EP261: The spectrum of CFTR and PRSS1 pathogenic variants in chronic pancreatitis

Abstract

Chronic pancreatitis is defined as persistent inflammation of the pancreas that is ongoing for 6 months or longer. Chronic pancreatitis often develops by early adulthood in affected individuals and can lead to permanent tissue damage and loss of pancreatic function, including both exocrine and endocrine pancreatic insufficiency. Chronic pancreatitis increases the risk for diabetes and pancreatic cancer, more so with smoking and use of alcohol. Variants in several genes have been identified to be causative for, or induce susceptibility to, chronic pancreatitis. Genetic testing for hereditary chronic pancreatitis can aid in differential diagnosis of chronic pancreatitis from other disorders which also present with pancreatitis and may inform treatment strategy. This study reports the spectrum of pathogenic variants in individuals referred for chronic pancreatitis panel testing. This study included 747 individuals who underwent chronic pancreatitis panel testing at a single clinical laboratory (PreventionGenetics) between June 15, 2018 and September 24, 2021. Clinical information was obtained from provider-completed test requisition forms. Next generation sequencing (NGS) with copy number variant (CNV) detection was performed on patient-derived DNA using the Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) and Sanger sequencing as necessary. Testing provided 100% coverage for the coding regions of the CASR, CFTR, CTRC, PRSS1, and SPINK1 genes plus ∼10 bases of non-coding DNA flanking each exon, as well as non-coding regions in which pathogenic variants had been identified by the clinical testing laboratory or reported elsewhere. The test also included sequencing of CFTR regions within intron 11 and intron 21, along with a complete analysis of the compound (TG)n(T)n sequence (5T/TG tract) in intron 8. Variations in the 5T/TG tract have been reported to cause congenital absence of the vas deferens, non-classic cystic fibrosis, and classic cystic fibrosis. At time of testing, the patients ranged in age from 1 week to 87 years, with a median age of 32 years. Of the patients tested, 68% were negative for variants in genes included on the panel that are likely to cause disease while 27% were found to be indeterminate, where variants were identified but the results were not diagnostic. Overall, 5% of patients were positive, with a clear molecular diagnosis identified. Pathogenic and likely pathogenic variants in CFTR and PRSS1 accounted for 90% of positive cases overall, with 42% of positive cases being attributed to CFTR-related pancreatitis (1 homozygous or 2 heterozygous causative variants identified) and 33% of positive cases attributed to PRSS1-related pancreatitis (1 heterozygous causative variant). An additional 15% of positive cases were found to have pathogenic or likely pathogenic variants in both CFTR and PRSS1 (1 heterozygous causative variant in both CFTR and PRSS1). The CFTR c.1210-34TG[12]T[5] variant (more commonly referred to as 5T/12TG) contributed to ∼21% of CFTR-related pancreatitis. Importantly, ∼72% of pathogenic and likely pathogenic variants identified in this patient cohort are approved as therapy responsive variants for FDA approved CFTR modulators. In approximately 40% of patients with PRSS1-related pancreatitis, we detected a ∼600kb copy number gain encompassing the whole PRSS1 gene, compared to an estimated 6% of patients in the literature. These data indicate that variants in CFTR are a common cause of chronic pancreatitis and highlights the clinic utility of including complete analysis of the compound (TG)n(T)n sequence (5T/TG tract) in intron 8 of CFTR in this patient cohort. Additionally, the high frequency of treatment responsive variants suggests that a molecular diagnosis in patients with chronic pancreatitis may alter treatment strategy, particularly in the context of CFTR-related pancreatitis. Furthermore, these data suggest that whole gene deletions/duplications may be more frequent that previously thought in this patient cohort and that complex copy number variants in the PRSS1 gene may escape detection by other NGS testing strategies.