BRAIN Publication Roundup – September 2016

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Advancements in cell classification strategies and steps toward a comprehensive mouse brain cell atlas…

One of the major goals of the BRAIN Initiative® is to identify, and provide experimental access to, the different brain cell types, in pursuit of the goal of determining their roles in health and disease. An important component of this goal is generating a census of brain cell types. Cells can be classified, for example, based on their morphological, molecular, or physiological characteristics, but the resulting taxonomies may not necessarily be consistent with each other. Further, the number of cells profiled in a given study can vary from dozens to a few thousand, and there are few populations of neurons that have been completely categorized into different cell types. To address these challenges, BRAIN Initiative Harvard University investigator Dr. Joshua Sanes and his colleagues used single-cell RNA profiling to create a complete classification of mouse retinal bipolar cells. They described this research in a recent article in Cell. Using a line of transgenic mice that expressed green fluorescent protein (GFP) in all bipolar cells, the team collected the GFP-positive cells using a fluorescence clustering analysis. Next, they prepared single-cell libraries using RNA sequencing techniques and performed principal component analysis clustering procedures. From an analysis of ~25,000 cells, the researchers identified 15 types of retinal bipolar neurons, which included 13 cell types that had been previously identified, along with two new types. The results were validated by matching gene expression to morphology for each cell type. It is hoped that this  team’s systematic strategy for characterizing retinal bipolar neurons can be applied to populations of neurons from other parts of the nervous system to build a comprehensive, validated atlas of cell types in the brain.

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Four bipolar cell types [B) BC5A, C) BC5B, D) Bc5C, and E) BC5D] and their respective markers/transcription factors (Sox6, Chrm2, Slitrk5, and Lrrtm1). Representative drawings based on electron microscope reconstructions are shown. Insets show localization of fluorescent in situ hybridization (FISH) with green fluorescent protein (GFP) positive cell bodies. Dashed gray lines denote the division between layers of the inner plexiform layer of the retina.
Four bipolar cell types [B) BC5A, C) BC5B, D) Bc5C, and E) BC5D] and their respective markers/transcription factors (Sox6, Chrm2, Slitrk5, and Lrrtm1). Representative drawings based on electron microscope reconstructions are shown. Insets show localization of fluorescent in situ hybridization (FISH) with green fluorescent protein (GFP) positive cell bodies. Dashed gray lines denote the division between layers of the inner plexiform layer of the retina.