Systems biology in inflammatory bowel diseases: on the way to precision medicine

Abstract

Inflammatory bowel diseases (IBD) are chronic and recurrent inflammatory disorders of the gastrointestinal tract. The elucidation of their etiopathology requires complex and multiple approaches. Systems biology has come to fulfill this need in approaching the pathogenetic mechanisms of IBD and its etiopathology, in a comprehensive way, by combining data from different scientific sources. In combination with bioinformatics and network medicine, it uses principles from computer science, mathematics, physics, chemistry, biology, medicine and computational tools to achieve its purposes. Systems biology utilizes scientific sources that provide data from omics studies (e.g., genomics, transcriptomics, etc.) and clinical observations, whose combined analysis leads to network formation and ultimately to a more integrative image of disease etiopathogenesis. In this review, we analyze the current literature on the methods and the tools utilized by systems biology in order to cover an innovative and exciting field: IBD-omics.

Differential genetic and functional background in inflammatory bowel disease phenotypes of a Greek population: a systems bioinformatics approach

“…As previous works [59–63] have shown, traditional IBD treatments like glucosteroids and azathioprine, but also newer approaches like anti-TNF, are all susceptible to inefficiency due to specific genetic polymorphisms. The IBD landscape is vast and includes many factors and pitfalls that should be considered when trying to identify “who” is responsible for disease onset, progression and treatment, by making use of various technical approaches, each targeting a different subsystem [64]. Highlighted among these factors, the microbiome, has become a scientific trend in recent years due to its apparent implication in various diseases, especially IBD.…”

Response to Anti-α4β7 Blockade in Patients With Ulcerative Colitis Is Associated With Distinct Mucosal Gene Expression Profiles at Baseline

“…36 This is coupled with bioinformatics, which further illuminates the principal mechanisms that may be associated with response to treatment, emphasizing the pathogenetic and therapeutic significance of specific pathways. 37 As such reports have started to accumulate, validation across patient cohorts will be of paramount importance. In our current study, we used a targeted microarray approach, which both confirms several already existing findings but also expands the number of potential biomarkers for vedolizumab response in UC.…”

Tailoring Multi-omics to Inflammatory Bowel Diseases: All for One and One for All

“…The current standard of care which includes histological examination (used currently only for diagnosis and not for therapeutic endpoints) following endoscopy does not capture the fine-prints of disease biology such as cellular heterogeneities, cell-type specific expression, interactions among cell-types and microbial influences. In response, new approaches like systems biology which integrates high-throughput datasets profiling different layers of biological organization and the network of molecular interactions have often been suggested as the "holy-grail" for understanding and treating IBD as well as other complex diseases [32][33][34][35][36] . However, despite the advances made in experimental (sequencing, high throughput genotyping etc) and computational methodologies (machine learning, data analysis tools etc), the -omic datasets in the IBD field are sparse and scattered leading to incomplete coverage across -omic layers (genome, transcriptome, proteome, metabolome etc).…”