A novel pathogenic APC variant identified in a Chinese pedigree with familial adenomatous polyposis

TL;DR

A new harmful APC gene variant was found in a Chinese family with a genetic disorder that causes colorectal cancer, expanding the known genetic causes of this condition.

Contribution

The study identifies and validates a novel APC germline variant (c.3799dup) as pathogenic in familial adenomatous polyposis.

Findings

The APC c.3799dup variant was present in all affected family members but absent in unaffected individuals.

The APC-mutant group showed significantly higher β-catenin protein levels compared to the APC-WT group.

The variant disrupts APC's role in β-catenin degradation, leading to Wnt/β-catenin pathway activation.

Abstract

Familial adenomatous polyposis (FAP) is an autosomal dominant genetic disorder characterized by the development of numerous colorectal polyps and a high predisposition to colorectal cancer, primarily caused by germline variants in the APC gene. This study aimed to identify and functionally validate a novel APC variant in a Chinese FAP pedigree.

A three-generation Chinese FAP pedigree was recruited. Peripheral blood samples were collected from family members to extract genomic DNA. Whole-exome sequencing (WES) was performed to screen candidate variants, and Sanger sequencing was used for verification. SW480 cells (endogenously deficient in functional APC) were divided into three groups: empty vector group, APC-wild-type (APC-WT) group, and APC-mutant group. Western blot analysis was conducted to detect β-catenin protein expression levels, to evaluate the functional impact of the identified variant.

The proband’s FAP-associated colorectal cancer was identified as exhibiting microsatellite instability high (MSI-H) with a classic MLH1/PMS2 dual loss pattern. A novel germline variant APC c.3799dup was identified in all affected family members but was absent in unaffected individuals. Western blot analysis showed that β-catenin protein levels in the APC-WT group were significantly lower than those in the APC-Mutant group (P < 0.05) and the empty vector group (P < 0.01). This indicated that the c.3799 dup variant abolished APC’s ability to promote β-catenin degradation, leading to sustained activation of the Wnt/β-catenin pathway.

The novel APC variant c.3799 dup is a pathogenic variant associated with FAP. Our findings expand the spectrum of known APC variants and provide functional evidence for the pathogenicity of this variant. The rare co-occurrence of FAP and MSI-H in the proband enriches the molecular phenotypic spectrum of FAP-related tumors.

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