Microarray analyses of laser-captured hippocampus reveal distinct gray and white matter signatures associated with incipient Alzheimer's disease

Abstract

Alzheimer’s disease (AD) is a devastating neurodegenerative disorder that threatens to reach epidemic proportions as our population ages. Although much research has examined molecular pathways associated with AD, relatively few such studies have focused on the disease’s critical early stages. In a prior microarray study we correlated gene expression in hippocampus with degree of Alzheimer’s disease and found close associations between upregulation of apparent glial transcription factor/epigenetic/tumor suppressor genes and incipient AD. The results suggested a new model in which AD pathology spreads along myelinated axons (Blalock et al., 2004). However, the microarray analyses were performed on RNA extracted from frozen hand-dissected hippocampal CA1 tissue blocks containing both gray and white matter, limiting the confidence with which transcriptional changes in gray matter could be distinguished from those in white matter. Here, we used laser capture microdissection (LCM) to exclude major white matter tracts while selectively collecting CA1 hippocampal gray matter from formalin-fixed, paraffin-embedded (FFPE) hippocampal sections of the same subjects assessed in our prior study. Microarray analyses of this gray matter-enriched tissue revealed many transcriptional changes similar to those seen in our past study and in studies by others, particularly for downregulated neuron-related genes. Additionally, the present analyses identified several previously undetected pathway alterations, including downregulation of molecules that stabilize ryanodine receptor Ca2+ release and upregulation of vasculature development. Conversely, we found a striking paucity of the upregulated changes in the putative glial and growth-related genes that had been strongly overrepresented in the prior mixed-tissue study. We conclude that FFPE tissue can be a reliable resource for microarray studies of brain tissue, that upregulation of growth-related epigenetic/transcription factors during incipient AD is predominantly localized in and around white matter (supporting our prior findings and model), and that novel alterations in vascular and ryanodine receptor-related pathways in gray matter are closely associated with incipient AD.

Robust Gene Dysregulation in Alzheimer's Disease Brains

“…The overlap was statistically significant with p-values 2.20e-16 and 4.95e-5 for the up-and down-regulated genes, respectively. Another work by Blalock et al identified 277 up-and 232 down-regulated genes [15], among which 8 and 6 were in our list of up-and down-regulated genes. The overlap was also statistically significant with p-values 6.10e-8 and 2.97e-7 for the up-and down-regulated genes, respectively.…”

“…This LOAD dataset included 17 AD cases and 16 controls. In another study, Blalock et al conducted a microarray analysis on the gray matter of hippocampus CA1 region using laser capture microdissection [15]. Although the same 30 subjects were included as in their earlier work [16], different tissue selection techniques were used (tissue with mixed gray and white matters in their earlier work).…”

Drosophila Shep and C. elegans SUP-26 are RNA-binding proteins that play diverse roles in nervous system development

“…Additionally, we found that the expression of RBMS1 and/ or RBMS2 are significantly altered in a variety of human neurological diseases including the neurodegenerative disorders Alzheimer disease, Parkinson disease, X-linked dystonia-parkinsonism, and the mental disorder schizophrenia (Table S2; Blalock et al 2011;Blalock et al 2004;Harris et al 2008;Lesnick et al 2007;Lewandowski et al 2010). Collectively, the data suggest that RBMS1/2/3 orthologs also play roles in neuronal function and may be factors in the pathogenesis of human neurological disease.…”

Overexpression of Heme Oxygenase 1 Causes Cognitive Decline and Affects Pathways for Tauopathy in Mice

“…The gene expression data used in this study were downloaded from the Gene Expression Omnibus (GEO) repository (accession numbers GDS 810 and GDS4136, http://www.ncbi.nlm.nih.gov) [32,33]. The GDS810 (31 samples) were detected using the Gene expression array (Affymetrix Human Genome U133A Array).…”