Gene expression profiling of 12633 genes in Alzheimer hippocampal CA1: Transcription and neurotrophic factor down‐regulation and up‐regulation of apoptotic and pro‐inflammatory signaling

Abstract

Alterations in transcription, RNA editing, translation, protein processing, and clearance are a consistent feature of Alzheimer's disease (AD) brain. To extend our initial study (Alzheimer Reports [2000] 3:161‐167), RNA samples isolated from control and AD hippocampal cornu ammonis 1 (CA1) were analyzed for 12633 gene and expressed sequence tag (EST) expression levels using DNA microarrays (HG‐U95Av2 Genechips; Affymetrix, Santa Clara, CA). Hippocampal CA1 tissues were carefully selected from several hundred potential specimens obtained from domestic and international brain banks. To minimize the effects of individual differences in gene expression, RNA of high spectral quality (A260/280 ≥ 1.9) was pooled from CA1 of six control or six AD subjects. Results were compared as a group; individual gene expression patterns for the most‐changed RNA message levels were also profiled. There were no significant differences in age, postmortem interval (mean ≤ 2.1 hr) nor tissue pH (range 6.6–6.9) between the two brain groups. AD tissues were derived from subjects clinically classified as CDR 2‐3 (CERAD/NIA). Expression data were analyzed using GeneSpring (Silicon Genetics, Redwood City, CA) and Microarray Data Mining Tool (Affymetrix) software. Compared to controls and 354 background/alignment markers, AD brain showed a generalized depression in brain gene transcription, including decreases in RNA encoding transcription factors (TFs), neurotrophic factors, signaling elements involved in synaptic plasticity such as synaptophysin, metallothionein III, and metal regulatory factor‐1. Three‐ or morefold increases in RNAs encoding DAXX, cPLA2, CDP5, NF‐κBp52/p100, FAS, βAPP, DPP1, NFIL6, IL precursor, B94, HB15, COX‐2, and CEX‐1 signals were strikingly apparent. These data support the hypothesis of widespread transcriptional alterations, misregulation of RNAs involved in metal ion homeostasis, TF signaling deficits, decreases in neurotrophic support and activated apoptotic and neuroinflammatory signaling in moderately affected AD hippocampal CA1. © 2002 Wiley‐Liss, Inc.

Human postmortem tissue: What quality markers matter?

“…However, since it has been shown that under certain circumstances some specific mRNA species are preferentially degraded (Barrachina et al, 2006;Buesa et al, 2004), it is advisable to verify individual mRNA integrity within an experiment. Our finding that RIN is the optimal marker for representing quality agrees with previously published studies that found RNA quality measures in assessing gene expression analysis (Colangelo et al, 2002;Jones et al, 2006;Ross et al, 1992). pH appears to be a good marker of peri-mortem tissue quality, but does not appear to be sensitive to freezer degradation, as shown in our tissue-thaw illustration.…”

RNA-Seq and human complex diseases: recent accomplishments and future perspectives

“…23,24 However, although promising, the clear difficulties in obtaining brain tissue and the fragile nature of isolated RNA render transcriptome studies quite difficult. 25,26 Microarray analysis, widely used for ND and neuropsychiatric disorders, provided much information about the transcriptional profiles in pathological states, [27][28][29] although discordant results have been often reported. The lack of convergence could be attributed to microarray drawbacks (discussed in 8,9,15 ), as well as to the variable quality/integrity of RNAs strictly influenced by pH, 25 which may dramatically alter the binding to the nucleotide probes, affecting the measure of gene expression levels.…”

Alterations in immunological and neurological gene expression patterns in Alzheimer's disease tissues

“…Several studies using this technique have already been reported examining the changes in AD patients with mild to moderate disease [2][3][4][5]. In one such study, the gene expression differences between AD samples and control tissues utilized pooled RNA from 5 patients and demonstrated differences in the expression of genes associated with amino acid metabolism and neurotransmitter release [3].…”

“…In one such study, the gene expression differences between AD samples and control tissues utilized pooled RNA from 5 patients and demonstrated differences in the expression of genes associated with amino acid metabolism and neurotransmitter release [3]. Similarly, using pooled RNA preparations, Colangelo and colleagues specifically examined the hippocampal cornu ammonis 1 and demonstrated a very general overall repression of transcription in this region in AD patients [5]. In a third study, gene expression differences were observed between the affected hippocampus to that of the unaffected parietal cortex of the same patient [4].…”