Gene expression profiling in postmortem brains classified by Braak neurofibrillary tangle staging

Abstract

Alzheimer's disease (AD) is the most common form of dementia in the elderly. Molecular mechanism of progression in the AD brain remains to be resolved. A high-dense microarray technology allows us to profile gene expression in every exon level. In this study, we used 213 postmortem brain tissues (entorhinal, temporal and frontal cortices [EC, TC and FC, respectively]) from 71 brain donors in the Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology Brain Bank. According to Braak neurofibrillary tangle (NFT) stage criteria, these donors were classified into four groups: Braak NFT stages 0 (N = 13), I - II (N = 20), III (N = 19) and V - VI (N = 19). Total RNA was isolated from these tissues and purified with an on-column DNaseI treatment, using the TRIzol® plus RNA purification system (Invitrogen). An RNA integrity number (RIN, 1 [degraded] - 10 [intact]) was computed to evaluate RNA quality by a 2100 BioAnalyzer system (Agilent). Whole exons transcribed in the brain were analysed by an Affymetrix GeneChip® platform (Human Exon 1.0 ST Array). We determined APOE genotypes by means of both sequencing and a TaqMan® assay. The statistical significance was set at P < 0.05. The genotypic distribution of the APOE is as follows: e2*3 = 4, e3*3= 55, e3*4 = 9, e4*4 = 3. In three brain regions, there were no significant differences of mean RIN values between Braak NFT stages: EC, P = 0.8684; TC, P = 0.8490; FC, P = 0.7141. No correlation between postmortem interval and RIN was observed. We selected more than 50 genes which were differentially expressed among Braak NFT stages and evaluated by independent statistical analyses. We identified candidate genes involved in AD pathogenesis depending on the brain regions. Several genes responsible for clinical manifestation of AD could be elucidated through gene expression profiling.