Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures

Ho, Ritchie; Workman, Michael J.; Mathkar, Pranav; Wu, Kathryn; Kim, Kevin J.; O’Rourke, Jacqueline G.; Kellogg, Mariko; Montel, Valérie; Bañuelos, Maria G.; Aladesuyi, Olubankole; Diaz-Garcia, Sandra; Oheb, Daniel; Khrebtukova, Irena; Watson, Lisa; Ravits, John; Taylor, K. L.; Baloh, Robert H.; Svendsen, Clive N.

doi:10.1101/2020.04.27.064584

Cited by 8 publications

(9 citation statements)

References 76 publications

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“…S11d). Upregulation of translation in ALS V1 IN was also observed in a recent single cell study of sporadic and C9ORF72 iPSC derived neurons[67]. On the other hand, genes involved in synaptic signalling were found to be downregulated, though to a lower extent than observed in ALS MN (Fig.…”

Section: Resultssupporting

confidence: 71%

“…Though the total number of cells captured in our study is less than typically seen in droplet-based assays, we were able to sequence each cell to a much greater depth (1.5e6 read per cells). This is in contrast to droplet-based studies that result in just 100,000 reads per cell[67]. As a result, our data identified almost thrice the number of genes typically seen in droplet-based experiments.…”

Section: Discussioncontrasting

confidence: 66%

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Single cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS motor neurons

Namboori

Thomas

Ames

et al. 2019

Preprint

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BackgroundBulk RNA-Seq has been extensively utilized to investigate the molecular changes accompanying motor neuron degeneration in Amyotrophic Lateral Sclerosis (ALS). However, due to the heterogeneity and degenerating phenotype of the neurons, it has proved difficult to assign specific changes to neuronal subtypes and identify which factors drive these changes. Consequently, we have utilized single cell transcriptomics of degenerating motor neurons derived from ALS patients to uncover key transcriptional drivers of dysfunctional pathways.ResultsSingle cell analysis of spinal neuronal cultures derived from ALS and isogenic iPSC allowed us to classify cells into neural subtypes including motor neurons and interneurons. Differential expression analysis between disease and control motor neurons revealed downregulation of genes involved in synaptic structure, neuromuscular junction, neuronal cytoskeleton and mitochondrial function. Interestingly, interneurons did not show similar suppression of these homeostatic functions. Single cell expression data enabled us to derive a context-specific transcriptional network relevant to ALS neurons. Master regulator analysis on this network identified core transcriptional factors driving the ALS disease signature. Specifically, we were able to correlate suppression of HOXA1 and HOXA5 to synaptic dysfunction in ALS motor neurons. Our results suggest that suppression of HOX genes may be a general phenomenon in SOD1 ALS.ConclusionsOur results demonstrate the utility of single cell transcriptomics in mapping disease-relevant gene regulatory networks driving neurodegeneration in ALS motor neurons. We propose that ALS-associated mutant SOD1 leads to inhibition of transcriptional networks driving homeostatic programs specific to motor neurons, thereby providing a possible explanation for the relative resistance of spinal interneurons to degeneration in ALS.

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Section: Resultssupporting

confidence: 71%

Section: Discussioncontrasting

confidence: 66%

Single cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS motor neurons

Namboori

Thomas

Ames

et al. 2019

Preprint

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“…These cellular phenotypes were specific to C9-ALS compared to controls, non-ALS or non-C9-ALS. RNA profiling of C9-ALS iPS cells revealed that ribosomal biogenesis is a main pathway dysregulated [19]. Similarly, decreases in ribosomal maturation have been reported in C9-ALS lymphoblasts and motor cortex [16].…”

Section: Introductionmentioning

confidence: 68%

Nucleolar stress in C9orf72 and sporadic ALS spinal motor neurons precedes TDP-43 mislocalization

Arogundade

Nguyen

Leung

et al. 2021

acta neuropathol commun

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Nucleolar stress has been implicated in the pathology and disease pathogenesis of amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) from repeat expansions of GGGGCC in C9orf72 (C9-ALS/FTLD) but not in sporadic ALS (SALS). Previously we reported that antisense RNA transcripts are unique in C9-ALS because of their nucleolar localization in spinal motor neurons and correlation with TDP-43 mislocalization, the hallmark proteinopathy of ALS and FTLD. Here we report our further studies of 11 SALS, 11 C9-ALS and 11 control spinal cords. We find that nucleolar stress manifests specifically as shrinkage in nucleoli of C9-ALS spinal motor neurons. Nucleolar size reduction is greatest in similarly sized alpha motor neurons from C9-ALS cases and results are not skewed by the number of surviving neurons from each ALS spinal cord. Surprisingly, nucleolar shrinkage occurs before main pathological hallmarks—TDP-43 mislocalization or antisense RNA foci—appear and this suggest that nucleolar stress can precede pathology in C9-ALS, findings previously identified in C9-FTLD using sense RNA foci and dipeptide repeat proteins as pathological markers. Importantly, these observations are also seen in SALS motor neurons and thus nucleolar stress appears to be a significant and probably upstream problem in sporadic disease.

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“…In an iPSC-neuron model, increased cell death was observed in FUS and TDP-43 mutants only after an extended maturation period of 40 days in vitro 31 . Studying these early time points have begun to reveal early molecular phenotypes which persist to end stages of disease 86 . Furthermore, therapeutics with neuroprotective mechanisms of action are likely to be most effective at the early stages of disease.…”

Section: -Aging and Maturationmentioning

confidence: 99%

Phenotyping Neurodegeneration in Human iPSCs

Fraenkel

2021

Annu. Rev. Biomed. Data Sci.

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Induced pluripotent stem cell (iPSC) technology holds promise for modeling neurodegenerative diseases. Traditional approaches for disease modeling using animal and cellular models require knowledge of disease mutations. However, many patients with neurodegenerative diseases do not have a known genetic cause. iPSCs offer a way to generate patient-specific models and study pathways of dysfunction in an in vitro setting in order to understand the causes and subtypes of neurodegeneration. Furthermore, iPSC-based models can be used to search for candidate therapeutics using high-throughput screening. Here we review how iPSC-based models are currently being used to further our understanding of neurodegenerative diseases, as well as discuss their challenges and future directions. Expected final online publication date for the Annual Review of Biomedical Data Science, Volume 4 is July 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

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Single-cell RNA-seq analysis of human iPSC-derived motor neurons resolves early and predictive ALS signatures

Cited by 8 publications

References 76 publications

Single cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS motor neurons

Single cell transcriptomics identifies master regulators of neurodegeneration in SOD1 ALS motor neurons

Nucleolar stress in C9orf72 and sporadic ALS spinal motor neurons precedes TDP-43 mislocalization

Phenotyping Neurodegeneration in Human iPSCs

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