Insertion of Alu elements at a PTEN hotspot in Cowden syndrome

Abstract

Cowden syndrome (CS) is an inherited autosomal dominant disorder associated with germline pathogenic variants of the PTEN tumor suppressor gene. Its phenotypical expression is highly variable and the existence of patients with a CS suggestive phenotype without pathogenic PTEN variant may be related to genetic heterogeneity. In order to explore this hypothesis through the detection of potentially deleterious variants enabling us to identify a new candidate gene, we performed whole-exome sequencing (WES) in a series of 22 CS patients without detectable PTEN pathogenic variant using conventional methods for mutation screening. We failed to identify a novel candidate gene, but interestingly in two patients WES revealed the presence of two distinct, previously undescribed Alu insertions with the same break points in exon 5. These insertions were not found in a series of 35 breast carcinomas that showed a loss of PTEN expression without a detectable alteration of this gene. This study reveals the presence of a PTEN Alu insertion hotspot involved in CS, and suggests that undetected PTEN pathogenic variants could contribute to CS.

Figure 1

Alu insertions in PTEN exon 5 in two Cowden disease patients. Schematic representation of the Alu elements inserted into exon 5 of PTEN and Sanger sequencing of break points from mutant alleles for patient 1 (a) and patient 2 (b). The insertion was in an antisense orientation compared to the reference sequence. (c) Gel electrophoresis of PTEN exon 5 PCR products from two control individuals (C1 and C2), and patients 1998101 (P1) and 2001012 (P2) harboring a full-length Alu element (P1) and a truncated Alu element (P2). The additional bands are probably derived from heteroduplexes between the wild-type and mutant alleles, neither of which are present in the controls. TSD, target site duplication; W, water control.