Transcriptomic continuity and an age-dependent onset of hemoglobin expression characterize morphological PV types in the hippocampus

The diversity reflected by >100 different neural cell types fundamentally contributes to brain function and a central idea is that neuronal identity can be inferred from genetic information. Recent large-scale transcriptomic assays seem to confirm this hypothesis, but a lack of morphological information has limited the identification of several known cell types. For example, parvalbumin interneurons (PV-INs) comprise of a main transcriptomic cluster within all inhibitory cells. However, transcriptomics alone has not resolved the different morphological PV types that exist. To close this gap, we used single-cell RNA-seq in morphologically identified PV-INs, sampled from 10 days to 3 months-old mice and studied their transcriptomic states in the morphological, physiological, and developmental domains. Our findings reveal a small number of genes whose expression is different between morphologically different types, but overall our analysis indicates high transcriptomic similarity among PV-INs. Furthermore, morphological PV types display uniform cell adhesion molecule (CAM) profiles, despite the fact that these types have very different wiring patterns, suggesting that CAM expression in mature PV cells do not reflect wiring specificity after development. Finally, our results reveal a pronounced change of transcriptomic states between postnatal days 20 and 25, during which PV-INs display a rapid onset of hemoglobin gene expression which remains stable in later development. Together, our results suggest that while morphological PV types in the CA1 are distinguished by their anatomy and in vivo activity, their largely continuous transcriptomic and homogenous biophysical landscapes are not predictive of these distinct identities. Pvalb positive cells were collected from mice between ages P10 and P77. There were 62 vertical basket cells (vBCs), 16 horizontal basket cells (hBCs), 9 vertical bistratified cells (vBICs), 14 horizontal bistratified cells (hBICs), 7 vertical axo-axonic cells (vAACs), 6 cortical cells (Corticals), and 14 unclassified cells (UCs) Please note that the readme_Series_design.tsv list the samples included in each processed data file.超过100种不同神经细胞类型所体现的多样性，是大脑功能得以实现的核心基础之一，而核心假说认为神经元身份可通过遗传信息进行推断。近年来的大规模转录组学检测似乎证实了这一假说，但形态学信息的缺失限制了多种已知细胞类型的鉴定。例如，小白蛋白中间神经元（parvalbumin interneurons, PV-INs）是所有抑制性神经元中的主要转录组聚类之一，但仅通过转录组学无法区分已发现的不同形态学PV神经元亚型。 为填补这一研究空白，我们对经形态学鉴定的PV-INs开展了单细胞RNA测序（single-cell RNA-seq），样本采集自出生10天至3月龄的小鼠，并从形态学、生理学及发育三个维度分析了它们的转录组状态。研究结果显示，仅存在少量基因在不同形态学亚型间存在表达差异，但整体分析表明PV-INs的转录组相似性极高。此外，尽管各类形态学PV亚型的神经连接模式差异显著，它们却表现出统一的细胞黏附分子（cell adhesion molecule, CAM）表达谱，这提示成熟PV细胞中的CAM表达并不能反映发育完成后的连接特异性。 最后，我们的研究发现出生后第20天至第25天之间，转录组状态发生了显著变化：在此阶段PV-INs快速启动血红蛋白基因的表达，且该表达模式在后续发育中保持稳定。综上，尽管CA1脑区的形态学PV亚型可通过其解剖结构与在体活动加以区分，但它们整体连续的转录组特征与均一的生物物理图谱，并无法预测这些独特的细胞身份。 本次研究共收集了P10至P77龄小鼠的Pvalb阳性细胞，其中包括62个垂直篮状细胞（vertical basket cells, vBCs）、16个水平篮状细胞（horizontal basket cells, hBCs）、9个垂直双分层细胞（vertical bistratified cells, vBICs）、14个水平双分层细胞（horizontal bistratified cells, hBICs）、7个垂直轴突-轴突细胞（vertical axo-axonic cells, vAACs）、6个皮层细胞（cortical cells, Corticals）以及14个未分类细胞（unclassified cells, UCs）。 请注意，readme_Series_design.tsv列出了每个处理后数据文件所包含的样本。