Shankar Subramaniam, Ph.D.

A study led by researchers at the University of California (UC) San Diego Jacobs School of Engineering has offered up new insights into the mechanisms of stem cell differentiation that could one day help scientists develop regenerative therapies for muscle disease, injury and atrophy. By studying how easily different pluripotent stem cell lines differentiated into muscle cells, and comparing time-dependent changes in the cells’ transcriptomic profiles, the researchers discovered epigenetic mechanisms that can be triggered to accelerate muscle cell growth at different stages of stem cell differentiation.

“Stem cell-based approaches that have the potential to aid muscle regeneration and growth would improve the quality of life for many people, from children who are born with congenital muscle disease to people who are losing muscle mass and strength due to aging,” said Shankar Subramaniam, PhD, distinguished professor of bioengineering, computer science and engineering, and cellular and molecular medicine at UC San Diego and lead corresponding author of the team’s study, which is published in Science Advances. “Here, we have discovered that specific factors and mechanisms can be triggered by external means to favor rapid growth.” Subramaniam and colleagues report their findings in a paper titled, “Temporal mechanisms of myogenic specification in human induced pluripotent stem cells… Continue reading.

With New Year’s resolutions in full swing and many focused on getting in shape, there is no better time to discuss a three-letter word that is often taboo for many health-conscious individuals: Fat, or scientifically speaking lipids. For almost two decades scientists have been ardently working to specify and classify these fatty acids in order to develop techniques, tools, and terms to better study them. Now, an international team of chemists and biochemists has finally begun to “feel the burn” as their newly published data on understanding the complex nature of lipids could reshape the diagnosis and treatment of various acute and chronic conditions—from diabetes and atherosclerosis to cancer and autoimmunity.

“While the LIPID MAPS Consortium included a dozen U.S. investigators sponsored by the U.S. NIH, we invited scientists from Asia and Europe to join us in developing the LIPID MAPS Classification, Nomenclature and Structural Drawing Standards that contributed to international acceptance of LIPID MAPS,” explained study investigator Edward Dennis, PhD, professor and chair of the department of chemistry and biochemistry at UC San Diego. “This led to the rapid development of the lipidomics field… Continue reading.

Bioengineers from the University of California, San Diego have created a new method for analyzing RNA transcripts from samples of 50 to 100 cells. The approach could be used to develop inexpensive and rapid methods for diagnosing cancers at early stages, as well as better tools for forensics, drug discovery and developmental biology.

The protocols, which were published in April 2013 in the journal Nature Scientific Reports, are now being applied to a wide range of biological and medical research questions from brain cancer, to liver function and stem cell biology.

The approach from the UC San Diego bioengineers is called Designed Primer-based RNA sequencing or “DP-seq.” It’s a new tool for generating comprehensive snapshots of RNA — the “transcriptome” — collected from as little as 50 picograms of RNA. Analysis of the transcriptome provides insights into what biological processes are occurring at a specific moment in time. RNA transcripts serve as a proxy for which genes are being expressed and at what levels.

“In the months since we published the DP-seq protocol, there has been tremendous interest from the scientific community,” said Shankar Subramaniam a bioengineering professor at the UC San Diego Jacobs School of Engineering and the corresponding author on the paper. “When you are not restricted to samples of thousands of cells, there are so many more system-wide gene expression questions you can ask, and answer,” said Subramaniam. Questions like: What transcription factors will determine cell fates, such as cancer versus normal? and what pathways are likely to be activated in a tissue upon treatment with a drug?

Atherosclerosis – the hardening of arteries that is a primary cause of cardiovascular disease and death – has long been presumed to be the fateful consequence of complicated interactions between overabundant cholesterol and resulting inflammation in the heart and blood vessels.

However, researchers at the University of California, San Diego School of Medicine and the Jacobs School of Engineering, with colleagues at institutions across the country, say the relationship is not exactly what it appears, and that a precursor to cholesterol actually suppresses inflammatory response genes. This precursor molecule could provide a new target for drugs designed to treat atherosclerosis, which kills tens of thousands of Americans annually.

The findings are published in the September 28, 2012 issue of Cell…

… The systems biology approach that identified the lipid molecules came from analysis of the vast amounts of data from the transcriptome and metabolome. “The interaction between researchers in medicine and engineering has the potential to lead to such discoveries and is the future,” said Shankar Subramaniam, professor and chair in the Department of Bioengineering, who is also a senior co-author in this paper. Subramanian was recently awarded a $6 million grant by the National Institutes of Health to accelerate the study of “metabolomics,” an emerging field of biomedical research that could transform how doctor’s assess patient health and diagnose disease.

With a $6 million grant over five years, bioengineers from the University of California, San Diego will play a central role in a new program from theNational Institutes of Health (NIH) to accelerate “metabolomics”, an emerging field of biomedical research that offers a path to a wealth of information about a person’s nutrition, infection, health, disease status and more. In addition to powerful tools for diagnosis and disease follow-up, metabolomics technologies will transform researchers’ ability to define the mechanisms underlying disease, such as diabetes and obesity, and to develop new strategies for treatment.

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

Shankar Subramaniam, professor and chair of the Department of Bioengineering at the UC San Diego Jacobs School of Engineering leads the metabolomics effort at UC San Diego, which involves coordinating the research cores and running the metabolome project’s Data Repository and Coordination Center (DRCC).

Shankar Subramaniam has been named a Distinguished Scientist at the San Diego Supercomputer Center (SDSC), to assist the Organized Research Unit of the University of California, San Diego, in identifying new opportunities and solutions in the area of bioinformatics. Subramaniam’s appointment is effective June 1, 2010.

Subramaniam, a professor of bioengineering, chemistry and biochemistry, cellular and molecular medicine and nano engineering, is currently Chair of UC San Diego’s Bioengineering Department. He holds the inaugural Joan and Irwin Jacobs Endowed Chair in Bioengineering and Systems Biology, and was the founding director of the Bioinformatics Graduate Program at the university, participating in campus-wide recruitment of leading researchers in systems biology.

“All of us at SDSC look forward to working with Dr. Subramaniam in his new role as a Distinguished Scientist,” said Michael L. Norman, SDSC’s interim director. “As a true pioneer in bioinformatics and systems biology, Dr. Subramaniam is uniquely qualified to identify new opportunities and propose innovative solutions as SDSC broadens its expertise in these exciting areas of scientific research.”