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Therapeutic Drug Monitoring Apr 2016Modern multianalyte "omics" technologies allow for the identification of molecular signatures that confer significantly more information than measurement of a single... (Review)
Review
Modern multianalyte "omics" technologies allow for the identification of molecular signatures that confer significantly more information than measurement of a single parameter as typically used in current medical diagnostics. Proteomics and metabolomics bioanalytical assays capture a large set of proteins and metabolites in body fluids, cells, or tissues and, complementing genomics, assess the phenome. Proteomics and metabolomics contribute to the development of novel predictive clinical biomarkers in transplantation in 2 ways: they can be used to generate a diagnostic fingerprint or they can be used to discover individual proteins and metabolites of diagnostic potential. Much fewer metabolomics than proteomics biomarker studies in transplant patients have been reported, and, in contrast to proteomics discovery studies, new lead metabolite markers have yet to emerge. Most clinical proteomics studies have been discovery studies. Several of these studies have assessed diagnostic sensitivity and specificity. Nevertheless, none of these newly discovered protein biomarkers have yet been implemented in clinical decision making in transplantation. The currently most advanced markers discovered in proteomics studies in transplant patients are the chemokines CXCL-9 and CXCL-10, which have successfully been validated in larger multicenter trials in kidney transplant patients. These chemokines can be measured using standard immunoassay platforms, which should facilitate clinical implementation. Based on the published evidence, it is reasonable to expect that these chemokine markers can help guiding and individualizing immunosuppressive regimens, may be able to predict acute and chronic T-cell-mediated and antibody-mediated rejection, and may be useful tools for risk stratification of kidney transplant patients.
Topics: Biomarkers; Humans; Immunosuppressive Agents; Kidney Transplantation; Metabolome; Metabolomics; Proteome; Proteomics
PubMed: 26418702
DOI: 10.1097/FTD.0000000000000243 -
International Journal of Molecular... Jun 2022In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics... (Review)
Review
In the past two decades, the post-genomic era envisaged high-throughput technologies, resulting in more species with available genome sequences. In-depth multi-omics approaches have evolved to integrate cellular processes at various levels into a systems biology knowledge base. Metabolomics plays a crucial role in molecular networking to bridge the gaps between genotypes and phenotypes. However, the greater complexity of metabolites with diverse chemical and physical properties has limited the advances in plant metabolomics. For several years, applications of liquid/gas chromatography (LC/GC)-mass spectrometry (MS) and nuclear magnetic resonance (NMR) have been constantly developed. Recently, ion mobility spectrometry (IMS)-MS has shown utility in resolving isomeric and isobaric metabolites. Both MS and NMR combined metabolomics significantly increased the identification and quantification of metabolites in an untargeted and targeted manner. Thus, hyphenated metabolomics tools will narrow the gap between the number of metabolite features and the identified metabolites. Metabolites change in response to environmental conditions, including biotic and abiotic stress factors. The spatial distribution of metabolites across different organs, tissues, cells and cellular compartments is a trending research area in metabolomics. Herein, we review recent technological advancements in metabolomics and their applications in understanding plant stress biology and different levels of spatial organization. In addition, we discuss the opportunities and challenges in multiple stress interactions, multi-omics, and single-cell metabolomics.
Topics: Chromatography, Liquid; Gas Chromatography-Mass Spectrometry; Mass Spectrometry; Metabolome; Metabolomics; Plants
PubMed: 35805979
DOI: 10.3390/ijms23136985 -
Database : the Journal of Biological... Jan 2020Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how breath...
Breathomics is a special branch of metabolomics that quantifies volatile organic compounds (VOCs) from collected exhaled breath samples. Understanding how breath molecules are related to diseases, mechanisms and pathways identified from experimental analytical measurements is challenging due to the lack of an organized resource describing breath molecules, related references and biomedical information embedded in the literature. To provide breath VOCs, related references and biomedical information, we aim to organize a database composed of manually curated information and automatically extracted biomedical information. First, VOCs-related disease information was manually organized from 207 literature linked to 99 VOCs and known Medical Subject Headings (MeSH) terms. Then an automated text mining algorithm was used to extract biomedical information from this literature. In the end, the manually curated information and auto-extracted biomedical information was combined to form a breath molecule database-the Human Breathomics Database (HBDB). We first manually curated and organized disease information including MeSH term from 207 literatures associated with 99 VOCs. Then, an automatic pipeline of text mining approach was used to collect 2766 literatures and extract biomedical information from breath researches. We combined curated information with automatically extracted biomedical information to assemble a breath molecule database, the HBDB. The HBDB is a database that includes references, VOCs and diseases associated with human breathomics. Most of these VOCs were detected in human breath samples or exhaled breath condensate samples. So far, the database contains a total of 913 VOCs in relation to human exhaled breath researches reported in 2766 publications. The HBDB is the most comprehensive HBDB of VOCs in human exhaled breath to date. It is a useful and organized resource for researchers and clinicians to identify and further investigate potential biomarkers from the breath of patients. Database URL: https://hbdb.cmdm.tw.
Topics: Breath Tests; Data Mining; Database Management Systems; Exhalation; Humans; Metabolome; Metabolomics; Volatile Organic Compounds
PubMed: 31976536
DOI: 10.1093/database/baz139 -
Genetics Jul 2017Metabolomic analysis provides a powerful new tool for studies of physiology. This approach allows investigators to detect thousands of chemical compounds in a single... (Review)
Review
Metabolomic analysis provides a powerful new tool for studies of physiology. This approach allows investigators to detect thousands of chemical compounds in a single sample, representing the combined contributions of gene expression, enzyme activity, and environmental context. Metabolomics has been used for a wide range of studies in , often providing new insights into gene function and metabolic state that could not be obtained using any other approach. In this review, we survey the uses of metabolomic analysis since its entry into the field. We also cover the major methods used for metabolomic studies in and highlight new directions for future research.
Topics: Animals; Drosophila; Drosophila Proteins; Metabolome; Metabolomics
PubMed: 28684601
DOI: 10.1534/genetics.117.200014 -
Journal of Proteome Research Jul 2020The integration of omics techniques has seen a step change in our understanding of biological systems. However, multiomics has been impaired by mutually exclusive omic...
The integration of omics techniques has seen a step change in our understanding of biological systems. However, multiomics has been impaired by mutually exclusive omic separation methods and the destructive nature of the techniques when sample is limited. We describe Simultaneous Trapping (SiTrap), a simple and effective detergent-free method that facilitates direct measurement of the proteome and metabolome in the same sample extract. This "single-pot" multiomics processing is particularly beneficial in cases when sample amounts are limited or are heterogeneous, for example, tissue biopsies. We demonstrate the value of the SiTrap methodology as an essential multiomics tool in a proof-of-principle integrated study of renal cancer tissue biopsy samples. We believe SiTrap has the potential to become an indispensable tool in translational medical research.
Topics: Metabolome; Metabolomics; Proteome; Proteomics
PubMed: 31743035
DOI: 10.1021/acs.jproteome.9b00662 -
Current Opinion in Biotechnology Oct 2021Single-cell metabolomics (SCM) is currently one of the most powerful tools for performing high-throughput metabolic analysis at the cellular level. The power of... (Review)
Review
Single-cell metabolomics (SCM) is currently one of the most powerful tools for performing high-throughput metabolic analysis at the cellular level. The power of single-cell metabolomics to determine the metabolic profiles of individual cells makes it very suitable for decoding cell heterogeneity. SCM bears great potential in cell type identification and differentiation within cell colonies. With the development of various equipment and techniques, SCM analysis has become possible for a wide range of biological samples. Many fields have incorporated this cutting-edge analytic tool to generate fruitful findings. This review article pays close attention to the prevalent techniques utilized in SCM and the exciting new findings and applications developed by studies in phytology, neurology, and oncology using SCM.
Topics: Metabolome; Metabolomics; Single-Cell Analysis
PubMed: 34339935
DOI: 10.1016/j.copbio.2021.07.015 -
Molecules (Basel, Switzerland) Jun 2022The authors of this paper conducted a comparative metabolomic analysis of (OS), providing the metabolic profiles of the stroma (OSBSz) and sclerotia (OSBSh) of OS by...
The authors of this paper conducted a comparative metabolomic analysis of (OS), providing the metabolic profiles of the stroma (OSBSz) and sclerotia (OSBSh) of OS by widely targeted metabolomics and untargeted metabolomics. The results showed that 778 and 1449 metabolites were identified by the widely targeted metabolomics and untargeted metabolomics approaches, respectively. The metabolites in OSBSz and OSBSh are significantly differentiated; 71 and 96 differentially expressed metabolites were identified by the widely targeted metabolomics and untargeted metabolomics approaches, respectively. This suggests that these 71 metabolites (riboflavine, tripdiolide, bromocriptine, lumichrome, tetrahymanol, citrostadienol, etc.) and 96 metabolites (sancycline, vignatic acid B, pirbuterol, rubrophen, epalrestat, etc.) are potential biomarkers. 4-Hydroxybenzaldehyde, arginine, and lumichrome were common differentially expressed metabolites. Using the widely targeted metabolomics approach, the key pathways identified that are involved in creating the differentiation between OSBSz and OSBSh may be nicotinate and nicotinamide metabolism, thiamine metabolism, riboflavin metabolism, glycine, serine, and threonine metabolism, and arginine biosynthesis. The differentially expressed metabolites identified using the untargeted metabolomics approach were mainly involved in arginine biosynthesis, terpenoid backbone biosynthesis, porphyrin and chlorophyll metabolism, and cysteine and methionine metabolism. The purpose of this research was to provide support for the assessment of the differences between the stroma and sclerotia, to furnish a material basis for the evaluation of the physical effects of OS, and to provide a reference for the selection of detection methods for the metabolomics of OS.
Topics: Arginine; Biomarkers; Cordyceps; Metabolome; Metabolomics
PubMed: 35684580
DOI: 10.3390/molecules27113645 -
Cellular and Molecular Life Sciences :... Oct 2021During the past decade metabolomics has emerged as one of the fastest developing branches of "-omics" technologies. Metabolomics involves documentation, identification,... (Review)
Review
During the past decade metabolomics has emerged as one of the fastest developing branches of "-omics" technologies. Metabolomics involves documentation, identification, and quantification of metabolites through modern analytical platforms in various biological systems. Advanced analytical tools, such as gas chromatography-mass spectrometry (GC/MS), liquid chromatography-mass spectroscopy (LC/MS), and non-destructive nuclear magnetic resonance (NMR) spectroscopy, have facilitated metabolite profiling of complex biological matrices. Metabolomics, along with transcriptomics, has an influential role in discovering connections between genetic regulation, metabolite phenotyping and biomarkers identification. Comprehensive metabolite profiling allows integration of the summarized data towards manipulation of biosynthetic pathways, determination of nutritional quality markers, improvement in crop yield, selection of desired metabolites/genes, and their heritability in modern breeding. Along with that, metabolomics is invaluable in predicting the biological activity of medicinal plants, assisting the bioactivity-guided fractionation process and bioactive leads discovery, as well as serving as a tool for quality control and authentication of commercial plant-derived natural products. Metabolomic analysis of human biofluids is implemented in clinical practice to discriminate between physiological and pathological state in humans, to aid early disease biomarker discovery and predict individual response to drug therapy. Thus, metabolomics could be utilized to preserve human health by improving the nutritional quality of crops and accelerating plant-derived bioactive leads discovery through disease diagnostics, or through increasing the therapeutic efficacy of drugs via more personalized approach. Here, we attempt to explore the potential value of metabolite profiling comprising the above-mentioned applications of metabolomics in crop improvement, medicinal plants utilization, and, in the prognosis, diagnosis and management of complex diseases.
Topics: Animals; Biological Products; Biomarkers; Crops, Agricultural; Humans; Metabolome; Metabolomics; Pharmaceutical Preparations
PubMed: 34410445
DOI: 10.1007/s00018-021-03918-3 -
Journal of Cellular Physiology Aug 2012The metabolome is a data-rich source of information concerning all the low-molecular-weight metabolites in a biofluid, which can indicate early biological changes to the... (Review)
Review
The metabolome is a data-rich source of information concerning all the low-molecular-weight metabolites in a biofluid, which can indicate early biological changes to the host due to perturbations in metabolic pathways. Major changes can be seen after minor stimuli, which make it a valuable target for analysis. Due to the diverse and sensitive nature of the metabolome, studies must be designed in a manner to maintain consistency, reduce variation between subjects, and optimize information recovery. Technological advancements in experimental design, mouse models and instrumentation have aided in this effort. Metabolomics has the ultimate potential to be valuable in a clinical setting where it could be used for early diagnosis of a disease and as a predictor of treatment response and survival. During drug treatment, the metabolic status of an individual could be monitored and used to indicate possible toxic effects. Metabolomics therefore has great potential for improving diagnosis, treatment and aftercare of disease.
Topics: Animals; Biomarkers; Body Fluids; Humans; Metabolic Networks and Pathways; Metabolome; Metabolomics; Mice; Precision Medicine
PubMed: 22034100
DOI: 10.1002/jcp.24002 -
Molecules (Basel, Switzerland) Jun 2019Metabolomics is a powerful tool used to understand comprehensive changes in the metabolic response and to study the phenotype of an organism by instrumental analysis. It... (Meta-Analysis)
Meta-Analysis Review
Metabolomics is a powerful tool used to understand comprehensive changes in the metabolic response and to study the phenotype of an organism by instrumental analysis. It most commonly involves mass spectrometry followed by data mining and metabolite assignment. For the last few decades, hair has been used as a valuable analytical sample to investigate retrospective xenobiotic exposure as it provides a wider window of detection than other biological samples such as saliva, plasma, and urine. Hair contains functional metabolomes such as amino acids and lipids. Moreover, segmental analysis of hair based on its growth rate can provide information on metabolic changes over time. Therefore, it has great potential as a metabolomics sample to monitor chronic diseases, including drug addiction or abnormal conditions. In the current review, the latest applications of hair metabolomics in animal studies and clinical settings are highlighted. For this purpose, we review and discuss the characteristics of hair as a metabolomics sample, the analytical techniques employed in hair metabolomics and the consequence of hair metabolome alterations in recent studies. Through this, the value of hair as an alternative biological sample in metabolomics is highlighted.
Topics: Animals; Chromatography, High Pressure Liquid; Hair; Humans; Mass Spectrometry; Metabolome; Metabolomics
PubMed: 31212725
DOI: 10.3390/molecules24122195