A Transcriptome Database for Astrocytes, Neurons, and Oligodendrocytes: A New Resource for Understanding Brain Development and Function

TLDR

Cell–cell interactions governing CNS development and function have been difficult to study because neural cell types cannot be cleanly separated. This study presents methods for prospectively isolating and purifying astrocytes, neurons, and oligodendrocytes from developing and mature mouse forebrain. Using FACS on EGFP‑expressing transgenic mice, the authors isolated each cell type and profiled over 20,000 genes with Affymetrix GeneChip arrays across postnatal days 1–30 to build a transcriptome database. The resulting database shows distinct gene expression profiles, identifies Aldh1L1 as a highly specific astrocyte marker, highlights astrocyte enrichment in metabolic, lipid, and phagocytic pathways, challenges the notion of a single glial class, and offers a resource for improved cell‑type markers and insights into neural development and disease.

Abstract

Understanding the cell–cell interactions that control CNS development and function has long been limited by the lack of methods to cleanly separate neural cell types. Here we describe methods for the prospective isolation and purification of astrocytes, neurons, and oligodendrocytes from developing and mature mouse forebrain. We used FACS (fluorescent-activated cell sorting) to isolate astrocytes from transgenic mice that express enhanced green fluorescent protein (EGFP) under the control of an S100β promoter. Using Affymetrix GeneChip Arrays, we then created a transcriptome database of the expression levels of >20,000 genes by gene profiling these three main CNS neural cell types at various postnatal ages between postnatal day 1 (P1) and P30. This database provides a detailed global characterization and comparison of the genes expressed by acutely isolated astrocytes, neurons, and oligodendrocytes. We found that Aldh1L1 is a highly specific antigenic marker for astrocytes with a substantially broader pattern of astrocyte expression than the traditional astrocyte marker GFAP. Astrocytes were enriched in specific metabolic and lipid synthetic pathways, as well as the draper/Megf10 and Mertk/integrin α v β 5 phagocytic pathways suggesting that astrocytes are professional phagocytes. Our findings call into question the concept of a “glial” cell class as the gene profiles of astrocytes and oligodendrocytes are as dissimilar to each other as they are to neurons. This transcriptome database of acutely isolated purified astrocytes, neurons, and oligodendrocytes provides a resource to the neuroscience community by providing improved cell-type-specific markers and for better understanding of neural development, function, and disease.