Genome sequencing plays increasing role in pediatric IBD

Over the past two decades, researchers have gained considerable insight into the pathogenesis of inflammatory bowel disease (IBD), which seems to involve complex interactions among genetic predisposition, environmental factors such as diet and microbiome composition, and immune response.

The role of genetics, in particular, has received increased attention as new technologies and analytic techniques have been developed, with testing evolving from family-based linkage analysis to genome-wide association studies and, most recently, next-generation sequencing.

Genome-wide association studies have identified at least 163 genetic loci containing susceptibility genes for Crohn's disease, ulcerative colitis or both. A major disadvantage of these studies, however, is that they are more likely to detect common variants than rare ones — a problem that can be remedied by exome sequencing, which can identify rare, highly damaging variants associated with familial forms of early- or very early-onset IBD (VEO-IBD).

At Mayo Clinic, a unique collaboration between pediatric gastroenterology and the Center for Individualized Medicine (CIM) offers young patients the opportunity for deep sequencing of DNA and in most cases exome sequencing to try to identify the genetic basis of their symptoms as well as a therapeutic strategy to treat them.

VEO-IBD: A case study

Children with very early-onset IBD (children younger than ages 6 to 10 years) usually have more-extensive inflammation (pancolitis) at time of diagnosis and more medically refractory disease than teens or adults do. In many cases, they have a more definable primary immunodeficiency that exhibits features similar to IBD. Unlike typical IBD inheritance, which is polygenetic, early-onset forms may involve a single, very rare genetic allele.

Michael C. Stephens, M.D., a pediatric gastroenterologist at Mayo Clinic's campus in Rochester, Minnesota, describes the case of a now 17-year-old patient who has had severe symptoms of IBD since infancy and is currently being treated in the pediatric gastroenterology-individualized medicine program.

Dr. Stephens explains: "He is about the size of a 10-year-old because inflammation and malabsorption have stunted his growth. In addition to gastrointestinal symptoms, he has arthritis, eye inflammation, and thyroid and skin manifestations.

"When he first came to us, we performed exome sequencing and discovered several possible candidate genes. We then met with the Genomic Odyssey Board, which is composed of genetics experts, researchers and counselors from all three Mayo campuses, to determine if any of the genetic mutations were medically actionable. The one that seemed most important was an LPS-responsive beige-like anchor (LRBA) gene mutation that affected protein expression.

"In talking to our colleagues across the country, we learned that less than 20 patients are known to have had problems with that gene. We also realized that the fusion protein abatacept, which is not a conventional therapy for either Crohn's disease or ulcerative colitis, might be helpful in this case. Several other patients with LRBA disorders had been treated with abatacept and had significant improvement. There were also existing data about the use of this drug in other immunodeficiencies that resulted in autoimmune enteropathy."

After two months of abatacept, the patient has shown some response, which is measured both by a reduction in inflammation markers and clinical improvement, including weight gain and reduced severity of arthritis and ophthalmic symptoms. "Although early, we are optimistic; no other therapy has generated such improvement in this patient," Dr. Stephens says.

Mayo Clinic researchers are also looking for medically actionable novel genes in a family with three generations affected by IBD. "The data are just coming back, and again, it looks like just one gene," Dr. Stephens says. "One of our goals is to use the integration across pediatric and adult GI as well as the CIM to provide a comprehensive multidisciplinary program for families with multiple affected members. The family could come to Mayo and have adult and pediatric specialists collaboratively build a treatment strategy. Where appropriate, this will utilize the genetic resources of the CIM, and the family will hopefully leave with a treatment plan specifically designed for them and their type of IBD."

Microbiome research

Dr. Stephens has been actively involved in an international effort to identify better ways to stratify patients with IBD, with a focus on factors that predict more-severe disease. A recent publication from this group found a marked increase in Enterobacteriaceae, Pasteurellaceae, Veillonellaceae and Fusobacteriaceae and decreased numbers of Erysipelotrichales, Bacteroidales and Clostridiales in a large cohort of pediatric patients with new-onset Crohn's disease. Early exposure to antibiotics was shown to increase gut dysbiosis.

Dr. Stephens notes that based on the study results, which were published in the March 2014 issue of Cell Host & Microbe, analysis of the rectal, but not the fecal, microbiome could provide accurate and convenient diagnosis of early Crohn's disease.

For more information

Gevers D, et al. The treatment-naive microbiome in new-onset Crohn's disease. Cell Host & Microbe. 2014;15:382.