Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations
Abstract Background Cell-free DNA (cfDNA) in plasma carries epigenetic signatures specific to tissue or cell of origin. Aberrant methylation patterns in circulating cfDNA have emerged as valuable tools for noninvasive cancer detection, prenatal diagnostics, and organ transplant assessment. Such epig...
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BMC
2025-02-01
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| Series: | Cell & Bioscience |
| Online Access: | https://doi.org/10.1186/s13578-025-01366-1 |
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| author | Yulin Jin Karen N Conneely Wenjing Ma Robert K. Naviaux Teepu Siddique Emily G. Allen Sandra Guingrich Robert M. Pascuzzi Peng Jin |
| author_facet | Yulin Jin Karen N Conneely Wenjing Ma Robert K. Naviaux Teepu Siddique Emily G. Allen Sandra Guingrich Robert M. Pascuzzi Peng Jin |
| author_sort | Yulin Jin |
| collection | DOAJ |
| description | Abstract Background Cell-free DNA (cfDNA) in plasma carries epigenetic signatures specific to tissue or cell of origin. Aberrant methylation patterns in circulating cfDNA have emerged as valuable tools for noninvasive cancer detection, prenatal diagnostics, and organ transplant assessment. Such epigenetic changes also hold significant promise for the diagnosis of neurodegenerative diseases, which often progresses slowly and has a lengthy asymptomatic period. However, genome-wide cfDNA methylation changes in neurodegenerative diseases remain poorly understood. Results We used whole-genome bisulfite sequencing (WGBS) to profile age-dependent and ALS-associated methylation signatures in cfDNA from 30 individuals, including young and middle-aged controls, as well as ALS patients with matched controls. We identified 5,223 age-related differentially methylated loci (DMLs) (FDR < 0.05), with 51.6% showing hypomethylation in older individuals. Our results significantly overlapped with age-associated CpGs identified in a large blood-based epigenome-wide association study (EWAS). Comparing ALS patients to controls, we detected 1,045 differentially methylated regions (DMRs) in gene bodies, promoters, and intergenic regions. Notably, these DMRs were linked to key ALS-associated pathways, including endocytosis and cell adhesion. Integration with spinal cord transcriptomics revealed that 31% of DMR-associated genes exhibited differential expression in ALS patients compared to controls, with over 20 genes significantly correlating with disease duration. Furthermore, comparison with published single-nucleus RNA sequencing (snRNA-Seq) data of ALS demonstrated that cfDNA methylation changes reflects cell-type-specific gene dysregulation in the brain of ALS patients, particularly in excitatory neurons and astrocytes. Deconvolution of cfDNA methylation profiles suggested altered proportions of immune and liver-derived cfDNA in ALS patients. Conclusions cfDNA methylation is a powerful tool for assessing age-related changes and ALS-specific molecular dysregulation by revealing perturbed locus, genes, and the proportional contributions of different tissues/cells to the plasma. This technique holds promise for clinical application in biomarker discovery across a broad spectrum of neurodegenerative disorders. |
| format | Article |
| id | doaj-art-cbc083d49e39464ab6823c8a6f94ee2d |
| institution | OA Journals |
| issn | 2045-3701 |
| language | English |
| publishDate | 2025-02-01 |
| publisher | BMC |
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| series | Cell & Bioscience |
| spelling | doaj-art-cbc083d49e39464ab6823c8a6f94ee2d2025-08-20T02:15:16ZengBMCCell & Bioscience2045-37012025-02-0115111610.1186/s13578-025-01366-1Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterationsYulin Jin0Karen N Conneely1Wenjing Ma2Robert K. Naviaux3Teepu Siddique4Emily G. Allen5Sandra Guingrich6Robert M. Pascuzzi7Peng Jin8Department of Human Genetics, Emory University School of MedicineDepartment of Human Genetics, Emory University School of MedicineDepartment of Biostatistics, University of MichiganDepartments of Medicine, Pediatrics, and Pathology, and the Mitochondrial and Metabolic Disease Center (MMDC), School of Medicine, University of California San DiegoFeinberg School of Medicine, Northwestern UniversityDepartment of Human Genetics, Emory University School of MedicineDepartment of Neurology, Indiana University School of MedicineDepartment of Neurology, Indiana University School of MedicineDepartment of Human Genetics, Emory University School of MedicineAbstract Background Cell-free DNA (cfDNA) in plasma carries epigenetic signatures specific to tissue or cell of origin. Aberrant methylation patterns in circulating cfDNA have emerged as valuable tools for noninvasive cancer detection, prenatal diagnostics, and organ transplant assessment. Such epigenetic changes also hold significant promise for the diagnosis of neurodegenerative diseases, which often progresses slowly and has a lengthy asymptomatic period. However, genome-wide cfDNA methylation changes in neurodegenerative diseases remain poorly understood. Results We used whole-genome bisulfite sequencing (WGBS) to profile age-dependent and ALS-associated methylation signatures in cfDNA from 30 individuals, including young and middle-aged controls, as well as ALS patients with matched controls. We identified 5,223 age-related differentially methylated loci (DMLs) (FDR < 0.05), with 51.6% showing hypomethylation in older individuals. Our results significantly overlapped with age-associated CpGs identified in a large blood-based epigenome-wide association study (EWAS). Comparing ALS patients to controls, we detected 1,045 differentially methylated regions (DMRs) in gene bodies, promoters, and intergenic regions. Notably, these DMRs were linked to key ALS-associated pathways, including endocytosis and cell adhesion. Integration with spinal cord transcriptomics revealed that 31% of DMR-associated genes exhibited differential expression in ALS patients compared to controls, with over 20 genes significantly correlating with disease duration. Furthermore, comparison with published single-nucleus RNA sequencing (snRNA-Seq) data of ALS demonstrated that cfDNA methylation changes reflects cell-type-specific gene dysregulation in the brain of ALS patients, particularly in excitatory neurons and astrocytes. Deconvolution of cfDNA methylation profiles suggested altered proportions of immune and liver-derived cfDNA in ALS patients. Conclusions cfDNA methylation is a powerful tool for assessing age-related changes and ALS-specific molecular dysregulation by revealing perturbed locus, genes, and the proportional contributions of different tissues/cells to the plasma. This technique holds promise for clinical application in biomarker discovery across a broad spectrum of neurodegenerative disorders.https://doi.org/10.1186/s13578-025-01366-1 |
| spellingShingle | Yulin Jin Karen N Conneely Wenjing Ma Robert K. Naviaux Teepu Siddique Emily G. Allen Sandra Guingrich Robert M. Pascuzzi Peng Jin Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations Cell & Bioscience |
| title | Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations |
| title_full | Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations |
| title_fullStr | Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations |
| title_full_unstemmed | Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations |
| title_short | Whole-genome bisulfite sequencing of cell-free DNA unveils age-dependent and ALS-associated methylation alterations |
| title_sort | whole genome bisulfite sequencing of cell free dna unveils age dependent and als associated methylation alterations |
| url | https://doi.org/10.1186/s13578-025-01366-1 |
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