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SDSC to House Data Repository for NIH Metabolomics Project

Published: Thursday, October 18, 2012
Last Updated: Thursday, October 18, 2012
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UC San Diego bioengineers to play key role in the five-year, $6 million program.

The San Diego Supercomputer Center (SDSC) at the University of California, San Diego, will house the data repository for a new project funded by the National Institutes of Health (NIH) aimed at accelerating the study of metabolomics, an emerging field of biomedical research that studies chemical processes that could help more clearly define the mechanisms underlying diseases, such as diabetes and obesity, and develop new strategies for treatment.

SDSC joins other UC San Diego research units and organizations, which were awarded $6 million over five years out of a larger NIH metabolome program investment. Shankar Subramaniam, a Distinguished Scientist with SDSC and chair of the Department of Bioengineering at the UC San Diego Jacobs School of Engineering, is principal investigator (PI) for the project. Subramaniam is also an associate director of the UC San Diego Institute of Engineering in Medicine.

“I’m very excited about the prospect of collaborating with researchers in the Jacobs School, the School of Medicine, the San Diego Supercomputer Center, and others across the campus and the country,” said Subramaniam. “This work will lead to a systematic understanding of human physiology at the molecular level.”

Specifically, metabolomics is the study of small molecules called metabolites, found within cells and biological systems. Metabolites are produced or consumed in the chemical reactions that take place in the body to sustain life. The sum of all metabolites at any given moment – the metabolome – is a form of chemical readout of the state of health of the cell or body.

“This project builds on SDSC’s long-standing collaboration with Professor Subramaniam and our world-class expertise in scientific data management,” said SDSC Director Michael Norman, co-PI on the project. “That we will become a national data hub for other NIH-funded metabolomics projects makes this exciting for us.”

The metabolome project will provide insights into the millions of microorganisms living within us. The human body contains many more bacterial cells than human cells, and the project will provide new opportunities for researchers to understand the role that microorganisms living within the body play in human health, according to Subramaniam, who has extensive experience integrating “omics” data as well as experience coordinating other large-scale projects.

One of the expected outcomes of the NIH project is the ability to “metabo-type” individuals to get a detailed picture of their current metabolite profile, and recognize problems, such as insulin resistance. The effects of interventions, such as changes in diet and exercise as well as pharmaceuticals, could then be seen in updated metabo-type readings.

Through the SDSC data repository, bioengineers and other researchers at UC San Diego will organize and present all data from the three metabolome core centers across the country, as well as other metabolomics efforts. The data repository, along with a coordination center, will serve as a coordinating hub so that the awardees can function as a consortium.

This metabolomics project at UC San Diego is an extension of the successful Lipid Maps project. Lipids are just one metabolite, and the metabolomics work will extend researchers’ view beyond this metabolite to others, such as sugars, nucleic acids, amino acids, and hormones.

The $6 million in funding is part of an overall $51.4 million investment by the NIH in metabolomics. The awards are supported by the NIH Common Fund, which is taking a comprehensive approach to increasing the research capacity in metabolomics by funding a variety of initiatives in this area, including training, technology development, standards synthesis, and data sharing capability for this new field.

“We are excited about the potential advances in technology that will enable metabolomics analysis to be conducted in basic and clinical settings, resulting in the discovery of new diagnostic tools and yielding important clues about disease mechanisms,” said James M. Anderson, director of the NIH Division of Program Coordination, Planning and Strategic Initiatives, which oversees trans-NIH program areas, including those supported through the NIH Common Fund. “The new cross-cutting metabolomics initiatives will allow for better data sharing and coordination of metabolomics efforts both nationally and internationally.”

Regional Comprehensive Metabolomics Resource Cores

In addition of the Data Repository and Coordination Center award to UC San Diego, the NIH has awarded three Regional Comprehensive Metabolomics Resource Cores, aimed at increasing the national capacity to provide metabolomics profiling and data analysis services to investigators. They are:

•    University of California, Davis. This resource core will serve clinical and biomedical researchers across the West Coast, with access to cutting-edge tools, collaborations, and interpretation of data.
•    University of Michigan: This resource core is a fully integrated program that will provide researchers nationwide with the expertise and infrastructure for metabolomics in addition to training opportunities.
•    Research Triangle Institute in Research Triangle Park, N.C.: This core will serve as a regional metabolomics center and will offer a comprehensive range of services and collaborative opportunities for metabolomics technologies.

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