1
|
Caggiano C, Morselli M, Qian X, Celona B, Thompson M, Wani S, Tosevska A, Taraszka K, Heuer G, Ngo S, Steyn F, Nestor P, Wallace L, McCombe P, Heggie S, Thorpe K, McElligott C, English G, Henders A, Henderson R, Lomen-Hoerth C, Wray N, McRae A, Pellegrini M, Garton F, Zaitlen N. Tissue informative cell-free DNA methylation sites in amyotrophic lateral sclerosis. medRxiv 2024:2024.04.08.24305503. [PMID: 38645132 PMCID: PMC11030489 DOI: 10.1101/2024.04.08.24305503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Cell-free DNA (cfDNA) is increasingly recognized as a promising biomarker candidate for disease monitoring. However, its utility in neurodegenerative diseases, like amyotrophic lateral sclerosis (ALS), remains underexplored. Existing biomarker discovery approaches are tailored to a specific disease context or are too expensive to be clinically practical. Here, we address these challenges through a new approach combining advances in molecular and computational technologies. First, we develop statistical tools to select tissue-informative DNA methylation sites relevant to a disease process of interest. We then employ a capture protocol to select these sites and perform targeted methylation sequencing. Multi-modal information about the DNA methylation patterns are then utilized in machine learning algorithms trained to predict disease status and disease progression. We applied our method to two independent cohorts of ALS patients and controls (n=192). Overall, we found that the targeted sites accurately predicted ALS status and replicated between cohorts. Additionally, we identified epigenetic features associated with ALS phenotypes, including disease severity. These findings highlight the potential of cfDNA as a non-invasive biomarker for ALS.
Collapse
Affiliation(s)
- C Caggiano
- Department of Neurology, UCLA, Los Angeles, California
- Institute of Genomic Health, Icahn School of Medicine at Mt Sinai, New York, New York
| | - M Morselli
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - X Qian
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - B Celona
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - M Thompson
- Department of Neurology, UCLA, Los Angeles, California
- Systems and Synthetic Biology, Centre for Genomic Regulation, Barcelona, Spain
| | - S Wani
- Cardiovascular Research Institute, UCSF, San Francisco, California
| | - A Tosevska
- Department of Molecular, Cell, and Developmental Biology, UCLA; Los Angeles, California
- Department of Internal Medicine III, Division of Rheumatology, Medical University of Vienna, Vienna, Austria
| | - K Taraszka
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts
| | - G Heuer
- Computational and Systems Biology Interdepartmental Program, UCLA, Los Angeles, California
| | - S Ngo
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Australia
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - F Steyn
- School of Biomedical Sciences, Faculty of Medicine, The University of Queensland, Brisbane, Australia
| | - P Nestor
- Queensland Brain Institute, Unviversity of Queensland, Brisbane, Australia
- Mater Public Hospital, Brisbane, Australia
| | - L Wallace
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - P McCombe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - S Heggie
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - K Thorpe
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | | | - G English
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A Henders
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - R Henderson
- Department of Neurology, Royal Brisbane and Women's Hospital, Brisbane, QLD, Australia
| | - C Lomen-Hoerth
- Department of Neurology, UCSF, San Francisco, California
| | - N Wray
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - A McRae
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - M Pellegrini
- Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - F Garton
- Institute for Molecular Biology, University of Queensland, Brisbane, Australia
| | - N Zaitlen
- Department of Neurology, UCLA, Los Angeles, California
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California
| |
Collapse
|
2
|
Painter JN, Willemsen G, Nyholt DR, Hoekstra C, Duffy D, Henders A, Wallace L, Healy S, Cannon-Albright LA, Skolnick M, Martin NG, Boomsma DI, Montgomery GW. 138. GENOME-WIDE LINKAGE SCAN FOR FAMILIAL DIZYGOTIC TWINNING. Reprod Fertil Dev 2010. [DOI: 10.1071/srb10abs138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
The tendency to conceive dizygotic (DZ) twins is a complex trait influenced by genetic and environmental factors. To search for new candidate loci for twinning we have conducted a genome-wide linkage scan in 525 families using microsatellite and single nucleotide polymorphism (SNP) marker panels. Non-parametric linkage analyses including 523 families containing a total of 1115 mothers of DZ twins (MODZT) from Australia and New Zealand (ANZ) and The Netherlands (NL) produced four linkage peaks above the threshold for suggestive linkage, including a highly suggestive peak at the extreme telomeric end of chromosome 6 with an exponential (exp)LOD score of 2.813 (P = 0.0002). Since the DZ twinning rate increases steeply with maternal age independent of genetic effects, we also investigated linkage including only families where at least one MODZT gave birth to her first set of twins before the age of 30. These analyses produced a maximum expLOD score of 2.718 (p = 0.0002), largely due to linkage signal from the ANZ cohort, however, ordered subset analyses indicated this result is most likely a chance finding in the combined dataset. Linkage analyses were also performed for two large DZ twinning families from the USA, one of which produced a peak on chromosome 2 in the region of two potential candidate genes. Sequencing of FSHR and FIGLA, along with INHBB in MODZTs from two large NL families with family-specific linkage peaks directly over this gene, revealed a potentially functional variant in the 5’ untranslated region of FSHR that segregated with the DZ twinning phenotype in the UT family. Work is continuing screening candidate genes. Our data provide further evidence for complex inheritance of familial DZ twinning.
Collapse
|