Smithmyer, M. E. | bioRxiv Science

bioRxiv2026

Heterogeneity of HCMV-Specific CD8+ T Cells is Established Early in Infection, Clonally Encoded, and Stable Over Time

Human cytomegalovirus (CMV) elicits lifelong memory T cell responses of striking size and phenotypic diversity, but how these diverse responses are established during acute infection and evolve over decades of chronic stimulation is poorly understood. We tracked CD8+ T cells specific for the viral antigens pp65 and IE1 by single-cell RNAseq, TCRseq, and CITEseq over a period of 16 months in a newly seroconverted donor, and in five latently infected donors over intervals ranging from 4.5 to 12.5 years. We found that individual T cell clones exhibited distinct, specificity-dependent transcriptional profiles, with pp65-specific cells skewed toward central memory phenotypes and IE1-specific cells enriched for effector and chronically activated states. Among pp65-specific T cells we identified a CMC1-expressing state not previously described in virus-specific T cells that shares transcriptional features with exhausted T cells in human tumors yet remains phenotypically stable and clonally intact for over a decade of viral latency. Distinct clonal phenotypes arose during acute infection and were remarkably stable during viral latency, and these phenotypes tracked with relative TCR avidity and TCR sequence. Our findings reveal that the phenotypic diversity of the human CMV-specific CD8+ T cell response is organized at the level of individual clones, with distinct functional identities established during acute infection and preserved with striking fidelity across decades of viral latency and chronic antigen exposure.

immunology↗

bioRxiv2026

UC-associated autoantibodies to αvβ6 inhibit mucosal TGFβ activation and predispose to intestinal inflammation

Ulcerative colitis (UC) is characterized by epithelial barrier dysfunction and dysregulated mucosal immune responses; however, the mechanisms driving disease onset remain poorly defined. Autoantibodies against the epithelial-restricted integrin v{beta}6 are a highly specific biomarker of UC that can precede clinical diagnosis by up to 10 years. Because v{beta}6 activates TGF{beta} at epithelial surfaces, we hypothesized that UC-associated v{beta}6 autoantibodies inhibit mucosal TGF{beta} activation and disrupt epithelial homeostasis. We showed that v{beta}6 autoantibodies were enriched in UC and that IgG from autoantibody-positive individuals inhibited v{beta}6-dependent activation of TGF{beta}. v{beta}6 blockade dampened TGF{beta} signaling and altered differentiation-associated gene programs in human intestinal epithelial cells. In mice, deletion of v caused expansion of inflammation-associated goblet cells in the colon and changes in intestinal immune cells. Using a novel mouse model, we showed that v{beta}6-specific autoantibody disrupted epithelial-immune crosstalk and increased susceptibility to DSS colitis. Together, these findings establish anti-v{beta}6 autoantibodies as active inhibitors of epithelial TGF{beta} signaling, constituting a de facto anti-cytokine response, rather than passive biomarkers. By linking preclinical seropositivity to impaired epithelial signaling and heightened susceptibility to colitis, this work identifies epithelial v{beta}6-dependent TGF{beta} activation as a pathway that may be leveraged to modify disease risk or limit disease severity. One Sentence SummaryUC-associated autoantibodies impair epithelial TGF{beta} activation, alter mucosal homeostasis, and predispose to colitis.

immunology↗

bioRxiv2026

Soluble LAG-3 Identifies a Dynamic Early T Cell Activation Window in self-reactivity, Type 1 Diabetes, and Broader Immune Responses.

Aims/hypothesisType 1 diabetes is a complex autoimmune disorder in which autoreactive CD4 and CD8 T cells destroy pancreatic beta-cells, resulting in insulin deficiency and hyperglycemia. Although genetic susceptibility, particularly certain HLA alleles, contributes to disease risk, not all genetically predisposed individuals develop Type 1 diabetes. Screening first degree relatives (FDRs) for islet autoantibodies (GAD65, IAA, IA-2, ZnT8) helps detect autoimmune activity. However, these serum markers arise only after T-helper cell activation, limiting early intervention opportunities. Since protein antigen recognition by B cells requires T-helper cell assistance through linked recognition, T cell activation precedes B cell activation and autoantibody production. Activation of these T cells leads to shedding of the immune-regulatory (activation) surface protein LAG-3 (Lymphocyte Activation Gene-3 or CD223), generating its soluble form, sLAG-3, that is detectable in circulation. We hypothesized that sLAG-3 may serve as an early biomarker of autoimmune activity preceding islet autoantibody development in type 1 diabetes. MethodsPlasma sLAG-3 levels were measured longitudinally in female diabetes-prone NOD mice and analyzed in relation to islet antigen-specific CD4 T cell expansion and diabetes onset. To mechanistically link autoreactive T cell activation to sLAG-3 release. Naive autoreactive C6.6.9 TCR-transgenic (TCR-Tg) CD4 T cells were adoptively transferred into NOD.SCID mice and longitudinal assessment for plasma sLAG-3, beta-cell antigen specific CD4 T cell tetramer profiles, and circulating insulin (Ins2) mRNA to determine ongoing beta-cell stress. In parallel, sLAG-3 levels were analyzed from different human cohorts, including FDRs of individuals with type 1 diabetes, using cross-sectional and longitudinal approaches. ResultsIn murine models, elevated sLAG-3 correlated with expansion of islet-specific CD4 T cells that preceded hyperglycemia and diabetes onset. In the adoptive transfer model, early increases in sLAG-3 and circulating Ins2 mRNA marked immune activation and emerging beta-cell stress prior to overt diabetes. In our human cohorts, sLAG-3 was detectable in autoantibody-negative and single-autoantibody-positive FDRs, with higher levels observed in progressors compared to non-progressors, and associated with high-risk HLA genotypes. Conclusions/interpretationThese findings identify sLAG-3 as a candidate biomarker of early T cell activation in type 1 diabetes that may precede islet autoantibody development. Integration of sLAG-3 with antigen-specific T cell and beta-cell stress markers could improve early risk stratification and inform preventive strategies before substantial loss of beta-cell. Prospective longitudinal studies aligned to seroconversion are required to validate sLAG-3 as a surrogate marker of early disease activity. Research in contextO_ST_ABSWhat is already known about this subject?C_ST_ABSO_LIBefore the clinical onset of hyperglycemia, type 1 diabetes is characterized by a prolonged preclinical phase in which autoreactive B and T cells mediate progressive beta-cell destruction. C_LIO_LICurrent risk stratification strategies rely mainly on genetic susceptibility (genomic DNA) and the detection of islet autoantibodies in plasma/serum. C_LIO_LIIslet autoantibodies arise only after CD4 T cell activation and therefore do not capture the earliest stages of immune dysregulation. C_LIO_LIConsequently, biomarkers that directly reflect early pathogenic T cell activity prior to, or independent of, seroconversion remain limited and insufficiently validated. C_LI What is the key question?Can plasma sLAG-3 levels, beta-cell antigen-specific CD4 T cell tetramer expression, and circulating Ins2 mRNA serve as very early biomarkers of autoimmune activity in type 1 diabetes and serve to better inform risk stratification, thereby informing preventive intervention strategies for the clinician? What are the new findings?O_LIsLAG-3 increases transiently during early antigen-specific CD4 T cell activation stage, precedes hyperglycemia in mouse models, and is elevated in autoantibody-negative and single-autoantibody-positive first-degree relatives who later progress to type 1 diabetes. C_LIO_LIsLAG-3 was associated with beta-cell antigen-specific CD4 T cell expansion, assessment of stress induced beta cell Ins2 mRNA release and high-risk HLA genotypes, indicating early autoimmune activation rather than established disease. C_LI How might this impact clinical practice in the foreseeable future?These findings support sLAG-3 as a candidate early biomarker of T cell activation, before or at the earliest stages of islet autoantibody development in some at-risk individuals. Integration of plasma sLAG-3 with beta-cell antigen specific CD4 T cell profiling and insulin mRNA measurements could complement current autoantibody-based screening, improve risk stratification, and enable earlier preventive interventions to preserve beta-cell function in patients at-risk for type 1 diabetes.

immunology↗