Laser-captured spinal cord motorneurons from ALS subjects show increased gene expression in vacuolar ATPase networks

Ladd, Amy C.; Brohawn, David G.; Bennett, James P.

doi:10.15761/jsin.1000182

Cited by 3 publications

(3 citation statements)

References 26 publications

(36 reference statements)

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“…We next sought to explore whether similar results would be obtained from other ALS datasets. To this end, we examined five other publicly available ALS datasets, consisting of two that used total RNA from blood (Linsley2014 82 , Gagliardi 2018 58 ), and three datasets from spinal cord (Brohawn2016 83 , Ladd2017 84 , Brohawn 2019 85 ). We have provided a summary table of datasets for all studies used in this paper (Table 2).…”

Section: Resultsmentioning

confidence: 99%

Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Melnick

Gonzales

LaRocca

et al. 2021

Preprint

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Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis (ALS) patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq data sets currently being generated.

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Section: Resultsmentioning

confidence: 99%

Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Melnick

Gonzales

LaRocca

et al. 2021

Preprint

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“…The application of laser capture microdissection (LCM) to post-mortem CNS tissue offers an approach for evaluating in situ motor neurons and their distinctive transcriptome signature in ALS patients ( Jiang et al, 2005 ; Cox et al, 2010 ; Rabin et al, 2010 ; Kirby et al, 2011 ; Highley et al, 2014 ; Cooper-Knock et al, 2015 ; Ladd et al, 2017 ; Krach et al, 2018 ; Nizzardo et al, 2020 ). LCM allows RNA to be isolated from a motor neuron-enriched cellular pool, with less contribution from surrounding cell types as would occur with bulk tissue analysis ( EmmertBuck et al, 1996 ).…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, most analyses have focused on newly generated data only, without comparisons to previously published data. Conclusions have thus varied, although functional annotations of ALS dysregulated genes in LCM studies have related to cytoskeleton structure, RNA metabolism, RNA splicing and phosphatidylinositol-3 kinase signaling ( Jiang et al, 2005 ; Cox et al, 2010 ; Rabin et al, 2010 ; Kirby et al, 2011 ; Highley et al, 2014 ; Cooper-Knock et al, 2015 ; Ladd et al, 2017 ; Krach et al, 2018 ; Nizzardo et al, 2020 ). There has been one meta-analysis study of three LCM-generated datasets comparing motor neuron expression between ALS and CTL samples, which identified 206 DEGs in common among datasets ( p < 0.05, FC ≥ 2 or FC ≤ 0.50) ( Lin et al, 2020 ).…”

Section: Introductionmentioning

confidence: 99%

Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords

Swindell

2024

Front. Genet.

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IntroductionALS is a fatal neurodegenerative disease for which underlying mechanisms are incompletely understood. The motor neuron is a central player in ALS pathogenesis but different transcriptome signatures have been derived from bulk analysis of post-mortem tissue and iPSC-derived motor neurons (iPSC-MNs).MethodsThis study performed a meta-analysis of six gene expression studies (microarray and RNA-seq) in which laser capture microdissection (LCM) was used to isolate lower motor neurons from post-mortem spinal cords of ALS and control (CTL) subjects. Differentially expressed genes (DEGs) with consistent ALS versus CTL expression differences across studies were identified.ResultsThe analysis identified 222 ALS-increased DEGs (FDR <0.10, SMD >0.80) and 278 ALS-decreased DEGs (FDR <0.10, SMD < −0.80). ALS-increased DEGs were linked to PI3K-AKT signaling, innate immunity, inflammation, motor neuron differentiation and extracellular matrix. ALS-decreased DEGs were associated with the ubiquitin-proteosome system, microtubules, axon growth, RNA-binding proteins and synaptic membrane. ALS-decreased DEG mRNAs frequently interacted with RNA-binding proteins (e.g., FUS, HuR). The complete set of DEGs (increased and decreased) overlapped significantly with genes near ALS-associated SNP loci (p < 0.01). Transcription factor target motifs with increased proximity to ALS-increased DEGs were identified, most notably DNA elements predicted to interact with forkhead transcription factors (e.g., FOXP1) and motor neuron and pancreas homeobox 1 (MNX1). Some of these DNA elements overlie ALS-associated SNPs within known enhancers and are predicted to have genotype-dependent MNX1 interactions. DEGs were compared to those identified from SOD1-G93A mice and bulk spinal cord segments or iPSC-MNs from ALS patients. There was good correspondence with transcriptome changes from SOD1-G93A mice (r ≤ 0.408) but most DEGs were not differentially expressed in bulk spinal cords or iPSC-MNs and transcriptome-wide effect size correlations were weak (bulk tissue: r ≤ 0.207, iPSC-MN: r ≤ 0.037).ConclusionThis study defines a robust transcriptome signature from LCM-based motor neuron studies of post-mortem tissue from ALS and CTL subjects. This signature differs from those obtained from analysis of bulk spinal cord segments and iPSC-MNs. Results provide insight into mechanisms underlying gene dysregulation in ALS and highlight connections between these mechanisms, ALS genetics, and motor neuron biology.

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Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Melnick

Gonzales

LaRocca

et al. 2021

G3 Genes|Genomes|Genetics

View full text Add to dashboard Cite

Numerous reports have suggested that infectious agents could play a role in neurodegenerative diseases, but specific etiological agents have not been convincingly demonstrated. To search for candidate agents in an unbiased fashion, we have developed a bioinformatic pipeline that identifies microbial sequences in mammalian RNA-seq data, including sequences with no significant nucleotide similarity hits in GenBank. Effectiveness of the pipeline was tested using publicly available RNA-seq data and in a reconstruction experiment using synthetic data. We then applied this pipeline to a novel RNA-seq dataset generated from a cohort of 120 samples from amyotrophic lateral sclerosis (ALS) patients and controls, and identified sequences corresponding to known bacteria and viruses, as well as novel virus-like sequences. The presence of these novel virus-like sequences, which were identified in subsets of both patients and controls, were confirmed by quantitative RT-PCR. We believe this pipeline will be a useful tool for the identification of potential etiological agents in the many RNA-seq data sets currently being generated.

show abstract

Laser-captured spinal cord motorneurons from ALS subjects show increased gene expression in vacuolar ATPase networks

Cited by 3 publications

References 26 publications

Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

Meta-analysis of differential gene expression in lower motor neurons isolated by laser capture microdissection from post-mortem ALS spinal cords

Application of a bioinformatic pipeline to RNA-seq data identifies novel virus-like sequence in human blood

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