基于三代测序和结构生物信息学分析的血小板CD109基因第19外显子缺失的研究*

doi:10.3969/j.issn.1671-2587.2026.04.017

临床输血与检验 ›› 2026, Vol. 28 ›› Issue (4): 573-581.DOI: 10.3969/j.issn.1671-2587.2026.04.017

基于三代测序和结构生物信息学分析的血小板CD109基因第19外显子缺失的研究^*

宋文倩¹, 白素宁², 余婉珍², 王丽颖¹, 邵林楠¹, 周世航¹, 梁晓华¹

¹大连市血液中心,血型研究室,辽宁大连 116001;
²大连医科大学,检验医学院,辽宁大连 116044

收稿日期:2026-07-06 出版日期:2026-08-20 发布日期:2026-08-26
通讯作者: 梁晓华,主要从事血液免疫和血液安全的研究,（E-mail）liangxiaohua1968@126.com。
作者简介:宋文倩,主要从事输血医学研究,（E-mail）wenqian_song@163.com。并列第一作者：白素宁,主要从事检验医学技术研究,（E-mail）suning_bai@163.com。
基金资助:
^*本课题受大连市科技创新基金项目（No.2025JJ13PT055）资助

Exon 19 Deletion of the Platelet CD109 Gene: Characterization via Third-generation Sequencing and Structural Bioinformatics Analysis

SONG Wenqian¹, BAI Suning², YU Wanzhen², WANG Liying¹, SHAO Linnan¹, ZHOU Shihang¹, LIANG Xiaohua¹

¹Blood Group Laboratory, Dalian Blood Center, Dalian 116001;
²College of Laboratory Medicine, Dalian Medical University, Dalian 116044

Received:2026-07-06 Online:2026-08-20 Published:2026-08-26

摘要/Abstract

摘要： 目的探讨CD109基因第19外显子缺失对HPA-15分型、蛋白结构及其与TGF-β1相互作用的潜在影响。方法以1例在常规HPA筛查中发现异常的血小板献血者为研究对象,采用PacBio Sequel Ⅱ三代测序进行HPA相关基因分析,结合AlphaGenome剪接效应预测、AlphaFold3结构建模、PyMOL叠加比对及HADDOCK蛋白-蛋白对接,评估突变对CD109构象及其与TGF-β1结合模式的影响,并辅以血常规、凝血功能、血小板聚集及流式细胞术检测进行功能评价。结果三代测序显示CD109第19外显子存在大片段缺失,导致移码并提前终止,使一条单体型无法按常规方式完成HPA-15分型。AlphaGenome分析显示,结构变异可能导致局部剪接识别失稳及异常转录本形成。结构分析提示该变异未完全破坏CD109整体折叠,但引起局部构象改变和结构域空间重排。分子对接显示突变型复合物界面作用方式发生改变,构象异质性增加,其与TGF-β1的结合模式可能异常。常规实验室检测未见明显异常,但流式细胞术显示CD42a/CD42b及CD62P/PAC-1表达不一致。结论 CD109第19外显子缺失是一种罕见结构变异,可干扰HPA-15常规分型,并可能通过改变CD109构象及其与TGF-β1的相互作用,导致血小板出现亚临床层面的功能偏移。该研究提示三代测序结合结构生物信息学分析有助于揭示复杂血小板抗原变异的潜在功能意义。

关键词: AlphaGenome, HPA-15, 三代测序, 分子对接, CD109基因

Abstract: Objective To characterize the potential impacts of a CD109 exon 19 deletion on human platelet antigen 15 (HPA-15) genotyping, protein structure, and its interaction with transforming growth factor-β1 (TGF-β1). Methods A platelet donor presenting with abnormal results on routine HPA screening was enrolled. HPA-related genes were performed using third-generation sequencing on the PacBio Sequel Ⅱ platform. The effects of the variant on CD109 conformation and its binding mode to TGF-β1 were evaluated through an integrated structural bioinformatics workflow, including AlphaGenome splicing effect prediction, AlphaFold3 structural modeling, PyMOL structural superposition and alignment, and HADDOCK protein-protein docking. Functional phenotyping was complemented by blood count, coagulation assays, platelet aggregation testing, and flow cytometric analysis. Results Third-generation sequencing detected a large intragenic deletion spanning CD109 exon 19, which introduces a frameshift mutation and premature stop codon, rendering conventional HPA-15 genotyping unassignable for one haplotype. AlphaGenome analysis predicted that this structural variant may destabilize local splice site recognition and give rise to aberrant transcripts. Structural modeling demonstrated that the variant did not abrogate the overall fold of CD109, but induced localized conformational remodeling and spatial rearrangement of functional domains. Molecular docking simulations revealed altered interaction patterns at the protein-protein interface, augmented conformational heterogeneity, and a potentially dysregulated binding mode between mutant CD109 and TGF-β1. No overt abnormalities were identified on routine testings, whereas flow cytometry showed discordant expression profiles of CD42a/CD42b and CD62P/PAC-1. Conclusion The CD109 exon 19 deletion is a rare structural genomic variant that disrupts routine HPA-15 genotyping. It may drive subclinical functional perturbations in platelets by altering CD109 conformation and its interaction with TGF-β1. This study demonstrates that integrating third-generation sequencing with structural bioinformatics provides a powerful approach to unraveling the functional consequences of complex platelet antigen variants.

Key words: AlphaGenome, HPA-15, Third-generation sequencing, Molecular docking, CD109 gene

中图分类号:

R394.3

宋文倩, 白素宁, 余婉珍, 王丽颖, 邵林楠, 周世航, 梁晓华. 基于三代测序和结构生物信息学分析的血小板CD109基因第19外显子缺失的研究^*[J]. 临床输血与检验, 2026, 28(4): 573-581.

SONG Wenqian, BAI Suning, YU Wanzhen, WANG Liying, SHAO Linnan, ZHOU Shihang, LIANG Xiaohua. Exon 19 Deletion of the Platelet CD109 Gene: Characterization via Third-generation Sequencing and Structural Bioinformatics Analysis[J]. JOURNAL OF CLINICAL TRANSFUSION AND LABORATORY MEDICINE, 2026, 28(4): 573-581.

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基于三代测序和结构生物信息学分析的血小板CD109基因第19外显子缺失的研究^*

Exon 19 Deletion of the Platelet CD109 Gene: Characterization via Third-generation Sequencing and Structural Bioinformatics Analysis

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