文章：

CDH1基因的RNA-seq剪接谱及其对CDH1变异临床致病性分类的影响：替代性与致病性剪接模式的描述

RNA-seq Splicing Profile of theCDH1Gene and Its Impact on the Clinical Pathogenicity Classification ofCDH1Variants: A Description of Alternative and Pathogenic Splicing Patterns

原文发布日期：14 October 2025

DOI: 10.3390/cancers17203320

类型: Article

开放获取: 是

英文摘要：

Background/Objectives:CDH1gene is widely studied, as pathogenic variants are involved in diffuse gastric cancers and lobular breast cancers.CDH1genotype contributes to the management of clinical practice recommendations for cancer prevention. We proposed a qualitative and quantitative description ofCDH1alternative splicing profile on lymphoblastoid cell lines (LCLs). The aim of this description was to allow a comprehensive interpretation of the effect of variants of uncertain significance (VUS) onCDH1splicing.Methods:We studied, using RNAseq, the splicing profile of 22 LCLs (untreated and treated with puromycin) with no pathogenic variant onCDH1and evaluated the effect onCDH1splicing of four VUS.Results:We highlighted a total of eleven alternative splicing events including four junctions starting from intron 2, defining novel isoforms ofCDH1. We also identified an isoform causing the skip of exon 11 and leading to a disruption of the reading frame with high levels of expression on negativeCDH1control LCLs, confirmed by ddPCR. Splicing RNAseq results forCDH1VUS: c.1008+1G>A and c.1936+5G>A showed complex splicing patterns but allowed their classification as pathogenic. We studiedCDH1VUS exon 4 to exon 11 duplication with RNA analysis combined with Bionano optical genome mapping. Depending on alternative splicing of proximal and distal exons 11 within the duplication, we identified four distinct transcripts, leading to truncated proteins, classifying the duplication as pathogenic.Conclusions:CDH1has a complex alternative splicing profile characterized by a dynamic splicing of intron 2 makingCDH1a good candidate for a study using long-read RNAseq.

摘要翻译： 

背景/目的：CDH1基因因其致病性变异与弥漫性胃癌及小叶乳腺癌相关而受到广泛研究。CDH1基因型对癌症预防临床实践指南的制定具有重要指导意义。本研究对淋巴母细胞系（LCLs）中CDH1基因的可变剪接谱进行了定性与定量描述，旨在为全面解读意义未明变异（VUS）对CDH1剪接的影响提供依据。 方法：通过RNA测序技术，分析了22个不携带CDH1致病性变异的LCLs（未经处理及嘌呤霉素处理）的剪接谱，并评估了四种VUS对CDH1剪接的影响。 结果：研究共发现11种可变剪接事件，其中包含4个起始于内含子2的剪接连接点，这些事件定义了CDH1的新型异构体。同时鉴定出一种导致外显子11跳跃的异构体，该异构体会引起阅读框破坏，并在阴性对照LCLs中呈现高表达水平，此结果经ddPCR验证。针对CDH1 VUS（c.1008+1G>A和c.1936+5G>A）的剪接RNA测序结果显示复杂的剪接模式，但仍可将其归类为致病性变异。通过RNA分析结合Bionano光学基因组图谱技术，研究了CDH1 VUS中外显子4至外显子11的重复变异。根据重复区域内近端与远端外显子11的可变剪接方式，共鉴定出四种不同的转录本，这些转录本均导致蛋白质截短，从而将该重复变异归类为致病性。 结论：CDH1基因具有复杂的可变剪接特征，其内含子2的动态剪接尤为突出，这使得CDH1成为适合采用长读长RNA测序技术进行深入研究的理想对象。

原文链接：

RNA-seq Splicing Profile of theCDH1Gene and Its Impact on the Clinical Pathogenicity Classification ofCDH1Variants: A Description of Alternative and Pathogenic Splicing Patterns