Application of spatial omics, multi-omics, and artificial intelligence in inflammatory bowel disease: Current applications and emerging opportunities

Table 2 Summary of representative multi-omics, spatial omics, and artificial intelligence studies in inflammatory bowel disease, highlighting datasets, methodologies, and principal findings

Ref.	Technology/modality	Sample type	Cohort size	Analytical approach	Key findings	Clinical/translational relevance
Uniken Venema et al[43]	Epigenomics (DNA methylation)	Blood	240 IBD, 190 controls	Epigenome-wide methylation profiling	Differential methylation at VMP1, ITGB2	Links genetic risk loci to environmental regulation
Chan et al[65]	Proteomics (LC-MS/MS)	Colonic biopsies	10 UC, 10 controls	Gel-free quantitative proteomics	High level of neutrophil-related proteins (calprotectin, lactotransferrin)	Tissue-level inflammatory biomarkers
Quiroga-Centeno et al[84]	Metabolomics (HPLC)	Serum	> 530 IBD	Targeted metabolite profiling	Low levels of tryptophan correlate with disease activity	Potential metabolic biomarker
Aichler and Walch[103]	Spatial transcriptomics, scRNA-seq	Intestinal tissue	Human IBD biopsies	Single-cell, spatial mapping	IDA macrophages, NRG1-dependent epithelial regeneration	Defines pathogenic immune niches
Lins Neto et al[97]	Imaging mass cytometry	Intestinal tissue	Human IBD	Multiplex spatial proteomics	Disease-specific immune-cell neighborhoods	Spatial immune architecture as a biomarker
Mund et al[104]	10 × Visium spatial transcriptomics	Postoperative CD biopsies	43 biopsies	Spatial pathway analysis	TNF, NF-κB, and JAK-STAT are conserved across sites	Shared inflammatory programs
Garrido-Trigo et al[113]	AI (CNN model)	Endoscopic images	Large UC dataset	Deep learning severity scoring	Continuous inflammation scoring (UCEGS)	Objective endoscopic grading
Nair et al[161]	Blood transcriptomics	Blood	IBD patients	Machine learning classifier	Prognostic biomarker for disease course	Patient stratification
Kim et al[132]	Spatial multi-omics (MicroCart)	Murine colitis	Experimental	Integrated host-microbiome mapping	Coordinated immune epithelial microbial niches	Spatial host-microbiome cartography

LC-MS/MS: Liquid chromatography-mass spectrometry/mass spectrometry; HPLC: High performance liquid chromatography; scRNA-seq: Single-cell RNA-sequencing; CNN: Convolutional neural network; AI: Artificial intelligence; MicroCart: Microbiome cartography; CD: Crohn’s disease; IBD: Inflammatory bowel disease; UC: Ulcerative colitis; VMP1: Vacuole membrane protein 1; ITGB2: Integrin subunit β2; IDA: Inflammation-dependent activated macrophages; TNF: Tumor necrosis factor; NF-κB: Nuclear factor kappa-B; JAK-STAT: Janus tyrosine kinase/signal transducer and activator of transcription; UCEGS: Ulcerative colitis endoscopic index of severity.