\u201cFlashMap\u201d - A Semi-Automatic Tool for Rapid and Accurate Spatial Analysis of Marker Expression in the Subventricular Zone

Stefan Zweifel,Lorenzo Caruso,Julie Buquet,Olivier Raineteau,David Rousseau

doi:10.1038/s41598-018-33939-1

Abstract

The subventricular zone (SVZ) is a region of ongoing postnatal germinal activity that shows complex spatial heterogeneity. For instance, different SVZ microdomains contain neural stem cells that express distinct transcription factors and generate different glial and neuronal progenies. These unique characteristics call for the development of new methods to integrate a spatial dimension to histological analyses performed in this germinal region. We developed “FlashMap”, a semi-automatic software that allows the segmentation and rapid measurement of optical densities throughout the full SVZ coordinates. “FlashMap” generates easily readable two-dimensional heatmaps that can be superimposed onto three-dimensional reconstructions of the ventricular system for optimal spatial exploration. Accurate heatmaps can be obtained, even following serial section subsampling thereby reducing the amount of tissue and time required for histological analysis. We first illustrate the potential of “FlashMap” by spatially exploring the correlation of SVZ thickness and cellular density with germinal activity throughout its rostro-caudal coordinates. We then used “FlashMap” to analyse the spatial expression of the transcription factors Dlx2, Tbr2 and Hopx as well as of the immature neuronal marker Dcx, to demonstrate the suitability of this approach to explore the regional production of cells of distinct lineages by defined SVZ microdomains.

Highlights

Recent research, driven by the development of new technologies, led to an accumulation of a large amount of transcriptional datasets of various subventricular zone (SVZ) cell types isolated from distinct microdomains
While these 3 microdomains are contiguous in the rostral most SVZ regions, their definition becomes more ambiguous in regions caudal to the 3rd ventricle
Dlx[2] was detected in the lSVZ and the medial SVZ (mSVZ) in the regions we previously identified as zones of high germinal activity (Fig. 4C–E; white dashed boxes)

Summary

Introduction

Driven by the development of new technologies, led to an accumulation of a large amount of transcriptional datasets of various SVZ cell types isolated from distinct microdomains. We recently described an unexpected level of transcriptional heterogeneity between the dSVZ and lSVZ, as well as between NSCs and transient-amplifying progenitors of those two microdomains[12]. Genes continuously increases, an appropriate tool for rapid analysis of their expression pattern in the SVZ is still missing. We aimed to develop a tool that allows rapid protein expression analysis along the full rostro-caudal and dorso-ventral extend of this germinal region. “FlashMap” is a software for semi-automatic marker expression analysis in the SVZ, based on optical density (OD) measurements. “FlashMap” allows subsampling of serial sections, in order to further reduce the time for analysis. “FlashMap” has the potential to be applied to a wide range of semi-automated analyses, and is of substantial interest for the field

Methods

Results

Conclusion