Abstract
The application of metabolomics towards cancer research has led to a renewed appreciation of metabolism in cancer development and progression. It has also led to the discovery of metabolite cancer biomarkers and the identification of a number of novel cancer causing metabolites. The rapid growth of metabolomics in cancer research is also leading to challenges. In particular, with so many cancer-associate metabolites being identified, it is often difficult to keep track of which compounds are associated with which cancers. It is also challenging to track down information on the specific pathways that particular metabolites, drugs or drug metabolites may be affecting. Even more frustrating are the difficulties associated with identifying metabolites from NMR or MS spectra. Fortunately, a number of metabolomics databases are emerging that are designed to address these challenges. One such database is the Human Metabolome Database (HMDB). The HMDB is currently the world’s largest and most comprehensive, organism-specific metabolomics database. It contains more than 40,000 metabolite entries, thousands of metabolite concentrations, >700 metabolic and disease-associated pathways, as well as information on dozens of cancer biomarkers. This review is intended to provide a brief summary of the HMDB and to offer some guidance on how it can be used in metabolomic studies of cancer.
Highlights
The 1D and 2D NMR Searches allow users to submit peak lists from 1 H or 13 C NMR spectra or 2D Total correlation spectroscopy (TOCSY) or 13 C Heteronuclear single-quantum correlation spectroscopy (HSQC) spectra, respectively, and to have these spectra compared to the NMR libraries contained in the Human Metabolome Database (HMDB)
The increased interest in metabolomics by cancer researchers is leading to a flood of novel, metabolite-based cancer biomarkers that could be used in the prediction, monitoring and diagnosis of cancer
The HMDB is attempting to capture as much of this information as possible and its curation team is working hard to make these data current and freely available to all through pathways, detailed compound descriptions, metabolite concentrations and a rich collection of references
Summary
The “re-discovery” of cancer as a metabolic disorder largely occurred in the last ten years [2,3] This shift in thinking has mostly been due to the increased accessibility of metabolomics, the identification of useful cancer metabolite biomarkers and the discovery, via metabolomics, of “oncometabolites” [4]. Since the discovery of 2-hydroxyglutarate many other oncometabolites have been identified including fumarate (renal cell carcinoma), succinate (paraganglioma), sarcosine (prostate cancer), asparagine (leukemia), choline (prostate, brain, breast cancer) and polyamines (most cancers). The HMDB is currently the world’s largest and most comprehensive, organism-specific metabolomics database It contains nearly 42,000 metabolite entries, more than 5000 normal and abnormal metabolite concentrations, nearly 800 metabolic and disease-associated pathways, and detailed information on dozens of cancer biomarkers. We will offer some guidance, selected case studies and simple examples on how to use the HMDB in metabolomic studies of cancer
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