Genome-wide coexpression of steroid receptors in the mouse brain: Identifying signaling pathways and functionally coordinated regions

Abstract

Steroid receptors are pleiotropic transcription factors that coordinate adaptation to different physiological states. An important target organ is the brain, but even though their effects are well studied in specific regions, brain-wide steroid receptor targets and mediators remain largely unknown due to the complexity of the brain. Here, we tested the idea that novel aspects of steroid action can be identified through spatial correlation of steroid receptors with genome-wide mRNA expression across different regions in the mouse brain. First, we observed significant coexpression of six nuclear receptors (NRs) [androgen receptor (Ar), estrogen receptor alpha (Esr1), estrogen receptor beta (Esr2), glucocorticoid receptor (Gr), mineralocorticoid receptor (Mr), and progesterone receptor (Pgr)] with sets of steroid target genes that were identified in single brain regions. These coexpression relationships were also present in distinct other brain regions, suggestive of as yet unidentified coordinate regulation of brain regions by, for example, glucocorticoids and estrogens. Second, coexpression of a set of 62 known NR coregulators and the six steroid receptors in 12 nonoverlapping mouse brain regions revealed selective downstream pathways, such as Pak6 as a mediator for the effects of Ar and Gr on dopaminergic transmission. Third, Magel2 and Irs4 were identified and validated as strongly responsive targets to the estrogen diethylstilbestrol in the mouse hypothalamus. The brain-and genome-wide correlations of mRNA expression levels of six steroid receptors that we provide constitute a rich resource for further predictions and understanding of brain modulation by steroid hormones. neuroendocrinology | nuclear receptors | transcription regulation | estrogens | glucocorticoids S teroid receptors are part of the superfamily of nuclear receptors (NRs) that act as transcription factors regulating expression of numerous biologically important target genes (1). Their transcriptional activity is induced by steroid hormones, which respond to changed demands in terms of reproductive status, mineral balance, or stressful physical and psychological challenges. A crucial site of action is the brain, where these hormones have strong modulatory effects on physiological regulation, cognitive function, mood, and behavior. They do so by changing cellular responsiveness to a variety of neurotransmitters and peptides, and by inducing morphological changes (2, 3).Understanding the effects of steroid hormones on the brain faces the challenge to identify in as many as 900 different brain nuclei (4) both the highly cell-specific target genes that mediate the hormone effects (5, 6) and the signaling factors that mediate or influence steroid receptor signaling. The latter include proteins affecting prereceptor metabolism, interacting transcription factors (7), and downstream NR coregulator proteins (1). Even if the effects of steroid hormones are well-studied in specific regions (1, 8), overall, the brain steroid receptor targets and mediators ...

Coexpression profiles reveal hidden gene networks

“…Consequently, there is a risk of falsenegative results that goes hand in hand with the use of a genome-wide approach to identify region-specific targets and coregulators. This is something that Mahfouz et al (2) …”

“…The findings of Mahfouz et al (2) convincingly show that the spatial correlation of steroid receptors with genome-wide mRNA expression across different regions of the mouse brain using webbased repositories provides a novel in silico assay with which to explore novel aspects of steroid hormone action and obtain a glimpse of how the brain, by integrating ever-fluctuating combinatorial levels of circulating steroid hormones, orchestrates the adaptive response of the organism. Could this study be the stepping-stone to deciphering even more unknown steroid receptor pathways and networks not only in the mouse brain but also in the human brain (Fig.…”

“…In PNAS, Mahfouz et al (2) use the ability of the ABA to pinpoint the anatomical locations of expressed genes to uncover transcripts whose expression profiles correlate with those of steroid receptors, to begin to understand their function and specificity of action in different brain regions. This study shows that mapping combinatorial interactions among specific sets of genes represents a significant leap forward in our understanding of how tissue specificity for a given signaling pathway is determined, and in identifying the potential relationship between otherwise unrelated brain areas in terms of the adaptive response to specific biological and environmental challenges.…”

“…These researchers used two complementary approaches to meet the challenge of obtaining both cell-level resolution and an unbiased expression profile of large anatomical regions: real-time PCR provided a broad estimate of nuclear receptor expression levels in selected brain regions, and spatial expression patterns were more closely studied using highresolution in situ hybridization (ISH). The study by Mahfouz et al (2) significantly extends this approach to identify novel aspects of steroid hormone action via the spatial correlation of the expression patterns of steroid receptors with those of genes that could potentially be steroid hormone targets or even downstream receptor coregulators.…”

“…Six well-studied steroid receptors were chosen by Mahfouz et al (2) to costar in the "guilt by association" play; their expression profiles, although already reported in the literature, were validated using 3D spatial gene-expression data from the ABA (1). Based on the "guilt by association" principle, genes with similar spatial expression profiles are assumed to share similar biological functions, forming a neighborhood network of potential partners (12).…”