Clonal relations in the mouse brain revealed by single-cell and spatial transcriptomics

Michael Ratz,Leonie Von Berlin,Jakub Orzechowski Westholm,Gioele La Manno,Joakim Lundeberg,Ludvig Larsson,Marcel Martin,Jonas Frisén

doi:10.1038/s41593-022-01011-x

Abstract

The mammalian brain contains many specialized cells that develop from a thin sheet of neuroepithelial progenitor cells. Single-cell transcriptomics revealed hundreds of molecularly diverse cell types in the nervous system, but the lineage relationships between mature cell types and progenitor cells are not well understood. Here we show in vivo barcoding of early progenitors to simultaneously profile cell phenotypes and clonal relations in the mouse brain using single-cell and spatial transcriptomics. By reconstructing thousands of clones, we discovered fate-restricted progenitor cells in the mouse hippocampal neuroepithelium and show that microglia are derived from few primitive myeloid precursors that massively expand to generate widely dispersed progeny. We combined spatial transcriptomics with clonal barcoding and disentangled migration patterns of clonally related cells in densely labeled tissue sections. Our approach enables high-throughput dense reconstruction of cell phenotypes and clonal relations at the single-cell and tissue level in individual animals and provides an integrated approach for understanding tissue architecture.

Highlights

High-throughput single-cell RNA sequencing revealed hundreds of molecularly distinct cell types across the entire mouse and human nervous system[1–6]
We injected about 0.6 μl of enhanced green fluorescent protein (EGFP)-cloneID virus corresponding to 0.94 × 106 unique cloneIDs and which resulted in labeling of 1.8 ± 0.25% of all cells or a total of 41,000 ± 3,500 cells per E11.5 mouse brain (Extended Data Fig. 2b,c)
We developed TREX and Space-TREX for simultaneous clonal tracing and gene expression profiling of dissociated mouse brain cells and tissue sections, respectively

Summary

Introduction

High-throughput single-cell RNA sequencing (scRNA-seq) revealed hundreds of molecularly distinct cell types across the entire mouse and human nervous system[1–6]. Advanced molecular tools have been used to record cell lineages[9–14] and combined with scRNA-seq to generate fate maps in cultivated cells[15,16], zebrafish[17–20] and mice[14,16,21,22]. These technologies are not readily employed to uniquely label many progenitor cells in the mouse brain in vivo, and most approaches require tissue dissociation, an in situ whole-transcriptome readout is crucial for studies of the nervous system where function arises from both differential gene expression and circuit-specific anatomy[23–26]. Our findings demonstrate the utility of high-throughput clonal tracing in the mouse brain to provide molecular insights into brain development at the single-cell and tissue level

Methods

Results

Conclusion