Evaluation of a biomarker for amyotrophic lateral sclerosis derived from a hypomethylated DNA signature of human motor neurons.

Publisher: BioMed Central Country of Publication: England NLM ID: 101319628 Publication Model: Electronic Cited Medium: Internet ISSN: 1755-8794 (Electronic) Linking ISSN: 17558794 NLM ISO Abbreviation: BMC Med Genomics Subsets: MEDLINE

Original Publication: London : BioMed Central

Amyotrophic Lateral Sclerosis*/genetics ; Amyotrophic Lateral Sclerosis*/blood ; Motor Neurons*/metabolism ; Motor Neurons*/pathology ; Biomarkers*/blood ; DNA Methylation*; Humans ; Cell-Free Nucleic Acids/blood ; Cell-Free Nucleic Acids/genetics ; Induced Pluripotent Stem Cells/metabolism

Amyotrophic lateral sclerosis (ALS) lacks a specific biomarker, but is defined by relatively selective toxicity to motor neurons (MN). As others have highlighted, this offers an opportunity to develop a sensitive and specific biomarker based on detection of DNA released from dying MN within accessible biofluids. Here we have performed whole genome bisulfite sequencing (WGBS) of iPSC-derived MN from neurologically normal individuals. By comparing MN methylation with an atlas of tissue methylation we have derived a MN-specific signature of hypomethylated genomic regions, which accords with genes important for MN function. Through simulation we have optimised the selection of regions for biomarker detection in plasma and CSF cell-free DNA (cfDNA). However, we show that MN-derived DNA is not detectable via WGBS in plasma cfDNA. In support of our experimental finding, we show theoretically that the relative sparsity of lower MN sets a limit on the proportion of plasma cfDNA derived from MN which is below the threshold for detection via WGBS. Our findings are important for the ongoing development of ALS biomarkers. The MN-specific hypomethylated genomic regions we have derived could be usefully combined with more sensitive detection methods and perhaps with study of CSF instead of plasma. Indeed we demonstrate that neuronal-derived DNA is detectable in CSF. Our work is relevant for all diseases featuring death of rare cell-types.
Competing Interests: Declarations. Ethics approval and consent to participate: The study was approved by the South Sheffield Research Ethics Committee. Also, this study followed study protocols approved by Medical Ethical Committees for each of the participating institutions. Written informed consent was obtained from all participating individuals. All methods were performed in accordance with relevant national and international guidelines and regulations. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests.
(© 2025. The Author(s).)

Update of: Res Sq. 2024 Nov 26:rs.3.rs-5397445. doi: 10.21203/rs.3.rs-5397445/v1. (PMID: 39649175)

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CEGS 5P50HG00773504 NIH (USA); 899-792 United Kingdom MNDA_ Motor Neurone Disease Association; NF-SI-0617-10077 National Institute for Health and Care Research; United Kingdom WT_ Wellcome Trust; IS-BRC-1215-20017 NIHR Sheffield Biomedical Research Centre; 216596/Z/19/Z United Kingdom WT_ Wellcome Trust

Keywords: Amyotrophic lateral sclerosis (ALS); Biomarker; Cell-free DNA; DNA methylation; IPSC-derived motor neuron; Whole-genome bisulfite sequencing

0 (Biomarkers)
0 (Cell-Free Nucleic Acids)

Date Created: 20250114 Date Completed: 20250114 Latest Revision: 20250129

20250129

PMC11734586

10.1186/s12920-025-02084-w

39810183