The Integration of Metabolomics with Other Omics: Insights into Understanding Prostate Cancer

Abstract

Our understanding of prostate cancer (PCa) has shifted from solely caused by a few genetic aberrations to a combination of complex biochemical dysregulations with the prostate metabolome at its core. The role of metabolomics in analyzing the pathophysiology of PCa is indispensable. However, to fully elucidate real-time complex dysregulation in prostate cells, an integrated approach based on metabolomics and other omics is warranted. Individually, genomics, transcriptomics, and proteomics are robust, but they are not enough to achieve a holistic view of PCa tumorigenesis. This review is the first of its kind to focus solely on the integration of metabolomics with multi-omic platforms in PCa research, including a detailed emphasis on the metabolomic profile of PCa. The authors intend to provide researchers in the field with a comprehensive knowledge base in PCa metabolomics and offer perspectives on overcoming limitations of the tool to guide future point-of-care applications.

Metabolomics and Proteomics in Prostate Cancer Research: Overview, Analytical Techniques, Data Analysis, and Recent Clinical Applications

“…The process of analyzing a proteome sample involves separation techniques such as gel electrophoresis for gel-based methods and liquid chromatography (LC) or LC coupled with mass spectrometry (LC-MS) for liquidbased methods [120]. It is worth noting that the cost of implementing proteomics has restricted the number of integrated proteomics-metabolomics studies in the literature, especially when compared to genomics-metabolomics or transcriptomics-metabolomics studies [121]. However, recent developments in proteome mapping and the emergence of top-down proteomics have made this approach more feasible [117].…”

“…For instance, distinguishing between PCa and normal prostate cells is achieved through a combination of proteomics and metabolomics, which enables the analysis of dysregulated lipid metabolism and increased protein phosphorylation [122]. The evolution of computing capabilities has allowed this integrated approach to move beyond simple pathway mapping [121]. In the future, through the integration of various metabolomic datasets and advancements in AI methodologies, novel biomarkers for early cancer detection could be discovered [123].…”

Primary Metabolite Screening Shows Significant Differences between Embryogenic and Non-Embryogenic Callus of Tamarillo (Solanum betaceum Cav.)

“…Unlike other omics, the metabolome is highly sensitive to stimuli and provides a snapshot of the real-time physiological state of the observed system. Additionally, complex mechanisms of information transfer between other omics layers (post-transcription and post-translation) do not always allow omics like transcriptomics and proteomics to correlate with the observed phenotype [92]. With this in mind, we performed an untargeted analysis of the calli metabolome to obtain insight into the principal metabolic mechanisms that drive somatic embryogenesis.…”

Controlling the confounding effect of metabolic gene expression to identify actual metabolite targets in microsatellite instability cancers

“…In addition, research has indicated the direct involvement of the metabolome in genome regulation [11]. Metabolomics also serves as an input that influences genomic alteration to form a feedback loop [12,13]. There are interactions between metabolites and gene expression [14,15].…”