Underlying Genetic Disease in Pediatric Inflammatory Bowel Disease

Link to text of accepted study (Gastroenterology, ahead of publication): Prevalence and Clinical Features of Inflammatory Bowel Diseases Associated with Monogenic Variants, Identified by Whole-exome Sequencing in 1000 Children at a Single Center 


Background & Aims: A proportion of infants and young children with inflammatory bowel diseases (IBD) have subtypes associated with a single gene variant (monogenic IBD). We aimed to determine the prevalence of monogenic disease in a cohort of pediatric patients with IBD.

Methods: We performed whole-exome sequencing analyses of blood samples from an
unselected cohort of 1005 children with IBD, 0–18 y old (median age at diagnosis, 11.96 y) at a single center in Canada and their family members (2305 samples total). Variants believed to cause IBD were validated using Sanger sequencing. Biopsies from patients were analyzed by immunofluorescence and histochemical analyses.

Results: We identified 40 rare variants associated with 21 monogenic genes among 31 of the 1005 children with IBD (including 5 variants in XIAP, 3 in DOCK8, and 2 each in FOXP3, GUCY2C, and LRBA). These variants occurred in 7.8% of children younger than 6 y and 2.3% of children 6–18 y old. Of the 17 patients with monogenic Crohn’s disease, 35% had abdominal pain, 24% had non-bloody loose stool, 18% had vomiting, 18% had weight loss, and 5% had intermittent bloody loose stool. The 14 patients with monogenic ulcerative colitis or IBD unclassified received their diagnosis at a younger age, and their most predominant feature was bloody loose stool (78%). Features associated with monogenic IBD, compared to cases of IBD not associated with a single variant, were age of onset younger than 2 y (odds ratio [OR], 6.30; P=.020), family history of autoimmune disease (OR, 5.12; P=.002), extraintestinal manifestations (OR, 15.36; P<.0001), and surgery (OR, 3.42; P=.042). Seventeen patients had variants in genes that could be corrected with allogeneic hematopoietic stem cell transplantation.

Conclusions: In whole-exome sequencing analyses of more than 1000 children with IBD at a single center, we found that 3% had rare variants in genes previously associated with pediatric IBD. These were associated with different IBD phenotypes, and 1% of the patients had variants that could be potentially corrected with allogeneic hematopoietic stem cell transplantation. Monogenic IBD is rare but should be considered in analysis of all patients with pediatric onset of IBD.
KEY WORDS: HSCT, genetics, risk factor, prevalence


Expanding VEO Variants

A recent study (Q Li, CH Lee, LA Peters, et al. Gastroenterol 2016; 150: 1196-1207) provides a description of a new genetic variant causing very early onset inflammatory bowel disease (VEOIBD), which designates cases of IBD which presents <6 years of age.

Using whole exome sequencing, the authors identified TRIM22 mutations in 3 infants with fistulizing perianal disease and granulomatous colitis.  The authors further characterized the defect using functional studies that showed TRIM22 is important in the regulation of nucleotide binding oligomerization domain containing 2 (NOD2)–dependednt activation of interferon-beta signaling and nuclear factor (NF)-κB.

“NOD2 has long been recognized as a critical player in Crohn’s disease pathogenesis, where it is proposed to regulate innate immunity through NF-κB induced proinflammatory responses triggered by peptidoglycan…Simarlarly, mutations in XIAP..are associate with loss of NOD-2-dependent mediated NF-κB signaling” and has a similar phenotype.

My take: Identification of the numerous mutations that lead to VEOIBD is likely to help understand the pathogenesis and ultimately to better therapies.

Related blog posts:

How Much Lower Would The Braves Be Without the Marlins?

How Much Lower Would The Braves Be Without the Marlins?

Just the Beginning: Mutations in Very Early Onset Inflammatory Bowel Disease

A recent study (Gastroenterol 2014; 146: 1028-39) indicates that mutations in tetratricopeptide repeat domain 7A (TTC7A) can result in a severe form of very early onset inflammatory bowel disease (VEOIBD).

After identifying a TTC7A heterozygote mutation in an infant by using whole exome sequencing of DNA, the authors subsequently identified 4 additional patients (2 siblings from 2 families) who also had loss of function mutations in VEOIBD.  Thus far, four of the five identified infants have died.

The manuscript has some terrific figures describing endoscopic/histologic characteristics, TTC7A genetic analysis, functional TTC7A enterocyte studies with immunofluorescence, impaired cell adhesion figure, tandem mass spectrometry, and a summary mechanistic figure (figure 6).  Hematopoietic stem cell transplantation has not been effective and might not work due to the enterocyte defect.

This study adds another VEOIBD gene mutation.  Previous mutations have involved in VEOIBD have included IL10RA/B, XIAP, ADAM17, NCF4, and NCF2/RAC2. The specific subtype matters as some defects may respond to stem cell transplantation.

Take-home message: there are a diverse number of pathways that can lead to VEOIBD.  Given the recent availability of whole exome sequencing, more mutations are sure to be identified soon.

Related blog post/link:

IL-10 and early onset IBD | gutsandgrowth In addition to the Toronto group (noted in this blog), a group in Boston with Harland Winter/CJ Moran is also interested in whole exome sequencing for VEOIBD patients.

Causes and Treatment of Very-Early Onset IBD -this link is to the AGA Journals blog post on the same subject.