ArticleNature communications2022
A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis.
Article in Nature communications, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 25 citations in OpenAlex.
- Decoding non-coding SNPs: systems genomics modelling dissects the heterogeneity of IBD.Molecular systems biology · 2026Article
- PatientProfiler: building patient-specific signaling models from proteogenomic data.Molecular systems biology · 2025Article
- WTAP-mediated mHuman cell · 2025Article
- Patient-Specific Regulatory Network Rewiring in Inflammatory Bowel Disease: How Genetic Polymorphisms Divert Incoming Signals and Contribute to Disease Pathogenesis.Inflammatory bowel diseases · 2025Article
- MicroRNA-microbiota interactions: Emerging strategies for modulating intestinal homeostasis and enhancing host health.iMetaOmics · 2025Review
- Phillygenin ameliorates tight junction proteins reduction, fibrosis, and apoptosis in mice with chronic colitis via TGR5-mediated PERK-eIF2α-CaJournal of pharmaceutical analysis · 2025Article
- Identifying patient subgroups in MASLD and MASH-associated fibrosis: molecular profiles and implications for drug development.Scientific reports · 2024Article
- Integrating multi-omics to unravel host-microbiome interactions in inflammatory bowel disease.Cell reports. Medicine · 2024Review
- Revolutionizing immune research with organoid-based co-culture and chip systems.Clinical and experimental immunology · 2024Review
- Individual-network based predictions of microbial interaction signatures for response to biological therapies in IBD patients.Frontiers in molecular biosciences · 2024Article
- Updated immunomodulatory roles of gut flora and microRNAs in inflammatory bowel diseases.Clinical and experimental medicine · 2023Review
- Investigating the Crime Scene-Molecular Signatures in Inflammatory Bowel Disease.International journal of molecular sciences · 2023Review
- A multi-omic analysis reveals the esophageal dysbiosis as the predominant trait of eosinophilic esophagitis.Journal of translational medicine · 2023Article
- Functional Genomics Analysis to Disentangle the Role of Genetic Variants in Major Depression.Genes · 2022Article
- Network Biology Approaches to Achieve Precision Medicine in Inflammatory Bowel Disease.Frontiers in genetics · 2021Review
- Review
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Authors and funding
19 authors at 8 institutions in 4 countries.
Funding
Abstract
We describe a precision medicine workflow, the integrated single nucleotide polymorphism network platform (iSNP), designed to determine the mechanisms by which SNPs affect cellular regulatory networks, and how SNP co-occurrences contribute to disease pathogenesis in ulcerative colitis (UC). Using SNP profiles of 378 UC patients we map the regulatory effects of the SNPs to a human signalling network containing protein-protein, miRNA-mRNA and transcription factor binding interactions. With unsupervised clustering algorithms we group these patient-specific networks into four distinct clusters driven by PRKCB, HLA, SNAI1/CEBPB/PTPN1 and VEGFA/XPO5/POLH hubs. The pathway analysis identifies calcium homeostasis, wound healing and cell motility as key processes in UC pathogenesis. Using transcriptomic data from an independent patient cohort, with three complementary validation approaches focusing on the SNP-affected genes, the patient specific modules and affected functions, we confirm the regulatory impact of non-coding SNPs. iSNP identified regulatory effects for disease-associated non-coding SNPs, and by predicting the patient-specific pathogenic processes, we propose a systems-level way to stratify patients.
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