Transcript co-variance with Nestin in two mouse genetic reference populations identifies Lef1 as a novel candidate regulator of neural precursor cell proliferation in the adult hippocampus

Abstract

Adult neurogenesis, the lifelong production of new neurons in the adult brain, is under complex genetic control but many of the genes involved remain to be identified. In this study, we have integrated publicly available gene expression data from the BXD and CXB recombinant inbred mouse lines to discover genes co-expressed in the adult hippocampus with Nestin, a common marker of the neural precursor cell population. In addition, we incorporated spatial expression information to restrict candidates to genes with high differential gene expression in the hippocampal dentate gyrus. Incorporating data from curated protein-protein interaction databases revealed interactions between our candidate genes and those already known to be involved in adult neurogenesis. Enrichment analysis suggested a link to the Wnt/β-catenin pathway, known to be involved in adult neurogenesis. In particular, our candidates were enriched in targets of Lef1, a modulator of the Wnt pathway. In conclusion, our combination of bioinformatics approaches identified six novel candidate genes involved in adult neurogenesis; Amer3, Eya3, Mtdh, Nr4a3, Polr2a, and Tbkbp1. Further, we propose a role for Lef1 transcriptional control in the regulation of adult hippocampal precursor cell proliferation.

Keywords: BXD; CXB; Lef1; Wnt pathway; adult neurogenesis; neuroinformatics; recombinant inbred mice; systems genetics.

Figure 1

The integration of data from two genetic reference populations revealed a set of 144 genes potentially expressed in adult hippocampal neural precursor cells. Principal component analysis was carried out using three probesets for Nes expression (1453997_a_at, 1418289_at, 1449022_at) in both the BXD and CXB genetic reference populations (A). The first principal component of these traits was used to create a meta-trait, Nes-PC1. This meta-trait was then correlated to all probesets in the two hippocampal expression data sets for the two genetic reference populations (B). The intersection of all probesets (r-value greater than 0.8 in both data sets) revealed 144 probesets in common (C). These genes were then filtered based on enriched expression in the dentate gyrus (highlighted in purple) using the Allen Brain Atlas to yield a subset of 6 candidate genes most likely to be expressed in neural precursor cells (D).

Figure 2

Expression of the six candidate genes in the hippocampus. Immunohistochemistry (ISH) is presented in the left column, the expression in the same sagittal slices in the right column. An atlas is shown above to help orientation. All images are taken from the Allen Mouse brain data (Lein et al., ; Allen Institute for Brain Science, ; http://www.brain-map.org).

Figure 3

The integration of data from several online tools identifies a novel role for Lef1 in adult hippocampal neurogenesis. Enrichment analysis was carried out on the six candidate genes identified (Figure 1) and for targets of the transcription factor Lef1. This was further investigated using enrichment of genes known to be expressed in Nestin positive cells, correlation analysis between our candidate genes and Lef1, and the use of interaction databases to find links between our candidates.

Figure 4

Interaction network between the six candidate genes, Lef1 and 35 MANGO genes expressed in Nestin-positive cells. Adapted from GeneMANIA (http://genemania.org; Mostafavi et al., ; Warde-Farley et al., 2010) with links based on co-expression, co-localization, physical and genetic interactions, as well as shared protein domains. The network is shown with all genes and all interactions highlighted (A), only genes with a connection to Lef1 highlighted (B), only genes with a connection to Amer3 highlighted (C), or highlighting restricted to genes with a physical, or predicted physical, interaction with Lef1 (D).

Figure 5

Summary of known interactions shows a central role for Lef1. The transcription factor Lef1 (dark blue octagon) is central in a network comprised of our six candidate genes (red triangles) and 35 genes expressed in Nestin positive cells (pale blue circles). Transcription factor targets (from WebGestalt) are shown as contiguous blue arrows, protein-protein interactions (from IntAct) as black lines and physical interactions (from GeneMANIA) as double red lines. Figure produced in Cytoscape.