Multiomic Patterns in Body Fluids: Technological Challenge With a Great Potential to Implement the Advanced Paradigm of 3p Medicine

Abstract

Liquid biopsy (LB) is defined as a sample of any of body fluids (blood, saliva, tear fluid, urine, sweat, amniotic, cerebrospinal and pleural fluids, cervicovaginal secretion, and wound efflux, amongst others), which can be ex vivo analysed to detect and quantity the target(s) of interest. LB represents diagnostic approach relevant for organ‐specific changes and systemic health conditions including both manifested diseases and their prestages such as suboptimal health. Further, experts emphasise that DNA‐based analysis alone does not provide sufficient information for optimal diagnostics and effective treatments. Consequently, of great scientific and clinical utility are molecular patterns detected by hybrid technologies such as metabolomic tools and molecular imaging. Future proposed strategies utilise multiomic pillars (generally genome, tanscriptome, proteome, metabolome, epigenome, radiome, and microbiome), system‐biological approach, and multivariable algorithms for diagnostic, prognostic, and therapeutic purposes. Current article analyses pros and cons of the mass spectrometry‐based technologies, provides eminent examples of a success story “from discovery to clinical application,” and demonstrates a “road‐map” for the technology‐driven paradigm change from reactive to predictive, preventive and personalised medical services as the medicine of the future benefiting the patient and healthcare at large. © 2019 The Authors. Mass Spectrometry Reviews published by John Wiley & Sons Ltd. Mass Spec Rev

Label-free quantitative identification of abnormally ubiquitinated proteins as useful biomarkers for human lung squamous cell carcinomas

“…Multiomics integration analysis as a powerful tool to promote PPPM Biological omics is driving the paradigm shift of cancer research and treatment from a single-parameter model to a multiparameter model [10,11]. Meanwhile, PPPM strategy in cancer requires multiomics integration analysis, which can systematically explore the molecular mechanisms behind tumorigenesis [8,9,[71][72][73], and this study is an excellent example. The integration analysis of DUP profile and transcriptomics data with clinical information from the TCGA database (n = 494 LSCC patients) identified two prognosisrelated DUPs (vimentin and MRP1), which emphasized the important clinical value of ubiquitination for LSCC patient prognosis.…”

“…It is well-known that LSCC is a complex chronic disease with a series of molecular alterations at the levels of genome, transcriptome, and proteome, and is involved in extensive chronic inflammation in its pathogenesis [6][7][8]. Predictive, preventive, and personalized medicine (PPPM) is an effective strategy to treat LSCC patients [6][7][8][9].…”

“…It is well-known that LSCC is a complex chronic disease with a series of molecular alterations at the levels of genome, transcriptome, and proteome, and is involved in extensive chronic inflammation in its pathogenesis [6][7][8]. Predictive, preventive, and personalized medicine (PPPM) is an effective strategy to treat LSCC patients [6][7][8][9]. Integrative omics-based biomarkers have important scientific merits for insights into the molecular mechanism, discovery of therapeutic targets, and service for early diagnosis and prognostic assessment of LSCC patients to reduce the mortality and improve patient prognosis [10,11].…”

Neutrophil Extracellular Trap Formation Correlates with Favorable Overall Survival in High Grade Ovarian Cancer

“…The tumor microenvironment, including the immune system, may have an important impact on tumor progression and treatment response [1,2]. Focusing on tumor-stroma interactions, we are applying molecular profiling via mass spectrometry (MS), especially by the combination of proteomics, lipidomics, and metabolomics [3][4][5][6]. This approach supports the analysis of pathomechanisms and related adaptative responses such as inflammation in great detail [7,8].…”

Neutrophil extracellular trap formation correlates with improved overall survival in ovarian cancer

“…The tumor microenvironment, including the immune system, may have an important impact on tumor progression and treatment response [1,2]. Focussing on tumor-stroma interactions, we are applying molecular profiling via mass spectrometry (MS), especially by the combination of proteomics, lipidomics and metabolomics [3][4][5][6]. This approach supports the analysis of pathomechanisms and related adaptative responses such as inflammation in great detail [7,8].…”