Special Issue "Integrative Multi-Omics in Biomedical Research"

A special issue of Biomolecules (ISSN 2218-273X). This special issue belongs to the section "Biochemistry".

Deadline for manuscript submissions: 30 September 2020.

Special Issue Editors

Prof. Christopher Gerner
Website
Guest Editor
Department of Analytical Chemistry, University of Vienna, 1090 Vienna, Austria
Interests: clinical proteomics; lipidomics; metabolomics; chronic inflammation; cancer research; mechanisms of drug action; drug resistance
Assoc. Prof. Michelle Hill
Website
Guest Editor
Precision & Systems Biomedicine Laboratory, QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
Faculty of Medicine, The University of Queensland, Brisbane, Australia
Interests: membrane lipids; cell biology; subcellular omics; integrative biology; clinical proteomics; clinical lipidomics; liquid biopsy; extracellular vesicles; clinical diagnostics

Special Issue Information

Dear Colleagues,

Postgenomic methods, typically based on mass spectrometry, comprise the analysis of metabolites, lipids, and proteins and are an essential complement to genomics and transcriptomics. Multidimensional omics is becoming established to provide accurate and comprehensive state descriptions and to support the understanding of molecular mechanisms in complex systems. In this Special Issue, we invite you to share laboratory and computational method innovations that enable the concurrent and integrative analysis of multiple omics data sets. We would also like to showcase novel findings as a result of application of multi-omics to address questions in biology and pathology. Both original research and review papers are welcome.

We look forward to reading your contributions to this rapidly advancing interdisciplinary field.

Assoc. Prof. Michelle Hill
Prof. Christopher Gerner
Guest Editors

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 papers will be 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. Biomolecules 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

  • mass spectrometry
  • bioinformatics
  • integrative biology
  • systems biology
  • biomarker discovery

Published Papers (2 papers)

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Research

Open AccessFeature PaperArticle
Chronic High-Fat Diet Induces Early Barrett’s Esophagus in Mice through Lipidome Remodeling
Biomolecules 2020, 10(5), 776; https://doi.org/10.3390/biom10050776 - 16 May 2020
Abstract
Esophageal adenocarcinoma (EAC) incidence has been rapidly increasing, potentially associated with the prevalence of the risk factors gastroesophageal reflux disease (GERD), obesity, high-fat diet (HFD), and the precursor condition Barrett’s esophagus (BE). EAC development occurs over several years, with stepwise changes of the [...] Read more.
Esophageal adenocarcinoma (EAC) incidence has been rapidly increasing, potentially associated with the prevalence of the risk factors gastroesophageal reflux disease (GERD), obesity, high-fat diet (HFD), and the precursor condition Barrett’s esophagus (BE). EAC development occurs over several years, with stepwise changes of the squamous esophageal epithelium, through cardiac metaplasia, to BE, and then EAC. To establish the roles of GERD and HFD in initiating BE, we developed a dietary intervention model in C57/BL6 mice using experimental HFD and GERD (0.2% deoxycholic acid, DCA, in drinking water), and then analyzed the gastroesophageal junction tissue lipidome and microbiome to reveal potential mechanisms. Chronic (9 months) HFD alone induced esophageal inflammation and metaplasia, the first steps in BE/EAC pathogenesis. While 0.2% deoxycholic acid (DCA) alone had no effect on esophageal morphology, it synergized with HFD to increase inflammation severity and metaplasia length, potentially via increased microbiome diversity. Furthermore, we identify a tissue lipid signature for inflammation and metaplasia, which is characterized by elevated very-long-chain ceramides and reduced lysophospholipids. In summary, we report a non-transgenic mouse model, and a tissue lipid signature for early BE. Validation of the lipid signature in human patient cohorts could pave the way for specific dietary strategies to reduce the risk of BE in high-risk individuals. Full article
(This article belongs to the Special Issue Integrative Multi-Omics in Biomedical Research)
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Open AccessArticle
Identification and Validation of VEGFR2 Kinase as a Target of Voacangine by a Systematic Combination of DARTS and MSI
Biomolecules 2020, 10(4), 508; https://doi.org/10.3390/biom10040508 - 27 Mar 2020
Abstract
Although natural products are an important source of drugs and drug leads, identification and validation of their target proteins have proven difficult. Here, we report the development of a systematic strategy for target identification and validation employing drug affinity responsive target stability (DARTS) [...] Read more.
Although natural products are an important source of drugs and drug leads, identification and validation of their target proteins have proven difficult. Here, we report the development of a systematic strategy for target identification and validation employing drug affinity responsive target stability (DARTS) and mass spectrometry imaging (MSI) without modifying or labeling natural compounds. Through a validation step using curcumin, which targets aminopeptidase N (APN), we successfully standardized the systematic strategy. Using label-free voacangine, an antiangiogenic alkaloid molecule as the model natural compound, DARTS analysis revealed vascular endothelial growth factor receptor 2 (VEGFR2) as a target protein. Voacangine inhibits VEGFR2 kinase activity and its downstream signaling by binding to the kinase domain of VEGFR2, as was revealed by docking simulation. Through cell culture assays, voacangine was found to inhibit the growth of glioblastoma cells expressing high levels of VEGFR2. Specific localization of voacangine to tumor compartments in a glioblastoma xenograft mouse was revealed by MSI analysis. The overlap of histological images with the MSI signals for voacangine was intense in the tumor regions and showed colocalization of voacangine and VEGFR2 in the tumor tissues by immunofluorescence analysis of VEGFR2. The strategy employing DARTS and MSI to identify and validate the targets of a natural compound as demonstrated for voacangine in this study is expected to streamline the general approach of drug discovery and validation using other biomolecules including natural products. Full article
(This article belongs to the Special Issue Integrative Multi-Omics in Biomedical Research)
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