Gene expression profiles in Parkinson disease prefrontal cortex implicate FOXO1 and genes under its transcriptional regulation

Abstract

Parkinson disease (PD) is a complex neurodegenerative disorder with largely unknown genetic mechanisms. While the degeneration of dopaminergic neurons in PD mainly takes place in the substantia nigra pars compacta (SN) region, other brain areas, including the prefrontal cortex, develop Lewy bodies, the neuropathological hallmark of PD. We generated and analyzed expression data from the prefrontal cortex Brodmann Area 9 (BA9) of 27 PD and 26 control samples using the 44K One-Color Agilent 60-mer Whole Human Genome Microarray. All samples were male, without significant Alzheimer disease pathology and with extensive pathological annotation available. 507 of the 39,122 analyzed expression probes were different between PD and control samples at false discovery rate (FDR) of 5%. One of the genes with significantly increased expression in PD was the forkhead box O1 (FOXO1) transcription factor. Notably, genes carrying the FoxO1 binding site were significantly enriched in the FDR-significant group of genes (177 genes covered by 189 probes), suggesting a role for FoxO1 upstream of the observed expression changes. Single-nucleotide polymorphisms (SNPs) selected from a recent meta-analysis of PD genome-wide association studies (GWAS) were successfully genotyped in 50 out of the 53 microarray brains, allowing a targeted expression-SNP (eSNP) analysis for 52 SNPs associated with PD affection at genome-wide significance and the 189 probes from FoxO1 regulated genes. A significant association was observed between a SNP in the cyclin G associated kinase (GAK) gene and a probe in the spermine oxidase (SMOX) gene. Further examination of the FOXO1 region in a meta-analysis of six available GWAS showed two SNPs significantly associated with age at onset of PD. These results implicate FOXO1 as a PD-relevant gene and warrant further functional analyses of its transcriptional regulatory mechanisms.

Figure 1. Top microarray probes.

Probes with FDR-adjusted p-values smaller than 0.05 and with expression differences between PD and control prefrontal cortex BA9 samples greater than 1.5 fold changes. Twenty-one probes (42%) were in genes with FoxO1 transcription factor binding sites. The GENE-E software (http://www.broadinstitute.org/cancer/software/GENE-E/) was used to generate the heatmap.

Figure 2. Expression by genotype relationship between the SMOX probe, A_23_P102731, and the GAK SNP, rs11731387.

The box whiskers extend to the most extreme data point, which is at most 1.5 times the interquartile range from the box. The result for the 2-degree of freedom test was p = 8.1E-6, and the eSNP relationship was stronger in PD (p = 7.47E-5, beta = −0.727) than in controls (p = 0.037, beta = −0.494). The minor allele frequency for rs11731387 in the used brain sample was 0.15, and the odds ratio for this SNP in the additive model affection study of the meta-GWAS was 1.35.