Single-cell analyses of axolotl forebrain organization, neurogenesis, and regeneration

Preprint: https://doi.org/10.1101/2022.03.21.485045

Abstract:

Salamanders are important tetrapod models to study brain organization and regeneration, however the identity and evolutionary conservation of brain cell types is largely unknown. Here, we delineate cell populations in the axolotl telencephalon during homeostasis and regeneration, representing the first single-cell genomic and spatial profiling of an anamniote tetrapod brain. We identify glutamatergic neurons with similarities to amniote neurons of hippocampus, dorsal and lateral cortex, and conserved GABAergic neuron classes. We infer transcriptional dynamics and gene regulatory relationships of postembryonic, region-specific direct and indirect neurogenesis, and unravel conserved signatures. Following brain injury, ependymoglia activate an injury-specific state before reestablishing lost neuron populations and axonal connections. Together, our analyses yield key insights into the organization, evolution, and regeneration of a tetrapod nervous system.

File description:

all_nuclei_clustered_highlevel_anno.rds - Seurat object including all snRNA-seq data from uninjured pallium, both from microdissections and whole pallium multiome.

pallium_metadata_simp.csv - csv file containing a simplified version of the metadata for the uninjured pallium

Edu_1_2_4_6_8_12_fil_highvarfeat.rds - Seurat object containing all Div-seq data for the pallium injury time course

divseq_predicted_metadata.csv - csv file containing a simplified version of the metadata for the pallium injury time course

ep_wpi_srat.rds - Seurat object containing an integrated version of ependymoglia cells from uninjured and injured pallium (see Fig 6 in the preprint).

D1_113_sub_b.rds - Seurat object containing a Visium data for the axolotl pallium

multiome_integATAC_SCT.rds - Signac object containing the data used for multiome analysis of the uninjured whole pallium

predictions_cell2loc.csv - csv file containing cell2location scores for the uninjured pallium cell types in the Visium dataset

预印本：https://doi.org/10.1101/2022.03.21.485045

摘要：

蝾螈是研究脑组织结构与再生的重要四足动物模型，但目前学界对其脑细胞类型的身份特征及进化保守性仍知之甚少。本研究对稳态与再生过程中的美西钝口螈（axolotl）端脑细胞群进行了系统解析，这是首次针对非羊膜类四足动物脑开展的单细胞基因组与空间谱分析研究。本研究鉴定出与羊膜类海马、背侧及外侧皮层神经元具有同源性的谷氨酸能神经元，以及保守的γ-氨基丁酸能神经元（GABAergic neuron）类群。本研究还解析了胚后期、区域特异性的直接与间接神经发生过程的转录动态及基因调控关系，并揭示了保守的分子特征。脑损伤发生后，室管膜胶质细胞（ependymoglia）会先激活损伤特异性状态，随后重建丢失的神经元群与轴突连接。综上，本研究为四足动物神经系统的组织结构、进化历程与再生机制提供了关键认知。

文件说明：

all_nuclei_clustered_highlevel_anno.rds - 包含未损伤端脑的所有单细胞核RNA测序（single-nucleus RNA sequencing, snRNA-seq）数据的Seurat对象，数据涵盖显微解剖样本与全端脑多组学（multiome）样本。

pallium_metadata_simp.csv - 包含未损伤端脑元数据（metadata）简化版本的CSV文件。

Edu_1_2_4_6_8_12_fil_highvarfeat.rds - 包含端脑损伤时间序列所有Div-seq数据的Seurat对象。

divseq_predicted_metadata.csv - 包含端脑损伤时间序列元数据简化版本的CSV文件。

ep_wpi_srat.rds - 包含未损伤与损伤端脑的室管膜胶质细胞整合数据的Seurat对象（详见预印本中图6）。

D1_113_sub_b.rds - 包含美西钝口螈端脑Visium空间转录组数据的Seurat对象。

multiome_integATAC_SCT.rds - 包含未损伤全端脑多组学分析所用数据的Signac对象。

predictions_cell2loc.csv - 包含Visium数据集内未损伤端脑细胞类型的cell2location评分的CSV文件。