For much of her research life, Rama Natarajan, Ph.D., has wanted to understand the causes behind diabetes’ complications and how resulting cellular changes can damage organs like the heart and kidney.
Now, through a powerful systems biology tool, she can identify molecular transformations potentially underlying those harmful events.
The technology, known as “ChIP-on-chip,” makes Natarajan, professor in the Department of Diabetes, Endocrinology & Metabolism, optimistic about finding answers to the molecular mysteries behind diabetes. “Five years back I wouldn’t have dreamt that such approaches would be available for our studies,” she said.
ChIP-on-chip enables investigators to conduct computer searches through the entire human genome for changes in gene expression. Researchers at City of Hope and elsewhere are turning to the technology to study biochemical changes associated with various diseases.
In a study published March 5 in the Journal of Biological Chemistry, Natarajan’s group identified such changes in diabetes using the technology. Led by Assistant Research Scientist Feng Miao, Ph.D., the group found that high glucose levels harmful to pancreatic, blood vessel and immune system cells are correlated with what are called epigenetic changes in several genes associated with diabetes.
Epigenetic changes occur when DNA or its associated proteins, known as histones, are biochemically modified through the addition of methyl groups. Such modifications can change the architecture of chromatin and determine, in part, whether genes are active or silent. (Chromatin is the complex of chromosomal DNA and histones found within the nucleus of a cell.)
Increased inflammation and oxidative stress likely promote many diabetic complications, including heart and kidney disease and nerve and vision problems. Natarajan is investigating whether alterations in chromatin’s biochemistry may cause some of these conditions.
Initially the group analyzed a modification called histone methylation in monocytes, cells of the immune system. They examined two distinct methylation patterns — one associated with active genes and the other with repressed genes — in cells grown in high-glucose conditions.
“We simulated diabetic conditions in monocytes and found very nice histone methylation perturbations and then mapped them in a genome-wise fashion,” said Natarajan. “Using ChIP-on-chip, in one shot you can look at 12,000 genes and see what kinds of changes occur in the two different methylation patterns.”
The group identified specific genes whose histone methylation and expression changed in response to high glucose. “We found a lot of genes related to diabetes were turned on,” said Natarajan, “as were signal transduction pathways related to inflammation.”
They saw similar patterns when they analyzed chromatin from monocytes of patients with diabetes. Among affected genes were those encoding the cytokine IL-1A, which is associated with inflammation, and the enzyme PTEN, which is activated downstream of insulin signaling. Overall, concludes Natarajan, following exposure to diabetes’ high-glucose conditions, “protective genes are downregulated and bad genes are being turned on.”
The study was the first to find genome-wide histone methylation variations in diabetes; other studies already under way at City of Hope and across the world seek similar illuminating patterns in other diseases.
Miao, who pioneered application of ChIP-on-chip in the lab, sees this study as a start to a deeper understanding of diabetes. “We are one step closer to a modern epigenetic study of diabetes,” he said. “I hope this technology will lead to new tests to diagnose diabetes and its complications.”
Natarajan’s group will now analyze entire gene families using cells from diabetic patients. “We are looking at these targets now for patterns and certain pathways that are turned on,” she said, “and are coming up with gene networks that could be related to inflammation as well as metabolic defects.”
The group conducts the research in the Leslie and Susan Gonda (Goldschmied) Diabetes and Genetic Research Center, a City of Hope building whose opening in 1997 significantly expanded basic and clinical diabetes research at the Duarte, Calif., campus.
Others contributing to the study were Yate-Ching Yuan, Ph.D., who manages the Biomedical Informatics Core Facility, Xiwei Wu, Ph.D., bioinformatician in the facility and director of the Affymetrix Core, Lingxiao Zhang of the Natarajan lab, and Arthur Riggs, Ph.D., director of Beckman Research Institute at City of Hope and professor in the Division of Biology.
Grants from the Juvenile Diabetes Research Foundation and the National Institutes of Health and a General Clinical Research Center grant from the National Center for Research Resources funded the study.