Mass-spectrometry based multi-omics profiling of human disease for early stage biomarker identification and functional pathway level analysis

Date
2025
DOI
Authors
Moore, Jarrod Robeson
Version
OA Version
Citation
Abstract
Human disease is driven by complex molecular cascades, genetic perturbations, and environmental factors. Systems biology research aims to address the challenge of mapping such complexity by employing high-throughput, multi-omics analyses (e.g. proteomics and metabolomics) to characterize the molecular basis of disease. Liquid chromatography-tandem mass spectrometry is one of the most important tools for functional proteomics and metabolomics-based systems biology approaches. In conjunction with computational tools, these analyses can identify and quantify thousands of potential biomarkers of disease progression for exploratory, mechanistic and clinical studies. Moreover, these analyses can reveal complex biological networks, which are useful for elucidating the fundamental biochemical cascades underlying a myriad of pathologies. Here, I utilized this framework to characterize early stage molecular profiles associated with two complex diseases, hypertrophic cardiomyopathy and Barrett’s esophagus, which impact cardiac and gastrointestinal health, respectively. In our hypertrophic cardiomyopathy study, I quantified changes in antioxidant and mitochondrial dynamics throughout early and advanced disease, both these processes are implicated in the altered function of diseased cardiomyocytes. In addition, using human induced pluripotent stem cell-derived mutant cardiomyocytes as a model of early stage disease, I demonstrated increased glutaminolysis that reflects biosynthetic remodeling , replenishing the Krebs cycle intermediate 2-oxoglutarate via transamination of glutamate, as well as providing a major precursor for glutathione synthesis. Our analysis of these mutant cell cultures showed increased metabolic activity supplemented by glutaminolysis concomitant with significant activation of the sarcoplasmic reticulum calcium-handling machinery. In contrast, advanced disease samples exhibited decreased glutamate degradation, a pathway downstream of glutamine anaplerosis. Further underscoring this opposite trend in advanced disease, I also observed decreased sarcoplasmic reticulum handling of calcium, correlated with decreased protein phosphorylation, suggesting a lower burden of ATPase-dependent activity, perhaps due to decompensated ATP production. From our Barrett’s esophagus investigation, I identified a robust proteomic signature that accurately classified the pathological status of samples from independent patient cohorts. Pathway-level analysis of these phosphoproteomic profiles revealed the dysregulation of specific cellular processes, including DNA repair, in afflicted tissue relative to paired unaffected controls. Comparative analysis with previously published transcriptomic profiles provided independent evidence in support of these preliminary findings. Together, these findings provide functional insights into disease-specific maladaptive changes during pathological progression, and demonstrate a generalizable strategy for applying mass spectrometry-based systems biology towards translational research.
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