Biology subjects

Herati, R. S.

Publications and source records attributed to Herati, R. S..

12 recordsLinked to original sources

bioRxiv2026

Tfh dysfunction underlies poor responses to HBV vaccination

The primary goal of vaccination is to induce durable protection through generation of antigen-specific humoral immunity and cellular immune memory. Yet the same vaccine may elicit durable protection in some and less durable responses in others. Antigen-specific antibody responses arise from germinal centers (GCs), where T follicular helper (Tfh) cells help cognate B cells undergo somatic hypermutation (SHM), affinity maturation to generate humoral protection and cellular immune memory. In humans, however, the mechanisms linking GC dynamics to downstream antibody output remain incompletely characterized. To identify the molecular and cellular events that underlie differential vaccine responsiveness, we leveraged the known, pronounced variability in vaccine antigen-specific antibody concentration and durability observed after Hepatitis B virus (HBV) immunization. We longitudinally profiled 101 healthy adults undergoing either de novo (n=59) or booster (n=42) immunization. We then stratified participants into High (>100 mIU/mL) and Low (<100 mIU/mL) responder groups based on vaccine antigen-specific antibody responses. From this cohort, we obtained core needle biopsies (CNBx) of vaccine-draining lymph nodes from 10 participants (High Responder n=6, Low Responder n=4), 10-21 days post-final vaccination and performed single-cell RNA sequencing with paired antigen receptor sequencing. Lymph node BCR repertoire analysis revealed convergent, semi-public clonotypes across unrelated participants with elevated SHM. Transcriptomic profiling of GC-B cells uncovered stark functional divergence between response groups, with High Responders showing robust activation across both dark zone (DZ) and light zone (LZ) compartments and enrichment of MYC and mTORC1 signaling. In contrast, Low Responders exhibited a contracted LZ compartment and a stalled GC B cell response. This divergence in B cell responses corresponded to changes in the T cell compartment. High Responders harbored an expanded Tfh subset marked by increased expression of CXCL13, ICOS, and GNG4, indicative of their GC localization and capacity to provide B cell help. Moreover, receptor-ligand analysis indicated that these GNG4+Tfh formed coordinated costimulatory networks capable of driving LZ GC-B cell licensing. Low Responders demonstrated a divergent program in which their GNG4+Tfh displayed aberrant inflammatory transcriptional activity. This inflammatory signaling was associated with reduced specificity of BCL6 regulon activity despite maintained expression of canonical Tfh genes. Together, these findings reveal that variable HBV vaccine responsiveness was associated with transcriptional network alterations in the GNG4+Tfh subset, offering a molecular framework for understanding poor vaccine responses. One Sentence SummaryLymph node Tfh dysfunction is associated with poor vaccine responses to Hepatitis B virus vaccination

immunology↗

bioRxiv2025

Cellular interactions in the sentinel lymph node predict melanoma recurrence

Melanoma outcomes have dramatically improved over the past decade, but some patients still experience disease recurrence, particularly those who present at later stage of disease. Prior studies identified an altered immune microenvironment in the sentinel lymph node (SLN) including the presence of dysfunctional CD8 T cells and CD4 T regulatory cells (Tregs), but the spatial organization of the SLN and the interactions of individual cell types have not been extensively studied. To understand how spatial organization of immune cells in the SLN is related to outcomes, we performed spatial proteomic profiling of Stage I and II melanoma SLN to generate an atlas of cell types. Following multiplexed immunofluorescence imaging, deep learning-based segmentation and clustering, we identified 33 subsets of T cells, B cells and Tumor cells. Lymphoid region analyses established a foundational spatial map of the melanoma SLN, revealing higher regional frequencies of activated and memory CD4 T cells in Stage I SLN and consistent positioning of T cells at functional spatial locations. To better understand cellular interactions, we evaluated the immediate neighbors around each index cell using Effect Size Interaction mapping (ESI-map), a novel computational toolkit for understanding spatial interactions. Nearest-neighbor analyses across biological replicates revealed rewiring in cell-cell interacting pairs across disease progression and patient outcomes, particularly with respect to exhausted TOX+ CD8 T cells. Stage II patients who experienced disease recurrence had notable enrichment of cellular interactions between Tregs and TOX+ CD8 T cells that was associated with reduced expression of granzyme B and interferon-{gamma} that was most pronounced in exhausted CD8 T cells. Together, these data demonstrate that the specific spatial interactions between Tregs and exhausted CD8 T cells in the SLN provide a novel immune signature for understanding melanoma outcomes. One Line SummaryTreg-CD8 T cell interactions in the sentinel lymph node predict recurrence outcomes in Stage II SLN+ melanoma patients.

immunology↗

bioRxiv2025

Coordinated circulating and tissue-based T cell responses precede xenograft rejection

Despite the life-saving successes of solid organ transplantation, the number of individuals needing organ transplant far exceeds the number of organs available for use each year. Porcine xenotransplantation, or the use of pig organs for transplantation in people, holds substantial promise but xenograft rejection in humans is poorly understood. T cell rejection by the host immune system is a major challenge for human allografts and may limit the longevity of porcine xenografts. To study the xenograft rejection, we evaluated T cell responses and repertoire dynamics across tissues following porcine thymokidney transplantation in a decedent model over 61 days after bilateral native kidney nephrectomy. Despite induction with anti-thymocyte globulin and ongoing immune suppression consisting of rituximab, corticosteroids, calcineurin inhibition, and mycophenolate mofetil, human T cell infiltration of the xenograft was observed and was associated with xenograft dysfunction. Longitudinal analysis of T cell clonotypes in biopsies of thymokidney revealed accumulation of clonal human CD4 and CD8 T cell responses. Moreover, circulating activated T cells, including circulating T follicular helper (cTfh), were xeno-reactive and increased in frequency around rejection events. We confirmed clonal dominance of a single CD8 clonotype - identified as donor-reactive in a mixed lymphocyte reaction - in the circulation leading up to the acute cellular rejection event. Following re-treatment with anti-thymocyte globulin and intensification of corticosteroids, the T cell clonotypes were dramatically diminished in frequency in thymokidney and lymph nodes, though not eliminated. Over time of observation, the T cell clonotypes were shared across multiple compartments, including xenograft, circulation and lymph nodes and formed clonal families with known xeno-reactive clonotypes, suggesting a coordinated immune response against a limited pool of antigenic targets. Together, these data demonstrate T cell repertoire dynamics across tissues in the setting of xenograft rejection and highlight opportunities for early surveillance, prediction and potential intervention. One-sentence summaryAfter pig-to-human kidney xenotransplantation, xenoreactive T cells form clonotypic families across blood, graft, and lymphoid tissues, indicating a coordinated and targeted response.

immunology↗

bioRxiv2025

Lymphatic constraint of germinal centers optimizes protective antibody responses

Immunization strategies are central to pathogen control, where efficacy relies on antigen uptake, distribution, persistence, and inflammatory context. We recently demonstrated that dermal lymphatic capillaries regulate antigen presentation in lymph nodes (LN) by restraining fluid and virion transport following vaccinia virus (VACV) infection by skin scarification. Concurrently, a perifollicular, LN lymphangiogenic response encapsulates expanding B cell follicles. Given the important role of antigen transport and uptake on humoral immunity, we tested the hypothesis that lymphatic remodeling in the skin and LNs regulates germinal center (GC)-dependent antibody responses during infection. Using a model of lymphatic-specific VEGFR2 inhibition, we found that inhibiting viral-induced lymphatic remodeling in skin and LNs prompted significant GC expansion but paradoxically decreases protective VACV-specific class-switched antibodies. While the larger GC responses appeared structurally normal, they failed to support a proliferative burst consistent with clonal selection. Mathematical modeling revealed that this disconnect between GC size and function arises from impaired productive T follicular cell interactions in larger GC volumes and consistent with this finding, the optimal GC size was evolutionarily conserved across diverse mammals. Finally, we found that the presence of virus in the LN initiates these changes in GC function, inhibits LN lymphangiogenesis, increases B cell follicle size, and reduces selection efficiency. Therefore, protecting LN lymphatic vessels from virus-induced interferons rescues perifollicular lymphatic growth and follicle size, indicating that LN lymphangiogenesis directly constrains the follicular response. In summary, this study underscores the central role of lymphatic remodeling in compartmentalizing antigen and inflammatory signals to optimize GC fitness and protective antibody responses.

immunology↗

bioRxiv2023

Multimodal characterization of antigen-specific CD8+ T cells across SARS-CoV-2 vaccination and infection.

The human immune response to SARS-CoV-2 antigen after infection or vaccination is defined by the durable production of antibodies and T cells. Population-based monitoring typically focuses on antibody titer, but there is a need for improved characterization and quantification of T cell responses. Here, we utilize multimodal sequencing technologies to perform a longitudinal analysis of circulating human leukocytes collected before and after BNT162b2 immunization. Our data reveal distinct subpopulations of CD8+ T cells which reliably appear 28 days after prime vaccination (7 days post boost). Using a suite of cross-modality integration tools, we define their transcriptome, accessible chromatin landscape, and immunophenotype, and identify unique biomarkers within each modality. By leveraging DNA-oligo-tagged peptide-MHC multimers and T cell receptor sequencing, we demonstrate that this vaccine-induced population is SARS-CoV-2 antigen-specific and capable of rapid clonal expansion. Moreover, we also identify these CD8+ populations in scRNA-seq datasets from COVID-19 patients and find that their relative frequency and differentiation outcomes are predictive of subsequent clinical outcomes. Our work contributes to our understanding of T cell immunity, and highlights the potential for integrative and multimodal analysis to characterize rare cell populations.

genomics↗

bioRxiv2022

Molecularly distinct memory CD4+ T cells are induced by SARS-CoV-2 infection and mRNA vaccination

Adaptive immune responses are induced by vaccination and infection, yet little is known about how CD4+ T cell memory differs when primed in these two contexts. Notably, viral infection is generally associated with higher levels of systemic inflammation than is vaccination. To assess whether the inflammatory milieu at the time of CD4+ T cell priming has long-term effects on memory, we compared Spike-specific memory CD4+ T cells in 22 individuals around the time of the participants third SARS-CoV-2 mRNA vaccination, with stratification by whether the participants first exposure to Spike was via virus or mRNA vaccine. Multimodal single-cell profiling of Spike-specific CD4+ T cells revealed 755 differentially expressed genes that distinguished infection- and vaccine-primed memory CD4+ T cells. Spike-specific CD4+ T cells from infection-primed individuals had strong enrichment for cytotoxicity and interferon signaling genes, whereas Spike-specific CD4+ T cells from vaccine-primed individuals were enriched for proliferative pathways by gene set enrichment analysis. Moreover, Spike-specific memory CD4+ T cells established by infection had distinct epigenetic landscapes driven by enrichment of IRF-family transcription factors, relative to T cells established by mRNA vaccination. This transcriptional imprint was minimally altered following subsequent mRNA vaccination or breakthrough infection, reflecting the strong bias induced by the inflammatory environment during initial memory differentiation. Together, these data suggest that the inflammatory context during CD4+ T cell priming is durably imprinted in the memory state at transcriptional and epigenetic levels, which has implications for personalization of vaccination based on prior infection history. One Sentence SummarySARS-CoV-2 infection versus SARS-CoV-2 mRNA vaccination prime durable transcriptionally and epigenetically distinct Spike-specific CD4+ T cell memory landscapes.

immunology↗

bioRxiv2022

Human T follicular helper clones seed the germinal center-resident regulatory pool

How FOXP3+ T follicular regulatory (Tfr) cells simultaneously steer antibody formation toward microbe/vaccine recognition and away from self-reactivity remains unsettled. To explore human Tfr cell provenance, function and location heterogeneity, we used paired TCRVA/TCRVB sequencing to distinguish tonsillar Tfr cells clonally related to natural Tregs (nTfr) from those likely induced from Tfh cells (iTfr). The proteins iTfr and nTfr cells differentially expressed were utilized to pinpoint their in situ locations via multi-plex microscopy and establish divergent functional roles. In-silico and tonsil organoid tracking models corroborated the existence of separate Treg-to-nTfr and Tfh-to-iTfr developmental trajectories. In total, we have identified human iTfr cells as a distinct CD38-expressing, GC-resident, Tfh-descended subset that gains suppressive function while retaining capacities for B-cell help whereas CD38- nTfr cells are elite suppressors primarily localized to follicular mantles. Interventions differentially targeting Tfr subsets may provide therapeutic opportunities to boost immunity or more precisely treat autoimmune diseases. One sentence summaryHuman tonsillar Tfr clones descend from either Treg or Tfh lineages and provenance predicts their TCR repertoires, locations and functional characteristics.

immunology↗

bioRxiv2022

Induction of a CD8 T cell intrinsic DNA damage and repair response is associated with clinical response to PD-1 blockade in uterine cancer.

Despite the success of immune checkpoint blockade (ICB), many patients fail to achieve durable clinical benefit, and the underlying immunological mechanisms remain poorly understood. Here, we investigated immune reinvigoration by ICB in advanced or recurrent hypermutated or microsatellite instability-high, mismatch repair deficient (MSI-H/MMRd) uterine cancer patients treated with anti-PD-1 (nivolumab). CD8 T cells underwent rapid pharmacodynamic proliferation 2-4 weeks after initiating PD-1 blockade. This immunological response, however, did not correlate with clinical response. We hypothesized that the T cell-intrinsic response to proliferative and genotoxic stress might contribute to the disparity between immunological and clinical response. We developed a high-dimensional single cell cytometric platform to simultaneously analyze T cell differentiation with changes in DNA damage and repair (DDR) pathways. This DDR-Immune platform revealed T cell subset-specific patterns of DDR, and distinct DDR pathways induced by different types of DNA damage. Applying this platform to MSI-H/MMRd or hypermutated uterine cancer patients revealed a signature of DDR exemplified by rapid increase in phosphorylated-ATM (pATM) intrinsic to CD8 T cells proliferating in response to PD-1 blockade that distinguished clinical responders and non-responders. ATM regulated transcriptional circuits in T cells were associated with better clinical response to PD-1 blockade. These findings highlight a previously unrecognized role for CD8 T cell-intrinsic DDR as a potential determinant of immune fitness and clinical outcome of PD-1 blockade therapy. STATEMENT OF SIGNIFICANCEUsing high-dimensional immune and DNA damage response (DDR) profiling in T cell subsets we identified distinct signatures in anti-PD-1 treated MSI-H/hypermutated uterine cancer patients associated with clinical response versus non-response. Thus, T cell-intrinsic DDR is a potential determinant of immune responsiveness and clinical outcome to PD-1 blockade therapy in cancer.

immunology↗

bioRxiv2021

Rapid induction of antigen-specific CD4+ T cells guides coordinated humoral and cellular immune responses to SARS-CoV-2 mRNA vaccination

The SARS-CoV-2 mRNA vaccines have shown remarkable clinical efficacy, but questions remain about the nature and kinetics of T cell priming. We performed longitudinal antigen-specific T cell analyses in healthy individuals following mRNA vaccination. Vaccination induced rapid near-maximal antigen-specific CD4+ T cell responses in all subjects after the first vaccine dose. CD8+ T cell responses developed gradually after the first and second dose and were variable. Vaccine-induced T cells had central memory characteristics and included both Tfh and Th1 subsets, similar to natural infection. Th1 and Tfh responses following the first dose predicted post-boost CD8+ T cell and neutralizing antibody levels, respectively. Integrated analysis of 26 antigen-specific T cell and humoral responses revealed coordinated features of the immune response to vaccination. Lastly, whereas booster vaccination improved CD4+ and CD8+ T cell responses in SARS-CoV-2 naive subjects, the second vaccine dose had little effect on T cell responses in SARS-CoV-2 recovered individuals. Thus, longitudinal analysis revealed robust T cell responses to mRNA vaccination and highlighted early induction of antigen-specific CD4+ T cells. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=192 HEIGHT=200 SRC="FIGDIR/small/440862v1_ufig1.gif" ALT="Figure 1"> View larger version (52K): org.highwire.dtl.DTLVardef@db812dorg.highwire.dtl.DTLVardef@fdc549org.highwire.dtl.DTLVardef@a34663org.highwire.dtl.DTLVardef@1621e52_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2021

Neutralization of viruses with European, South African, and United States SARS-CoV-2 variant spike proteins by convalescent sera and BNT162b2 mRNA vaccine-elicited antibodies

The increasing prevalence of SARS-CoV-2 variants with mutations in the spike protein has raised concerns that recovered individuals may not be protected from reinfection and that current vaccines will become less effective. The B.1.1.7 isolate identified in the United Kingdom and B.1.351 isolate identified in the Republic of South Africa encode spike proteins with multiple mutations in the S1 and S2 subunits. In addition, variants have been identified in Columbus, Ohio (COH.20G/677H), Europe (20A.EU2) and in domesticated minks. Analysis by antibody neutralization of pseudotyped viruses showed that convalescent sera from patients infected prior to the emergence of the variant viruses neutralized viruses with the B.1.1.7, B.1.351, COH.20G/677H Columbus Ohio, 20A.EU2 Europe and mink cluster 5 spike proteins with only a minor decrease in titer compared to that of the earlier D614G spike protein. Serum specimens from individuals vaccinated with the BNT162b2 mRNA vaccine neutralized D614G virus with titers that were on average 7-fold greater than convalescent sera. Vaccine elicited antibodies neutralized virus with the B.1.1.7 spike protein with titers similar to D614G virus and neutralized virus with the B.1.351 spike with, on average, a 3-fold reduction in titer (1:500), a titer that was still higher than the average titer with which convalescent sera neutralized D614G (1:139). The reduction in titer was attributable to the E484K mutation in the RBD. The B.1.1.7 and B.1.351 viruses were not more infectious than D614G on ACE2.293T cells in vitro but N501Y, an ACE2 contacting residue present in the B.1.1.7, B.1.351 and COH.20G/677H spike proteins caused higher affinity binding to ACE2, likely contributing to their increased transmissibility. These findings suggest that antibodies elicited by primary infection and by the BNT162b2 mRNA vaccine are likely to maintain protective efficacy against B.1.1.7 and most other variants but that the partial resistance of virus with the B.1.351 spike protein could render some individuals less well protected, supporting a rationale for the development of modified vaccines containing E484K.

microbiology↗

bioRxiv2019

Chronic viral infection promotes early germinal center exit of B cells and impaired antibody development.

Chronic viral infections disrupt B cell responses leading to impaired affinity maturation and delayed control of viremia. Previous studies have identified early pre-germinal center (GC) B cell attrition but the impact of chronic infections on B cell fate decisions in the GC remains poorly understood. To address this question, we used single-cell transcriptional profiling of virus-specific GC B cells to test the hypothesis that chronic viral infection disrupted GC B cell fate decisions leading to suboptimal humoral immunity. These studies revealed a critical GC differentiation checkpoint that is disrupted by chronic infection, specifically at the point of dark zone re-entry. During chronic viral infection, virus-specific GC B cells were shunted towards terminal plasma cell (PC) or memory B cell (MBC) fates at the expense of continued participation in the GC. Early GC exit was associated with decreased B cell mutational burden and antibody quality. Persisting antigen and inflammation independently drove facets of dysregulation, with a key role for inflammation in directing premature terminal GC B cell differentiation and GC exit. Thus, these studies define GC defects during chronic viral infection and identify a critical GC checkpoint that is short-circuited, preventing optimal maturation of humoral immunity.

immunology↗

bioRxiv2019

Vaccine-induced ICOS+CD38+ cTfh are sensitive biosensors of age-related changes in inflammatory pathways

Humoral immune responses are dysregulated with aging but details remain incompletely understood. In particular, little is known about the effects of aging on T follicular helper (Tfh) CD4 cells, the subset that provides critical help to B cells for effective humoral immunity. We previously demonstrated that influenza vaccination increases a circulating Tfh (cTfh) subset that expresses ICOS and CD38, contains influenza-specific memory cells, and is correlated with antibody responses. To directly study the effects of aging on the cTfh response, we performed transcriptional profiling and cellular analysis before and after influenza vaccination in young and elderly adults. Several key differences in cTfh responses were revealed in the elderly. First, whole blood transcriptional profiling defined cross-validated genesets of youth versus aging and these genesets were, compared to other T cells, preferentially enriched in ICOS+CD38+ cTfh from young and elderly subjects, respectively, following vaccination. Second, vaccine-induced ICOS+CD38+ cTfh from the elderly were enriched for transcriptional signatures of inflammation including TNF-NFkB pathway activation. Indeed, we reveal a paradoxical positive effect of TNF signaling on Tfh providing help to B cells linked to survival circuits that may explain detrimental effects of TNF blockade on vaccine responses. Finally, vaccine-induced ICOS+CD38+ cTfh displayed strong enrichment for signatures of underlying age-associated biological changes. Thus, these data reveal key biological changes in cTfh during aging and also demonstrate the sensitivity of vaccine-induced cTfh to underlying changes in host physiology. This latter observation suggests that vaccine-induced cTfh could function as sensitive biosensors of underlying inflammatory and/or overall immune health.\n\nOne sentence summaryTranscriptional profiling of vaccine-induced circulating T follicular helper cell responding to influenza vaccination reveals age-associated effects on Tfh such as alterations in TNF-NFkB signaling.

immunology↗