Pseudoexons provide a mechanism for allele-specific expression of APC in familial adenomatous polyposis.

Taina T Nieminen,Noora Porkka,Matti Kankainen,Anna Lepistö,Heikki J Järvinen,Walter Pavicic,Päivi Peltomäki

doi:10.18632/oncotarget.12206

Abstract

Allele-specific expression (ASE) of the Adenomatous Polyposis Coli (APC) gene occurs in up to one-third of families with adenomatous polyposis (FAP) that have screened mutation-negative by conventional techniques. To advance our understanding of the genomic basis of this phenomenon, 54 APC mutation-negative families (21 with classical FAP and 33 with attenuated FAP, AFAP) were investigated. We focused on four families with validated ASE and scrutinized these families by sequencing of the blood transcriptomes (RNA-seq) and genomes (WGS). Three families, two with classical FAP and one with AFAP, revealed deep intronic mutations associated with pseudoexons. In all three families, intronic mutations (c.646-1806T>G in intron 6, c.1408+729A>G in intron 11, and c.1408+731C>T in intron 11) created new splice donor sites resulting in the insertion of intronic sequences (of 127 bp, 83 bp, and 83 bp, respectively) in the APC transcript. The respective intronic mutations were absent in the remaining polyposis families and the general population. Premature stop of translation as the predicted consequence as well as co-segregation with polyposis supported the pathogenicity of the pseudoexons. We conclude that next generation sequencing on RNA and genomic DNA is an effective strategy to reveal and validate pseudoexons that are regularly missed by traditional screening methods and is worth considering in apparent mutation-negative polyposis families.

Highlights

Familial adenomatous polyposis (FAP; OMIM #175100) is characterized by a dominant predisposition to multiple adenomatous polyps throughout the colon and rectum as a consequence of germline mutations in the Adenomatous Polyposis Coli (APC) gene [1]
We conclude that generation sequencing on RNA and genomic DNA is an effective strategy to reveal and validate pseudoexons that are regularly missed by traditional screening methods and is worth considering in apparent mutation-negative polyposis families
We focused on three families with adenomatous polyposis (FAP) families (42, 85, and 103) from the research-based cohort (Figure 1 and Table 1)

Summary

Introduction

Familial adenomatous polyposis (FAP; OMIM #175100) is characterized by a dominant predisposition to multiple adenomatous polyps throughout the colon and rectum as a consequence of germline mutations in the Adenomatous Polyposis Coli (APC) gene [1]. The number of adenomatous polyps in the bowel is used to stratify APC-associated polyposis into a classical form (FAP; 100 adenomas or more) and attenuated form (AFAP; below 100 adenomas). These two phenotypes differ relative to the onset of polyposis (in the second or third decades of life in FAP vs later in AFAP), colonic location (left-sided disease in FAP vs frequently right-sided disease in AFAP), and life-time risk of colorectal cancer (100% in FAP vs up to 70% in AFAP) [1, 3]. In a large cohort of individuals who had undergone clinical genetic testing because of a personal or family history of polyposis, www.impactjournals.com/oncotarget

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