Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq

Kim, TaeHyun; Lim, Chae‐Seok; Kaang, Bong‐Kiun

doi:10.5483/bmbrep.2015.48.7.218

Cited by 20 publications

(13 citation statements)

References 49 publications

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“…For instance, Map1b gene expression was downregulated in AD temporal cortex [123], whereas downregulation of Synpo protein in dendritic spines occurred in frontal cortex neurons in AD [9] similar to that found in our LC gene array experiments. Future studies employing single population RNA-sequencing, Fluidigm, and/or Nanostring nCounter analyses are warranted when transcriptomic technologies become more standardized and economical [22, 66, 73]. …”

Section: Resultsmentioning

confidence: 99%

Locus coeruleus cellular and molecular pathology during the progression of Alzheimer’s disease

Kelly

Perez

et al. 2017

acta neuropathol commun

236

230

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A major feature of Alzheimer’s disease (AD) is the loss of noradrenergic locus coeruleus (LC) projection neurons that mediate attention, memory, and arousal. However, the extent to which the LC projection system degenerates during the initial stages of AD is still under investigation. To address this question, we performed tyrosine hydroxylase (TH) immunohistochemistry and unbiased stereology of noradrenergic LC neurons in tissue harvested postmortem from subjects who died with a clinical diagnosis of no cognitive impairment (NCI), amnestic mild cognitive impairment (aMCI, a putative prodromal AD stage), or mild/moderate AD. Stereologic estimates of total LC neuron number revealed a 30% loss during the transition from NCI to aMCI, with an additional 25% loss of LC neurons in AD. Decreases in noradrenergic LC neuron number were significantly associated with worsening antemortem global cognitive function as well as poorer performance on neuropsychological tests of episodic memory, semantic memory, working memory, perceptual speed, and visuospatial ability. Reduced LC neuron numbers were also associated with increased postmortem neuropathology. To examine the cellular and molecular pathogenic processes underlying LC neurodegeneration in aMCI, we performed single population microarray analysis. These studies revealed significant reductions in select functional classes of mRNAs regulating mitochondrial respiration, redox homeostasis, and neuritic structural plasticity in neurons accessed from both aMCI and AD subjects compared to NCI. Specific gene expression levels within these functional classes were also associated with global cognitive deterioration and neuropathological burden. Taken together, these observations suggest that noradrenergic LC cellular and molecular pathology is a prominent feature of prodromal disease that contributes to cognitive dysfunction. Moreover, they lend support to a rational basis for targeting LC neuroprotection as a disease modifying strategy.Electronic supplementary materialThe online version of this article (doi:10.1186/s40478-017-0411-2) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Locus coeruleus cellular and molecular pathology during the progression of Alzheimer’s disease

Kelly

Perez

et al. 2017

acta neuropathol commun

236

230

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“…On the other hand, the upregulation of neuronal Chrna7 during AD has been reported by both in situ hybridization and immunohistochemical approaches (Counts et al, 2007; Hellström-Lindahl et al, 1999; Teaktong et al, 2004). Future studies employing single population RNA-sequencing, Fluidigm, and/or Nanostring nCounter analyses are warranted when single population transcriptomic technologies become more standardized and economical (Buettner et al, 2015; Kim et al, 2015; Macosko et al, 2015) for human postmortem tissue use.…”

Section: Resultsmentioning

confidence: 99%

Pretangle pathology within cholinergic nucleus basalis neurons coincides with neurotrophic and neurotransmitter receptor gene dysregulation during the progression of Alzheimer's disease

Tiernan

Ginsberg

et al. 2018

Neurobiology of Disease

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Cholinergic basal forebrain neurons of the nucleus basalis of Meynert (nbM) regulate attentional and memory function and are exquisitely prone to tau pathology and neurofibrillary tangle (NFT) formation during the progression of Alzheimer’s disease (AD). nbM neurons require the neurotrophin nerve growth factor (NGF), its cognate receptor TrkA, and the pan-neurotrophin receptor p75NTR for their maintenance and survival. Additionally, nbM neuronal activity and cholinergic tone are regulated by the expression of nicotinic (nAChR) and muscarinic (mAChR) acetylcholine receptors as well as receptors modulating glutamatergic and catecholaminergic afferent signaling. To date, the molecular and cellular relationships between the evolution of tau pathology and nbM neuronal survival remain unknown. To address this knowledge gap, we profiled cholinotrophic pathway genes within nbM neurons immunostained for pS422, a pretangle phosphorylation event preceding tau C-terminal truncation at D421, or dual-labeled for pS422 and TauC3, a later stage tau neo-epitope revealed by this same C-terminal truncation event, via single-population custom microarray analysis. nbM neurons were obtained from postmortem tissues from subjects who died with an antemortem clinical diagnosis of no cognitive impairment (NCI), mild cognitive impairment (MCI), or mild/moderate AD. Quantitative analysis revealed significant downregulation of mRNAs encoding TrkA as well as TrkB, TrkC, and the Trk-mediated downstream pro-survival kinase Akt in pS422+ compared to unlabeled, pS422-negative nbM neurons. In addition, pS422+ neurons displayed a downregulation of transcripts encoding NMDA receptor subunit 2B, metabotropic glutamate receptor 2, D2 dopamine receptor, and β1 adrenoceptor. By contrast, transcripts encoding p75NTR were downregulated in dual-labeled pS422+/TauC3+ neurons. Appearance of the TauC3 epitope was also associated with an upregulation of the α7 nAChR subunit and differential downregulation of the β2 nAChR subunit. Notably, we found that gene expression patterns for each cell phenotype did not differ with clinical diagnosis. However, linear regression revealed that global cognition and Braak stage were predictors of select transcript changes within both unlabeled and pS422+/TauC3™ neurons. Taken together, these cell phenotype-specific gene expression profiling data suggest that dysregulation of neurotrophic and neurotransmitter signaling is an early pathogenic mechanism associated with NFT formation in vulnerable nbM neurons and cognitive decline in AD, which may be amenable to therapeutic intervention early in the disease process.

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“…This leaves a significant fraction of genes whose parent of origin cannot be defined in this particular cross (see Supplemental Figure 4 for analysis of accession combinations providing additional coverage). Despite this limitation, the ease of experimental setup and noninvasive nature of the technique argue for this approach, which does not require the extensive postharvesting purification steps required for alternative biochemical approaches such as TRAP-seq (Lin et al, 2014;Kim et al, 2015) or isolation of nuclei tagged in specific cell types (INTACT; Deal and Henikoff, 2011). Our analysis of Cvi x Col cross-pollinations revealed that ;8% of pollinated A. thaliana pistil RNA is derived from the pollen tube and we found strong correlations between our analysis and previous microarray analyses of the component cell types (microarray experiments recently reviewed in Rutley and Twell [2015]; Figure 2).…”

Section: Discussionmentioning

confidence: 99%

The Molecular Dialog between Flowering Plant Reproductive Partners Defined by SNP-Informed RNA-Sequencing

et al. 2017

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Cell type-specific gene expression profiling in brain tissue: comparison between TRAP, LCM and RNA-seq

Cited by 20 publications

References 49 publications

Locus coeruleus cellular and molecular pathology during the progression of Alzheimer’s disease

Locus coeruleus cellular and molecular pathology during the progression of Alzheimer’s disease

Pretangle pathology within cholinergic nucleus basalis neurons coincides with neurotrophic and neurotransmitter receptor gene dysregulation during the progression of Alzheimer's disease

The Molecular Dialog between Flowering Plant Reproductive Partners Defined by SNP-Informed RNA-Sequencing

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