Biology subjects

Caspi, R. R.

Publications and source records attributed to Caspi, R. R..

7 recordsLinked to original sources

bioRxiv2025

Gut microbial interaction networks control autoimmunity to neuroretina

The gut microbiome influences the development of immune-mediated inflammatory diseases, including autoimmune uveitis, a sight-threatening ocular inflammation driven by retina-specific T cells1. Using a model of spontaneous autoimmune uveitis (sEAU) we showed that gut commensals provide immune stimuli that trigger disease2. Here we report that uveitis-promoting microbes are present in human gut flora and that colonization of germ-free (GF) mice with commensals from healthy human donors was sufficient to provoke disease. Severity of sEAU correlated with expansion of Akkermansia and contraction of short-chain fatty acid (SCFA)-producing Firmicutes, followed by decreased SCFA levels and a dominant gut Th1 effector response. Mechanistic gain-of-function experiments, enriching GF sEAU mice with Akkermansia, reproduced these microbiome, metabolite and immune phenotype shifts, and exacerbated disease, suggesting that Akkermansia promotes autoimmunity by outcompeting SCFA-producers and enhancing Th1-type responses. An inverse correlation between Akkermansia (Verrucomicrobia) and Firmicutes was also present in patients with uveitis, multiple sclerosis and Crohns disease. These findings reveal a stereotypic gut microbial interaction network that regulates systemic immune balance, and may represent an ecologically conserved mechanism through which the gut microbiome modulates autoimmune and inflammatory diseases.

immunology↗

bioRxiv2025

Laquinimod treatment attenuates EAU by inhibiting both the inductive and effector phases in an APC-dependent manner

PurposeTo evaluate the immunomodulatory effects on experimental autoimmune uveitis (EAU) of the aryl hydrocarbon receptor (AhR) agonist Laquinimod (LAQ), and its active metabolite DELAQ, with a focus on dendritic cell- and T cell-mediated mechanisms. MethodsEAU was induced in mice by active immunization or by adoptive transfer of activated T cells. Mice were treated with LAQ either from the time of immunization or from 7 days after. Effects of LAQ were examined in wild-type, global AhR-knockout, or dendritic cell-conditional AhR knockout mice. Direct vs. indirect effects of AhR agonism on dendritic cells and T cells were studied in vitro using DELAQ, a major active metabolite of LAQ. ResultsLAQ treatment from Day 0 fully suppressed EAU, while delayed treatment (Day 7) provided only partial protection. In the adoptive transfer model, LAQ-treated recipients showed reduced pathology. Global AhR-deficient mice developed severe EAU comparable to that of wild-type mice, with an elevated Th17 response. LAQ-treated mice displayed increased frequencies of cDC1 and FoxP3 regulatory T cells. In vitro, DELAQ activated AhR signaling and induced Ido1 and Ido2 expression in dendritic cells. DELAQ inhibited the activation of naive and memory mouse T cells in an APC-dependent manner, as the response to anti-CD3/CD28 stimulation was unaffected. Importantly, DELAQ suppressed recall responses of human PBMC to tetanus toxoid. ConclusionsLAQ protects against EAU by acting on AhR-expressing antigen-presenting cells to impair both priming and reactivation of pathogenic T cells. Its active metabolite DELAQ does not suppress T cells directly, but re-programs dendritic cells toward a tolerogenic, IDO-expressing phenotype that promotes immune regulation.

immunology↗

bioRxiv2025

Vitamin A is necessary for acquisition, but not for expression or progression, of CNS autoimmunity

Vitamin A (VitA) and its derivative retinoic acid (RA) are essential for immunological responses. In VitA deficient (VAD) mice, acquisition of effector responses is impeded, but little is known about maintenance and expression of previously acquired effector function under the VAD conditions. We examined the impact of VAD on progression of autoimmune diseases using two models of uveitis, experimental autoimmune uveitis (EAU) induced by active immunization and spontaneous uveitis in retina-specific T cell receptor transgenic (R161H) mice, and in the model of experimental autoimmune encephalomyelitis (EAE). VAD was induced by dietary lack of VitA from before birth, or by daily injections of a pan-RA receptor inhibitor BMS493 in adult mice fed with the standard diet. VAD mice were essentially resistant to induction of EAU or EAE and displayed impaired effector T cell responses. Defective priming/acquisition of effector function by VAD T cells was also evident. By contrast, spontaneously uveitic R161H mice fed with VAD diet, in which priming of pathogenic T cells occurs before onset of full VAD, only moderately attenuated uveitis compared to VitA sufficient R161H mice. To reconcile somewhat different results between induced model and spontaneous model of uveitis, we examined EAU in partial VAD mice or adoptive transfer into VAD hosts. The results supported that effector T cells primed in VitA-sufficient environment were able to function in VAD environment and induced EAU. We conclude that although priming of naive T cells in the VAD environment is defective, effector function acquired under VitA sufficient conditions is maintained and can be expressed under VAD conditions. Because dietary lack of VitA is rarely profound and may be seasonal, our findings may shed light on immunity and autoimmunity in geographical regions where dietary VitA is limiting.

immunology↗

bioRxiv2025

Chromosome-scale genome assembly of B10.RIII, an autoimmune susceptible mouse strain

BackgroundA vast majority of potential drug candidates are initially tested in mice before human trials, resulting in life-saving treatments and preventive measures. Hundreds of autoimmune disorders, including arthritis, lupus etc., affect millions of people all over the world. Studying those disorders using mouse models is crucial for understanding the disease mechanisms. Knowing the genome sequence of these mouse models would help with those vital studies. B10.RIII is one of the most susceptible mouse strains used as a model to understand autoimmune diseases but did not have its genome sequenced until now. FindingsIn this study, we generated the first, high-quality chromosome level genome sequence of B10.RIII, using a combination of long read, short read and optical mapping techniques. The B10.RIII genome sequence scored higher than the reference mouse genome both in assembly completeness and assembly quality. The B10.RIII genome annotation based on the reference genome identified about 98% of the known reference genes. ConclusionsWe believe the availability of B10.RIII genome sequence will help advance the understanding of autoimmune diseases, giving the researchers a better idea on its unique genetic makeup. Comparative studies of B10.RIII with other mouse models could also significantly enhance the power of these models towards their clinical applications.

immunology↗

bioRxiv2025

IAN: An Intelligent System for Omics Data Analysis and Discovery

IAN is an R package that addresses the challenge of integrating, analyzing and interpreting high-throughput "omics" data, using a multi-agent artificial intelligence (AI) system. IAN leverages popular pathway and regulatory datasets (KEGG, WikiPathways, Reactome, GO, ChEA) and the STRING database for protein-protein interactions to perform standard enrichment analysis. The individual enrichment results are then used to generate insightful summaries, for each of the datasets, using a large language model (LLM) through a multi-agent architecture. These summaries are then contextually integrated and interpreted by the LLM, guided by carefully engineered prompts and grounding instructions, to provide insightful explanations, system overview, key regulators, novel observations etc. We demonstrate IANs potential to facilitate biological discovery from complex omics data, by reanalyzing two already published data and evaluating the results. We also show remarkable performance of IAN, in terms of avoiding hallucination. IAN package, along with installation instructions and example usage, is available on https://github.com/NIH-NEI/IAN.

bioinformatics↗

bioRxiv2025

AI-Driven Analysis Unveils Functional Dynamics of Müller Cells in Autoimmune Inflammation

Muller cells are the most abundant glial cell type in the human and mouse retina, playing a crucial role in maintaining retinal homeostasis. However, many aspects of Muller cell function remain poorly characterized. In this study, we reanalyzed a single-cell RNA-seq (scRNA-seq) dataset from Aire-/- mice, focusing on Muller cells and T cells. We identified nine distinct Muller cell subgroups and five T cell subgroups, with activated Muller cells comprising the majority of the Muller cells in the inflamed retina. Using SCassist, an AI-based workflow assistant for single-cell analysis, we created a comparison matrix to quantify pathway involvement in each Muller cell subset. This approach unveils the functional dynamics of Muller cells during retinal inflammation. Activated Muller cells primarily exhibit enhanced inflammatory activity and adopt a macrophage or dendritic-cell-like phenotype, in the presence or absence of increased neuronal activity. These changes are primarily driven by Interferon Regulatory Factors (IRFs), acting alone or in concert with Neuronal Differentiation 1 (NEUROD1). We further inferred the interactions between Muller cells and T cells and found that activated Muller cells do not appear to exhibit extra chemoattraction to Th1 cells compared to other Muller cell subsets, but they do show such effects on the Th1-like regulatory T cells (Tregs). Activated Muller cells display nearly exclusive expression of immune checkpoint molecules, primarily targeting Th1 cells. These findings may uncover a previously unrecognized role for activated Muller cells in attenuating Th1 cell activity.

immunology↗

bioRxiv2025

Ocular immune privilege in action: the living eye imposes unique regulatory and anergic gene signatures on uveitogenic T cells

Despite ocular immune privilege, circulating retina-specific T cells can trigger autoimmune uveitis, yet intraocular bleeding--a relatively common event--rarely leads to disease. Using an in vivo immune privilege model, we previously reported that all naive retina-specific T cells entering the eye become primed in situ; about Ob% become FoxpO+ T-regulatory cells (Tregs), while the rest fail to induce pathology. Here, single-cell transcriptomics and functional validation revealed distinct phenotypes in both populations: ocular Tregs were highly suppressive, whereas non-Tregs expressed suppression- and anergy-associated genes and lacked regulatory function. Trajectory analyses suggested that Tregs and anergic cells arise from a common proliferative precursor in parallel, rather than sequentially. Our data indicate a key checkpoint governing the divergence of anergic and regulatory fates. These findings provide molecular-level insights into ocular immune privilege and may inform strategies to silence autoimmune effector cells or reverse T cell unresponsiveness in cancer, vaccination, or chronic infection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=160 SRC="FIGDIR/small/640701v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@1e13f5org.highwire.dtl.DTLVardef@b065feorg.highwire.dtl.DTLVardef@f83014org.highwire.dtl.DTLVardef@1ca8f0_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIEye-primed retina-specific T cells develop distinct tolerance-associated phenotypes. C_LIO_LIEye-induced anergic T cells remain hyporesponsive to antigen re-stimulation. C_LIO_LIRegulatory and anergic T cells differentiate in parallel from a common precursor. C_LIO_LIInduction of T cell anergy is a novel feature of ocular immune privilege. C_LI

immunology↗