Single cell gene expression profiling in Alzheimer’s disease

Abstract

Summary: Development and implementation of microarray techniques to quantify expression levels of dozens to hundreds to thousands of transcripts simultaneously within select tissue samples from normal control subjects and neurodegenerative diseased brains has enabled scientists to create molecular fingerprints of vulnerable neuronal populations in Alzheimer's disease (AD) and related disorders. A goal is to sample gene expression from homogeneous cell types within a defined region without potential contamination by expression profiles of adjacent neuronal subpopulations and nonneuronal cells. The precise resolution afforded by single cell and population cell RNA analysis in combination with microarrays and real-time quantitative polymerase chain reaction (qPCR)-based analyses allows for relative gene expression level comparisons across cell types under different experimental conditions and disease progression. The ability to analyze single cells is an important distinction from global and regional assessments of mRNA expression and can be applied to optimally prepared tissues from animal models of neurodegeneration as well as postmortem human brain tissues. Gene expression analysis in postmortem AD brain regions including the hippocampal formation and neocortex reveals selectively vulnerable cell types share putative pathogenetic alterations in common classes of transcripts, for example, markers of glutamatergic neurotransmission, synaptic-related markers, protein phosphatases and kinases, and neurotrophins/neurotrophin receptors. Expression profiles of vulnerable regions and neurons may reveal important clues toward the understanding of the molecular pathogenesis of various neurological diseases and aid in identifying rational targets toward pharmacotherapeutic interventions for progressive, late-onset neurodegenerative disorders such as mild cognitive impairment (MCI) and AD.

S3‐03‐01: Transcriptional vulnerability of brain regions in Alzheimer's disease and dementia

“…The advent of high throughput gene expression technologies has raised our capacities by permitting the study of the expression level of multiple genes simultaneously and defining ADassociated changes in numerous molecular biological systems (Blalock et al 2004;Blalock et al 2005;Emilsson et al 2006;Ginsberg et al 2000;Ginsberg et al 2004;Ginsberg et al 2006;Loring et al 2001;Parachikova et al 2006;Pasinetti 2001;Ricciarelli et al 2004;Xu et al 2006;Yao et al 2003). In addition, microarray techniques have been combined with microdissection capabilities to hone in on gene expression abnormalities in discrete neurons and in brain regions known to be affected by AD neuropathology (Ginsberg et al 2000;Ginsberg et al 2004;Ginsberg et al 2006).…”

“…In addition, microarray techniques have been combined with microdissection capabilities to hone in on gene expression abnormalities in discrete neurons and in brain regions known to be affected by AD neuropathology (Ginsberg et al 2000;Ginsberg et al 2004;Ginsberg et al 2006). Despite the breadth of our current technical abilities and understanding of transcriptional abnormalities in AD, most of the studies cited above have approached the question of abnormal gene expression in AD by examining gene expression in a limited number of brain regions and/or at specific neuropathologically or cognitively distinct stages of the disease.…”

Liquid chromatography with tandem mass spectrometry-based proteomic discovery in aging and Alzheimer’s disease

“…1 Genomics, the unbiased simultaneous assessment of relative changes in thousands of gene transcripts, is now a widely employed approach to assess relevance of molecular pathways using a variety of platforms that are becoming standardized; for examples, see the reviews by Ginsberg and coworkers, 2 as well as Miller and Federoff 3 in this issue. Proteomics, also an unbiased method that simultaneously assesses thousands of proteins, is less standardized than genomics, but likely will have an equally large influence on our understanding of molecular physiology and pathophysiology.…”

Single-Cell and Regional Gene Expression Analysis in Alzheimer’s Disease

“…However, the human brain is a complex tissue that contains hundreds of anatomically and histologically distinct areas (Sugino et al 2006), including thousands of different neuronal and non-neuronal cell types and subtypes (Ginsberg et al 2006b;Nelson et al 2006a). The effects of AD on two nearby neurons can be very different, where one neuron may exhibit markers of AD while the adjacent neuron appears normal (Chow et al 1998).…”