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Copyright ©The Author(s) 2023.
World J Gastroenterol. Sep 28, 2023; 29(36): 5211-5225
Published online Sep 28, 2023. doi: 10.3748/wjg.v29.i36.5211
Table 1 Studies utilizing multiomics in inflammatory bowel disease
No.
Ref.
Type of study
Number of participants
Type of omics utilized
Results
1Lloyd-Price et al[75]Cohort study132 IBDMicrobiome; genome; metagenome; meta; transcriptome; metabolome profiles; proteomeFound functional dysbiosis in the gut microbiome, changes in metabolite pools, and increased levels of antibodies in serum during periods of inflammatory bowel disease activity
2Mills et al[83]Cohort study-40 UC, -validation cohort: 73 UC, 117 CD, 20 controlsProteome; metaproteome; metabolome; metagenome; meta peptidomeUC patients with active disease had increased protease activity that originated from the bacterium Bacteroides vulgatus
3Zhang et al[84]Cohort study25 CD, 22 UC, 24 controlsMetaproteome; microbiomeIdentified functional alterations of microbiome and associated microbial proteins in the intestinal mucosa in new-onset pediatric IBD patients which contributed to abnormal host-microbiota interactions
4Lee et al[74]Prospective study108 CD, 77 UCMetabolome; microbiome; metagenome; proteomeMicrobial, metagenomic diversity and metabolomics (serum secondary bile acid concentrations) predicted response in moderate-to-severe Crohn’s disease or ulcerative colitis patients initiating anti-cytokine therapy (anti-TNF or -IL12/23) or anti-integrin therapy
5Dai et al[85]Prospective study5956 CD, 21770 controlsGenome; epigenome; transcriptomeIdentified strongly associated CD genes involved in immune response, MHC class II receptor activity, and immunological disorders. Involvement of constitutive photomorphogenesis 9 signalosome in CD pathogenesis. Interactions among CD genes with CD drug target genes
6Suskind et al[86]Randomized controlled trial10 CDMicrobiome; metagenome; metaproteome; metabolomeDiet had a positive effect on CD patient symptoms and inflammation; Specific exclusionary diets were associated with a better resolution of inflammation
7Borren et al[87]Cohort study108 CD, 56 UCProteome; metabolome; microbiomeIdentified proteomic, metabolomic, and microbiome biomarkers that characterized a proinflammatory state in quiescent IBD patients and predicted clinical relapse
8Liu et al[88]Prospective study42 UC, 11 controlsMetabonome; microbiomeIdentified that the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the prediction of early remission to anti-integrin therapy
9Huang et al[89]Cohort study140 CD, 73 UC, 86 controlsMetagenome; meta transcriptome; proteome; metabolome; virome; microbiomeEstablished artificial intelligence models that can subtype IBD with high accuracy using simple noninvasive fecal biomarkers and avoiding invasive procedures
10Mishra et al[60]Cohort study37 IBDGenome; epigenomeIdentified biomarkers of early shifts in gene expression and DNA methylation for early prediction of anti-TNF treatment success
11Gonzalez et al[90]Cohort study200 IBDMicrobiome; metabolome; metaproteome; metagenomeIdentified colonic- and ileal-isolated CD subtypes had different pathologies. Colonic CD was similar to ulcerative colitis with neutrophil and Bacteroides vulgatus involvement while Ileal-isolated CD had a bile acid-driven profile
12Xu et al[91]Cohort studyDiscovery: 6 datasets, Validation: 46 CD, 44 controlsGenome; transcriptome; Epigenome; microbiomeIdentified that CD onset results from a number of oxidative stress genes through DNA methylation, gene expression, and host-microbiota interactions
13Gao et al[92]Cohort study30 CD, 5 controlsProteome; microbiome; metagenomeIdentified alterations in proteins, microbiome, and metabolic processes across multi-tissues in CD patients that are imprinted in serum and fecal samples as potential diagnostic biomarkers, allowing a non-invasive precision diagnosis
14Baran et al[93]Cohort study18 IBDEpigenome; transcriptome; genomeTherapeutic response causes transcriptional changes in the mucosa and early changes in gene expression in peripheral blood that are regulated epigenetically