GRASP

 




 

 

 

 

 


"What has become evident is that not only will patients benefit from this large-scale effort, but the broader community of scleroderma researchers will benefit as well."

- Deann Wright, Member SRF Board of Directors

Dr. Dan Kastner and Dr. Fred Wigley chuckled as they sat down for dinner together at the SRF Workshop. Both were interested in meeting the many new scientists present that evening, but as the last people to join the table, the two old friends were seated together. They had known each other for years, but they did not often have a chance to sit and just talk. And, after listening to scientific presentations all day, they had plenty to discuss. As it happened, it was a fortuitous moment: they conceived the Genome Research in African American Scleroderma Patients (GRASP) project over dinner that night.

Dr. Fred Wigley, Director of the Johns Hopkins (JH) Scleroderma Center has been treating patients for more than 35 years. Wigley is the kind of physician who listens and observes closely, and has developed patient care into an art. With support from the SRF, he has built his practice into a premier multi-specialty Scleroderma Center, with four full-time rheumatologists serving one of the largest groups of patients in the country. The SRF also has helped Dr. Wigley build a large clinical database to track patients and their data, as well as a biorepository filled with patient samples, which together give him unique abilities to study scleroderma. Located in Baltimore, his patients include members of the strong African American community there. Dr. Wigley, knowing that African Americans have an increased incidence and prevalence of scleroderma and often a more severe presentation of the disease has, for many years, been interested to try to figure out why, and what can be done for his patients.

SRF-Scientific Advisor, Dan Kastner, MD, PhD, is widely known for his research into the causes of autoinflammatory diseases, such as Behçet’s. As Scientific Chief of the intramural program at the National Human Genome Research Institute (NHGRI), he oversees the work of more than 50 genomics researchers within the NIH. Having traveled the world to identify extended families afflicted by unusual fever syndromes, Kastner, together with his own research group, has identified the genes mutated in several of these rare autoinflammatory disorders. These discoveries have not only identified therapeutic targets for these disorders, but they have advanced our understanding of many key molecules and processes of the immune system.

ASKING THE RIGHT QUESTIONS

Could it be, the two researchers asked, that African Americans’ increased risk for scleroderma and severe form of disease are at least partially genetically driven? Would it be possible to sequence DNA from a sufficiently large number of African American scleroderma patients to reveal any such underlying genetic factors? And, most importantly, could this help researchers and clinicians discover biological pathways to target in treating these and other patients?

Scleroderma does not have a clear-cut genetic basis, unlike some diseases, like cystic fibrosis, which results from a mutation in a single gene. These single-gene diseases clearly run in families, whereas others, known as complex diseases, are different. However, scientists are discovering that many complex diseases also have a genetic component. Complex diseases, which include many autoimmune disorders like scleroderma and lupus, but also diseases like Alzheimer’s and heart disease, arise from a combination of several genetic and environmental factors. Many of these factors are not well understood. Further, complex diseases often do not have readily discernible inheritance patterns, making it harder to pinpoint genetic contributors to disease. This means that studying the genetics of complex diseases requires analyzing greater numbers of patients in order to tease apart truly relevant disease associations from inadvertent associations.

Often, in studying complex diseases, genomic researchers try to improve the likelihood of finding disease-relevant associations by studying so-called “enriched populations”, in which genetics may play a more significant role, for one reason or another. Compared to patients of European ancestry, African American patients have increased incidence and severity of scleroderma, leading Dr. Wigley and Dr. Kastner to speculate that genetics might play an enhanced role in these patients.

Enriched populations can be defined in other ways too. For example, the SRF is supporting genetic analyses in another enriched population of systemic sclerosis patients—those diagnosed before the age of eight. The very early onset of scleroderma, which most commonly presents in mid-life, may indicate a stronger genetic component in pediatric patients. This, too, may provide an opportunity to find a gene or genes that play a role in the disease.

Knowing the genes that play a role in disease can be important in assessing risk for a patient as well as identifying therapeutic targets. “The GRASP study has the potential to provide novel insight into the genetic basis for the disease expression in African Americans by discovering specific genes or genetic areas that associate with a specific clinical picture,” explains Dr. Wigley. “For example, if we discover that a group of African Americans who all have gene X develop severe scleroderma lung disease, while members of another ethnic group without gene X never get lung disease; then we know that gene X associates with the risk of getting severe lung disease. Knowing this will allow us to identify individuals at risk for lung disease. Then we can not only detect the lung disease early, but we can intervene before irreversible damage is done. Likewise, if we know patients lacking gene X are unlikely to progress to severe lung disease, then we can personalize their therapy without subjecting them to toxic or unnecessary medications.” Dr. Wigley adds, “it will also open the opportunity to study how having gene X causes lung disease by studying the specific gene and its biological function. We might even be able to develop a drug for the biological pathway driven by gene X that would prevent or reduce lung disease.”

ENGAGING A BROAD COMMUNITY TO FIND ANSWERS

Shortly after that SRF Workshop dinner, Drs. Kastner and Wigley enlisted Dr. Francesco Boin, then a scleroderma physician in the JH Scleroderma Center, to work with them on a plan for the GRASP project. The Hopkins group would enroll the patients, do the clinical work-ups and analyze the clinical data, while Dr. Kastner’s group at the NHGRI would sequence their DNA and perform the genomic analyses.

Since that evening, more than four years ago, the GRASP project has progressed in important ways. Under the leadership of Drs. Kastner, Wigley and Boin (now Director of the Scleroderma Center at UCSF) and in partnership with the Scleroderma Research Foundation, the GRASP project has evolved from a partnership between the JH Scleroderma Center and the NHGRI into a multi-center, national effort. Dr. Boin, a talented physician and native of Italy with considerable charm and an inclusive leadership style, has been critical in this expansion.

The GRASP project now includes a consortium of physicians from 23 U.S. scleroderma clinics and centers that enrolls African American patients into a national registry, located at Johns Hopkins. The SRF supports the consortium, clinical data and sample collection, the database and the expert staff that runs it at the JH Center, as well as investigator time devoted to the project. Biological samples are shipped directly to the NHGRI, where post-doctoral fellow Dr. Pravitt Gourh supervises the DNA sequencing and performs much of the genomic analysis.

Today, the GRASP registry includes more than 1,200 African American Scleroderma patients. Clinical data has been collected on all patients and is stored in the GRASP database at Johns Hopkins. Extensive genomic analyses are being conducted at the NHGRI. The initial step was sequencing a large fraction of the DNA from the first 400 patients, plus a comparable number of age- and ancestry-matched control subjects. This initial phase looked for variants that would have a very strong effect, such as those likely to result in changes to a protein’s structure. This helped identify genes and other DNA regions of interest. These results were then used to customize tools for a much broader, genome-wide analysis of samples from all 1,200 patients, plus the control group. Specific commercial tools that have been designed for studying the genetics in African American subjects have also been used. The DNA areas of highest interest are being further analyzed through targeted “re-sequencing” of samples from 600 patients plus controls. This will confirm the initial “hit” and collect additional data on those areas. Importantly, the NHGRI group employs sophisticated biostatistical methods at every step for analyzing the massive amount of data generated.

RESULTS ARE EVIDENT; ENGAGEMENT IS HIGH

The GRASP project is beginning to produce results. At the most recent meeting of the American College of Rheumatology (ACR), the GRASP investigator group was granted three oral presentations—an extremely high rate of acceptance. Dr. Nadia Morgan of the JH Center presented her findings regarding clinical manifestations of the disease in African American scleroderma patients. Notably, while scleroderma is overall a heterogeneous disease, meaning that it does not present in one way, with a predictable path of progression, the GRASP clinical data suggests that African American patients, as a group, have some clearly definable characteristics. For example, compared to patients of European ancestry, African Americans are more likely to have diffuse scleroderma with anti-topoisomerase antibodies and less likely to have limited scleroderma with anti-centromere antibodies—two quite different forms of scleroderma. Further, African American patients are more likely to develop a severe form of interstitial lung disease and pulmonary hypertension, both serious, life-threatening complications of scleroderma. These findings support the importance of research into inherited or genetic factors that may play a role in the incidence and severity of disease in this at-risk group. They also provide much-needed insight for physicians and other healthcare providers involved in the care of African American scleroderma patients.

With respect to the genomic analyses, the emerging results are very encouraging. With just the initial analysis done, several candidate genes have popped out as having statistically significant associations with disease, giving researchers confidence that the project will yield important insights into some of the subtle genetic elements of the disease. Dr. Elaine Remmers, PhD, of the NHGRI, noted that certain HLA genes particularly stood out. HLA genes play critical roles in shaping immune responses in both health and disease, and specific HLA alleles, or “flavors” of those genes, are known to be associated with different autoimmune diseases. Often an HLA allele will have a stronger association with an autoimmune disease than any other gene. This is also the case in scleroderma. Dr. Remmers discovered unique scleroderma-associated HLA alleles in the African American patients that differ from those previously identified in patients of European ancestry. And, in pediatric patients still other scleroderma-associated HLA alleles have been found. Intriguingly, the biological mechanisms that cause particular HLA alleles to be strongly associated with autoimmune diseases are beginning to be unraveled. Thus, Dr. Remmers’ discovery will certainly lead to intense interest and further inquiry.

Another exciting early result is that Dr. Gourh has found DNA differences in the gene control regions of TGFβ-3, a gene that is known to play a role in fibrosis. Dr. Gourh’s ability to connect these particular DNA variants to the TGFβ-3 gene stemmed from his collaboration with Dr. Howard Chang’s group at Stanford. For DNA variants that occur outside of protein-coding sequences, Chang’s newly developed technique pinpoints the specific gene(s) they affect. In this case, although the DNA variants are distant from the TGFβ-3 gene, the technique shows that they lie within a region that controls the gene. This technique is broadly applicable and will vastly improve researchers’ abilities to interpret their genetic data.

Since the goal of any genomic study is to identify DNA variants that cause or contribute to disease, the next step is a “functional study”−actually showing that a DNA variant functions in the disease. In Dr. Gourh’s work, because DNA variants affecting TGFβ-3 popped out as having a statistically strong association with scleroderma in African Americans, he identified TGFβ-3 as a “candidate” gene. Since TGFβ-3 is known to be involved in fibrosis in many contexts, he hypothesizes that these DNA variants may change its function, thereby contributing to fibrosis. And he has already begun his first experiments aimed at proving it. Using powerful new gene-editing tools, he can introduce these same variants into normal human fibroblasts to see if they change the function of the TGFβ-3 gene in a manner that would lead to fibrosis.

While the research progress is encouraging, the GRASP project’s goals have continued to grow. Last February, the SRF sponsored a meeting of the entire GRASP consortium at the NHGRI, where new research ideas were considered. The group decided to collect serum from enrolled patients in order to conduct a number of different experiments, including more extensive autoantibody screening. This will add to the group’s ability to correlate measurable data with clinical outcomes and to confirm involvement of genes identified in the genomic analyses.

“We are very proud of the GRASP project and the SRF’s role in moving this project forward,” says SRF Board member Deann Wright. “Additionally, the impact of the SRF’s funding has really been amplified by working with the NHGRI. Funds from our donors have been leveraged more than four-to-one, with combined support for this project totaling over $2 million at this point.”

“I believe this project will yield insights about disease in African American patients, leading to improved patient care in this at-risk population,” she adds. “Also, it is likely to produce significant insights into the biological processes involved in scleroderma, enhancing our understanding of the disease and potentially leading us to new therapeutic targets that could benefit all patients.”

“In terms of its effect on the research community,” Wright notes, “everyone involved−the GRASP leadership, investigators and consortium members−has come together, with incredible spirit and enthusiasm, to take part in this collaborative effort. I really think the progress achieved in GRASP is changing the way members of the scleroderma research community work together. What has become clear is that not only will patients benefit from this large-scale effort, but the broader community of scleroderma researchers will benefit as well.” The GRASP consortium is allowing its members and selected outside investigators to submit proposals to query the data with questions relevant to their own research. In this way, the GRASP data is becoming a rich resource for the broader scleroderma research community, aiding a broad range of projects. Ultimately, the data will be made even more widely available, further amplifying the impact of the project.

From Wright’s perspective, “the GRASP project embodies the two principal tenets of the SRF−supporting strong research and encouraging collaboration. Working together on this large and complex effort, we will significantly advance scleroderma research.”

Watch the SRF GRASP video, featuring Drs. Fred Wigley and Dan Kastner here>

 

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