Shankar UCSD

Researchers led by Shankar Subramaniam (left) at the University of California at San Diego have received a $12 million grant by the National Institutes of Health to continue its research on human metabolism. ( photo)

Researchers at U.C. San Diego, led by the university’s Jacobs School of Engineering bioengineering professor Shankar Subramaniam, have been provided a sizeable grant from the National Institutes of Health to further research on human metabolism.

The $12 million, four-year grant from NIH comes with the expectation that the Indian American professor-led team will expand the Metabolomics Workbench, a searchable, interactive repository of data for all research in the field of metabolism, the study of the small molecules called metabolites that are found within cells and biological systems, the university said in a news report.

The Metabolomics Workbench project launched in 2012 with a $6 million grant from the NIH. This new infusion of funds will allow Subramaniam and colleagues to add a wide range of clinical data to the Workbench and take the project into the clinic itself, the university said.

This in turn will allow researchers and physicians to develop better tools to diagnose diseases through metabolite markers in blood, it said.

Subramaniam is one of the pioneers of the field of developing data and analysis environments for metabolomics. His research group focuses on systems biology and systems medicine, including diseases of the liver, muscles, brain and vascular system, according to the report.

Metabolites are produced and consumed in the chemical reactions that take place in the body to sustain life, UCSD said.

Today, some metabolites are used to diagnose a range of diseases. But Subramaniam said researchers want to be able to analyze the collection of all metabolites at any given moment as a chemical readout of the state of health of the cell or body, the report added.

Over the past six years, the Workbench has helped scientists elucidate the role that metabolomics play in diabetes and cancer. Researchers are now hoping to do the same for other conditions, such as obesity, heart disease, liver disease and more. Subramaniam himself is trying to determine if any metabolomics markers could help diagnose Alzheimer’s disease in its early stages, the university report said.

Metabolomics used to be considered the missing piece in the puzzle that systems biology is trying to solve, Subramanian said. But a series of advances in mass spectrometry has made it possible for researchers to better analyze metabolites and understand the role they play in human health, the report said.

The NIH funds will allow Subramaniam to hire more personnel for the Workbench, doubling the group’s size to about a dozen experts in computer science, computational biology and of course metabolomics.

Workbench data are housed in the cloud at the San Diego Supercomputer Center, with support from Christine Kirkpatrick, SDSC’s division director for IT Systems & Services.

Researchers at the UC San Diego School of Medicine said they are looking forward to using the next generation of the Metabolomics Workbench, according to the report.

Subramaniam and his team are uniquely placed to identify novel prognostic biomarkers of disease severity of chronic metabolic diseases such as nonalcoholic fatty liver disease, said Dr. Rohit Loomba, director of the UC San Diego NAFLD Research Center, in the report.

Since its inception in 2012, the Metabolomics Workbench has made available data from more than 1,000 projects around the nation and the world. It has established the only national metabolomics database with over 50,000 experimentally annotated metabolites along with over one million computationally generated metabolites described in terms of their structure, classification and computed spectra, the university noted.

The project’s next generation will house enormous amounts of clinical data from human subjects, as metabolomics measurements are increasingly being used in epidemiological, observational, and interventional clinical studies.

The National Metabolomics Data Repository will work with the Stakeholder Engagement and Program Coordination Center to ensure that the appropriate computational tools are available and, when possible, can be used in the cloud environment, it said.

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