Transcriptomics Analyses of ALS Post-mortem Motor Cortex highlight alteration and potential biomarkers in the Neuropeptide Signalling pathway

Background: Amyotrophic lateral sclerosis (ALS) is a fatal heterogeneous neurodegenerative disease that typically leads to death from respiratory failure within two to five years. Despite the identification of several genetic risk factors, the biological processes involved in ALS pathogenesis remain poorly understood. The motor cortex is an ideal region to study dysregulated pathological processes in ALS as it is affected from the earliest stages of the disease. In this study, we investigated motor-cortex gene expression of cases and controls to gain new insight into the molecular footprint of ALS. Methods: We performed a large case-control differential expression analysis of two independent post-mortem motor cortex bulk RNA-sequencing (RNAseq) datasets from the King's College London BrainBank (N = 171) and TargetALS (N = 132). Differentially expressed genes from both datasets were subjected to gene and pathway enrichment analysis. Genes common to both datasets were also reviewed for their involvement with known mechanisms of ALS pathogenesis to identify potential candidate genes. Finally, we performed a correlation analysis of genes implicated in pathways enriched in both datasets with clinical outcomes such as the age of onset and survival. Results: Differential expression analysis identified 2,290 and 402 differentially expressed genes in KCL BrainBank and TargetALS cases, respectively. Enrichment analysis revealed significant synapse-related processes in the KCL BrainBank dataset, while the TargetALS dataset carried an immune system-related signature. There were 44 differentially expressed genes which were common to both datasets, which represented previously recognised mechanisms of ALS pathogenesis, such as lipid metabolism, mitochondrial energy homeostasis and neurovascular unit dysfunction. Differentially expressed genes in both datasets were significantly enriched for the neuropeptide signalling pathway. By looking at the relationship between the expression of neuropeptides and their receptors with clinical measures, we found that in both datasets NPBWR1, TAC3 and SSTR1 correlated with age of onset, and GNRH1, TACR1 with survival. We provide access to gene-level expression results to the broader research community through a publicly available web application (https://alsgeexplorer.er.kcl.ac.uk). Conclusion: This study identified motor-cortex specific pathways altered in ALS patients, potential molecular targets for therapeutic disease intervention and a set of neuropeptides and receptors for investigation as potential biomarkers. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement RK is funded by MND Scotland, grant number RE14937. HM is funded by GlaxoSmithKline and the KCL funded centre for Doctoral Training (CDT) in Data-Driven Health. GH is funded by Perron Institute for Neurological and Translational Science and the KCL funded centre for Doctoral Training (CDT) in Data-Driven Health.RJBD is supported by the following: (1) NIHR Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London, London, UK; (2) Health Data Research UK, which is funded by the UK Medical Research Council, Engineering and Physical Sciences Research Council, Economic and Social Research Council, Department of Health and Social Care (England), Chief Scientist Office of the Scottish Government Health and Social Care Directorates, Health and Social Care Research and Development Division (Welsh Government), Public Health Agency (Northern Ireland), British Heart Foundation and Wellcome Trust; (3) The BigData@Heart Consortium, funded by the Innovative Medicines Initiative-2 Joint Undertaking under grant agreement No. 116074. This Joint Undertaking receives support from the European Union's Horizon 2020 research and innovation programme and EFPIA; it is chaired by DE Grobbee and SD Anker, partnering with 20 academic and industry partners and ESC; (4) the National Institute for Health Research University College London Hospitals Biomedical Research Centre; (5) the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London; (6) the UK Research and Innovation London Medical Imaging & Artificial Intelligence Centre for Value Based Healthcare; (7) the National Institute for Health Research (NIHR) Applied Research Collaboration South London (NIHR ARC South London) at King's College Hospital NHS Foundation Trust. AAC is an NIHR Senior Investigator (NIHR202421). This research is part an EU Joint Programme - Neurodegenerative Disease Research (JPND) project. The project is supported through the following funding organisations under the aegis of JPND: Medical Research Council; Economic and Social Research Council and the Motor Neurone Disease Association. Funding for open access charge: UKRI. AI is funded by the Motor Neurone Disease Association. This study represents independent research partly funded by the National Institute for Health Research (NIHR) Biomedical Research Centre at South London and Maudsley NHS Foundation Trust and King's College London. BA acknowledges funding through a Pre-doctoral Fellowship from the NIHR (NIHR301067). We acknowledge use of the research computing facility at King's College London, Rosalind (https://rosalind.kcl.ac.uk), which is delivered in partnership with the National Institute for Health Research (NIHR) Biomedical Research Centres at South London & Maudsley and Guy's & St. Thomas' NHS Foundation Trusts and part-funded by capital equipment grants from the Maudsley Charity (award 980) and Guy's and St Thomas' Charity (TR130505). The views expressed are those of the author(s) and not necessarily those of the NHS, the NIHR, King's College London, or the Department of Health and Social Care. ### 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: Ethical approval to process and analyse post-mortem samples stored at King's College London was provided by a local ethics committee at the Institute of Psychiatry, Psychology & Neuroscience, King's College London, and the MRC London Neurodegenerative Diseases Brain Bank. 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, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes KCL BrainBank RNAseq data is available, on reasonable request, from the corresponding author. All raw RNAseq data from TargetALS samples can be requested by emailing cgnd\_help@nygenome.org. Results for individual genes can be visually explored at https://alsgeexplorer.er.kcl.ac.uk/. All data analysis scripts used in this study are available at https://github.com/rkabiljo/RNASeq\_Genes\_ERVs and https://github.com/rkabiljo/DifferentialExpression\_Genes . [https://github.com/rkabiljo/RNASeq\_Genes\_ERVs][1] [1]: https://github.com/rkabiljo/RNASeq_Genes_ERVs