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

Abstract

Background: Inflammatory Bowel Disease (IBD) is a multifactorial chronic disease. Understanding only one aspect of IBD pathogenesis does not reflect the complex nature of IBD nor will it improve its clinical management. Therefore, it is vital to dissect the interactions between the different players in IBD pathogenesis in order to understand the biology of the disease and enhance its clinical outcomes. Aims:To provide an overview of the available omics data used to assess the potential mechanisms through which various players are contributing to IBD pathogenesis and propose a precision medicine model to fill the current knowledge gap in IBD.Results: Several studies have reported microbial dysbiosis, immune and metabolic dysregulation in IBD patients, however, this data is not sufficient to create signatures that can differentiate between the disease subtypes or between disease relapse and remission. Conclusions:We summarized the current knowledge in the application of omics in IBD patients, and we showed that the current knowledge gap in IBD hinders the improvements of clinical decision for treatment as well as the prediction of disease relapse. We propose one way to fill this gap by implementing integrative analysis of various omics datasets generated from one patient at a single time point.

A literature-based approach for curating gene signatures in multifaceted diseases

“…However, the available data is a valuable resource for large-scale mining of genes associated/reported with IBD. Systems biology and reductionist approaches have identified several key genes or pathways for determining and characterizing the cause and progression of IBD [ 12 , 13 ]. However, extrapolating and summarizing the results have been difficult due to the heterogeneity of datasets and experimental designs.…”

“…LitLab Gene Retriever application ( https://www.acumenta.com/generetriever ) retrieves genes associated with a publication list and is useful in specific search strategies or under less known conditions, as for the case of IBDU. As IBD etiology has a major immune component [ 12 ], we focused our targeted panel by retrieving genes associated with PubMed IDs (PMIDs) supporting the association between IBD and mucosal immunity (List 5, Fig. 1 —Gene lists).…”

“…Preliminary results from this cohort showed that the gene panel contained the necessary element to differentiate the transcriptomic signatures of UC patients in remission versus flare (data not shown). Nevertheless, our results may provide a promising base for future transcriptomic analyses, in the context of extrapolating and summarizing publicly available gene biomarker studies or multi-omics approach-type of studies [ 12 ].…”

Enteric Viruses and Inflammatory Bowel Disease

“…Real-time integrated studies are needed to decipher the mechanisms underlying IBD pathogenesis. Such studies would then contribute to the development of personalized therapeutic approaches to IBD [ 97 , 98 , 99 ]. With the advent of artificial intelligence and big data, analysis of the “integratome” (from the so-called “integrated omics”) should also open new avenues of research for enteric virus infections in IBD [ 100 ].…”

NADPH oxidase inhibition rescues keratinocytes from elevated oxidative stress in a 2D atopic dermatitis and psoriasis model

“…The novel inhibitors ML171 and GKT136901 selectively inhibit NOX1 and NOX1/NOX4, respectively. [46][47][48][49][50] Clinical trials with 170 patients have demonstrated that the novel inhibitors are well-tolerated and non-toxic, and thus provide a good alternative for DPI. [50] In this study, we controlled for the possible unspecific effects of DPI by additionally analysing intracellular ROS levels after inhibition of NOX1 and NOX1/4 by the selective inhibitors.…”