Inside Salk; Salk Institute

Decoding Chronic Disease

Salk scientists use genome mapping, bioinformatics and powerful computers to study chronic diseases and find new therapies.

On the surface, chronic diseases such as cancer, diabetes and Parkinson's look very different. Each has its particular symptoms, prognosis and therapies, and scientists have tended to study each disease in isolation, searching for the particular key that will unlock its mysteries.

Inder Verma, professor in the Laboratory of Genetics, and Manching Ku of the Genome Sequencing Core Facility

Inder Verma, professor in the Laboratory of Genetics, and Manching Ku of the Genome Sequencing Core Facility

Deeper down, however, these diseases have much in common. In recent years, scientists have discovered that certain genetic programs are involved in all chronic illnesses, suggesting that these programs might serve as targets for treating multiple diseases. In particular, many chronic diseases involve inflammation, the body's first defense against stressors such as disease and injury. When inflammation becomes chronic, due to long-term stresses such as infections, toxins or obesity, it can damage cells and organs, leading to clinical illness.

The Salk Institute's new Helmsley Center for Genomic Medicine, launched in January with a $42 million gift from the Leona M. and Harry B. Helmsley Charitable Trust, was established to study these links between chronic diseases, with a focus on the role of chronic inflammation. The center's three major programs—cancer, stem cell and metabolism research—are focused on deciphering the common molecular and genetic mechanisms that go awry in chronic illness.

One of four major scientific initiatives of the Campaign for Salk, the Institute's first major fundraising campaign, the Genomic Medicine Initiative is leveraging new technologies that allow scientists to map the entire human genome—the DNA sequences containing the blueprint for human life. In addition to a core facility for genomic sequencing, the Helmsley Center includes a bioinformatics core devoted to managing and analyzing the massive amounts of data produced by sequencing machines. Other new facilities allow researchers to study the molecules that make up cells' biochemical machinery and to produce potential new drugs that can be tested in cellular and animal models. The center also supports postdoctoral researchers through the Helmsley Fellows Program, as well as a monthly Helmsley Symposium, where Salk scientists discuss their research in an open forum.

Already, the center is allowing Salk scientists to greatly expand on their research into the genomic underpinnings of disease, generating ideas for new scientific directions and building on the promise of past findings. "The ability to sequence an organism's genome offers an unprecedented window into what's happening in our cells and how those processes impact our health," says Inder M. Verma, one of the center's lead researchers and holder of the Irwin and Joan Jacobs Chair in Exemplary Life Science. "When you combine this with the other new core facilities and expertise, you have an incredibly powerful platform for studying the role of stress and chronic inflammation in disease."

In one line of research, Verma's laboratory has developed mouse models of lung cancers to study the links between cancer and inflammation. Using these animal models, they are exploring how the same biochemical players that protect the body by controlling the inflammation response of cells can be hijacked by genetic mutations involved in the development of cancer. Whole-genome sequencing allows them to observe the changes in the genome and in gene expression as a cancer progresses.

"For a cell to become cancerous, a sequence of several genetic mutations must occur," says Yifeng Xia, a postdoctoral researcher in Verma's laboratory who works on the project. "Sequencing the entire of doing the same for more complex disorders that may involve multiple genetic mutations.

In the past, Salk researchers sent their cellular samples as far as China to be sequenced and wouldn't get the results back for weeks. Thanks to the Helmsley Center's new genomic sequencing core, they now have in-house access to the latest technology.

The Helmsley Center is also allowing Salk to recruit scientists with expertise in bioinformatics, who use powerful computers and statistical modeling to analyze and manage the genomic data produced by the sequencers. "The technologies are critical, but you also need great people to work with the data—it has become an entirely new field of science," says Ronald M. Evans, holder of the March of Dimes Chair in Molecular and Developmental Biology and co-lead researcher of the center. "We often look at the genetic signatures from healthy versus unhealthy tissue to determine what's different at the genomic level. To find those signatures, you have to set up the experiments so they produce the right kind of data, and you need expertise in computational analysis to comb the data for answers."

Evans's laboratory is combining whole-genome sequencing with technology to pinpoint genes that control inflammation. "The genome is the control center for our cells, and it adapts to stress to keep us healthy," Evans says. "However, when that stress is persistent, the genome's adaptation leads to chronic inflammation and persistent illness. We are integrating multiple technology platforms to find delinquent genes and develop drugs that can reset the genome to a healthy state. This is where the Helmsley Center therapeutic core comes in. When we have an idea for resetting the genome, we can generate molecules to test as potential drugs."

In one project, the Evans team is exploring how long-term inflammation results in liver fibrosis, an excessive accumulation of tough, fibrous scar tissue found in people with chronic liver diseases. The causes of fibrosis include chronic hepatitis virus infection, excess alcohol consumption and obesity. With the help of high-throughput sequencing, Ning Ding, a postdoctoral fellow on Evans's team, recently discovered that a synthetic form of vitamin D, calcipotriol (a drug already approved by the FDA for the treatment of psoriasis), deactivates the genetic switch governing the fibrotic response in mouse liver cells, suggesting a potential new therapy for liver fibrosis.

Evans's lab has already begun working with the laboratories of Salk professors Marc Montminy, Salk's J.W. Kieckhefer Foundation Chair, and Greg Lemke, the Françoise Gilot-Salk Chair, to further develop this disease model. "A prominent part of the vision for the Helmsley Center is to help those of us working in different areas to collaborate more seamlessly," says Evans.

Fibrosis occurs in a wide range of body tissues—heart, lungs, intestines, skin—and Evans is exploring ways to leverage his research on liver fibrosis to understand other types of fibrotic disease. Another postdoctoral researcher on his team, Mara Sherman, has found that fibrosis is a particularly powerful driver of inflammation of the pancreas, known as "pancreatitis," which if not controlled, progresses to pancreatic cancer.

Evans's laboratory and other Salk laboratories are adapting sequencing machines to map more than just the DNA code. With rapidly evolving technology, scientists can determine which genes are active in a cell at any given time—a process known as gene expression—and can chart an extra code of chemical markers on DNA known as the epigenome. Computational technology developed at the Salk can overlay maps of DNA sequences with those of the epigenetic code, as well as measurements of gene expression, to produce a three-dimensional view of our cellular machinery in action.

Fred H. Gage, also a lead researcher in the Helmsley Center and holder of the Vi and John Adler Chair for Research on Age-Related Neurodegenerative Diseases, is combining these sequencing approaches with stem cell research to study chronic neurological conditions, such as schizophrenia, autism and Parkinson's disease. Gage and his team reprogram skin cells from patients with these disorders to become induced pluripotent stem cells (iPSCs), then coax these cells into becoming neurons. This overcomes hurdles to obtaining neurons from patients' brains and allows the investigators to study the cells in the laboratory.

By using this iPSC technology to generate neurons and other brain cells, known as glia, from Parkinson's patients, Gage and his team are investigating the role of inflammation in the disease. "The primary risk factor for Parkinson's disease is aging, and we know that inflammation in the brain increases dramatically when people get older," Gage says. "It's clear that inflammation plays a role, but we don't know the precise mechanisms that lead to the neuron death seen in Parkinson's. It could be that the neurons become more sensitive to inflammation or that the glia malfunction to damage the neurons."

Salk researchers Apua Paquola and Jennifer Erwin

Salk researchers Apua Paquola and Jennifer Erwin

Sequencing the genomes of iPSC-derived neurons shows what genes are regulated differently in Parkinson's patients, which may provide targets for drugs that prevent or reverse the disease. The scientists are also exploring whether it is possible to measure brain-related inflammation through a simple blood test, which might provide an early warning that a person is at risk of Parkinson's. In that case, drugs to reduce that inflammation could help head off the disease.

In another line of research, Gage and his team want to know whether these neurological disorders are linked to so-called "jumping genes," bits of DNA known as retrotransposons that move freely about the genome. "This is the dark matter of the genome," says Gage. "This movement of DNA sequences may explain why people with ostensibly similar genetic profiles have a very different disease history."

In some sets of identical twins, for instance, one twin will develop schizophrenia while the other remains healthy. Also, twins might respond differently to the same drug. By comparing the twins' genomes, Gage's team is discerning what genetic differences explain these variations in health and drug responses. "There's so much we don't know about retrotransposons," says Jennifer Erwin, a postdoctoral researcher in Gage's lab. "We are trying to figure out how many copies of these genes there are in the genome, how often they move and where they are located. Once we know those basics, we will have a better idea of their role in neurological disorders."

If genomic medicine at Salk is a marriage between the best molecular biology research and powerful bioinformatic and computational approaches, Erwin and her husband, Apua Paquola, a staff scientist in Gage's lab, could be the poster children for the Helmsley Center. Erwin's specialty is molecular genetics, focusing on gene expression and cell culture, while Paquola has a computer engineering background and a doctorate in bioinformatics.

Combining their expertise, the couple is studying the role of jumping genes in Rett syndrome, a rare neurodevelopmental disease that affects mostly girls and is considered one of the autism spectrum disorders. Already Gage's lab has shown that people with the syndrome have more movement of genetic material in their DNA, a groundbreaking study that provided the first evidence of a link between genomic instability and a mental disorder.

"Now we want to find out whether this instability is related to a defect in neurons or glia to explain the symptoms of the syndrome," Paquola says. "The genome is a big, complicated place, but now wešve got the right people and the right tools to make much more rapid advances in understanding the relationship between the genome and diseases."

The technologies that drive genomic medicine

When a clinician gives a patient a prognosis based on genomic research, it's the tip of a very large technical iceberg. Backing up the analysis are years of laboratory research based on gene sequencers and other specialized tools and techniques.

DNA sequencing (whole genome)

Whole-genome sequencing maps the sequences of nucleotides that make up the genetic code stored in DNA. Understanding the genomes of other species is essential to the biomedical research at Salk that underlies successful therapies. In clinical settings, the genomes of patients may be compared to a baseline "normal" human genome to see if there are any mutations or variations that the patients have in common. In personalized medicine, a person's genome might be analyzed to determine whether a particular drug could work within his or her body.

RNA sequencing (gene expression)

While DNA sequencing provides a static view of all the letters in our genome, RNA sequencing offers a dynamic glimpse at how that genomic blueprint actually controls cellular function. RNA sequencing detects what genes are turned on or off, which provides insight into how diseases disrupt the genomic programs that normally keep us healthy. For example, Salk scientists use RNA sequencing to examine the patterns and changes in gene expression as a tumor grows.

Bioinformatics (computational analysis techniques)

One of the greatest challenges of genomics is trying to sort through raw sequencing data, which can run to trillions of letters, to find useful information. It's like trying to find one phrase in all of the books in the Library of Congress. Specialists in bioinformatics, such as Chris Benner, director of the Integrative Genomics and Bioinformatics Core, combine a background in computer science with knowledge of biology to mine the data using computer code that seeks out patterns. In addition, they develop new algorithms to solve specific research questions, as well as make "missing piece" predictions about molecular structures.

Laboratory modeling of disease

Disease causes change at the cellular level, and scientists have long hoped to track the progression of these changes throughout the course of an illness. Salk researchers now have the ability to study diseases in animal models, which is far faster and more affordable than studying humans. They can also take skin or blood cells from patients with diseases such as autism, Parkinson's or hemophilia and convert them into stem cells, which can then be differentiated into any cell type. This will allow them to follow the entire cycle of disease progression, yielding insight into both drug development and when best to target therapies in individual patients.

Advanced imaging of disease

Equipment to visualize tumors in different organs, such as MicroCT to visualize tumor size, PET imaging to track tumor usage of glucose, and bioluminescence to track tumor growth in labeled cells, are all critical tools in the cancer researcher's arsenal. They are now available for use with laboratory mice, allowing scientists to track therapeutic responses in the best mouse models for human cancers.