The Integrated Cellular and Molecular Landscape of Autoimmunity
Appierdo, R.; Pepe, G.; Helmer-Citterich, M.; Sirota, M.; Vallania, F.; Gherardini, P. F.
Show abstract
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 particular, was associated with disease severity and predicted treatment response across multiple conditions. This modular framework offers a powerful tool for understanding immune dysregulation and advancing precision medicine in autoimmune diseases. To support reproducibility and enable others to build upon this work, we developed an interactive app to explore and download the complete dataset and associated results.
Matching journals
The top 10 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- High throughput profiling of the B cell repertoire identifies systematic changes in the repertoire of individuals with Crohn's disease 95%
- Interleukin-36 upregulates type-I interferon responses in systemic lupus erythematosus by promoting the accumulation of self-nucleic acids 94%
- Cross-Tissue Transcriptomic Analysis Leveraging Machine Learning Approaches Identifies New Biomarkers for Rheumatoid Arthritis 94%
Similar papers in this journal
- Enhanced NF-κB signaling in type-2 dendritic cells at baseline predicts non-response to adalimumab in psoriasis 95%
- Plasmacytoid dendritic cells are functionally exhausted while non-haematopoietic sources of type I interferon dominate human autoimmunity 95%
- Immunosuppression causes dynamic changes in expression QTLs in psoriatic skin 94%
Similar papers in this journal
Similar papers in this journal
- Interpretable machine learning identifies paediatric Systemic Lupus Erythematosus subtypes based on gene expression data 95%
- Large-scale Analyses of Disease Biomarkers and Apremilast Pharmacodynamic Effects 94%
- Integrated Single Cell and Spatial Transcriptomics Reveal Autoreactive Differentiated B Cells in Joints of Early Rheumatoid Arthritis 94%
Similar papers in this journal
- Multimodal repertoire analysis unveils B cell biology in immune-mediated diseases 95%
- Distinct immune-effector and metabolic profile of CD8 + T Cells in patients with autoimmune polyarthritis induced by therapy with immune-checkpoint inhibitors 94%
- Meta-analysis of 208,370 East Asians identifies 113 genomic loci and yields new non-immune cell relevant biological insights for systemic lupus erythematosus 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.