Illustration: Ron Chan
Gene machines find the answers to diseases amid thousands of bits of DNA
Now, through a powerful technique used to search the entire human genome for genes that are either expressed or silenced in different disease states, Natarajan can identify molecular transformations potentially underlying diabetes’ harmful events.
That technology, known as “ChIPon-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.
In a study published in the March 5 issue of 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 associated with what are called epigenetic changes in several genes associated with diabetes.
Inherited changes in gene expression may occur in two ways. They either happen through genetic mutations, which damage the sequence of the DNA, or by the way the DNA and its associated proteins — known collectively as chromatin — are “packaged” in a cell’s nucleus. These are referred to as epigenetic changes.
One type of epigenetic alteration is the addition of methyl groups to DNA or proteins, in a process called methylation. This often promotes the formation of tightly coiled chromatin associated with gene silencing, when genes are “turned off.” In contrast, different modifications that unwind or relax the DNA strand can “turn on” gene expression.
When such changes occur, increased inflammation likely promotesmany complications of diabetes, including heart and kidney disease, and nerve and vision problems. Natarajan is investigating whether biochemical modifications that alter chromatin’s structure may cause some of these conditions.
Initially, the group analyzed chromatin modification in certain cells of the immune system. They examined two different methylation patterns — one associated with active genes and the other with silenced genes — in cells grown in conditions that mimic diabetes.
“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,” Natarajan said.
The group identified specific genes of interest through the study. “We found a lot of genes related to diabetes were turned on,” said Natarajan.
When they analyzed chromatin from the same type of immune cells drawn from patients with diabetes, they saw similar patterns. Among affected genes were some associated with inflammation, as well as an enzyme linked to insulin signaling. Overall, concluded Natarajan, after exposure to diabetes’ high-glucose conditions, “protective genes are ‘downregulated’
and bad genes are being turned on.”
The study was the first to find variations in these particular methylation patterns across the genome in diabetes; other studies already under way at City of Hope and around the world seek similar illuminating patterns in other diseases.
Miao, who pioneered the 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. The center significantly expanded basic and clinical diabetes research at City of Hope when it opened in 1997.
Grants from the Juvenile Diabetes Research Foundation and the National Institutes of Health, as well as a General Clinical Research Center grant from the National Center for Research Resources, funded the study.
Markie RamirezRama Natarajan