Clinical trans-omics: an integration of clinical phenomes with molecular multiomics

Wang, Xiangdong

doi:10.1007/s10565-018-9431-3

Cited by 56 publications

(44 citation statements)

References 18 publications

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“…While multi‐omics investigates the networks and correlations amongst genes, proteins, and metabolites, it is believed that trans‐omics will provide the full picture of patient phenome‐based molecular networks, making a step forward toward personalized medicine. [ 117 ] Despite trans‐omics is still in its early days, it represents a step forward in integrative medicine and it is anticipated that it will help characterizing patients, identifying new disease‐specific biomarkers and targets, and uncovering mechanisms underlying drug responsiveness.…”

Section: Discussionmentioning

confidence: 99%

Proteomic and Transcriptomic Approaches for Studying Bone Regeneration in Health and Systemically Compromised Conditions

Calciolari

Donos

2020

Proteomics Clinical Apps

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Bone regeneration is a complex biological process, where the molecular mechanisms are only partially understood. In an ageing population, where the prevalence of chronic diseases with an impact on bone metabolism is increasing, it becomes crucial to identify new strategies that would improve regenerative outcomes also in medically compromised patients. In this context, omics are demonstrating a great potential, as they offer new insights on the molecular mechanisms regulating physiologic/pathologic bone healing and, at the same time, allow the identification of new diagnostic and therapeutic targets. This review provides an overview on the current evidence on the use of transcriptomic and proteomic approaches in bone regeneration research, particularly in relation to type 1 diabetes and osteoporosis, and discusses future scenarios and potential benefits and limitations on the integration of multi-omics. It is suggested that future research will leverage the synergy of omics with statistical modeling and bioinformatics to prompt the understanding of the biology underpinning bone formation in health and medically compromised conditions. With an eye toward personalized medicine, new strategies combining the mining of large datasets and bioinformatic data with a detailed characterization of relevant phenotypes will need to be pursued to further the understanding of disease mechanisms.

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Section: Discussionmentioning

confidence: 99%

Proteomic and Transcriptomic Approaches for Studying Bone Regeneration in Health and Systemically Compromised Conditions

Calciolari

Donos

2020

Proteomics Clinical Apps

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“…It is also a challenge to achieve optimization of the used methodologies, explain the variations of data generated from different measurements, as well as define the meanings of altered 3D genome organization in the disease. The finding that 20% of genomic regions switched the chromatin A/B compartment types may have any correlation and association with clinical phenomes, any regulation of clinical trans-omics, or any link with therapeutic responses (Wang 2018).…”

Section: Toxicity Regulatorsmentioning

confidence: 99%

Genome dimensions control biological and toxicological functions; myth or reality?

Wang

2018

Cell Biol Toxicol

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The multidimensional genome offers a new perspective to understand molecular mechanisms of genotoxicity and provide deeper knowledge of how genome organization and reorganization in dimensions can alter cell sensitivity, tolerance, resistance, or toxicity to drugs, whether drugs per se can influence the 3D architecture of the genome directly or indirectly through transcriptional factors, and how we can improve cell sensitivity to drugs through the reorganization of genome and regulation of gene expression. We address roles of 3D genome organization and reorganization in the pathogenesis and progression of disease by evaluating various methodologies of studying the 3D genome, and in the genome integrity and stability susceptible to chemicals as mechanisms of genotoxicity. We discuss the value of imaging, visualizing, and nuclear proximity ligation-based methods of 3D genome organization to measure spatial proximity and visualize spatial distances between genomic loci. We also list a number of dynamic genome changes during genome function and call for further investigations on the interaction of drugs with genome-specific regulators, key enzymes, or spliceosome.

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“…It is important to think clinical lipidomics as the part of clinical trans-omics which was coined as a new emerging scientific discipline where clinical phenomes are integrated with molecular multiomics, in order to further understand molecular mechanisms of disease pathogenesis and progression, patient sensitivity to therapy and prognosis, and therapy design and development [3]. Multiomics is defined as a biological analysis approach where more than two omics measurements are performed simultaneously in one cell, organ/tissue, or body, for the identification of disease-specific biomarker and therapeutic targets.…”

mentioning

confidence: 99%

Clinical lipidomics: a new way to diagnose human diseases

Zhang

Yan

et al. 2018

Clinical & Translational Med

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Lipidomics is a measurement of a large scale of lipid species to understand roles of their carbon atoms, dual bonds, or isomerism in the lipid molecule. Clinical lipidomics was recently defined “as a new integrative biomedicine to discover the correlation and regulation between a large scale of lipid elements measured and analyzed in liquid biopsies from patients with those patient phenomes and clinical phenotypes”. The first step to translate lipidomics into clinical lipidomics is to settle a number of standard operation procedures and protocols of lipidomics performance and measurement. Clinical lipidomics is the part of clinical trans-omics which was coined as a new emerging scientific discipline where clinical phenomes are integrated with molecular multiomics. We believe it is the time to translate lipid science and lipidomics into clinical application and to understand the importance of clinical lipidomics as one of the most helpful approaches during the design and decision-making of therapeutic strategies for individuals. We emphasize here that clinical lipidomics should be merged with clinical phenomes, e.g. patient signs and symptoms, biomedical analyses, pathology, images, and responses to therapies, although it is difficult to integrate and fuse the information of clinical lipidomics with clinical phenomes. It will be a great achievement if we can draw the networks of lipidomic species fused with networks of genes and proteins to describe the molecular mechanisms of the disease in multi-dimensions.

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Clinical trans-omics: an integration of clinical phenomes with molecular multiomics

Cited by 56 publications

References 18 publications

Proteomic and Transcriptomic Approaches for Studying Bone Regeneration in Health and Systemically Compromised Conditions

Proteomic and Transcriptomic Approaches for Studying Bone Regeneration in Health and Systemically Compromised Conditions

Genome dimensions control biological and toxicological functions; myth or reality?

Clinical lipidomics: a new way to diagnose human diseases

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