Nikhat, Sameena

Autoimmune diseases arise from a breakdown of immune tolerance and complex interplay of genetic susceptibility, environmental triggers, tissue-specific immune responses, microbiota, and regulatory pathways. Mouse models remain essential for dissecting these mechanisms, but no single model fully reproduces the heterogeneity, chronicity, and immune complexity of autoimmune disease in humans. This review summarizes classical murine and humanized mouse models used to study inflammatory bowel disease (IBD), multiple sclerosis (MS), type-1 diabetes (T1D), and rheumatoid arthritis (RA). We also highlight disease-specific scoring systems, including clinical indices, histopathology, imaging, cytokine profiling, autoantibody assessment, and human immune-cell readouts, as essential tools for standardized interpretation. Conventional murine models provide experimental control and mechanistic clarity, whereas humanized models improve assessment of human immune responses, patient-specific biology, and therapeutic translation. However, humanized systems remain limited by incomplete immune reconstitution, graft-versus-host disease, donor variability, cost, and incomplete tissue architecture. By providing a comparative framework spanning both conventional and humanized models, this review aims to guide informed model selection tailored to specific research questions in autoimmune disease biology and translational therapeutic development.

ABSTRACT We report the optimization of a 38‐parameter spectral flow cytometry panel to identify, phenotype, and assess lineage plasticity of human regulatory T cells (Tregs). Tregs are an indispensable T cell lineage with pleiotropic tolerogenic functions whose activities contribute critically to numerous disease settings including cancer, autoimmunity, and infectious disease, among others. Phenotypic and functional heterogeneity within the Treg lineage has been appreciated, but the etiology and impact of Treg plasticity across disease states remain incompletely understood. Better tools are thus needed to deeply characterize human Treg phenotypic heterogeneity at the single cell level to advance discovery of Treg‐based biomarkers in disease and to assess the effects of Treg‐directed therapeutics. To this end, our 38‐parameter panel consists of a 13‐marker PBMC backbone module to broadly phenotype PBMCs while specifically discriminating Tregs, and a 25‐marker Treg phenotyping module to determine Treg differentiation state, activation profile, and lineage subtype. In contrast to many high‐parameter OMIPs that rely on surface staining only, we incorporated several intracellular targets in this panel. This afforded the opportunity to thoroughly evaluate binding characteristics of all antibodies in both pre‐fixation and post‐fixation and permeabilization settings; we identify several antibodies eligible for overnight post‐fixation staining that require substantially reduced titers as compared to traditional pre‐fixation staining, resulting in significant cost savings. Dimensionality reduction and semi‐supervised clustering on healthy donor PBMC‐derived Tregs profiled by our panel reveal up to 14 discrete Treg phenotypes. In sum, this panel enables deep phenotypic characterization of human Treg heterogeneity in peripheral blood specimens by spectral flow cytometry.