Genetic regulation of expression in the granule cell layer of the human dentate gyrus

Specific cell populations may have unique contributions to schizophrenia, but may be missed in studies of homogenate tissue. Laser capture microdissection followed by RNA-seq (LCM-seq) was used to transcriptomically profile the granule cell layer of the dentate gyrus (DG-GCL) in human hippocampus, and contrast these data to those from bulk hippocampal homogenate tissue. We identified widespread cell type-enriched aging and genetic effects in the DG-GCL that were either absent or directionally discordant in bulk hippocampus data. Of the ~9 million eQTLs identified in the DG-GCL, 15% were not detected in bulk hippocampus, including 15 schizophrenia risk variants. We created transcriptome-wide association study (TWAS) genetic weights from the DG-GCL, which identified many novel schizophrenia-associated genetic signals not found in TWAS from bulk hippocampus, including GRM3 and CACNA1C. These results highlight the improved biological resolution provided by targeted sampling strategies like LCM, and complement homogenate and single nuclei approaches in human brain.

特定细胞群对精神分裂症或具有独特的致病贡献，但在整体组织匀浆的研究中往往被忽视。本研究采用激光捕获显微切割联合RNA测序（Laser capture microdissection followed by RNA-seq，LCM-seq）技术，对人类海马齿状回颗粒细胞层（dentate gyrus granule cell layer，DG-GCL）开展转录组分析，并将所得数据与整体海马组织匀浆的测序数据进行对比。我们在DG-GCL中鉴定出广泛存在的细胞类型富集型衰老与遗传效应，这类效应在整体海马组织数据中要么缺失，要么效应方向相悖。在DG-GCL中鉴定出的约900万个表达数量性状位点（expression quantitative trait locus，eQTL）中，有15%无法在整体海马组织数据中被检测到，其中包含15个精神分裂症风险变异位点。我们基于DG-GCL的数据构建了转录组全基因组关联分析（transcriptome-wide association study，TWAS）的遗传权重模型，由此鉴定出多个此前在整体海马组织的TWAS分析中未被发现的新型精神分裂症相关遗传信号，包括GRM3与CACNA1C基因。本研究结果凸显了激光捕获显微切割这类靶向采样策略所带来的更高生物学分辨率，同时也为人类脑组织研究中的整体组织匀浆分析与单细胞核分析方法提供了有益补充。