NanoString has started an ambitious project called the "Spatial Organ Atlas." The goal of this initiative is to map the architecture of tissues with spatially resolved whole transcriptomics. In this study, we used the GeoMx® Mouse Whole Transcriptome Atlas (WTA) to segment and profile different structures of the mouse brain at the cellular and molecular level. Spatial whole transcriptomic data was benchmarked to orthogonal platforms as an independent validation of the results.
In a follow-up study done in conjunction with our collaborators at Emory University in Ellen Hess’ lab, we performed deep spatial transcriptomic profiling using GeoMx Mouse WTA on subpopulations of spiny projection neurons (SPNs) in the mouse striatum. SPN subpopulations are generally divided into those that express D1 dopamine receptors and those that express D2 dopamine receptors. Recently, it was shown that these subpopulations are more complex than previously thought whereby gene expression in SPNs is, in part, mediated by their position within regional striatal subdivisions.
To analyze SPNs, 10um fresh frozen coronal sections from six C57/BL6 (WT) mice (n=3 female, n=3 male) were placed across two slides. D1 and D2 SPNs were identified using Drd1 and Adora2a RNAScope probes respectively in combination with Syto13 for visualization of all nuclei. Regions of interest (ROIs) were selected in dorsomedial, dorsolateral, and ventrolateral striatum to identify cell-type specific gene expression signatures in regions previously associated with unique functional roles within the striatum. GeoMx data was benchmarked against bulk and single-cell RNAseq from matched samples with high concordance across all metrics, and spatial analysis yielded novel insights into striatal organization of SPNs in WT mice.
FOR RESEARCH USE ONLY. Not for use in diagnostic procedures.
1. Explain the concept of the Spatial Organ Atlas and how the Whole Transcriptome Atlas works.
2. Describe the different structures and substructures of the mouse brain and how their gene expression differs spatially.
3. Summarize the transcriptional differences between D1 and D2 spiny projection neurons in the mouse brain and how their gene expression is regulated by position in the striatum.