Hereditary pancreatitis – managing patient clinical information and sequence variants in the CFTR, PRSS1 and SPINK1 genes

Abstract

Hereditary pancreatitis is a rare inherited disorder, characterized by recurrent episodes of acute pancreatitis usually within the first two decades of life progressing to chronic pancreatitis. Disease progression includes pancreatic calcifications, exocrine insufficiency, and diabetes mellitus in most patients. Some cases progress to pancreatic cancer. The mode of inheritance suggests an autosomal dominance trait with incomplete penetrance. PRSSI is a one of eight trypsinogen genes. Mutations in the PRSS1 gene are believed to be mostly gain-of-function leading to increased activity or stability of trypsin and / or decreased trypsin inactivation resulting in autolysis of the pancreatic tissue. Almost all the PRSS1 pancreatitis-associated mutations discovered to date seem to cluster in exons 2 and 3. The two most common c.365G>A, p.R122H and c.86A>T, p.N29I are missense mutations and are reported to have a penetrance of 80% for hereditary pancreatitis. Two other genes, SPINK1 (serine protease inhibitor Kazal type 1) and CFTR are risk factors for pancreatitis. Mutations in these two genes may be inherited in an autosomal recessive or multifactorial fashion. SPINK1, is a specific trypsin inhibitor expressed within the pancreas, providing an important defense against prematurely activated trypsinogen. 15% of adults, and 25% of children, with idiopathic pancreatitis have SPINK1 mutations. The primary mutation found in the SPINK1 gene, c.101A>G, p.N34S, increases the risk for pancreatitis by 14 fold. Approximately 30% of individuals with idiopathic pancreatitis have at least one CFTR mutation. Hereditary pancreatitis is an autosomal disease with variable expression caused by mutations in the PRSS1 gene. Two other genes, SPINK1 and CFTR, are risk factors for pancreatitis and can be inherited in an autosomal recessive or multifactorial fashion. Gene sequencing of all three genes aids in the diagnosis of hereditary pancreatitis which can be difficult to distinguish from a mild cystic fibrosis phenotype. Manageability of data derived from the patient’s clinical presentation and sequencing results is vital to understand genotype/phenotype correlation, to help classify variants and to assure quality in laboratory reporting. To this end, we have employed the clinical data management software, Progeny, to track genotypic and phenotypic information on individuals and pedigrees. The database was customized for pancreatitis patients. Data entered includes patient demographics and clinical presentation, laboratory sequencing results (nucleotide and amino acid changes for CFTR, PRSS1 and SPINK1; mutation type and effect; and significance of the variant) and evidence for reclassification of variants. Analysis of 59 pancreatitis cases (classified as idiopathic, acute or chronic) found 10.2% of the patients carried one CFTR mutation, 5.1% carried one CFTR and one SPINK1 mutation, 5.1% carried one PRSS1 mutation, 1.7% carried two CFTR mutations, 1.7% carried one CFTR mutation and two SPINK1 mutations and 6.8% carried one SPINK1 mutation. No mutations were found in 69.5% of the cases. Progeny software allows customized databases for combining clinical and laboratory information, providing a means for accessible collection and querying of data. Samples Patient samples were sent to ARUP Laboratories (Salt Lake City, Utah) for clinical testing. Sequencing Patient samples requesting an idiopathic pancreatitis panel (IP panel) were sequenced in the clinical laboratory. An IP panel composed of full gene sequencing (FGS) for all three genes CFTR, PRSS1 and SPINK1 was ordered on 45 samples. Seven patient samples had FGS ordered only for PRSS1, 5 had FGS for SPINK1 only and 2 patient samples had FGS ordered both for PRSS1 and SPINK1. Thirty-three samples sent in for only CFTR FGS were selected for additional analysis due to their singular diagnosis of pancreatitis. The samples were de-identified and sequencing for PRSS1 and SPINK1 was performed in the R&D laboratory.