Linkage of cDNA expression profiles of mesencephalic dopaminergic neurons to a genome-wide in situ hybridization database

Kambiz N Alavian,Horst H Simon

doi:10.1186/1750-1326-4-6

Kambiz N Alavian, Horst H Simon

Open Access

https://doi.org/10.1186/1750-1326-4-6

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Abstract

Midbrain dopaminergic neurons are involved in control of emotion, motivation and motor behavior. The loss of one of the subpopulations, substantia nigra pars compacta, is the pathological hallmark of one of the most prominent neurological disorders, Parkinson's disease. Several groups have looked at the molecular identity of midbrain dopaminergic neurons and have suggested the gene expression profile of these neurons. Here, after determining the efficiency of each screen, we provide a linked database of the genes, expressed in this neuronal population, by combining and comparing the results of six previous studies and verification of expression of each gene in dopaminergic neurons, using the collection of in situ hybridization in the Allen Brain Atlas.

Highlights

The population of dopaminergic (DA) neurons in the ventral midbrain is divided into three distinct groups, substantia nigra pars compacta (SNpc) or the A9 group, ventral tegmental area (VTA) or the A10 group, and retrorubral field
In order to combine the lists of genes from the six studies, as a first step, we determined the association of sequences in the cDNA differential display-based studies (Stewart et al, Barrett et al and Thuret et al.) to genes and published ESTs, by checking location of each hit on the mouse genome on Map Viewer http://www.ncbi.nlm.nih.gov/mapview/ and by performing BLAST search
In order to determine whether the genes, presented in these screens, are present in VTA and/or SNpc, we looked for above-background cellular expression in the ventral midbrain, using Allen's Brain Atlas in situ hybridization (ISH) database at http:/ /www.brain-map.org

Summary

Introduction

The population of dopaminergic (DA) neurons in the ventral midbrain is divided into three distinct groups, substantia nigra pars compacta (SNpc) or the A9 group, ventral tegmental area (VTA) or the A10 group, and retrorubral field. Neurons of the VTA innervate the nucleus accumbens and olfactory tubercle, comprising the mesolimbic and mesocortical pathways, and the target for SNpc innervation is the dorsal striatum, thereby constituting the nigrostriatal pathway [1]. These three pathways are involved in control of emotion, motivation and motor behavior and are connected to neurological conditions such as addiction, schizophrenia and to the second most common neurodegenerative disorder, Parkinson's disease (PD) [2,3]. The main pathological characteristic of PD is the progressive degeneration of DA neurons in the SNpc. The functional and pathological relevance of the neurons in SNpc and VTA necessitates in depth study of their gene expression profile. Several such studies have been carried out to identify the genes, expressed in these neuronal populations [49]

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