The Identification of Large Rearrangements Involving Intron 2 of the CDH1 Gene in BRCA1/2 Negative and Breast Cancer Susceptibility

Abstract

E-cadherin, a CDH1 gene product, is a calcium-dependent cell-cell adhesion molecule playing a critical role in the establishment of epithelial architecture, maintenance of cell polarity, and differentiation. Germline pathogenic variants in the CDH1 gene are associated with hereditary diffuse gastric cancer (HDGC), and large rearrangements in the CDH1 gene are now being reported as well. Because CDH1 pathogenic variants could be associated with breast cancer (BC) susceptibility, CDH1 rearrangements could also impact it. The aim of our study is to identify rearrangements in the CDH1 gene in 148 BC cases with no BRCA1 and BRCA2 pathogenic variants. To do so, a zoom-in CGH array, covering the exonic, intronic, and flanking regions of the CDH1 gene, was used to screen our cohort. Intron 2 of the CDH1 gene was specifically targeted because it is largely reported to include several regulatory regions. As results, we detected one large rearrangement causing a premature stop in exon 3 of the CDH1 gene in a proband with a bilateral lobular breast carcinoma and a gastric carcinoma (GC). Two large rearrangements in the intron 2, a deletion and a duplication, were also reported only with BC cases without any familial history of GC. No germline rearrangements in the CDH1 coding region were detected in those families without GC and with a broad range of BC susceptibility. This study confirms the diversity of large rearrangements in the CDH1 gene. The rearrangements identified in intron 2 highlight the putative role of this intron in CDH1 regulation and alternative transcripts. Recurrent duplication copy number variations (CNV) are found in this region, and the deletion encompasses an alternative CDH1 transcript. Screening for large rearrangements in the CDH1 gene could be important for genetic testing of BC.

Keywords: BRCA1/2 negative cases; CDH1 rearrangements; CGH array; CNV; breast carcinoma; gastric carcinoma.

Figure 1

Family history of the three index cases harboring the exon 3, the intron 2 deletions and intron 2 duplication of the CDH1 gene. (A) Pedigree of the index case’s family carrying the exon 3 deletion, with proband filled in black and indicated by arrow. (B) Pedigree of the index case’s family carrying the intron 2 duplication. (C) Pedigree of the index case’s family carrying the intron 2 deletion with ages of affected individuals at onset of disease in years (BC: breast cancer, CRC: colorectal cancer; black arrows: sampled individuals carrying identified variants).

Figure 2

(A) Array CGH profile obtained for the heterozygous exon 3 deletion of the CDH1 gene. Intron 2 is represented in blue dots. (B) Sequencing chromatogram of the mapped breakpoint for the exon 3 deletion from chr16: 67,387,135 to 67,394,109. Gray box: exons; green line: deletion locus. Red arrows: position of sequencing primers.

Figure 3

(A) Array CGH profiles obtained for the heterozygous intron 2 deletion of the CDH1 gene. Intron 2 is represented in blue dots. (B) Sequencing chromatogram of the mapped breakpoint for the intron 2 deletion from chr16: 67,358,862–67,362,674 (NM_0043603: c.163+29048_c.164−30401del). Gray box: exons; blue box; EST; green line: deletion locus. Red arrows: position of sequencing primers.

Figure 4

(A) Array CGH profiles obtained for the heterozygous intron 2 duplication of the CDH1 gene. Intron 2 is represented in blue dots. (B) Sequencing chromatogram of the mapped breakpoint for the intron 2 duplication from chr16: 67,345,633–67,350,721(NM_0043603: c.163+15817_c.163+20905dup). Gray box: exons; red line: duplication locus; red arrows: position of sequencing primers.

Figure 5

(A) Immunohistochemical staining for E-cadherin in bilateral invasive lobular carcinoma, showing an homogenous loss of E-cadherin expression and presence of E-cadherin in normal tissue X 200. (B) Immunohistochemical staining for E-cadherin in in situ ductal and lobular carcinoma, showing a heterogeneous loss of E-cadherin expression X 200.