整合基因组学与单细胞转录组学分析提示梅尼埃病中存在一个假定的锌转运-免疫轴

文献信息

中文摘要

目的： 梅尼埃病是一种致残性内耳疾病，其分子基础仍知之甚少。免疫失调和遗传易感性已被认为与疾病病因有关，但将遗传易感性与疾病相关分子改变联系起来的基因和免疫细胞程序仍未被完全阐明。聚焦于锌转运和免疫信号传导，我们旨在优先筛选具有遗传学支持的候选基因，并识别这些基因所嵌入的免疫细胞程序。
方法： 我们整合了外周血批量转录组、外周血单个核细胞的单细胞RNA测序、大规模血液eQTL数据以及梅尼埃病的全基因组关联汇总统计。采用差异表达分析和WGCNA定义批量转录特征，随后将其与scRNA-seq衍生的细胞类型标志基因整合，生成具有互补的批量疾病关联和细胞类型定位证据的候选基因集。应用两样本孟德尔随机化和共定位分析，检验这些候选基因的遗传预测表达是否影响梅尼埃病风险。随后在单细胞分辨率下将优先基因映射至免疫细胞亚群、配体-受体通讯网络和CD4+ T细胞分化轨迹，并在一个独立临床队列中于mRNA和蛋白水平验证其表达变化。
结果： 批量与单细胞分析产生了202个梅尼埃病相关候选基因，富集于RNA加工、染色质调控和免疫相关通路。两样本孟德尔随机化发现SLC39A10、GAB1和XCL2的遗传预测表达与梅尼埃病风险之间存在名义关联。结合批量转录组证据，优先筛选出SLC39A10表达升高以及GAB1和XCL2表达降低以供进一步分析。免疫特征富集和单细胞分析将其表达相关程序定位至CD4+ T细胞、NK细胞、单核细胞、B细胞及其他外周免疫细胞群。CellChat和拟时序分析对推断的细胞间通讯和CD4+ T细胞状态转换提供了互补描述。在一个独立临床队列中，SLC39A10、GAB1和XCL2在转录本和蛋白水平均显示出一致的变化。
结论： 我们的多层基因组学和单细胞分析优先将SLC39A10、GAB1和XCL2确定为与梅尼埃病相关的候选基因，并将其表达相关程序映射至CD4+ T细胞、NK细胞及其他外周免疫区室。总体而言，这些发现支持一个可能促成梅尼埃病系统性免疫失调的假定锌转运-免疫框架。该框架应被视为由整合基因组学和转录组学证据产生的假说，需要通过锌稳态、转运体活性及下游免疫功能的直接测量加以验证。

英文摘要

OBJECTIVE: Meniere's disease is a disabling inner-ear disorder whose molecular basis remains poorly understood. Immune dysregulation and genetic susceptibility have been implicated in disease etiology, but the genes and immune-cell programs linking genetic susceptibility to disease-associated molecular alterations remain incompletely defined. Focusing on zinc transport and immune signaling, we aimed to prioritize genetically supported candidate genes and identify the immune-cell programs in which they are embedded.
METHODS: We combined bulk peripheral blood transcriptomes, single-cell RNA sequencing of peripheral blood mononuclear cells, large-scale blood eQTL data, and genome-wide association summary statistics for Meniere's disease. Differential expression analysis and WGCNA were used to define bulk transcriptional signatures, which were then integrated with scRNA-seq-derived cell-type marker genes to generate a candidate-gene set with complementary bulk disease-association and cell-type localization evidence. Two-sample Mendelian randomization and colocalization were applied to test whether genetically predicted expression of these candidate genes influences Meniere's disease risk. Prioritized genes were then mapped to immune-cell subsets, ligand-receptor communication networks, and CD4+ T-cell differentiation trajectories at single-cell resolution, and their expression changes were validated at the mRNA and protein levels in an independent clinical cohort.
RESULTS: Bulk and single-cell analyses yielded 202 Meniere's disease-associated candidate genes enriched in RNA processing, chromatin regulation, and immune-related pathways. Two-sample Mendelian randomization identified nominal associations between genetically predicted expression of SLC39A10, GAB1, and XCL2 and Meniere's disease risk. Integration with bulk transcriptomic evidence prioritized increased SLC39A10 expression and reduced GAB1 and XCL2 expression for further analysis. Immune-signature enrichment and single-cell analyses localized their expression-related programs to CD4+ T cells, NK cells, monocytes, B cells, and other peripheral immune populations. CellChat and pseudotime analyses provided complementary descriptions of inferred intercellular communication and CD4+ T-cell state transitions. In an independent clinical cohort, SLC39A10, GAB1, and XCL2 showed concordant changes at the transcript and protein levels.
CONCLUSION: Our multi-layered genomic and single-cell analyses prioritize SLC39A10, GAB1, and XCL2 as candidate genes associated with Meniere's disease and map their expression-related programs to CD4+ T-cell, NK-cell, and other peripheral immune compartments. Together, these findings support a putative zinc transport-immune framework that may contribute to systemic immune dysregulation in Meniere's disease. This framework should be regarded as a hypothesis generated by integrative genomic and transcriptomic evidence and requires direct validation through measurements of zinc homeostasis, transporter activity, and downstream immune function.