Biology subjects

Eisenlohr, L. C.

Publications and source records attributed to Eisenlohr, L. C..

11 recordsLinked to original sources

bioRxiv2026

Generation and MHC class II loading of an endogenous influenza epitope revealed by a T cell receptor-like antibody

CD4+ T cells coordinate immune responses to infections and cancers and initiate many autoimmune diseases, yet the intracellular pathways that generate the peptide antigens they recognize remain incompletely understood. Progress has been limited in part by the scarcity of reagents that directly detect defined peptide:MHC class II (pMHC-II) complexes. Here, we established an mRNA vaccine-based pipeline to generate and characterize T cell receptor (TCR)-like antibodies. One result was 1D6, a monoclonal antibody specific for NA25:Ab, an influenza A/PR8 neuraminidase-derived epitope presented by MHC-II. 1D6 bound NA25:Ab with high affinity and specificity. 1D6 recognizes NA25:Ab through binding determinants partially distinct from those used by the cognate TCR. Using this reagent, we confirmed the proteasome dependence of NA25 presentation and showed that NA25:Ab accumulates in intracellular MHC-II loading compartments without a major requirement for canonical macroautophagy, pointing to an unconventional mode of antigen presentation. These findings establish TCR-like antibodies as powerful tools for dissecting noncanonical MHC-II antigen processing pathways. One Sentence SummaryAn mRNA immunization strategy generated a highly specific antibody to study how a noncanonical natural epitope from influenza virus is produced and loaded onto MHC-II.

immunology↗

bioRxiv2026

AI-enabled virtual immunopeptidomics links quantitative neoantigen presentation to immunogenicity

Effective anti-tumor T cell response depends on both neoantigen quality (non-selfness) and quantity (abundance). However, existing methods for neoantigen prioritization largely overlook peptide abundance because it is difficult to measure and model. To bridge this gap, we developed epiVIP, a deep learning framework that predicts the abundance of individual HLA-I peptides using widely available (sc)RNA-seq data. Trained on 1.7 million immune peptides paired with gene expression profiles, epiVIP demonstrated strong generalizability across unseen samples. Analyzing 33,711 neoantigens from clinical datasets revealed a compensatory relationship between abundance and non-selfness in determining antigenicity, providing quantitative support for the TCR avidity theory. Importantly, abundance independently predicted tumor reactivity and patient survival across multiple neoantigen vaccine cohorts and immune checkpoint blockade cohorts. Mechanistic interpretation of epiVIP further identified directional regulation of MAGEA3 epitope presentation by PSME4, which was validated experimentally using T cell functional assays. Together, these findings established AI-enabled virtual immunopeptidomics as a powerful strategy to improve cancer immunotherapy.

bioinformatics↗

bioRxiv2026

Generation and characterization of a novel MHC-II tetramer for tracking and characterization of toxin B-specific CD4+ T cell responses

The gastrointestinal pathogen Clostridioides difficile, is a major burden for health systems due to high rates of recurrence. C. difficile pathogenesis is mediated by two virulence factors, toxin A (TcdA) and Toxin B (TcdB). Antibodies specific for TcdA and TcdB are correlated with protection from symptomatic recurrence, however, the role for CD4+ T cells is poorly understood in part due to the lack of tools to study the toxin-specific CD4+ T cell response. Our group recently demonstrated the antibody and CD4+ T cell response to C. difficile toxins is impaired via the glucosyltransferase activity of the toxins; however, tools do not exist to study the protective capacity and the phenotype of toxin-specific CD4+ T cells. Therefore, we developed an MHC-II tetramer to identify TcdB-specific CD4+ T cells via flow cytometry. Herein, we identified an immunodominant epitope (TcdB1961-1975) in the CROPs region of TcdB and optimized an MHC-II tetramer for use in tracking and phenotyping TcdB-specific CD4+ T cell responses following multiple different immunization strategies in mice. Utilizing the tetramer, TcdB-specific T follicular helper (Tfh) cells were detected following TcdB-CROPs mRNA-LNP vaccination validating the advantage of the tetramer. Furthermore, using a modular mRNA vector expressing the TcdB1961 peptide covalently bound to the beta chain of MHC-II (MHC-II{beta}) we were able to generate a robust population of TcdB-specific CD4+ T cells. These data outline the generation of new tools for the C. difficile field and lay the groundwork for future studies of toxin-specific CD4+ T cell responses.

immunology↗

bioRxiv2025

Cutting Edge: An mRNA Platform to Create Isolated, Monospecific Th1 Responses

Helper T cells (TCD4) are lynchpins of adaptive immune responses. Since each TCD4 expresses a single T cell receptor, recognizing an epitope within major histocompatibility complex class II (MHCII), it is often desirable to study a population that responds to the same epitope. We devised a novel method of selective immunization to produce a robust, monospecific TCD4 in mice using a modular mRNA vector. The vector encodes the target epitope attached via flexible linker to MHCII. Immunization with this mRNA selectively elicits TCD4 responses across a range of epitopes and MHCII alleles. These TCD4 show robust, polyfunctional Th1 cytokine release when evaluated in vitro. Additionally, we tested the activity of these TCD4 cells during Salmonella enterica infection, a model of Th1-dependent immune response, and demonstrated their efficacy in vivo in curtailing infection.

immunology↗

bioRxiv2025

Multimodal induction of fulminant HLH by IL-18 includes virus-specific NK immunodeficiency

Macrophage Activation Syndrome (MAS) is a cytokine storm syndrome associated with Stills Disease, XIAP deficiency, and elevation of both total and free IL-18. Modeling excess IL-18 using Il18tg mice, we found mild NK-cytopenia and cytotoxic T lymphocyte (CTL) activation in resting mice reminiscent of Stills patients. Infection with Lymphocytic Choriomeningitis Virus (LCMV) triggered MAS via and IFN{gamma}, despite normal viral clearance. Il18tg NK cell transcriptomes showed replicative activity, but few changes in canonical NK function or maturation pathways. LCMV clearance is NK-independent, so we challenged Il18tg mice with mousepox in which NK cells are critical early orchestrators of clearance. Il18tg mices NK cells failed to activate or expand, but mousepox further activated their CTL and early viral control was normal. Il18tg mice soon developed "MAS" including hepatosplenic necrosis, but (contrasting with LCMV) they showed poor virus-specific CTL expansion and viral clearance. Though more normal at rest, Il18bpKO mices NK cells were similarly inert upon mousepox infection, and the mice succumbed to viremic MAS like Il18tg. Rescue of Il18tg mice, and mousepox-specific CTL responses, by NK cell transfer required in vitro NK pre-activation. Thus, IL-18 can induce both hyperinflammation (CTL hyperactivation) and immunodeficiency (NK cell hypoactivation) depending on the nature of the infectious trigger.

immunology↗

bioRxiv2025

Endogenous antigen processing promotes mRNA vaccine CD4+ T cell responses

Lipid nanoparticle (LNP)-encapsulated nucleoside-modified mRNA vaccines elicit robust CD4+ T cell responses, which are essential for antiviral immunity1-3. While peptides presented to CD4+ T cells via major histocompatibility complex class II (MHC II) are traditionally thought to be derived from extracellular sources that are processed by antigen presenting cells (APCs) through the classical exogenous pathway4,5, the precise mechanisms of mRNA-LNP vaccine-specific CD4+ T cell priming remain unknown. Here, we investigated the role of alternative, endogenous antigen presentation pathways6,7 in inducing CD4+ T cell responses to mRNA-LNP vaccines. APCs treated with mRNA-LNP vaccines were consistently superior in activating T cells under conditions of endogenous, rather than exogenous, presentation. Immunization with an mRNA-LNP vaccine that excludes antigen expression in APCs resulted in lower antigen-specific CD4+ T cell, T follicular helper cell, and antibody responses than mice receiving control vaccine. In contrast, depletion of vaccine antigen from exogenous sources such as muscle cells resulted in little to no reduction in antigen-specific CD4+ T cells. Our findings demonstrate that direct presentation of endogenous antigen on MHC II is crucial to mRNA-LNP vaccine-induced immune responses and adds to a growing body of literature that redefines the paradigm of MHC II-restricted antigen processing and presentation.

immunology↗

bioRxiv2024

Human erythroid progenitors express antigen presentation machinery

Early-life immune exposures can profoundly impact lifelong health. However, functional mechanisms underlying fetal immune development remain incomplete. Erythrocytes are not typically considered active immune mediators, primarily because erythroid precursors discard their organelles as they mature, thus losing the ability to alter gene expression in response to stimuli. Erythroid progenitors and precursors circulate in human fetuses and neonates. Although there is limited evidence that erythroid precursors are immunomodulatory, our understanding of the underlying mechanisms remains inadequate. To define the immunobiological role of fetal and perinatal erythroid progenitors and precursors, we analyzed single cell RNA-sequencing data and found that transcriptomics support erythroid progenitors as putative immune mediators. Unexpectedly, we discovered that human erythroid progenitors constitutively express Major Histocompatibility Complex (MHC) class II antigen processing and presentation machinery, which are hallmarks of specialized antigen presenting immune cells. Furthermore, we demonstrate that erythroid progenitors internalize and cleave foreign proteins into peptide antigens. Unlike conventional antigen presenting cells, erythroid progenitors express atypical costimulatory molecules and immunoregulatory cytokines that direct the development of regulatory T cells, which are critical for establishing maternal-fetal tolerance. Expression of MHC II in definitive erythroid progenitors begins during the second trimester, coinciding with the appearance of mature T cells in the fetus, and is absent in primitive progenitors. Lastly, we demonstrate physical and molecular interaction potential of erythroid progenitors and T cells in the fetal liver. Our findings shed light on a unique orchestrator of fetal immunity and provide insight into the mechanisms by which erythroid cells contribute to host defense.

immunology↗

bioRxiv2024

Influenza virus antibodies inhibit antigen-specific de novo B cell responses in mice

Antibody responses to influenza vaccines tend to be focused on epitopes encountered during prior influenza exposures, with little production of de novo responses to novel epitopes. To examine the contribution of circulating antibody to this phenomenon, we passively transferred a hemagglutinin (HA)-specific monoclonal antibody (mAb) into mice before immunizing with whole inactivated virions. The HA mAb inhibited de novo HA-specific antibodies, plasmablasts, germinal center B cells, and memory B cells, while responses to a second antigen in the vaccine, neuraminidase (NA), were uninhibited. The HA mAb potently inhibited de novo antibody responses against epitopes near the HA mAb binding site. The HA mAb also promoted IgG1 class switching, an effect that, unlike the inhibition of HA responses, relied on signaling through Fc-gamma receptors. These studies suggest that circulating antibodies inhibit de novo B cell responses in an antigen-specific manner, which likely contributes to differences in antibody specificities elicited during primary and secondary influenza virus exposures.

immunology↗

bioRxiv2024

Early-life exposures to specific commensal microbes prevent type 1 diabetes.

Early-life disruptions of the gut microbiome have long-lasting impacts on the risk of developing autoimmune diseases. How the composition of the early-life microbiota contributes to autoimmunity and whether manipulating it can prove therapeutically beneficial remains largely unexplored. Here we demonstrate that a simple consortium of nine early-life commensal bacteria (PedsCom) prevents type 1 diabetes (T1D) in diabetes-susceptible NOD mice. Remarkably, we find that this protection is completely dependent upon early-life colonization. During this critical time window of early-life colonization and immune development, specific microbes unexpectedly translocate from the gut to peripheral tissues and induce the tolerogenic responses required for T1D protection. These findings highlight how the timing and localization of microbial interactions during a pivotal stage of immune development contribute to protection from T1D. Altogether, these findings suggest an opportunity to develop microbial therapies for human infants to prevent autoimmune diseases. One sentence summaryA defined consortium of early-life microbes shapes immune development and prevents type 1 diabetes.

immunology↗

bioRxiv2022

The ectromelia virus virulence factor C15 facilitates early viral spread by inhibiting NK cell-infected cell contacts

The success of poxviruses as pathogens depends upon their antagonism of host responses by multiple immunomodulatory proteins. The largest of these expressed by ectromelia virus (the agent of mousepox) is C15, one member of a well-conserved poxviral family previously shown to inhibit T cell activation. Here, we demonstrate by quantitative immunofluorescence imaging that C15 also limits contact between natural killer (NK) cells and infected cells in vivo. This corresponds to an inhibition in the number of total and degranulating NK cells, ex vivo and in vitro, with no detectable impact on NK cell cytokine production nor the transcription of factors related to NK cell recruitment or activation. Thus, in addition to its previously identified capacity to antagonize CD4 T cell activation, C15 inhibits NK cell cytolytic function, which results in increased viral replication and dissemination in vivo. This work builds on a body of literature demonstrating the importance of early restriction of virus within the draining lymph node. summaryPoxvirus B22 family proteins are important virulence factors known to inhibit T cell functions. Peauroi et al. identify a novel function of the ectromelia virus homolog, C15, which inhibits NK cell-target contact and cytolytic function to facilitate early viral spread. (Provide a short, [~]40-word summary statement for the online JEM table of contents and alerts. This summary should describe the context and significance of the findings for a general readership; it should be written in the present tense and refer to the work in the third person.)

immunology↗

bioRxiv2021

Type II alveolar cells with constitutive expression of MHCII and limited antigen presentation capacity contribute to improved respiratory viral disease outcomes

Type II alveolar cells (AT2s) are critical for basic respiratory homeostasis and tissue repair after lung injury. Prior studies indicate that AT2s also express major histocompatibility complex II (MHCII) molecules, but how MHCII expression by AT2s is regulated and how it contributes to host defense remain unclear. Here we show that AT2s express high levels of MHCII independent of conventional inflammatory stimuli, and that selective loss of MHCII from AT2s in mice results in the worsening of respiratory virus disease following influenza and Sendai virus infections. We also find that AT2s exhibit MHCII presentation capacity that is substantially limited in comparison to professional antigen presenting cells. The combination of constitutive MHCII expression and restrained presentation may position AT2s to contribute to lung adaptive immune responses in a measured fashion, without over-amplifying damaging inflammation.

immunology↗