Proteomics and Lipidomics in Inflammatory Bowel Disease Research: From Mechanistic Insights to Biomarker Identification

Abstract

Inflammatory bowel disease (IBD) represents a group of progressive disorders characterized by recurrent chronic inflammation of the gut. Ulcerative colitis and Crohn′s disease are the major manifestations of IBD. While our understanding of IBD has progressed in recent years, its etiology is far from being fully understood, resulting in suboptimal treatment options. Complementing other biological endpoints, bioanalytical “omics” methods that quantify many biomolecules simultaneously have great potential in the dissection of the complex pathogenesis of IBD. In this review, we focus on the rapidly evolving proteomics and lipidomics technologies and their broad applicability to IBD studies; these range from investigations of immune-regulatory mechanisms and biomarker discovery to studies dissecting host–microbiome interactions and the role of intestinal epithelial cells. Future studies can leverage recent advances, including improved analytical methodologies, additional relevant sample types, and integrative multi-omics analyses. Proteomics and lipidomics could effectively accelerate the development of novel targeted treatments and the discovery of complementary biomarkers, enabling continuous monitoring of the treatment response of individual patients; this may allow further refinement of treatment and, ultimately, facilitate a personalized medicine approach to IBD.

Integrating omics for a better understanding of Inflammatory Bowel Disease: a step towards personalized medicine

“…Previous studies have showed differences in the metabolic and lipidomic profiles of IBD patients when compared with the healthy controls [146] [77]. Recent analysis of the lipidome profiles of IBD patients also reflected the role of several pathways that are crucial for epithelial homeostasis, including barrier function and innate immune response [150]. Moreover, Scoville et al showed that the serum metabolomic profile in IBD patients reflected differences in a number of lipid, amino acid, and tricarboxylic acid cycle related metabolites when compared to the healthy controls [151].…”

Comparison of the systemic phospholipid profile in dogs diagnosed with idiopathic inflammatory bowel disease or food-responsive diarrhea before and after treatment

“…Former studies have demonstrated phosphatidylcholine to possess anti-inflammatory properties and to be beneficial in humans with ulcerative colitis [61,81]. Moreover, patients with ulcerative colitis were reported to have significantly lower levels of phosphatidylcholine and lysophosphatidylcholine compared to healthy controls [82,83]. In the current study, lysophosphatidylcholine species were also significantly relevant to differentiate between treatment statuses in dogs with FRD, with lysophosphatidylcholine species being important after treatment.…”

Proteomic analysis-based discovery of a novel biomarker that differentiates intestinal Behçet’s disease from Crohn’s disease

“…Proteomic analysis is a promising technology that is a powerful tool for identifying biomarkers to help diagnose and choose personalized treatment. It allows high-throughput study of protein expression with high accuracy, sensitivity, and repeatability, and it enables the identification of molecular mechanisms that are responsible for the development of a specific disease 11 , 12 . The tandem mass tag (TMT)-liquid chromatography-tandem mass spectrometric (LC–MS/MS) method has been recently developed to identify and quantify proteins.…”