biostudies-literatureUnknownAppierdo RNIAMS NIH HHSWe performed a large-scale immunogenomic analysis of ~13,000 transcriptomic profiles from 10 autoimmune diseases, integrating publicly available datasets from both blood and tissue. Using meta-analysis, we identified core immune mechanisms underlying autoimmunity, including strong interferon responses, inflammation, and adaptive immune suppression, alongside disease-specific signatures. To enhance biological interpretability, we derived higher-order immune features - such as cell type proportions, cytokine levels, pathway activity, transcription factor regulation, and miRNA activity - and organized them into 15 coherent immune modules. These modules enabled systematic cross-disease comparisons, revealing shared and distinct immunopathological patterns. The inflammation module, in particulabioRxiv : the preprint server for biology2025.09.12.675833https://www.ebi.ac.uk/biostudies/studies/S-EPMC12458282biostudies-literatureThe Integrated Cellular and Molecular Landscape of Autoimmunity.PMC12458282P30 AR070155Appierdo RPepe GSirota MHelmer-Citterich MGherardini PFVallania FfalseThe Integrated Cellular and Molecular Landscape of Autoimmunity.We performed a large-scale immunogenomic analysis of ~13,000 transcriptomic profiles from 10 autoimmune diseases, integrating publicly available datasets from both blood and tissue. Using meta-analysis, we identified core immune mechanisms underlying autoimmunity, including strong interferon responses, inflammation, and adaptive immune suppression, alongside disease-specific signatures. To enhance biological interpretability, we derived higher-order immune features - such as cell type proportions, cytokine levels, pathway activity, transcription factor regulation, and miRNA activity - and organized them into 15 coherent immune modules. These modules enabled systematic cross-disease comparisons, revealing shared and distinct immunopathological patterns. The inflammation module, in particula2025-01-01T00:00:00Z2025 Sep2026-05-05T03:13:22.045Z2026-05-05T03:12:18.008ZS-EPMC124582824100068010.1101/2025.09.12.675833