A Comprehensive Analysis of Metabolomics and Transcriptomics in Cervical Cancer

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Abstract

Cervical cancer (CC) still remains a common and deadly malignancy among females in developing countries. More accurate and reliable diagnostic methods/biomarkers should be discovered. In this study, we performed a comprehensive analysis of metabolomics (285 samples) and transcriptomics (52 samples) on the potential diagnostic implication and metabolic characteristic description in cervical cancer. Sixty-two metabolites were different between CC and normal controls (NOR), in which 5 metabolites (bilirubin, LysoPC(17:0), n-oleoyl threonine, 12-hydroxydodecanoic acid and tetracosahexaenoic acid) were selected as candidate biomarkers for CC. The AUC value, sensitivity (SE), and specificity (SP) of these 5 biomarkers were 0.99, 0.98 and 0.99, respectively. We further analysed the genes in 7 significantly enriched pathways, of which 117 genes, that were expressed differentially, were mainly involved in catalytic activity. Finally, a fully connected network of metabolites and genes in these pathways was built, which can increase the credibility of our selected metabolites. In conclusion, our biomarkers from metabolomics could set a path for CC diagnosis and screening. Our results also showed that variables of both transcriptomics and metabolomics were associated with CC.

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HMDB: a knowledgebase for the human metabolome

David Wishart, Craig Knox, An Guo … (2009)

The Human Metabolome Database (HMDB, http://www.hmdb.ca) is a richly annotated resource that is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. Since its first release in 2007, the HMDB has been used to facilitate the research for nearly 100 published studies in metabolomics, clinical biochemistry and systems biology. The most recent release of HMDB (version 2.0) has been significantly expanded and enhanced over the previous release (version 1.0). In particular, the number of fully annotated metabolite entries has grown from 2180 to more than 6800 (a 300% increase), while the number of metabolites with biofluid or tissue concentration data has grown by a factor of five (from 883 to 4413). Similarly, the number of purified compounds with reference to NMR, LC-MS and GC-MS spectra has more than doubled (from 380 to more than 790 compounds). In addition to this significant expansion in database size, many new database searching tools and new data content has been added or enhanced. These include better algorithms for spectral searching and matching, more powerful chemical substructure searches, faster text searching software, as well as dedicated pathway searching tools and customized, clickable metabolic maps. Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users.

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Author and article information

Journal

Journal ID (nlm-ta): Sci Rep

Journal ID (iso-abbrev): Sci Rep

Title: Scientific Reports

Publisher: Nature Publishing Group

ISSN (Electronic): 2045-2322

Publication date (Electronic): 22 February 2017

Publication date Collection: 2017

Volume: 7

Electronic Location Identifier: 43353

Affiliations

[1 ]Department of Epidemiology and Biostatistics, School of Public Health, Harbin Medical University , Harbin, 150086, P.R. China

[2 ]Department of Gynecology Oncology, the Tumor Hospital, Harbin Medical University , Harbin, 150086, P.R. China

[3 ]State Key Laboratory of Natural Products, Jiangsu Key Laboratory of TCM Evaluation; Translational Research Department of Complex Prescription of TCM, Pharmaceutical University , 639 Longmian Road, Nanjing 211198, P.R. China

[4 ]School of Basic Medical Sciences, Heilongjiang University of Chinese Medicine , Harbin, Heilongjiang 150040, P.R. China

[5 ]Harbin Medical University , Harbin, 150086, P.R. China

[6 ]Key Laboratory of Cardiovascular Medicine Research, Harbin Medical University, Ministry of Education , Harbin, 150086, P.R. China

Author notes

[a ] houyan@ 123456ems.hrbmu.edu.cn

[b ] likang@ 123456ems.hrbmu.edu.cn

[c ] louge@ 123456ems.hrbmu.edu.cn

[*]

These authors contributed equally to this work.

Article

Publisher Item ID: srep43353

DOI: 10.1038/srep43353

PMC ID: 5320559

PubMed ID: 28225065

SO-VID: 617ce4d5-0484-4983-bfd9-19b8f414de84

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A Comprehensive Analysis of Metabolomics and Transcriptomics in Cervical Cancer

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Cancer Metabolism

Most cited references 36

The meaning and use of the area under a receiver operating characteristic (ROC) curve.

MassBank: a public repository for sharing mass spectral data for life sciences.

HMDB: a knowledgebase for the human metabolome

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