Transcriptional signatures mediated by acetylation overlap with early-stage Alzheimer's disease

Abstract

The mechanisms by which environmental influences lead to the development of complex neurodegenerative diseases are largely unknown. It is known, however, that epigenetic mechanisms can mediate alterations in transcription due to environmental influences. In order to identify genes susceptible to regulation in the adult cortex by one type of epigenetic mechanism, histone, and protein acetylation, we treated mice with the histone deacetylase inhibitor Trichostatin A (TSA). After 1 week of treatment with TSA, RNA was extracted from the brain cortices of mice and gene expression differences were analyzed by microarray profiling. The altered genes were then compared with genes differentially expressed in microarray studies of disease by database and literature searches. Genes regulated by TSA were found to significantly overlap with differentially expressed genes in the Alzheimer's disease (AD) brain. Several TSA-regulated genes involved in chromatin remodeling and epigenetic reprogramming including histone cluster 1, H4 h (Hist1H4 h), methionine adenosyltransferase II, alpha (Mat2a), and 5-methyltetrahydrofolate homocysteine reductase (Mtrr) overlapped with genes altered in early-stage AD in gray matter. We also show that the expression of hemoglobin, which has been shown to be altered in neurons in the AD brain, is regulated by TSA treatment. This analysis suggests involvement of epigenetic mechanisms in neurons in early stages of AD.

Fig. 1

Representative western blot showing increased acetyl-lysine immunoreactive proteins (denoted by arrows) in nuclear extracts isolated from the brains of TSA-treated compared to control (vehicle-treated) mice

Fig. 2

TSA-regulated genes overlap with genes differentially expressed in AD. Overlaps were identified by a combination of gene set enrichment analysis and literature searches. Heat maps show relative gene expression levels for TSA-regulated genes by expression microarray profiling. Red denotes increased expression and blue denotes decreased expression of genes in TSA-treated mice compared to controls (vehicle-treated, veh.). a Heat map of genes upregulated by TSA, which overlap with genes altered in AD. b Heat map of genes downregulated by TSA treatment, which overlap with genes altered in AD. ^aOverlap identified by gene set enrichment analysis (Blalock et al. 2004, which analyzed early and later stages of AD), ^boverlap in gray matter (Blalock et al. 2011, which analyzed early-stage disease in laser-captured hippocampal gray matter), ^coverlap with Bossers et al. (2010), which analyzed cortical gene expression in early-stage AD, ^doverlap with Tan et al. (2010), which analyzed neocortex. *TSA-regulated genes that overlap in early-stage AD. FC indicates fold change, TSA treated relative to control

Fig. 2

TSA-regulated genes overlap with genes differentially expressed in AD. Overlaps were identified by a combination of gene set enrichment analysis and literature searches. Heat maps show relative gene expression levels for TSA-regulated genes by expression microarray profiling. Red denotes increased expression and blue denotes decreased expression of genes in TSA-treated mice compared to controls (vehicle-treated, veh.). a Heat map of genes upregulated by TSA, which overlap with genes altered in AD. b Heat map of genes downregulated by TSA treatment, which overlap with genes altered in AD. ^aOverlap identified by gene set enrichment analysis (Blalock et al. 2004, which analyzed early and later stages of AD), ^boverlap in gray matter (Blalock et al. 2011, which analyzed early-stage disease in laser-captured hippocampal gray matter), ^coverlap with Bossers et al. (2010), which analyzed cortical gene expression in early-stage AD, ^doverlap with Tan et al. (2010), which analyzed neocortex. *TSA-regulated genes that overlap in early-stage AD. FC indicates fold change, TSA treated relative to control

Fig. 3

Quantitative RT-PCR confirms altered expression of genes found to be differentially expressed due to TSA treatment by microarray profiling. By qRT-PCR of RNA isolated from the cortex of TSA-treated and control mice, the expression of S100a8 was increased 3.70-fold, Ung was increased 1.29-fold, Mat2a was decreased 1.21-fold, and the hemoglobin β1 and β2 transcripts (Hbb1 and Hbb2) were decreased by 1.40- and 1.28-fold, respectively. Black bars represent gene expression levels from control mice, and gray bars represent gene expression levels from TSA-treated mice. For Hbb, the dark gray bar represents Hbb1 expression and the lighter gray bar represents Hbb2 expression. Gene expression levels in TSA-treated mice are shown as percent of control from at least two experiments performed in triplicate. Error bars represent SEM, *p < 0.05