Integration and implementation of precision medicine in the multifaceted inflammatory bowel disease

Table 1 Studies utilizing multiomics in inflammatory bowel disease

No.	Ref.	Type of study	Number of participants	Type of omics utilized	Results
1	Lloyd-Price et al[75]	Cohort study	132 IBD	Microbiome; genome; metagenome; meta; transcriptome; metabolome profiles; proteome	Found functional dysbiosis in the gut microbiome, changes in metabolite pools, and increased levels of antibodies in serum during periods of inflammatory bowel disease activity
2	Mills et al[83]	Cohort study	-40 UC, -validation cohort: 73 UC, 117 CD, 20 controls	Proteome; metaproteome; metabolome; metagenome; meta peptidome	UC patients with active disease had increased protease activity that originated from the bacterium Bacteroides vulgatus
3	Zhang et al[84]	Cohort study	25 CD, 22 UC, 24 controls	Metaproteome; microbiome	Identified 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
4	Lee et al[74]	Prospective study	108 CD, 77 UC	Metabolome; microbiome; metagenome; proteome	Microbial, 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
5	Dai et al[85]	Prospective study	5956 CD, 21770 controls	Genome; epigenome; transcriptome	Identified 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
6	Suskind et al[86]	Randomized controlled trial	10 CD	Microbiome; metagenome; metaproteome; metabolome	Diet had a positive effect on CD patient symptoms and inflammation; Specific exclusionary diets were associated with a better resolution of inflammation
7	Borren et al[87]	Cohort study	108 CD, 56 UC	Proteome; metabolome; microbiome	Identified proteomic, metabolomic, and microbiome biomarkers that characterized a proinflammatory state in quiescent IBD patients and predicted clinical relapse
8	Liu et al[88]	Prospective study	42 UC, 11 controls	Metabonome; microbiome	Identified that the combination of Verrucomicrobiota, butyric acid, and isobutyric acid improved the prediction of early remission to anti-integrin therapy
9	Huang et al[89]	Cohort study	140 CD, 73 UC, 86 controls	Metagenome; meta transcriptome; proteome; metabolome; virome; microbiome	Established artificial intelligence models that can subtype IBD with high accuracy using simple noninvasive fecal biomarkers and avoiding invasive procedures
10	Mishra et al[60]	Cohort study	37 IBD	Genome; epigenome	Identified biomarkers of early shifts in gene expression and DNA methylation for early prediction of anti-TNF treatment success
11	Gonzalez et al[90]	Cohort study	200 IBD	Microbiome; metabolome; metaproteome; metagenome	Identified 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
12	Xu et al[91]	Cohort study	Discovery: 6 datasets, Validation: 46 CD, 44 controls	Genome; transcriptome; Epigenome; microbiome	Identified that CD onset results from a number of oxidative stress genes through DNA methylation, gene expression, and host-microbiota interactions
13	Gao et al[92]	Cohort study	30 CD, 5 controls	Proteome; microbiome; metagenome	Identified 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
14	Baran et al[93]	Cohort study	18 IBD	Epigenome; transcriptome; genome	Therapeutic response causes transcriptional changes in the mucosa and early changes in gene expression in peripheral blood that are regulated epigenetically

IBD: Inflammatory bowel disease; UC: Ulcerative colitis; CD: Crohn’s Disease; IL: Interleukin; TNF: Tumor necrosis factor.