HIV Infection Prematurely Ages People by an Average of Five Years

Epigenetic changes also associated with 19 percent increased risk of mortality —

Thanks to combination antiretroviral therapies, many people with HIV can expect to live decades after being infected. Yet doctors have observed these patients often show signs of premature aging. Researchers at University of California San Diego School of Medicine and the University of Nebraska Medical Center have applied a highly accurate biomarker to measure just how much HIV infection ages people at the cellular level — an average of almost five years.

The study is published April 21 in Molecular Cell. … Read the Full Story from the UC San Diego Newsroom


Trey Ideker, PhD

Trey Ideker, PhD

Trey Ideker, PhD, Professor of Medicine and Professor of Bioengineering, is co-corresponding author of the study report in Molecular Cell (article access for UC San Diego only).

Other Department of Medicine authors include Andrew M. Gross, Philipp A. Jaeger, Jason F. Kreisberg and Katherine Licon.

How DNA Damage Affects Golgi – The Cell’s Shipping Department

In studying the impact of DNA damage on the Golgi, a research team from the University of California, San Diego School of Medicine and the Ludwig Institute for Cancer Research have discovered a novel pathway activated by DNA damage, with important consequences for the body’s cellular response to chemotherapy. … Read the full story from the UC San Diego News Center


Dr. Seth FieldStudy principal investigator Seth J. Field, MD, PhD, is associate professor of medicine in the Division of Endocrinology and Metabolism.

Visit Dr. Field’s Laboratory Website

Citation for the study report in Cell: Suzette E. Farber-Katz, Holly C. Dippold, Matthew D. Buschman, Marshall C. Peterman, Mengke Xing, Christopher J. Noakes, John Tat, Michelle M. Ng, Juliati Rahajeng, David M. Cowan, Greg J. Fuchs, Huilin Zhou, Seth J. Field, DNA Damage Triggers Golgi Dispersal via DNA-PK and GOLPH3, Cell, Volume 156, Issue 3, 30 January 2014, Pages 413-427, ISSN 0092-8674. Summary | Full text (UCSD only)

The Role of “Master Regulators” in Gene Mutations and Disease

Researchers identify key proteins that help establish cell function

Researchers at the University of California, San Diego School of Medicine have developed a new way to parse and understand how special proteins called “master regulators” read the genome, and consequently turn genes on and off. … Read the full story from the UC San Diego News Center


Christopher K. Glass, MD, PhDThe principal investigator of the reported study is Christopher K. Glass, MD, PhD, professor of medicine in the Division of Endocrinology & Metabolism and professor of cellular and molecular medicine at UC San Diego.

He is on the faculty of the UC San Diego Institute for Genomic Medicine.

Visit the Glass Laboratory website.

Related UC San Diego news stories:

Potential New Way to Suppress Tumor Growth Discovered

Researchers at the University of California, San Diego School of Medicine, with colleagues at the University of Rochester Medical Center, have identified a new mechanism that appears to suppress tumor growth, opening the possibility of developing a new class of anti-cancer drugs. … Read the full story from the UCSD Newsroom


Dr. Willis X. Li

Dr. Willis X. Li

Senior author of the study report in the Proceedings of the National Academy of Sciences is Willis X. Li, PhD, professor of medicine in the Division of Pulmonary & Critical Care Medicine and faculty member in the Biomedical Sciences graduate program.

Li’s UC San Diego Department of Medicine coauthors are postdoctoral fellow Pranabananda Dutta, PhD; pulmonary/critical care physician-scientist Jinghong Li, MD, PhD, and senior undergraduate student Jingtong Wang.

Coauthors Xiaoyu Hu, Amy Tsurumi and Hartmut Land are colleagues at the University of Rochester, where Li was a faculty member and researcher at the Wilmot Cancer Center before he joined the faculty at UC San Diego.

At the University of Rochester, LI received the 2008 Davey Memorial Award for Outstanding Cancer Research for his work in the cellular and molecular signaling in cancer development.

He is now principal investigator of an R01 research grant from the National Cancer Institute for the project, Epigenetic Tumor Induction by Heterochromatin Instability.

Citation for the study report:  

Xiaoyu Hu, Pranabananda Dutta, Amy Tsurumi, Jinghong Li, Jingtong Wang, Hartmut Land, and Willis X. Li. Unphosphorylated STAT5A stabilizes heterochromatin and suppresses tumor growth. PNAS 2013 ; published ahead of print June 3, 2013, doi:10.1073/pnas.1221243110  |  Abstract  |  Full text (PDF)

In Epigenomics, Location is Everything

Researchers exploit gene position to test “histone code”

In a novel use of gene knockout technology, researchers at the University of California, San Diego School of Medicine tested the same gene inserted into 90 different locations in a yeast chromosome – and discovered that while the inserted gene never altered its surrounding chromatin landscape, differences in that immediate landscape measurably affected gene activity. … Read the full story from the UCSD Newsroom


Trey Ideker, PhD

Led by Trey Ideker, PhD, researchers in the UCSD departments of bioengineering, biological sciences, and medicine collaborated in the study, which was published online this week in Cell Reports.

Ideker is professor of bioengineering and medicine and chief of the Division of Medical Genetics in the Department of Medicine.

The study investigators include Lorraine Pillus, PhD, professor and chair of the Section of Molecular Biology in the Division of Biological Sciences at UCSD, whose laboratory focuses on investigating chromosomal and chromatin effects on the expression of genes.

Citation for the study report: Chen M, Licon K, Otsuka R, Pillus L, and Ideker T. (2013) Decoupling Epigenetic and Genetic Effects through Systematic Analysis of Gene Position. 10.1016/j.celrep.2012.12.003   Read the article abstract.

UC San Diego Moores Cancer Center Launches Bold Campaign to Personalize Cancer Treatment

“My Answer to Cancer” will analyze patient tumor DNA to individualize cancer care

UC San Diego Moores Cancer Center launched a bold plan today aimed at personalizing cancer treatment.  The “My Answer to Cancer” team of oncologists, bioinformaticians, pathologists and geneticists pledges to “sequence” or analyze the DNA of large numbers of patients with cancer in order to match each patient to the best available drug for his or her particular tumor. There will be two parallel approaches: a research approach to discover new mutations that cause cancer and a patient-care approach that will use confirmed mutations and other DNA abnormalities to direct patients to clinical studies of agents targeting these abnormalities. … Read the full story from the UC San Diego Newsroom.

More about the “My Answer to Cancer” Program:

DNA Mismatch Repair Happens Only During A Brief Window of Opportunity

In eukaryotes – the group of organisms that include humans – a key to survival is the ability of certain proteins to quickly and accurately repair genetic errors that occur when DNA is replicated to make new cells.

In a paper published in the December 23, 2011 issue of the journal Science, researchers at the Ludwig Institute for Cancer Research and the University of California, San Diego School of Medicine have solved part of the mystery of how these proteins do their job… Read the full story from the UCSD Newsroom

The new findings come from the Laboratory of Cancer Genetics in the San Diego branch of the Ludwig Institute for Cancer Research, the departments of Medicine and Cellular and Molecular Medicine, the Moores Cancer Center, and the Institute for Genomic Medicine in the UCSD School of Medicine.

Senior investigator Richard D. Kolodner, PhD, head of the Laboratory of Cancer Genetics, is a professor in the departments of Medicine and Cellular and Molecular Medicine. First author Christopher D. Putnam, PhD, is assistant professor of medicine and coauthors Hans Hombauer and Anjana Srivatsan are postdoctoral fellows in the Kolodner laboratory.

Read the study report in Science

Plasticity of Hormonal Response Permits Rapid Gene Expression Reprogramming

Gene expression reprogramming may allow cancer cell growth as well as normal differentiation

Gene expression is the process of converting the genetic information encoded in DNA into a final gene product such as a protein or any of several types of RNA. Scientists have long thought that the gene programs regulated by different physiological processes throughout the body are robustly pre-determined and relatively fixed for every specialized cell. But a new study by researchers from the University of California, San Diego School of Medicine reveals the unsuspected plasticity of some of these gene expression programs. … Read the full story from the UCSD Newsroom

M. Geoffrey Rosenfeld, MD

Co-principal investigator of the study is Dr. M. Geoffrey Rosenfeld (pictured at left). M. Geoffrey Rosenfeld, MD, is Professor of Medicine in the Division of Endocrinology and Metabolism and Howard Hughes Medical Institute investigator.

Department of Medicine coauthor Christopher K. Glass, MD, PhD, is Professor of Medicine in the Division of Endocrinology and Metabolism and Professor of Cellular and Molecular Medicine.

Read the published study in Nature (free full text).

Scientists Map Changes in Genetic Networks Caused By DNA Damage

Using a new technology called “differential epistasis maps,” an international team of scientists, led by researchers at the University of California, San Diego School of Medicine, has documented for the first time how a cellular genetic network completely rewires itself in response to stress by DNA-damaging agents… Read the full story from the UCSD Newsroom


Dr. Trey Ideker

Senior author of the study is Trey Ideker, Ph.D., Professor and Chief of the Division of Medical Genetics in the Department of Medicine and Professor of Bioengineering (pictured above).  Department of Medicine faculty coauthors include Richard D. Kolodner, Ph.D., Professor in the Division of Hematology-Oncology.

Read the abstract of the article in the December 3 issue of Science.