Evolving systems biology approaches to understanding non-coding RNAs in pulmonary hypertension

Comprehensive review for non-coding RNAs: From mechanisms to therapeutic applications

Non-coding RNAs (ncRNAs) are an assorted collection of transcripts that are not translated into proteins. Since their discovery, ncRNAs have gained prominence as crucial regulators of various biological functions across diverse cell types and tissues, and their abnormal functioning has been implicated in disease. Notably, extensive research has focused on the relationship between microRNAs (miRNAs) and human cancers, although other types of ncRNAs, such as long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs), are also emerging as significant contributors to human disease. In this review, we provide a comprehensive summary of our current knowledge regarding the roles of miRNAs, lncRNAs, and circRNAs in cancer and other major human diseases, particularly cancer, cardiovascular, neurological, and infectious diseases. Moreover, we discuss the potential utilization of ncRNAs as disease biomarkers and as targets for therapeutic interventions.

Evolving Schema for Employing Network Biology Approaches to Understand Pulmonary Hypertension

Reductionist approaches have served as the cornerstone for traditional mechanistic endeavors in biomedical research. However, for pulmonary hypertension (PH), a relatively rare but deadly vascular disease of the lungs, the use of traditional reductionist approaches has failed to define the complexities of pathogenesis. With the development of new -omics platforms (i.e., genomics, transcriptomics, proteomics, and metabolomics, among others), network biology approaches have offered new pipelines for discovery of human disease pathogenesis. Human disease processes are driven by multiple genes that are dysregulated which are affected by regulatory networks. Network theory allows for the identification of such gene clusters which are dysregulated in various disease states. This framework may in part explain why current therapeutics that seek to target a single part of a dysregulated cluster may fail to provide clinically significant improvements. Correspondingly, network biology could further the development of novel therapeutics which target clusters of "disease genes" so that a disease phenotype can be more robustly addressed. In this chapter, we seek to explain the theory behind network biology approaches to identify drivers of disease as well as how network biology approaches have been used in the field of PH. Furthermore, we discuss an example of in silico methodology using network pharmacology in conjunction with gene networks tools to identify drugs and drug targets. We discuss similarities between the pathogenesis of PH and other disease states, specifically cancer, and how tools developed for cancer may be repurposed to fill the gaps in research in PH. Finally, we discuss new approaches which seek to integrate clinical health record data into networks so that correlations between disease genes and clinical parameters can be explored in the context of this disease.

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

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.