Evidence map›Paper›PMID 37080969›Full record

ArticleNature communications2023

Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology.

Oliver J Ziff, Jacob Neeves, Jamie Mitchell, Giulia Tyzack, Carlos Martinez-Ruiz, Raphaelle Luisier, Anob M Chakrabarti, Nicholas McGranahan, Kevin Litchfield, Simon J Boulton and 4 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
48citing papers in PubMed, 1 pooled it
12.1field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

48 citing papers in PubMed, 1 synthesis or guideline pooled it, 59 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 6 institutions in 3 countries.

Oliver J ZiffThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. o.ziff@ucl.ac.uk.ORCID 0000-0002-1504-7245
Jacob NeevesThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Jamie MitchellThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
Giulia TyzackThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.ORCID 0000-0001-5730-2112
Carlos Martinez-RuizCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0002-4817-0565
Raphaelle LuisierGenomics and Health Informatics Group, Idiap Research Institute, Martigny, Switzerland.
Anob M ChakrabartiThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.ORCID 0000-0002-6841-5718
Nicholas McGranahanCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.ORCID 0000-0001-9537-4045
Kevin LitchfieldCancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
Simon J BoultonThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.ORCID 0000-0001-6936-6834
Ammar Al-ChalabiMaurice Wohl Clinical Neuroscience Institute, Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK.ORCID 0000-0002-4924-7712
Gavin KellyThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.ORCID 0000-0001-7219-560X
Jack HumphreyNash Family Department of Neuroscience & Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.ORCID 0000-0002-6274-6620
Rickie PataniThe Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK. rickie.patani@ucl.ac.uk.ORCID 0000-0002-3825-7675
The Francis Crick Institute · GBCancer Research UK · GBUniversity College London Hospitals NHS Foundation Trust · GBAllen Institute for Brain Science · USIdiap Research Institute · CHKing's College London · GB

Funding

Cancer Research UKMedical Research Council MR/S006591/1Medical Research Council MR/V033077/1Wellcome Trust
6 · The paper itself

Abstract

Amyotrophic Lateral Sclerosis (ALS) causes motor neuron degeneration, with 97% of cases exhibiting TDP-43 proteinopathy. Elucidating pathomechanisms has been hampered by disease heterogeneity and difficulties accessing motor neurons. Human induced pluripotent stem cell-derived motor neurons (iPSMNs) offer a solution; however, studies have typically been limited to underpowered cohorts. Here, we present a comprehensive compendium of 429 iPSMNs from 15 datasets, and 271 post-mortem spinal cord samples. Using reproducible bioinformatic workflows, we identify robust upregulation of p53 signalling in ALS in both iPSMNs and post-mortem spinal cord. p53 activation is greatest with C9orf72 repeat expansions but is weakest with SOD1 and FUS mutations. TDP-43 depletion potentiates p53 activation in both post-mortem neuronal nuclei and cell culture, thereby functionally linking p53 activation with TDP-43 depletion. ALS iPSMNs and post-mortem tissue display enrichment of splicing alterations, somatic mutations, and gene fusions, possibly contributing to the DNA damage response.

Indexed as

Amyotrophic Lateral SclerosisDNA-Binding ProteinsGenomic InstabilityTranscriptomeAlternative SplicingC9orf72 ProteinCadaverCohort StudiesDatasets as TopicDNA DamageGene FusionHumansInduced Pluripotent Stem CellsMotor NeuronsMutationRNA-Binding Protein FUSC9orf72 ProteinC9orf72 protein, humanDNA-Binding ProteinsFUS protein, humanRNA-Binding Protein FUSSOD1 protein, humanSuperoxide Dismutase-1TARDBP protein, humanTP53 protein, humanTumor Suppressor Protein p53

Identifiers

PMID37080969
PMCPMC10119258
OpenAlexW4366595964

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.