Introduction
Gastroparesis is a severe medical condition characterized by delayed gastric emptying and symptoms of nausea, vomiting, bloating, fullness after meals, and abdominal pain. Thus far, little is known about the underlying genetic risk factors for nausea in gastroparesis patients. We explored the association of genetic variants with nausea severity in a set of WGS data from a clinical gastroparesis study.
Aims & Methods
Blood samples were obtained from adults with a diagnosis of diabetic or idiopathic gastroparesis, having evidence of delayed gastric emptying, and moderate to severe nausea, daily average nausea score of >2.5, at least one episode of vomiting, PAGI-SYM nausea score of ≥2 at screening, and controlled blood glucose levels. WGS was conducted with 30x read depth using whole blood samples. Nausea score was assessed from a daily symptom dairy with a range from 0 mild to 5 severe. GWAS using linear model was conducted on variants with MAF ≥0.01 with adjustment of the subject’s age, sex, BMI, etiology, and the first 3 PCs.
Results
Variant clusters from multiple genes are significantly associated with baseline nausea score at p=1e-5 level. Among the top scoring variants are loci within ATF3, PP2D1, CNTN4, BMP2, ABL1, CTNNA3 and KIF6. Interestingly, upon comparing our results with a published transcriptomic analysis that included both diabetic and idiopathic gastroparesis subjects, we found that ATF3 and BMP2 were overlapping with genes differentially expressed in both diabetic and idiopathic gastroparesis when compared with controls. ABL1 was however differentially expressed in diabetic cases whereas CNTN4 was differentially expressed in idiopathic controls.
We expanded the analysis with single gene tests which shows that ATF3 is significant especially for MAF>0.05 variants (SKAT p=0.02). The top variant in ATF3 is rs79151334 (beta= 0.68, p=5.76e-6), whose minor allele associates with higher nausea score.
Conclusion
Additionally, we report new potential associations CTNNA3, PP2D1, and KIF6 as well as a cluster of variants between CDH2 and MIR302F, that associated with baseline nausea score. Among those, both CTNNA3 and CDH2 encode cadherin related proteins, suggesting this type of junction could play a role in the underlying mechanism.
Disclosure
I am an employee at Vanda Pharmaceuticals Inc.