Advances and Applications of Metabolomics in Human Diseases

A special issue of Diseases (ISSN 2079-9721).

Deadline for manuscript submissions: closed (31 July 2015) | Viewed by 18662

Special Issue Editor

Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD 21287, USA
Interests: metabolomics; mass spectrometry; metabolite profiling; toxicology; chromatography; biomarker discovery; proteomics

Special Issue Information

Dear Colleagues,

Metabolomics, as an emerging field of ‘omics’ technologies, is defined as comparative analysis of the metabolites present in a biological system or a specified physiological state. It aims to characterize and identify metabolites – the end products of cellular metabolism. As an interdisciplinary field of science, metabolomics combines analytical chemistry, bioinformatics, statistics, and biochemistry. When applied to human disease studies, metabolomics also includes aspects of patho-biochemistry, systems biology, and molecular diagnostics.

This Special Issue will focus on the advances and applications of metabolomics in human diseases. Metabolomics has been in the focus for the past few years as diagnostic and screening tool for disease recognition. There are already plenty of test cases demonstrating the validity of such approaches. However, there are also severe practical and theoretical constraints known if applying metabolic profiling as universal tool for improved understanding and diagnostics of disease patterns. Potential topics related to this special issue include, but not limited to:

  • Analytical methods development in metabolomics;
  • Bioinformatics tools for data processing and pathway analysis;
  • Method development for metabolite identification;
  • Discovery of new markers for human diseases;
  • Methods for ‘omics’ data integration for human disease study;
  • Integration of metabolomics and clinical data for diagnosis or therapeutic applications;

I highly encourage authors to submit original papers and reviews for this Special Issue.

Dr. Liang Zhao
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Diseases is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1800 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.


Keywords

  • metabolomics
  • metabolic profiling
  • untargeted approach
  • targeted approach
  • mass spectrometry
  • biomarker
  • diagnostics
  • plasma
  • serum
  • urine
  • mammalian cells
  • multivariate statistics
  • pathway analysis
  • omics technology
  • systems biology

Published Papers (3 papers)

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Research

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Article
Renal Cell Carcinoma: A Study through NMR-Based Metabolomics Combined with Transcriptomics
by Rosa Ragone, Fabio Sallustio, Sara Piccinonna, Monica Rutigliano, Galleggiante Vanessa, Silvano Palazzo, Giuseppe Lucarelli, Pasquale Ditonno, Michele Battaglia, Francesco Paolo Fanizzi and Francesco Paolo Schena
Diseases 2016, 4(1), 7; https://doi.org/10.3390/diseases4010007 - 22 Jan 2016
Cited by 62 | Viewed by 5221
Abstract
Renal cell carcinoma (RCC) is a heterogeneous cancer often showing late symptoms. Until now, some candidate protein markers have been proposed for its diagnosis. Metabolomics approaches have been applied, predominantly using Mass Spectrometry (MS), while Nuclear Magnetic Resonance (NMR)-based studies remain limited. There [...] Read more.
Renal cell carcinoma (RCC) is a heterogeneous cancer often showing late symptoms. Until now, some candidate protein markers have been proposed for its diagnosis. Metabolomics approaches have been applied, predominantly using Mass Spectrometry (MS), while Nuclear Magnetic Resonance (NMR)-based studies remain limited. There is no study about RCC integrating NMR-based metabolomics with transcriptomics. In this work, 1H-NMR spectroscopy combined with multivariate statistics was applied on urine samples, collected from 40 patients with clear cell RCC (ccRCC) before nephrectomy and 29 healthy controls; nine out of 40 patients also provided samples one-month after nephrectomy. We observed increases of creatine, alanine, lactate and pyruvate, and decreases of hippurate, citrate, and betaine in all ccRCC patients. A network analysis connected most of these metabolites with glomerular injury, renal inflammation and renal necrosis/cell death. Interestingly, intersecting metabolites with transcriptomic data from CD133+/CD24+ tumoral renal stem cells isolated from ccRCC patients, we found that both genes and metabolites differentially regulated in ccRCC patients belonged to HIF-α signaling, methionine and choline degradation, and acetyl-CoA biosynthesis. Moreover, when comparing urinary metabolome of ccRCC patients after nephrectomy, some processes, such as the glomerular injury, renal hypertrophy, renal necrosis/cell death and renal proliferation, were no more represented. Full article
(This article belongs to the Special Issue Advances and Applications of Metabolomics in Human Diseases)
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Review

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Review
An Integrated Outlook on the Metagenome and Metabolome of Intestinal Diseases
by Wanping Aw and Shinji Fukuda
Diseases 2015, 3(4), 341-359; https://doi.org/10.3390/diseases3040341 - 06 Nov 2015
Cited by 6 | Viewed by 6971
Abstract
Recently, metagenomics and metabolomics are the two most rapidly advancing “omics” technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites) that specific cellular [...] Read more.
Recently, metagenomics and metabolomics are the two most rapidly advancing “omics” technologies. Metagenomics seeks to characterize the composition of microbial communities, their operations, and their dynamically co-evolving relationships with the habitats they occupy, whereas metabolomics studies unique chemical endpoints (metabolites) that specific cellular processes leave behind. Remarkable progress in DNA sequencing and mass spectrometry technologies has enabled the comprehensive collection of information on the gut microbiome and its metabolome in order to assess the influence of the gut microbiota on host physiology on a whole-systems level. Our gut microbiota, which consists of prokaryotic cells together with its metabolites, creates a unique gut ecosystem together with the host eukaryotic cells. In this review, we will highlight the detailed relationships between gut microbiota and its metabolites on host health and the pathogenesis of various intestinal diseases such as inflammatory bowel disease and colorectal cancer. Therapeutic interventions such as probiotic and prebiotic administrations and fecal microbiota transplantations will also be discussed. We would like to promote this unique biology-wide approach of incorporating metagenome and metabolome information as we believe that this can help us understand the intricate interplay between gut microbiota and host metabolism to a greater extent. This novel integration of microbiome, metatranscriptome, and metabolome information will help us have an improved holistic understanding of the complex mammalian superorganism, thereby allowing us to gain new and unprecedented insights to providing exciting novel therapeutic approaches for optimal intestinal health. Full article
(This article belongs to the Special Issue Advances and Applications of Metabolomics in Human Diseases)
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Review
Metabolomic Approaches in Cancer Epidemiology
by Mukesh Verma and Hirendra Nath Banerjee
Diseases 2015, 3(3), 167-175; https://doi.org/10.3390/diseases3030167 - 11 Aug 2015
Cited by 5 | Viewed by 5879
Abstract
Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) that can measure hundreds of thousands of unique chemical entities (UCEs). The [...] Read more.
Metabolomics is the study of low molecular weight molecules or metabolites produced within cells and biological systems. It involves technologies such as mass spectrometry (MS) and nuclear magnetic resonance spectroscopy (NMR) that can measure hundreds of thousands of unique chemical entities (UCEs). The metabolome provides one of the most accurate reflections of cellular activity at the functional level and can be leveraged to discern mechanistic information during normal and disease states. The advantages of metabolomics over other “omics” include its high sensitivity and ability to enable the analysis of relatively few metabolites compared with the number of genes and messenger RNAs (mRNAs). In clinical samples, metabolites are more stable than proteins or RNA. In fact, metabolomic profiling in basic, epidemiologic, clinical, and translational studies has revealed potential new biomarkers of disease and therapeutic outcome and has led to a novel mechanistic understanding of pathogenesis. These potential biomarkers include novel metabolites associated with cancer initiation, regression, and recurrence. Unlike genomics or even proteomics, however, the degree of metabolite complexity and heterogeneity within biological systems presents unique challenges that require specialized skills and resources to overcome. This article discusses epidemiologic studies of altered metabolite profiles in several cancers as well as challenges in the field and potential approaches to overcoming them. Full article
(This article belongs to the Special Issue Advances and Applications of Metabolomics in Human Diseases)
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