Liu Na, Bai Jingyi, Huang Nan, Xu Yi, Long Xiangyun, Hu Xinyi, Wu Jiaxin, Liu Fei, Lu Zheng
Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Xuhui District, Shanghai 200030, China.
Department of Psychiatry, Tongji Hospital of Tongji University, Tongji University School of Medicine, Shanghai 200065, China.
Sex Med. 2025 Aug 22;13(4):qfaf062. doi: 10.1093/sexmed/qfaf062. eCollection 2025 Aug.
Genetic factors contributing to sex-associated dimorphic brain development may also underlie gender identity-related anxiety disorders.
To establish a high-throughput whole-exome sequencing (WES) and bioinformatics pipeline for identifying rare variants in sex-dimorphic neural pathways and explore their association with gender identity-related anxiety.
Peripheral genomic DNA was collected from 23 patients (13 Assigned male at birth (AMAB), 10 Assigned female at birth (AFAB)) presenting with gender identity-related anxiety at Shanghai Mental Health Centre between March 2020 and February 2022. WES libraries were prepared and sequenced to an average depth of 100×. Raw reads underwent stringent quality control, alignment, variant calling, and annotation against public databases (gnomAD, ClinVar). Rare (minor allele frequency [MAF] < 1%) high-confidence variants were filtered to focus on exonic, splice-site, and insertion and deletion (indel) events. Candidate genes were subjected to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment and Gene Ontology (GO) analyses to identify overrepresented neural development pathways, with particular emphasis on estrogen receptor-mediated signaling.
A total of 479 rare, potentially pathogenic variants across 19 estrogen receptor-mediated neurodevelopmental genes were identified for further validation.
After quality control, 266 265 high-confidence variants were retained; of 217 757 exomic calls, 48 508 (22.3%) were exonic (49.8% nonsynonymous), including 4.1% splice-site, 225 missense, 27 nonsense, 43 frameshift, and various indels. KEGG analysis highlighted significant enrichment in axon guidance signaling, while GO terms pointed to neuronal projection and synaptic assembly. Nineteen genes within the estrogen receptor pathway harbored rare deleterious variants, suggesting disruptions in sex hormone-driven neural differentiation.
This WES-based framework enables the identification of novel candidate loci for diagnostic panels and may inform personalized interventions for gender identity-related anxiety.
This study leveraged high-depth whole-exome sequencing, stringent bioinformatics filtering, and a pathway-focused approach to pinpoint rare variants in sex-dimorphic neurodevelopmental genes; however, its small sample size, lack of functional validation, potential population stratification bias, and cross-sectional design limit causal inference.
Our integrated WES and bioinformatics pipeline uncovers rare variants in estrogen receptor-mediated neurodevelopmental genes, providing new insights into the genetic architecture of sex-dimorphic brain development and its role in gender identity-related anxiety.
The article was registered at the ISRCTN Registry https://www.isrctn.com/ISRCTN18336816 (no. 18336816) under an observational study record.
导致性别相关脑发育二态性的遗传因素可能也是性别认同相关焦虑症的基础。
建立一种高通量全外显子组测序（WES）和生物信息学流程，以识别性别二态性神经通路中的罕见变异，并探索它们与性别认同相关焦虑的关联。
2020年3月至2022年2月期间，从上海精神卫生中心的23例患有性别认同相关焦虑的患者（13例出生时被指定为男性（AMAB），10例出生时被指定为女性（AFAB））中收集外周基因组DNA。制备WES文库并测序至平均深度为100×。原始读数经过严格的质量控制、比对、变异检测，并与公共数据库（gnomAD、ClinVar）进行注释。筛选罕见（次要等位基因频率[MAF]<1%）的高置信度变异，重点关注外显子、剪接位点以及插入和缺失（indel）事件。对候选基因进行京都基因与基因组百科全书（KEGG）通路富集和基因本体论（GO）分析，以识别过度富集的神经发育通路，特别强调雌激素受体介导的信号传导。
共鉴定出19个雌激素受体介导的神经发育基因中的479个罕见、潜在致病性变异，以待进一步验证。
经过质量控制后，保留了266265个高置信度变异；在217757个外显子变异检测中，48508个（22.3%）为外显子变异（49.8%为非同义变异），包括4.1%的剪接位点变异、225个错义变异、27个无义变异、43个移码变异以及各种indel。KEGG分析突出了轴突导向信号通路的显著富集，而GO术语指向神经元投射和突触组装。雌激素受体通路中的19个基因含有罕见的有害变异，表明性激素驱动的神经分化受到破坏。
这种基于WES的框架能够识别诊断面板的新候选基因座，并可能为性别认同相关焦虑的个性化干预提供依据。
本研究利用高深度全外显子组测序、严格的生物信息学筛选以及以通路为重点的方法来确定性别二态性神经发育基因中的罕见变异；然而，其样本量小、缺乏功能验证以及潜在的群体分层偏差和横断面设计限制了因果推断。
我们整合的WES和生物信息学流程揭示了雌激素受体介导的神经发育基因中的罕见变异，为性别二态性脑发育的遗传结构及其在性别认同相关焦虑中的作用提供了新见解。
本文已在ISRCTN注册中心https://www.isrctn.com/ISRCTN18336816（编号18336816）注册，属于一项观察性研究记录。
