. Adoptive transfer of OT-II T cells together with ovalbumin-coated N. brasiliensis larvae confirms that WAT accumulates bona fide antigen-experienced T cells. Diet-induced obesity selectively disrupts depot establishment, while leaving acute lung-stage immune cell recruitment, parasite clearance, and the intrinsic competence of cells that do accumulate largely intact. Despite preserved early lung recruitment, obese mice show exacerbated peri-alveolar tissue damage, consistent with an uncoupling of immune cell infiltration from productive type 2-dependent wound repair. Together, these findings establish WAT as a broadly competent type 2 immunological memory niche, identify obesity as a selective disruptor of depot formation rather than effector function, and provide a cellular framework for the impaired vaccine and infection responses associated with obesity.

immunology↗