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

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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

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Rodent Models of Amyotrophic Lateral Sclerosis

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C9orf72 Hexanucleotide Expansions Are Associated with Altered Endoplasmic Reticulum Calcium Homeostasis and Stress Granule Formation in Induced Pluripotent Stem Cell-Derived Neurons from Patients with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia

inferredcites →https://doi.org/10.1002/wsbm.1159openalex-snapshot

Reverse‐engineering human regulatory networks

inferredcites →https://doi.org/10.1007/s00401-007-0337-zopenalex-snapshot

Phosphorylated Smad2/3 immunoreactivity in sporadic and familial amyotrophic lateral sclerosis and its mouse model

inferredcites →https://doi.org/10.1007/s00401-018-1870-7openalex-snapshot

Transcriptome–pathology correlation identifies interplay between TDP-43 and the expression of its kinase CK1E in sporadic ALS

inferredcites →https://doi.org/10.1007/s00401-020-02252-5openalex-snapshot

Mitochondrial bioenergetic deficits in C9orf72 amyotrophic lateral sclerosis motor neurons cause dysfunctional axonal homeostasis

inferredcites →https://doi.org/10.1007/s12031-010-9467-1openalex-snapshot

The “Dying-Back” Phenomenon of Motor Neurons in ALS

inferredcites →https://doi.org/10.1016/j.cell.2013.07.034openalex-snapshot

Transcription Factor Binding in Human Cells Occurs in Dense Clusters Formed around Cohesin Anchor Sites

inferredcites →https://doi.org/10.1016/j.celrep.2015.03.053openalex-snapshot

Astrocyte-Derived TGF-β1 Accelerates Disease Progression in ALS Mice by Interfering with the Neuroprotective Functions of Microglia and T Cells

inferredcites →https://doi.org/10.1016/j.celrep.2015.06.019openalex-snapshot

The Regulatory Machinery of Neurodegeneration in In Vitro Models of Amyotrophic Lateral Sclerosis

inferredcites →https://doi.org/10.1016/j.celrep.2017.05.024openalex-snapshot

Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS

inferredcites →https://doi.org/10.1016/j.cels.2015.12.004openalex-snapshot

The Molecular Signatures Database Hallmark Gene Set Collection

inferredcites →https://doi.org/10.1016/j.cels.2020.10.010openalex-snapshot

Cross-Comparison of Human iPSC Motor Neuron Models of Familial and Sporadic ALS Reveals Early and Convergent Transcriptomic Disease Signatures

inferredcites →https://doi.org/10.1016/j.expneurol.2003.10.004openalex-snapshot

Amyotrophic lateral sclerosis is a distal axonopathy: evidence in mice and man

inferredcites →https://doi.org/10.1016/j.jcmgh.2018.09.005openalex-snapshot

Enhancer of Zeste Homologue 2 Inhibition Attenuates TGF-β Dependent Hepatic Stellate Cell Activation and Liver Fibrosis

inferredcites →https://doi.org/10.1016/j.nbd.2020.104877openalex-snapshot

Single-cell RNA-seq analysis of the brainstem of mutant SOD1 mice reveals perturbed cell types and pathways of amyotrophic lateral sclerosis

inferredcites →https://doi.org/10.1016/j.neuron.2013.02.007openalex-snapshot

Circuits for Grasping: Spinal dI3 Interneurons Mediate Cutaneous Control of Motor Behavior

inferredcites →https://doi.org/10.1016/j.neuron.2013.09.020openalex-snapshot

Hox Genes: Choreographers in Neural Development, Architects of Circuit Organization

inferredcites →https://doi.org/10.1016/j.neuron.2015.11.013openalex-snapshot

Purification and Characterization of Progenitor and Mature Human Astrocytes Reveals Transcriptional and Functional Differences with Mouse

inferredcites →https://doi.org/10.1016/j.neuron.2016.09.015openalex-snapshot

Poly(GR) in C9ORF72 -Related ALS/FTD Compromises Mitochondrial Function and Increases Oxidative Stress and DNA Damage in iPSC-Derived Motor Neurons

inferredcites →https://doi.org/10.1016/j.neuron.2017.12.029openalex-snapshot

Origin and Segmental Diversity of Spinal Inhibitory Interneurons

inferredcites →https://doi.org/10.1016/j.neuron.2019.03.014openalex-snapshot

Disruption of RNA Metabolism in Neurological Diseases and Emerging Therapeutic Interventions

inferredcites →https://doi.org/10.1016/j.semcdb.2018.05.001openalex-snapshot

Pathway perturbations in signaling networks: Linking genotype to phenotype

inferredcites →https://doi.org/10.1016/j.stem.2014.02.004openalex-snapshot

Modeling ALS with iPSCs Reveals that Mutant SOD1 Misregulates Neurofilament Balance in Motor Neurons

inferredcites →https://doi.org/10.1016/j.stem.2014.03.004openalex-snapshot

Pathways Disrupted in Human ALS Motor Neurons Identified through Genetic Correction of Mutant SOD1

inferredcites →https://doi.org/10.1016/j.stem.2016.09.011openalex-snapshot

A Single-Cell Roadmap of Lineage Bifurcation in Human ESC Models of Embryonic Brain Development

inferredcites →https://doi.org/10.1016/j.stemcr.2015.02.018openalex-snapshot

Deterministic HOX Patterning in Human Pluripotent Stem Cell-Derived Neuroectoderm

inferredcites →https://doi.org/10.1016/j.stemcr.2017.02.019openalex-snapshot

Genetic Correction of SOD1 Mutant iPSCs Reveals ERK and JNK Activated AP1 as a Driver of Neurodegeneration in Amyotrophic Lateral Sclerosis

inferredcites →https://doi.org/10.1016/j.stemcr.2017.09.004openalex-snapshot

FUS Mutant Human Motoneurons Display Altered Transcriptome and microRNA Pathways with Implications for ALS Pathogenesis

inferredcites →https://doi.org/10.1016/j.stemcr.2020.03.023openalex-snapshot

Impairment of Mitochondrial Calcium Buffering Links Mutations in C9ORF72 and TARDBP in iPS-Derived Motor Neurons from Patients with ALS/FTD

inferredcites →https://doi.org/10.1016/j.tig.2016.12.003openalex-snapshot

Single-Cell Multiomics: Multiple Measurements from Single Cells

inferredcites →https://doi.org/10.1016/s0896-6273(04)00017-0openalex-snapshot

Cell Cycle Activation Linked to Neuronal Cell Death Initiated by DNA Damage

inferredcites →https://doi.org/10.1038/nature20413openalex-snapshot

Decoding ALS: from genes to mechanism

inferredcites →https://doi.org/10.1038/nature25980openalex-snapshot

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

inferredcites →https://doi.org/10.1038/nbt.2859openalex-snapshot

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

inferredcites →https://doi.org/10.1038/nbt.3049openalex-snapshot

Combinatorial analysis of developmental cues efficiently converts human pluripotent stem cells into multiple neuronal subtypes

inferredcites →https://doi.org/10.1038/nbt.4314openalex-snapshot

Dimensionality reduction for visualizing single-cell data using UMAP

inferredcites →https://doi.org/10.1038/ncomms12139openalex-snapshot

Laser capture microscopy coupled with Smart-seq2 for precise spatial transcriptomic profiling

inferredcites →https://doi.org/10.1038/ncomms3464openalex-snapshot

Master regulators of FGFR2 signalling and breast cancer risk

inferredcites →https://doi.org/10.1038/ncomms6999openalex-snapshot

Human iPSC-derived motoneurons harbouring TARDBP or C9ORF72 ALS mutations are dysfunctional despite maintaining viability

inferredcites →https://doi.org/10.1038/ng1532openalex-snapshot

Reverse engineering of regulatory networks in human B cells

inferredcites →https://doi.org/10.1038/nmeth.1923openalex-snapshot

Fast gapped-read alignment with Bowtie 2

inferredcites →https://doi.org/10.1038/nmeth.4236openalex-snapshot

SC3: consensus clustering of single-cell RNA-seq data

inferredcites →https://doi.org/10.1038/nn.3490openalex-snapshot

Saltatory remodeling of Hox chromatin in response to rostrocaudal patterning signals

inferredcites →https://doi.org/10.1038/nn.4273openalex-snapshot

Modeling ALS with motor neurons derived from human induced pluripotent stem cells

inferredcites →https://doi.org/10.1038/nn.4345openalex-snapshot

ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks

inferredcites →https://doi.org/10.1038/nrdp.2017.85openalex-snapshot

Correction: Amyotrophic lateral sclerosis

inferredcites →https://doi.org/10.1038/nrm3434openalex-snapshot

TGFβ signalling in context

inferredcites →https://doi.org/10.1038/s41467-017-00911-yopenalex-snapshot

HDAC6 inhibition reverses axonal transport defects in motor neurons derived from FUS-ALS patients

inferredcites →https://doi.org/10.1038/s41467-017-02729-0openalex-snapshot

C9ORF72 repeat expansion causes vulnerability of motor neurons to Ca2+-permeable AMPA receptor-mediated excitotoxicity

inferredcites →https://doi.org/10.1038/s41467-018-04373-8openalex-snapshot

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS

inferredcites →https://doi.org/10.1038/s41467-019-08831-9openalex-snapshot

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

inferredcites →https://doi.org/10.1038/s41586-019-0969-xopenalex-snapshot

The single-cell transcriptional landscape of mammalian organogenesis

inferredcites →https://doi.org/10.1038/s41598-020-68794-6openalex-snapshot

Proteomics analysis of FUS mutant human motoneurons reveals altered regulation of cytoskeleton and other ALS-linked proteins via 3′UTR binding

inferredcites →https://doi.org/10.1056/nejmra1603471openalex-snapshot

Amyotrophic Lateral Sclerosis

inferredcites →https://doi.org/10.1073/pnas.1006869107openalex-snapshot

Deficits in axonal transport precede ALS symptoms in vivo

inferredcites →https://doi.org/10.1073/pnas.1704294114openalex-snapshot

Distinct roles for motor neuron autophagy early and late in the SOD1 G93A mouse model of ALS

inferredcites →https://doi.org/10.1093/bioinformatics/btg405openalex-snapshot

affy—analysis of Affymetrix GeneChip data at the probe level

inferredcites →https://doi.org/10.1093/bioinformatics/btu638openalex-snapshot

HTSeq—a Python framework to work with high-throughput sequencing data

inferredcites →https://doi.org/10.1093/brain/awq167openalex-snapshot

Global gene expression profiling of somatic motor neuron populations with different vulnerability identify molecules and pathways of degeneration and protection

inferredcites →https://doi.org/10.1093/brain/awt250openalex-snapshot

Transcriptomic indices of fast and slow disease progression in two mouse models of amyotrophic lateral sclerosis

inferredcites →https://doi.org/10.1093/hmg/ddp498openalex-snapshot

Sporadic ALS has compartment-specific aberrant exon splicing and altered cell–matrix adhesion biology

inferredcites →https://doi.org/10.1093/hmg/ddw105openalex-snapshot

Axonal transport defects are a common phenotype in Drosophila models of ALS

inferredcites →https://doi.org/10.1093/nar/27.1.29openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot

KEGG: Kyoto Encyclopedia of Genes and Genomes

inferredcites →https://doi.org/10.1093/nar/gkn923openalex-snapshot

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

inferredcites →https://doi.org/10.1093/nar/gkv007openalex-snapshot

limma powers differential expression analyses for RNA-sequencing and microarray studies

inferredcites →https://doi.org/10.1093/nar/gkz972openalex-snapshot

ClinVar: improvements to accessing data

inferredcites →https://doi.org/10.1101/2019.12.29.889543openalex-snapshot

Species-specific developmental timing is associated with global differences in protein stability in mouse and human

inferredcites →https://doi.org/10.1101/2020.08.26.268631openalex-snapshot

ALS-FUS mutation affects the activities of HuD/ELAVL4 and FMRP leading to axon phenotypes in motoneurons

inferredcites →https://doi.org/10.1101/217737openalex-snapshot

K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data

inferredcites →https://doi.org/10.1101/gr.135350.111openalex-snapshot

GENCODE: The reference human genome annotation for The ENCODE Project

inferredcites →https://doi.org/10.1101/gr.223313.117openalex-snapshot

Single-cell gene expression analysis reveals regulators of distinct cell subpopulations among developing human neurons

inferredcites →https://doi.org/10.1111/pcmr.12483openalex-snapshot

TGF ‐β induces SOX 2 expression in a time‐dependent manner in human melanoma cells

inferredcites →https://doi.org/10.1126/science.aaa1934openalex-snapshot

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

inferredcites →https://doi.org/10.1159/000064943openalex-snapshot

Hox Genes and Spinal Cord Development

inferredcites →https://doi.org/10.1186/1471-2105-9-559openalex-snapshot

WGCNA: an R package for weighted correlation network analysis

inferredcites →https://doi.org/10.1186/gb-2013-14-4-r36openalex-snapshot

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

inferredcites →https://doi.org/10.1186/s12864-018-4772-0openalex-snapshot

Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics

inferredcites →https://doi.org/10.1186/s13059-016-0888-1openalex-snapshot

Classification of low quality cells from single-cell RNA-seq data

inferredcites →https://doi.org/10.1242/dev.173807openalex-snapshot

Single cell transcriptomics reveals spatial and temporal dynamics of gene expression in the developing mouse spinal cord

inferredcites →https://doi.org/10.1242/dmm.020099openalex-snapshot

ALS mutant FUS proteins are recruited into stress granules in induced Pluripotent Stem Cells (iPSCs) derived motoneurons

inferredcites →https://doi.org/10.1242/dmm.029058openalex-snapshot

Modelling amyotrophic lateral sclerosis: progress and possibilities

inferredcites →https://doi.org/10.1242/jcs.01130openalex-snapshot

Axonal mitochondrial transport and potential are correlated

inferredcites →https://doi.org/10.1371/journal.pone.0138425openalex-snapshot

Transforming Growth Factor Beta (TGF-β) Is a Muscle Biomarker of Disease Progression in ALS and Correlates with Smad Expression

inferredcites →https://doi.org/10.1371/journal.pone.0177649openalex-snapshot

ALS skeletal muscle shows enhanced TGF-β signaling, fibrosis and induction of fibro/adipogenic progenitor markers

inferredcites →https://doi.org/10.15252/emmm.201707850openalex-snapshot

G‐quadruplex‐binding small molecules ameliorate C9orf72 FTD/ALS pathology in vitro and in vivo

inferredcites →https://doi.org/10.2119/molmed.2009.00149openalex-snapshot

Attenuation of the Transforming Growth Factor β-Signaling Pathway in Chronic Venous Ulcers

inferredcites →https://doi.org/10.2202/1544-6115.1128openalex-snapshot

A General Framework for Weighted Gene Co-Expression Network Analysis

inferredcites →https://doi.org/10.3389/fnmol.2017.00369openalex-snapshot

Conditional Loss of Hoxa5 Function Early after Birth Impacts on Expression of Genes with Synaptic Function

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1016/j.neuroscience.2021.10.025openalex-snapshot

Single-cell Transcriptional Changes in Neurodegenerative Diseases

inferred← citeshttps://doi.org/10.1186/s12860-021-00343-zopenalex-snapshot

Global transcriptome profile of the developmental principles of in vitro iPSC-to-motor neuron differentiation

inferred← citeshttps://doi.org/10.3389/fnins.2020.577755openalex-snapshot

From Multi-Omics Approaches to Precision Medicine in Amyotrophic Lateral Sclerosis

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