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. 2011 Oct;42(2):118-26.
doi: 10.1016/j.jchemneu.2011.06.007. Epub 2011 Jul 2.

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

Eric M Blalock  1 , Heather M Buechel, Jelena Popovic, James W Geddes, Philip W Landfield
Affiliations

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

Eric M Blalock et al. J Chem Neuroanat. 2011 Oct.

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.

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Figures

Figure 1
Figure 1. Representative images of laser capture process
A. Reconstructed image of human hippocampal section of CA1 region before laser cut and capture process. Associated white matter tracts, which appear as dark bundles, are labeled (alveus, perforant path). Calibration bar (yellow) = 1 mm. B. Same section after cut and capture process. Note that sampling region largely excludes white matter tracts. Inset: Laser pressure micro-catapulted sections in the capture region. Calibration bar (yellow) = 300 μm.
Figure 2
Figure 2. Flowchart of microarray correlation analysis procedure
Pre-statistical filtering omitted probe sets with poor annotation and/or low quality signal. Each of the remaining genes was correlated (Pearson’s test) with MMSE scores and NFT counts across all 30 subjects (Overall correlation). If genes were found to correlate significantly with either marker overall, then a post-hoc correlation test across the subset of 15 subjects in the control and incipient groups (incipient correlation) was also performed. Numbers of significant genes were separated based on the AD marker (MMSE or NFT, or both) with which they were correlated. All genes significant in MMSE and/or NFT were used for subsequent functional overrepresentation analysis (Table 1).
Figure 3
Figure 3. Comparing tissue block and laser capture dissection gene signatures
The two studies were conducted six years apart using different microarray platforms. For the 7537 gene probes that were present and annotated in both studies, the number of genes that showed correlations with an AD marker in both the tissue block and laser dissection samples (overlap) was determined. At extremely high (relaxed) p-value criteria for correlation significance (right), all genes are expected by chance to correlate with AD in both studies and all genes were found in the overlap (found:expected = 1.0). As p-value criterion stringency increases toward the left, the number of genes expected to correlate significantly in both studies by chance alone falls precipitously, as would the number actually found if there were little true overlap (maintaining a ratio of ~ 1.0). However, with increasing p-value stringency the found:expected ratio rises sharply, particularly at p-values below 0.05, indicating that far more genes were found to agree between studies than would be expected by chance. Inset- Venn Diagram: Using the 0.05 cutoff (gray shaded area, arrow), ~34 times as many overlapping genes as expected by chance was identified. Functional overrepresentation analysis was performed for genes encompassed within each region of the Venn diagram (section 3.2).
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References

    1. Abdueva D, Wing M, Schaub B, Triche T, Davicioni E. Quantitative expression profiling in formalin-fixed paraffin-embedded samples by affymetrix microarrays. J Mol Diagn. 2010;12:409–417. - PMC - PubMed
    1. Ambati J. Age-related macular degeneration and the other double helix. The Cogan Lecture. Investigative ophthalmology & visual science. 2011;52:2165–2169. - PMC - PubMed
    1. Arendt T, Holzer M, Stobe A, Gartner U, Luth HJ, Bruckner MK, Ueberham U. Activated mitogenic signaling induces a process of dedifferentiation in Alzheimer’s disease that eventually results in cell death. Ann N Y Acad Sci. 2000;920:249–255. - PubMed
    1. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–29. - PMC - PubMed
    1. Barrett T, Edgar R. Gene expression omnibus: microarray data storage, submission, retrieval, and analysis. Methods Enzymol. 2006;411:352–369. - PMC - PubMed

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