Characterizing cellular subpopulations critical to treatment response in autoimmune diseases

Single-cell RNA sequencing provides a powerful approach for characterizing cell types, states, and lineages within heterogeneous tissues. However, identifying cell subpopulations that drive phenotypes, particularly treatment responses, remains a challenge. In this study, we performed comprehensive analyses to identify treatment response-associated cell subpopulations in autoimmune diseases by mapping bulk response information onto single-cell data. We integrated single-cell and bulk biopsy data from 314 responders and 619 non-responders treated with six therapeutics targeting tumor necrosis factor (TNF), integrin, or interleukin pathways in inflammatory bowel diseases (IBD) and psoriasis (PsO). Our analyses captured 128,428 interactions among 3,617 differentially expressed genes (DEGs), 852 pathways, and nine cell types spanning immune, stromal, and epithelial compartments. The importance of epithelial barrier integrity and enterocyte-mediated permeability in responses and inflammatory signaling in macrophages in non-responses in all tested therapies were highlighted by the presence of shared DEGs and pathways in both Crohns disease (CD) and ulcerative colitis (UC). In PsO, keratinocytes drove non-response to integrin-targeting therapies via disrupted adhesion, migration, and sustained epidermal inflammation. Additionally we introduce SCTRAD (https://immbioinfoabbv.shinyapps.io/SCTRAD/), an online web-based platform that allows exploration of mechanisms that influence the heterogeneity of cellular responses through DEGs and pathways at the single-cell level, as well as analysis of the cell-type-specific drug-related gene network. Our findings provide a comprehensive analysis of the role of cellular heterogeneity in treatment outcomes and for advancing precision medicine strategies in autoimmune diseases.