Meta-analysis of the amyotrophic lateral sclerosis spectrum uncovers genome instability

Amyotrophic Lateral Sclerosis (ALS) is characterised by progressive motor neuron degeneration but there is marked genetic and clinical heterogeneity[1][1]. Identifying common mechanisms of ALS amongst this diversity has been challenging, however, a systematic framework examining motor neurons across the ALS spectrum may reveal unifying insights. Here, we present the most comprehensive compendium of ALS human-induced pluripotent stem cell-derived motor neurons (iPSNs) from 429 donors across 15 datasets including Answer ALS and NeuroLINCS, spanning 10 ALS mutations and sporadic ALS. Using gold-standard reproducible bioinformatic workflows, we identify that ALS iPSNs show common activation of the DNA damage response and p53 signalling, which was replicated in the NYGC ALS postmortem cohort of 203 spinal cord samples. The strongest p53 activation was observed in C9orf72 repeat expansions but was also independently increased in TARDBP, FUS and sporadic subgroups. ALS iPSNs showed extensive splicing alterations and enrichment of SNVs, indels and gene fusions, which may contribute to their damage-induced mutation signature. Our results integrate the global landscape of motor neuron alterations in ALS, revealing that genome instability is a common hallmark of ALS motor neurons and provides a resource to identify future ALS drug targets. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This work was funded by the Francis Crick Institute, which receives its core funding from Cancer Research UK (FC010110), the UK Medical Research Council (FC010110), and the Wellcome Trust (FC010110). O.J.Z. holds a Crick Clinical PhD Fellowship supported by the University College London Hospitals Biomedical Research Centre (BRC689/ED/CB/100130). R.P. holds an MRC Senior Clinical Fellowship (MR/S006591/1) and a Lister Research Prize Fellowship. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: All iPSN sequencing datasets used in this study are publicly available through Gene Expression Omnibus, European Nucleotide Archive, and dbGap and their accession numbers are stated in Table 1, with the exception being Answer ALS. Answer ALS is an anonymized publicly available dataset at [answerals.org][2] that requires a signed data user agreement with John Hopkins University, in which the user must agree to protect the security of the data. Postmortem data were accessed from The New York Genome Centre (NYGC) ALS Consortium database which is also publicly available on the Gene Expression Omnibus under accession GSE137810. The NYGC samples were acquired through various IRB protocols from member sites and the Target ALS postmortem tissue core and transferred to the NYGC in accordance with all applicable foreign, domestic, federal, state, and local laws and regulations for processing, sequencing, and analysis. The Biomedical Research Alliance of New York (BRANY) Institutional Review Board serves as the central ethics oversight body for NYGC ALS Consortium. Ethical approval was given. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes All raw and processed sequencing data generated in this study are available on public repositories under accession numbers shown in Table 1. [1]: #ref-1 [2]: http://answerals.org