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Li JZ, Ramalingam N, Li S. Targeting epigenetic mechanisms in amyloid-β-mediated Alzheimer's pathophysiology: unveiling therapeutic potential. Neural Regen Res 2025; 20:54-66. [PMID: 38767476 PMCID: PMC11246147 DOI: 10.4103/nrr.nrr-d-23-01827] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/07/2024] [Indexed: 05/22/2024] Open
Abstract
Alzheimer's disease is a prominent chronic neurodegenerative condition characterized by a gradual decline in memory leading to dementia. Growing evidence suggests that Alzheimer's disease is associated with accumulating various amyloid-β oligomers in the brain, influenced by complex genetic and environmental factors. The memory and cognitive deficits observed during the prodromal and mild cognitive impairment phases of Alzheimer's disease are believed to primarily result from synaptic dysfunction. Throughout life, environmental factors can lead to enduring changes in gene expression and the emergence of brain disorders. These changes, known as epigenetic modifications, also play a crucial role in regulating the formation of synapses and their adaptability in response to neuronal activity. In this context, we highlight recent advances in understanding the roles played by key components of the epigenetic machinery, specifically DNA methylation, histone modification, and microRNAs, in the development of Alzheimer's disease, synaptic function, and activity-dependent synaptic plasticity. Moreover, we explore various strategies, including enriched environments, exposure to non-invasive brain stimulation, and the use of pharmacological agents, aimed at improving synaptic function and enhancing long-term potentiation, a process integral to epigenetic mechanisms. Lastly, we deliberate on the development of effective epigenetic agents and safe therapeutic approaches for managing Alzheimer's disease. We suggest that addressing Alzheimer's disease may require distinct tailored epigenetic drugs targeting different disease stages or pathways rather than relying on a single drug.
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Affiliation(s)
- Jennie Z Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
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2
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC v1.0 BeadChip microarrays. Epigenetics 2024; 19:2333660. [PMID: 38564759 PMCID: PMC10989698 DOI: 10.1080/15592294.2024.2333660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC v1.0 arrays. We conducted a comprehensive assessment of the EPIC v1.0 array probe reliability using 69 blood DNA samples, each measured twice, generated by the Alzheimer's Disease Neuroimaging Initiative study. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliability information for probes on the EPIC v1.0 array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Juan I Young
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
| | - Brian Kunkle
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Eden R Martin
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL, USA
- Dr. John T MacDonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL, USA
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3
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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retro-age: A unique epigenetic biomarker of aging captured by DNA methylation states of retroelements. Aging Cell 2024:e14288. [PMID: 39092674 DOI: 10.1111/acel.14288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 08/04/2024] Open
Abstract
Reactivation of retroelements in the human genome has been linked to aging. However, whether the epigenetic state of specific retroelements can predict chronological age remains unknown. We provide evidence that locus-specific retroelement DNA methylation can be used to create retroelement-based epigenetic clocks that accurately measure chronological age in the immune system, across human tissues, and pan-mammalian species. We also developed a highly accurate retroelement epigenetic clock compatible with EPICv.2.0 data that was constructed from CpGs that did not overlap with existing first- and second-generation epigenetic clocks, suggesting a unique signal for epigenetic clocks not previously captured. We found retroelement-based epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, and responsive to antiretroviral therapy. Our findings highlight the utility of retroelement-based biomarkers of aging and support a renewed emphasis on the role of retroelements in geroscience.
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Affiliation(s)
- Lishomwa C Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | - Matthew L Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | | | - Alina P S Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | | | | | - Douglas F Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
| | - Michael J Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York, New York City, USA
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4
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Fernandes S, Revanna J, Pratt J, Hayes N, Marchetto MC, Gage FH. Modeling Alzheimer's disease using human cell derived brain organoids and 3D models. Front Neurosci 2024; 18:1434945. [PMID: 39156632 PMCID: PMC11328153 DOI: 10.3389/fnins.2024.1434945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2024] [Accepted: 07/10/2024] [Indexed: 08/20/2024] Open
Abstract
Age-related neurodegenerative diseases, like Alzheimer's disease (AD), are challenging diseases for those affected with no cure and limited treatment options. Functional, human derived brain tissues that represent the diverse genetic background and cellular subtypes contributing to sporadic AD (sAD) are limited. Human stem cell derived brain organoids recapitulate some features of human brain cytoarchitecture and AD-like pathology, providing a tool for illuminating the relationship between AD pathology and neural cell dysregulation leading to cognitive decline. In this review, we explore current strategies for implementing brain organoids in the study of AD as well as the challenges associated with investigating age-related brain diseases using organoid models.
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Affiliation(s)
- Sarah Fernandes
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Jasmin Revanna
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Biological Sciences, University of California, San Diego, La Jolla, CA, United States
| | - Joshua Pratt
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Biology, San Diego State University, San Diego, CA, United States
| | - Nicholas Hayes
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
- Department of Biological Sciences, California State University, San Marcos, CA, United States
| | - Maria C. Marchetto
- Department of Anthropology, Center for Academic Research and Training in Anthropogeny (CARTA), University of California, San Diego, La Jolla, CA, United States
| | - Fred H. Gage
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, United States
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5
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Murthy M, Fodder K, Miki Y, Rambarack N, De Pablo Fernandez E, Pihlstrøm L, Mill J, Warner TT, Lashley T, Bettencourt C. DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson's disease, and progressive supranuclear palsy: a cross-comparative investigation. Acta Neuropathol 2024; 148:4. [PMID: 38995454 PMCID: PMC11245434 DOI: 10.1007/s00401-024-02764-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 07/04/2024] [Accepted: 07/04/2024] [Indexed: 07/13/2024]
Abstract
Multiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCIs) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders, such as Parkinson's disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported alterations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate genome-wide DNA methylation patterns in the frontal lobe white matter of individuals with MSA (n = 17), PD (n = 17), and PSP (n = 16) along with controls (n = 15) using the Illumina EPIC array, to identify shared and disease-specific DNA methylation alterations. Genome-wide DNA methylation profiling of frontal lobe white matter in the three parkinsonian disorders revealed substantial commonalities in DNA methylation alterations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signaling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport to be shared between these parkinsonian disorders. Our overall analysis points toward more similarities in DNA methylation patterns between MSA and PD, both synucleinopathies, compared to that between MSA and PD with PSP, which is a tauopathy. Our results also highlight several shared DNA methylation changes and pathways indicative of converging molecular mechanisms in the white matter contributing toward neurodegeneration in all three parkinsonian disorders.
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Affiliation(s)
- Megha Murthy
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Katherine Fodder
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Yasuo Miki
- Department of Neuropathology, Institute of Brain Science, Hirosaki University Graduate School of Medicine, Hirosaki, Japan
| | - Naiomi Rambarack
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
| | - Eduardo De Pablo Fernandez
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Lasse Pihlstrøm
- Department of Neurology, Oslo University Hospital, Oslo, Norway
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, UK
| | - Thomas T Warner
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK
- Department of Clinical and Movement Neurosciences, UCL Queen Square Institute of Neurology, London, UK
- Reta Lila Weston Institute, UCL Queen Square Institute of Neurology, London, UK
| | - Tammaryn Lashley
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK
| | - Conceição Bettencourt
- Queen Square Brain Bank for Neurological Disorders, UCL Queen Square Institute of Neurology, London, UK.
- Department of Neurodegenerative Disease, UCL Queen Square Institute of Neurology, London, UK.
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Whitman ET, Ryan CP, Abraham WC, Addae A, Corcoran DL, Elliott ML, Hogan S, Ireland D, Keenan R, Knodt AR, Melzer TR, Poulton R, Ramrakha S, Sugden K, Williams BS, Zhou J, Hariri AR, Belsky DW, Moffitt TE, Caspi A. A blood biomarker of the pace of aging is associated with brain structure: replication across three cohorts. Neurobiol Aging 2024; 136:23-33. [PMID: 38301452 PMCID: PMC11017787 DOI: 10.1016/j.neurobiolaging.2024.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 01/16/2024] [Accepted: 01/19/2024] [Indexed: 02/03/2024]
Abstract
Biological aging is the correlated decline of multi-organ system integrity central to the etiology of many age-related diseases. A novel epigenetic measure of biological aging, DunedinPACE, is associated with cognitive dysfunction, incident dementia, and mortality. Here, we tested for associations between DunedinPACE and structural MRI phenotypes in three datasets spanning midlife to advanced age: the Dunedin Study (age=45 years), the Framingham Heart Study Offspring Cohort (mean age=63 years), and the Alzheimer's Disease Neuroimaging Initiative (mean age=75 years). We also tested four additional epigenetic measures of aging: the Horvath clock, the Hannum clock, PhenoAge, and GrimAge. Across all datasets (total N observations=3380; total N individuals=2322), faster DunedinPACE was associated with lower total brain volume, lower hippocampal volume, greater burden of white matter microlesions, and thinner cortex. Across all measures, DunedinPACE and GrimAge had the strongest and most consistent associations with brain phenotypes. Our findings suggest that single timepoint measures of multi-organ decline such as DunedinPACE could be useful for gauging nervous system health.
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Affiliation(s)
- Ethan T Whitman
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA.
| | - Calen P Ryan
- Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, USA
| | | | - Angela Addae
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - David L Corcoran
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Maxwell L Elliott
- Department of Psychology, Center for Brain Science, Harvard University, Cambridge, MA, USA
| | - Sean Hogan
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - David Ireland
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Ross Keenan
- Brain Research New Zealand-Rangahau Roro Aotearoa, Centre of Research Excellence, Universities of Auckland and Otago, New Zealand; Christchurch Radiology Group, Christchurch, New Zealand
| | - Annchen R Knodt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Tracy R Melzer
- Brain Research New Zealand-Rangahau Roro Aotearoa, Centre of Research Excellence, Universities of Auckland and Otago, New Zealand; Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Richie Poulton
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Sandhya Ramrakha
- Dunedin Multidisciplinary Health and Development Research Unit, Department of Psychology, University of Otago, Dunedin, New Zealand
| | - Karen Sugden
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | | | - Jiayi Zhou
- Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, USA
| | - Ahmad R Hariri
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA
| | - Daniel W Belsky
- Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, USA; Department of Epidemiology, Columbia University Mailman School of Public Health, New York, USA
| | - Terrie E Moffitt
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC, USA; King's College London, Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, London, UK; PROMENTA, Department of Psychology, University of Oslo, Norway; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
| | - Avshalom Caspi
- Department of Psychology and Neuroscience, Duke University, Durham, NC, USA; Center for Genomic and Computational Biology, Duke University, Durham, NC, USA; King's College London, Social, Genetic, and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology, & Neuroscience, London, UK; PROMENTA, Department of Psychology, University of Oslo, Norway; Department of Psychiatry and Behavioral Sciences, Duke University, Durham, NC, USA
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7
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Zhang Y, Shen S. Epigenome-wide DNA methylation analysis of late-stage mild cognitive impairment. Front Cell Dev Biol 2024; 12:1276288. [PMID: 38298218 PMCID: PMC10824854 DOI: 10.3389/fcell.2024.1276288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 01/05/2024] [Indexed: 02/02/2024] Open
Abstract
Background: Patients with late-stage mild cognitive impairment (LMCI) have a higher risk of progression to Alzheimer's disease (AD) than those with early-stage mild cognitive impairment (EMCI). However, previous studies have often pooled EMCI and LMCI patients into a single MCI group, with limited independent investigation into the pathogenesis of LMCI. Methods: In this study, we employed whole-genome methylation association analysis to determine the differences in peripheral blood methylation profiles between 663 cognitive aging (CN) and 554 LMCI patients. Results: Our results revealed 2,333 differentially methylated probes (DMPs) and 85 differentially methylated regions (DMRs) specific to LMCI. The top hit methylation sites or regions were associated with genes such as SNED1, histone deacetylases coding gene HDACs, and HOX and ZNF gene family. The DNA methylations upregulated the expression of HDAC4, HDAC8, and HOX family genes HOXC5 and HOXC9, but they downregulated the expression of SNED1, ADCYAP1, and ZNF family genes ZNF415 and ZNF502. Gene Ontology (GO) and KEGG analysis showed that the genes associated with these methylation sites were predominantly related to the processes of addiction disorders, neurotransmission, and neurogenesis. Out of the 554 LMCI patients included in this study, 358 subjects (65%) had progressed to AD. Further association analysis between the LMCI subjects with a stable course (sLMCI) and those who progressed to AD (pLMCI) indicated that the methylation signal intensities of HDAC6, ZNF502, HOXC5, HOXC6, and HOXD8 were associated with increased susceptibility to AD. Protective effects against progression to AD were noticed when the methylation of SNED1 and ZNF727 appeared in LMCI patients. Conclusion: Our findings highlight a substantial number of LMCI-specific methylated biomarkers that differ from those identified in previous MCI case-control studies. These biomarkers have the potential to contribute to a better understanding of the pathogenesis of LMCI.
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Affiliation(s)
- Yi Zhang
- Institute of Neuroscience, Panzhihua University, Panzhihua, China
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8
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Ulrich A, Wu Y, Draisma H, Wharton J, Swietlik EM, Cebola I, Vasilaki E, Balkhiyarova Z, Jarvelin MR, Auvinen J, Herzig KH, Coghlan JG, Lordan J, Church C, Howard LS, Pepke-Zaba J, Toshner M, Wort SJ, Kiely DG, Condliffe R, Lawrie A, Gräf S, Morrell NW, Wilkins MR, Prokopenko I, Rhodes CJ. Blood DNA methylation profiling identifies cathepsin Z dysregulation in pulmonary arterial hypertension. Nat Commun 2024; 15:330. [PMID: 38184627 PMCID: PMC10771427 DOI: 10.1038/s41467-023-44683-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 12/28/2023] [Indexed: 01/08/2024] Open
Abstract
Pulmonary arterial hypertension (PAH) is characterised by pulmonary vascular remodelling causing premature death from right heart failure. Established DNA variants influence PAH risk, but susceptibility from epigenetic changes is unknown. We addressed this through epigenome-wide association study (EWAS), testing 865,848 CpG sites for association with PAH in 429 individuals with PAH and 1226 controls. Three loci, at Cathepsin Z (CTSZ, cg04917472), Conserved oligomeric Golgi complex 6 (COG6, cg27396197), and Zinc Finger Protein 678 (ZNF678, cg03144189), reached epigenome-wide significance (p < 10-7) and are hypermethylated in PAH, including in individuals with PAH at 1-year follow-up. Of 16 established PAH genes, only cg10976975 in BMP10 shows hypermethylation in PAH. Hypermethylation at CTSZ is associated with decreased blood cathepsin Z mRNA levels. Knockdown of CTSZ expression in human pulmonary artery endothelial cells increases caspase-3/7 activity (p < 10-4). DNA methylation profiles are altered in PAH, exemplified by the pulmonary endothelial function modifier CTSZ, encoding protease cathepsin Z.
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Affiliation(s)
- Anna Ulrich
- Department of Clinical and Experimental Medicine, University of Surrey, Surrey, UK
| | - Yukyee Wu
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Harmen Draisma
- Department of Clinical and Experimental Medicine, University of Surrey, Surrey, UK
- Section of Genetics & Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - John Wharton
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Emilia M Swietlik
- VPD Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Inês Cebola
- Section of Genetics & Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Eleni Vasilaki
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Zhanna Balkhiyarova
- Department of Clinical and Experimental Medicine, University of Surrey, Surrey, UK
- Section of Genetics & Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
| | - Marjo-Riitta Jarvelin
- MRC Centre for Environment and Health, Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
- Unit of Primary Care, Oulu University Hospital, Oulu, Finland
- Department of Life Sciences, College of Health and Life Sciences, Brunel University London, London, UK
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Karl-Heinz Herzig
- Institute of Biomedicine, Medical Research Center Oulu, Oulu University and Oulu University Hospital, Oulu, Finland
- Department of Pediatric Gastroenterology and Metabolic Diseases, Poznan University of Medical Sciences, Poznan, Poland
| | | | | | - Colin Church
- Golden Jubilee National Hospital and University of Glasgow, Glasgow, UK
| | - Luke S Howard
- National Heart and Lung Institute, Imperial College London, London, UK
| | | | - Mark Toshner
- VPD Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Stephen J Wort
- National Heart and Lung Institute, Imperial College London, London, UK
- National PH Service, Royal Brompton Hospital, London, UK
| | - David G Kiely
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, UK
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield, UK
- NIHR Biomedical Research Centre Sheffield, Sheffield, UK
| | - Robin Condliffe
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, UK
- Sheffield Pulmonary Vascular Disease Unit, Royal Hallamshire Hospital, Sheffield, UK
| | - Allan Lawrie
- National Heart and Lung Institute, Imperial College London, London, UK
- Department of Infection, Immunity & Cardiovascular Disease, University of Sheffield, Sheffield, UK
| | - Stefan Gräf
- VPD Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
- NIHR BioResource for Translational Research, Cambridge Biomedical Campus, Cambridge, UK
| | - Nicholas W Morrell
- VPD Heart & Lung Research Institute, University of Cambridge, Cambridge, UK
| | - Martin R Wilkins
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Inga Prokopenko
- Department of Clinical and Experimental Medicine, University of Surrey, Surrey, UK
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9
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Costantini E, Carrarini C, Calisi D, De Rosa M, Simone M, Di Crosta A, Palumbo R, Cipollone A, Aielli L, De Laurentis M, Colarusso L, Pilotto A, Padovani A, Konstantinidou F, Gatta V, Stuppia L, Cipollone F, Di Nicola M, Reale M, Bonanni L. Search in the Periphery for Potential Inflammatory Biomarkers of Dementia with Lewy Bodies and Alzheimer's Disease. J Alzheimers Dis 2024; 99:1147-1158. [PMID: 38759010 PMCID: PMC11191525 DOI: 10.3233/jad-231471] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/04/2024] [Indexed: 05/19/2024]
Abstract
Background Neuroinflammation, with altered peripheral proinflammatory cytokine production, plays a major role in the pathogenesis of neurodegenerative diseases, such as Alzheimer's disease (AD), while the role of inflammation in dementia with Lewy bodies (DLB) is less known and the results of different studies are often in disagreement. Objective The present study aimed to investigate the levels of TNFα and IL-6 in serum and supernatants, and the related DNA methylation in patients affected by DLB and AD compared to healthy controls (HCs), to clarify the role of epigenetic mechanisms of DNA promoter methylation on of pro-inflammatory cytokines overproduction. Methods Twenty-one patients with DLB and fourteen with AD were frequency-matched for age and sex with eleven HCs. Clinical evaluation, TNFα and IL-6 gene methylation status, cytokine gene expression levels and production in serum and peripheral blood mononuclear cell (PBMC) supernatants were performed. Results In AD and DLB patients, higher serum levels of IL-6 and TNFα were detected than in HCs. Differences in LPS-stimulated versus spontaneous PBMCs were observed between DLB, AD, and HC in the levels of TNFα (p = 0.027) and IL-6 (p < 0.001). Higher levels were also revealed for sIL-6R in DLB (p < 0.001) and AD (p < 0.001) in comparison with HC.DNA hypomethylation in IL-6 and TNFα CpG promoter sites was detected for DLB and AD patients compared to the corresponding site in HCs. Conclusions Our preliminary study documented increased levels of IL-6 and TNFα in DLB and AD patients to HCs. This overproduction can be due to epigenetic mechanisms regarding the hypomethylation of DNA promoters.
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Affiliation(s)
- Erica Costantini
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Claudia Carrarini
- Department of Neuroscience, Catholic University of Sacred Heart, Rome, Italy
- IRCCS San Raffaele, Rome, Italy
| | - Dario Calisi
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Matteo De Rosa
- Department of Neurosciences, Imaging and Clinical Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Marianna Simone
- Clinics of Neurology SS. Annunziata Hospital of Chieti, Chieti, Italy
| | - Adolfo Di Crosta
- Department of Psychological Health and Territorial Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Rocco Palumbo
- Department of Psychological Health and Territorial Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Alessia Cipollone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Lisa Aielli
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d’Annunzio”, Chieti, Italy
| | | | | | - Andrea Pilotto
- Department of Clinical and Experimental Sciences, Neurology Unit, University of Brescia, Brescia, Italy
- Parkinson’s Disease Rehabilitation Centre, FERB ONLUS-S, Isidoro Hospital, Trescore Balneario, Italy
| | - Alessandro Padovani
- Department of Clinical and Experimental Sciences, Neurology Unit, University of Brescia, Brescia, Italy
| | - Fani Konstantinidou
- Department of Psychological Health and Territorial Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Valentina Gatta
- Department of Psychological Health and Territorial Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Liborio Stuppia
- Department of Psychological Health and Territorial Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Francesco Cipollone
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti, Italy
| | - Marta Di Nicola
- Department of Medical and Oral Sciences and Biotechnologies, University “G. d’Annunzio”, Chieti, Italy
| | - Marcella Reale
- Department of Innovative Technologies in Medicine and Dentistry, University “G. d’Annunzio”, Chieti, Italy
| | - Laura Bonanni
- Department of Medicine and Aging Sciences, University “G. d’Annunzio”, Chieti, Italy
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10
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Albala B, Appelmans E, Burress R, De Santi S, Devins T, Klein G, Logovinsky V, Novak GP, Ribeiro K, Schmidt ME, Schwarz AJ, Scott D, Shcherbinin S, Siemers E, Travaglia A, Weber CJ, White L, Wolf‐Rodda J, Vasanthakumar A. The Alzheimer's Disease Neuroimaging Initiative and the role and contributions of the Private Partners Scientific Board (PPSB). Alzheimers Dement 2024; 20:695-708. [PMID: 37774088 PMCID: PMC10843521 DOI: 10.1002/alz.13483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/24/2023] [Accepted: 08/27/2023] [Indexed: 10/01/2023]
Abstract
The Alzheimer's Disease Neuroimaging Initiative (ADNI) Private Partners Scientific Board (PPSB) encompasses members from industry, biotechnology, diagnostic, and non-profit organizations that have until recently been managed by the Foundation for the National Institutes of Health (FNIH) and provided financial and scientific support to ADNI programs. In this article, we review some of the major activities undertaken by the PPSB, focusing on those supporting the most recently completed National Institute on Aging grant, ADNI3, and the impact it has had on streamlining biomarker discovery and validation in Alzheimer's disease. We also provide a perspective on the gaps that may be filled with future PPSB activities as part of ADNI4 and beyond. HIGHLIGHTS: The Private Partners Scientific board (PPSB) continues to play a key role in enabling several Alzheimer's Disease Neuroimaging Initiative (ADNI) activities. PPSB working groups have led landscape assessments to provide valuable feedback on new technologies, platforms, and methods that may be taken up by ADNI in current or future iterations.
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Affiliation(s)
- Bruce Albala
- Eisai Inc.NutleyNew JerseyUSA
- Present address:
Program in Public HealthIrvine and Department of NeurologyUCI School of MedicineUniversity of California856 Health Sciences QuadIrvineCalifornia92697‐3957USA
| | - Eline Appelmans
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
| | - Ramona Burress
- Janssen Research & Development, LLCTitusvilleNew JerseyUSA
- Present address:
Takeda95, Hayden AvenueLexingtonMassachusetts02421USA
| | - Susan De Santi
- Eisai Inc.NutleyNew JerseyUSA
- Life Molecular ImagingBerlinGermany
- Present address:
Eisai Inc.NutleyNew JerseyUSA
| | - Theresa Devins
- Eisai Inc.NutleyNew JerseyUSA
- Present address:
Cognition Therapeutics2500 Westchester AvenuePurchaseNew York10577USA
| | | | - Veronika Logovinsky
- Eisai Inc.NutleyNew JerseyUSA
- Present address:
Lundbeck6 Parkway NDeerfieldIllinois60015USA
| | | | | | | | | | | | | | | | - Alessio Travaglia
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
| | | | - Leah White
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
- Present address:
Veranex5420 Wade Park Blvd Suite 204RaleighNorth Carolina27607USA
| | - Julie Wolf‐Rodda
- Foundation for the National Institutes of HealthNorth BethesdaMarylandUSA
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11
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Ndhlovu LC, Bendall ML, Dwaraka V, Pang APS, Dopkins N, Carreras N, Smith R, Nixon DF, Corley MJ. Retroelement-Age Clocks: Epigenetic Age Captured by Human Endogenous Retrovirus and LINE-1 DNA methylation states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.06.570422. [PMID: 38106164 PMCID: PMC10723416 DOI: 10.1101/2023.12.06.570422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Human endogenous retroviruses (HERVs), the remnants of ancient viral infections embedded within the human genome, and long interspersed nuclear elements 1 (LINE-1), a class of autonomous retrotransposons, are silenced by host epigenetic mechanisms including DNA methylation. The resurrection of particular retroelements has been linked to biological aging. Whether the DNA methylation states of locus specific HERVs and LINEs can be used as a biomarker of chronological age in humans remains unclear. We show that highly predictive epigenetic clocks of chronological age can be constructed from retroelement DNA methylation states in the immune system, across human tissues, and pan-mammalian species. We found retroelement epigenetic clocks were reversed during transient epigenetic reprogramming, accelerated in people living with HIV-1, responsive to antiretroviral therapy, and accurate in estimating long-term culture ages of human brain organoids. Our findings support the hypothesis of epigenetic dysregulation of retroelements as a potential contributor to the biological hallmarks of aging.
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Affiliation(s)
- Lishomwa C. Ndhlovu
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Matthew L. Bendall
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | - Alina PS Pang
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Nicholas Dopkins
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | | | | | - Douglas F. Nixon
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
| | - Michael J. Corley
- Department of Medicine, Division of Infectious Diseases, Weill Cornell Medicine, New York City, New York, USA
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12
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Lukacsovich D, O’Shea D, Huang H, Zhang W, Young JI, Steven Chen X, Dietrich ST, Kunkle B, Martin ER, Wang L. MIAMI-AD (Methylation in Aging and Methylation in AD): an integrative knowledgebase that facilitates explorations of DNA methylation across sex, aging, and Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.12.04.23299412. [PMID: 38105943 PMCID: PMC10723513 DOI: 10.1101/2023.12.04.23299412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder with a significant impact on aging populations. DNA methylation (DNAm) alterations have been implicated in both the aging processes and the development of AD. Given that AD affects more women than men, it is also important to explore DNAm changes that occur specifically in each sex. We created MIAMI-AD, a comprehensive knowledge base containing manually curated summary statistics from 97 published tables in 37 studies, all of which included at least 100 participants. MIAMI-AD enables easy browsing, querying, and downloading DNAm associations at multiple levels - at individual CpG, gene, genomic regions, or genome-wide, in one or multiple studies. Moreover, it also offers tools to perform integrative analyses, such as comparing DNAm associations across different phenotypes or tissues, as well as interactive visualizations. Using several use case examples, we demonstrated that MIAMI-AD facilitates our understanding of age-associated CpGs in AD and the sex-specific roles of DNAm in AD. This open-access resource is freely available to the research community, and all the underlying data can be downloaded. MIAMI-AD (https://miami-ad.org/) facilitates integrative explorations to better understand the interplay between DNAm across aging, sex, and AD.
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Affiliation(s)
- David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Deirdre O’Shea
- Department of Neurology, Comprehensive Center for Brain Health, University of Miami Miller School of Medicine, Boca Raton, FL, 33433
| | - Hanchen Huang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Sven-Thorsten Dietrich
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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13
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Karlsson IK, Ploner A, Wang Y, Gatz M, Pedersen NL, Hägg S. Leukocyte DNA methylation in Alzheimer´s disease associated genes: replication of findings from neuronal cells. Epigenetics 2023; 18:2158285. [PMID: 36573011 PMCID: PMC9980709 DOI: 10.1080/15592294.2022.2158285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Differences in gene-wide DNA methylation of the Alzheimer's disease (AD)-associated genes BIN1, HLA-DRB5, SORL1, SLC24A4, and ABCA7 are reported to be associated with AD in post-mortem brain samples. We investigated whether the same associations could be found in leukocytes collected pre-mortem. Using cohort data of 544 Swedish twins (204 dementia diagnoses), we replicated the findings in HLA-DRB5 and SLC24A4 at P < 0.05. However, co-twin control analyses indicated that the associations were partly explained by familial confounding. Thus, DNA methylation differences in HLA-DRB5 and SLC24A4 are present in both neuronal cells and leukocytes, and not fully explained familial factors.
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Affiliation(s)
- Ida K Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Alexander Ploner
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Yunzhang Wang
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Margaret Gatz
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Center for Economic and Social Research, University of Southern California, Los Angeles, CA, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden.,Department of Psychology, University of Southern California, Los Angeles, CA, USA
| | - Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
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14
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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15
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Kunkle B, Martin ER, Wang L. Critical evaluation of the reliability of DNA methylation probes on the Illumina MethylationEPIC BeadChip microarrays. RESEARCH SQUARE 2023:rs.3.rs-3068938. [PMID: 37461726 PMCID: PMC10350239 DOI: 10.21203/rs.3.rs-3068938/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2023]
Abstract
DNA methylation (DNAm) plays a crucial role in a number of complex diseases. However, the reliability of DNAm levels measured using Illumina arrays varies across different probes. Previous research primarily assessed probe reliability by comparing duplicate samples between the 450k-450k or 450k-EPIC platforms, with limited investigations on Illumina EPIC arrays. We conducted a comprehensive assessment of the EPIC array probe reliability using 138 duplicated blood DNAm samples generated by the Alzheimer's Disease Neuroimaging Initiative study. We introduced a novel statistical measure, the modified intraclass correlation, to better account for the disagreement in duplicate measurements. We observed higher reliability in probes with average methylation beta values of 0.2 to 0.8, and lower reliability in type I probes or those within the promoter and CpG island regions. Importantly, we found that probe reliability has significant implications in the analyses of Epigenome-wide Association Studies (EWAS). Higher reliability is associated with more consistent effect sizes in different studies, the identification of differentially methylated regions (DMRs) and methylation quantitative trait locus (mQTLs), and significant correlations with downstream gene expression. Moreover, blood DNAm measurements obtained from probes with higher reliability are more likely to show concordance with brain DNAm measurements. Our findings, which provide crucial reliable information for probes on the EPIC array, will serve as a valuable resource for future DNAm studies.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Juan I. Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Michael A. Schmidt
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - X. Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
| | - Brian Kunkle
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Eden R. Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
- John P. Hussman Institute for Human Genomics, the University of Miami Miller School of Medicine, Miami, FL 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136, USA
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16
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Jeremic D, Jiménez-Díaz L, Navarro-López JD. Targeting epigenetics: A novel promise for Alzheimer's disease treatment. Ageing Res Rev 2023; 90:102003. [PMID: 37422087 DOI: 10.1016/j.arr.2023.102003] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Revised: 05/30/2023] [Accepted: 07/03/2023] [Indexed: 07/10/2023]
Abstract
So far, the search for a cure for Alzheimer Disease (AD) has been unsuccessful. The only approved drugs attenuate some symptoms, but do not halt the progress of this disease, which affects 50 million people worldwide and will increase its incidence in the coming decades. Such scenario demands new therapeutic approaches to fight against this devastating dementia. In recent years, multi-omics research and the analysis of differential epigenetic marks in AD subjects have contributed to our understanding of AD; however, the impact of epigenetic research is yet to be seen. This review integrates the most recent data on pathological processes and epigenetic changes relevant for aging and AD, as well as current therapies targeting epigenetic machinery in clinical trials. Evidence shows that epigenetic modifications play a key role in gene expression, which could provide multi-target preventative and therapeutic approaches in AD. Both novel and repurposed drugs are employed in AD clinical trials due to their epigenetic effects, as well as increasing number of natural compounds. Given the reversible nature of epigenetic modifications and the complexity of gene-environment interactions, the combination of epigenetic-based therapies with environmental strategies and drugs with multiple targets might be needed to properly help AD patients.
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Affiliation(s)
- Danko Jeremic
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain
| | - Lydia Jiménez-Díaz
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain.
| | - Juan D Navarro-López
- University of Castilla-La Mancha, NeuroPhysiology & Behavior Lab, Biomedical Research Center (CRIB), School of Medicine of Ciudad Real, Spain.
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17
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Wu S, Yang F, Chao S, Wang B, Wang W, Li H, Yu L, He L, Li X, Sun L, Qin S. Altered DNA methylome profiles of blood leukocytes in Chinese patients with mild cognitive impairment and Alzheimer's disease. Front Genet 2023; 14:1175864. [PMID: 37388929 PMCID: PMC10300350 DOI: 10.3389/fgene.2023.1175864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 06/01/2023] [Indexed: 07/01/2023] Open
Abstract
Objective: DNA methylation plays a potential role in the pathogenesis of Alzheimer's disease (AD). However, little is known about the global changes of blood leukocyte DNA methylome profiles from Chinese patients with mild cognitive impairment (MCI) and with AD, or the specific DNA methylation-based signatures associated with MCI and AD. In this study, we sought to dissect the characteristics of blood DNA methylome profiles in MCI- and AD-affected Chinese patients with the aim of identifying novel DNA methylation biomarkers for AD. Methods: In this study, we profiled the DNA methylome of peripheral blood leukocytes from 20 MCI- and 20 AD-affected Chinese patients and 20 cognitively healthy controls (CHCs) with the Infinium Methylation EPIC BeadChip array. Results: We identified significant alterations of the methylome profiles in MCI and AD blood leukocytes. A total of 2,582 and 20,829 CpG sites were significantly and differentially methylated in AD and MCI compared with CHCs (adjusted p < 0.05), respectively. Furthermore, 441 differentially methylated positions (DMPs), aligning to 213 unique genes, were overlapped by the three comparative groups of AD versus CHCs, MCI versus CHCs, and AD versus MCI, of which 6 and 5 DMPs were continuously hypermethylated and hypomethylated in MCI and AD relative to CHCs (adjusted p < 0.05), respectively, such as FLNC cg20186636 and AFAP1 cg06758191. The DMPs with an area under the curve >0.900, such as cg18771300, showed high potency for predicting MCI and AD. In addition, gene ontology and pathway enrichment results showed that these overlapping genes were mainly involved in neurotransmitter transport, GABAergic synaptic transmission, signal release from synapse, neurotransmitter secretion, and the regulation of neurotransmitter levels. Furthermore, tissue expression enrichment analysis revealed a subset of potentially cerebral cortex-enriched genes associated with MCI and AD, including SYT7, SYN3, and KCNT1. Conclusion: This study revealed a number of potential biomarkers for MCI and AD, also highlighted the presence of epigenetically dysregulated gene networks that may engage in the underlying pathological events resulting in the onset of cognitive impairment and AD progression. Collectively, this study provides prospective cues for developing therapeutic strategies to improve cognitive impairment and AD course.
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Affiliation(s)
- Shaochang Wu
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Fan Yang
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Shan Chao
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - Bo Wang
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Department of Obstetrics and Gynecology, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Wuqian Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
| | - He Li
- Department of Geriatrics, Lishui Second People’s Hospital, Lishui, China
| | - Limei Yu
- Key Laboratory of Cell Engineering in Guizhou Province, Affiliated Hospital of Zunyi Medical University, Zunyi, China
| | - Lin He
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Xingwang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
| | - Liya Sun
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
- Research Center for Lin He Academician New Medicine, Institutes for Shanghai Pudong Decoding Life, Shanghai, China
- Shanghai Mental Health Center, Editorial Office, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
| | - Shengying Qin
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, China
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18
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Milicic L, Porter T, Vacher M, Laws SM. Utility of DNA Methylation as a Biomarker in Aging and Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:475-503. [PMID: 37313495 PMCID: PMC10259073 DOI: 10.3233/adr-220109] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 04/23/2023] [Indexed: 06/15/2023] Open
Abstract
Epigenetic mechanisms such as DNA methylation have been implicated in a number of diseases including cancer, heart disease, autoimmune disorders, and neurodegenerative diseases. While it is recognized that DNA methylation is tissue-specific, a limitation for many studies is the ability to sample the tissue of interest, which is why there is a need for a proxy tissue such as blood, that is reflective of the methylation state of the target tissue. In the last decade, DNA methylation has been utilized in the design of epigenetic clocks, which aim to predict an individual's biological age based on an algorithmically defined set of CpGs. A number of studies have found associations between disease and/or disease risk with increased biological age, adding weight to the theory of increased biological age being linked with disease processes. Hence, this review takes a closer look at the utility of DNA methylation as a biomarker in aging and disease, with a particular focus on Alzheimer's disease.
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Affiliation(s)
- Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
| | - Michael Vacher
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- CSIRO Health and Biosecurity, Australian e-Health Research Centre, Floreat, Western Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, Western Australia, Australia
- Collaborative Genomics and Translation Group, Edith Cowan University, Joondalup, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Curtin Medical School, Curtin University, Bentley, Western Australia, Australia
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Martin ER, Wang L. Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects. Alzheimers Res Ther 2023; 15:78. [PMID: 37038196 PMCID: PMC10088180 DOI: 10.1186/s13195-023-01216-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 03/21/2023] [Indexed: 04/12/2023]
Abstract
BACKGROUND Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer's disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis. METHODS We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ42, phosphorylated tau181 (pTau181), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset. RESULTS We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau181 in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker. CONCLUSIONS Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.
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Affiliation(s)
- Wei Zhang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA
| | - Juan I Young
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lissette Gomez
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Michael A Schmidt
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - David Lukacsovich
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA
| | - Achintya Varma
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - X Steven Chen
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Eden R Martin
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Lily Wang
- Division of Biostatistics, Department of Public Health Sciences, University of Miami Miller School of Medicine, 1120 NW 14Th Street, Miami, FL, 33136, USA.
- Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL, 33136, USA.
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20
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Nho K, Risacher SL, Apostolova L, Bice PJ, Brosch J, Deardorff R, Faber K, Farlow MR, Foroud T, Gao S, Rosewood T, Kim JP, Nudelman K, Yu M, Aisen P, Sperling R, Hooli B, Shcherbinin S, Svaldi D, Jack CR, Jagust WJ, Landau S, Vasanthakumar A, Waring JF, Doré V, Laws SM, Masters CL, Porter T, Rowe CC, Villemagne VL, Dumitrescu L, Hohman TJ, Libby JB, Mormino E, Buckley RF, Johnson K, Yang HS, Petersen RC, Ramanan VK, Vemuri P, Cohen AD, Fan KH, Kamboh MI, Lopez OL, Bennett DA, Ali M, Benzinger T, Cruchaga C, Hobbs D, De Jager PL, Fujita M, Jadhav V, Lamb BT, Tsai AP, Castanho I, Mill J, Weiner MW, Saykin AJ. Novel CYP1B1-RMDN2 Alzheimer's disease locus identified by genome-wide association analysis of cerebral tau deposition on PET. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.02.27.23286048. [PMID: 36993271 PMCID: PMC10055458 DOI: 10.1101/2023.02.27.23286048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Determining the genetic architecture of Alzheimer's disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. Here, we performed a genome-wide association study of cortical tau quantified by positron emission tomography in 3,136 participants from 12 independent studies. The CYP1B1-RMDN2 locus was associated with tau deposition. The most significant signal was at rs2113389, which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. rs2113389 was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4 , and Aβ positivity. CYP1B1 expression was upregulated in AD. rs2113389 was associated with higher CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not Aβ. These results may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD.
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21
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Peng X, Zhang W, Cui W, Ding B, Lyu Q, Wang J. ADmeth: A Manually Curated Database for the Differential Methylation in Alzheimer's Disease. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:843-851. [PMID: 35617175 DOI: 10.1109/tcbb.2022.3178087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease. More and more evidence show that DNA methylation is closely related to the pathological mechanism of AD. Many AD-associated differentially methylated genes, regions and CpG sites have been identified in recent researches, which may have great potential in clinical research. However, there is no dedicated database to collect AD-related differential methylation up to now. To provide a reference to researchers, we design a database named ADmeth by manually curating relevant articles, which contains a total of 16,709 AD-related differentially methylated items identified from different brain regions and different cell types in the blood, involving 209 genes, 2,229 regions and 14,271 CpG sites. The ADmeth database provides user-friendly pages to search, submit and download data. We hope that the ADmeth database can facilitate researchers to select candidate AD-associated methylation markers in revealing the pathological mechanism of AD and promote the cell-free DNA based non-invasive diagnosis of AD. The ADmeth database is available at http://www.biobdlab.cn/ADmeth.
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Zhang W, Young JI, Gomez L, Schmidt MA, Lukacsovich D, Varma A, Chen XS, Martin ER, Wang L. Distinct CSF biomarker-associated DNA methylation in Alzheimer's disease and cognitively normal subjects. RESEARCH SQUARE 2023:rs.3.rs-2391364. [PMID: 36865230 PMCID: PMC9980279 DOI: 10.21203/rs.3.rs-2391364/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
Abstract
Background Growing evidence has demonstrated that DNA methylation (DNAm) plays an important role in Alzheimer's disease (AD) and that DNAm differences can be detected in the blood of AD subjects. Most studies have correlated blood DNAm with the clinical diagnosis of AD in living individuals. However, as the pathophysiological process of AD can begin many years before the onset of clinical symptoms, there is often disagreement between neuropathology in the brain and clinical phenotypes. Therefore, blood DNAm associated with AD neuropathology, rather than with clinical data, would provide more relevant information on AD pathogenesis. Methods We performed a comprehensive analysis to identify blood DNAm associated with cerebrospinal fluid (CSF) pathological biomarkers for AD. Our study included matched samples of whole blood DNA methylation, CSF Aβ 42 , phosphorylated tau 181 (pTau 181 ), and total tau (tTau) biomarkers data, measured on the same subjects and at the same clinical visits from a total of 202 subjects (123 CN or cognitively normal, 79 AD) in the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. To validate our findings, we also examined the association between premortem blood DNAm and postmortem brain neuropathology measured on a group of 69 subjects in the London dataset. Results We identified a number of novel associations between blood DNAm and CSF biomarkers, demonstrating that changes in pathological processes in the CSF are reflected in the blood epigenome. Overall, the CSF biomarker-associated DNAm is relatively distinct in CN and AD subjects, highlighting the importance of analyzing omics data measured on cognitively normal subjects (which includes preclinical AD subjects) to identify diagnostic biomarkers, and considering disease stages in the development and testing of AD treatment strategies. Moreover, our analysis revealed biological processes associated with early brain impairment relevant to AD are marked by DNAm in the blood, and blood DNAm at several CpGs in the DMR on HOXA5 gene are associated with pTau 181 in the CSF, as well as tau-pathology and DNAm in the brain, nominating DNAm at this locus as a promising candidate AD biomarker. Conclusions Our study provides a valuable resource for future mechanistic and biomarker studies of DNAm in AD.
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Affiliation(s)
- Wei Zhang
- University of Miami, Miller School of Medicine
| | - Juan I Young
- Dr. John T Macdonald Foundation, University of Miami, Miller School of Medicine
| | | | - Michael A Schmidt
- Dr. John T Macdonald Foundation, University of Miami, Miller School of Medicine
| | | | | | | | - Eden R Martin
- Dr. John T Macdonald Foundation, University of Miami, Miller School of Medicine
| | - Lily Wang
- University of Miami, Miller School of Medicine
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Schäfer Hackenhaar F, Josefsson M, Nordin Adolfsson A, Landfors M, Kauppi K, Porter T, Milicic L, Laws SM, Hultdin M, Adolfsson R, Degerman S, Pudas S. Sixteen-Year Longitudinal Evaluation of Blood-Based DNA Methylation Biomarkers for Early Prediction of Alzheimer's Disease. J Alzheimers Dis 2023; 94:1443-1464. [PMID: 37393498 PMCID: PMC10473121 DOI: 10.3233/jad-230039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/30/2023] [Indexed: 07/03/2023]
Abstract
BACKGROUND DNA methylation (DNAm), an epigenetic mark reflecting both inherited and environmental influences, has shown promise for Alzheimer's disease (AD) prediction. OBJECTIVE Testing long-term predictive ability (>15 years) of existing DNAm-based epigenetic age acceleration (EAA) measures and identifying novel early blood-based DNAm AD-prediction biomarkers. METHODS EAA measures calculated from Illumina EPIC data from blood were tested with linear mixed-effects models (LMMs) in a longitudinal case-control sample (50 late-onset AD cases; 51 matched controls) with prospective data up to 16 years before clinical onset, and post-onset follow-up. Novel DNAm biomarkers were generated with epigenome-wide LMMs, and Sparse Partial Least Squares Discriminant Analysis applied at pre- (10-16 years), and post-AD-onset time-points. RESULTS EAA did not differentiate cases from controls during the follow-up time (p > 0.05). Three new DNA biomarkers showed in-sample predictive ability on average 8 years pre-onset, after adjustment for age, sex, and white blood cell proportions (p-values: 0.022-<0.00001). Our longitudinally-derived panel replicated nominally (p = 0.012) in an external cohort (n = 146 cases, 324 controls). However, its effect size and discriminatory accuracy were limited compared to APOEɛ4-carriership (OR = 1.38 per 1 SD DNAm score increase versus OR = 13.58 for ɛ4-allele carriage; AUCs = 77.2% versus 87.0%). Literature review showed low overlap (n = 4) across 3275 AD-associated CpGs from 8 published studies, and no overlap with our identified CpGs.
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Affiliation(s)
- Fernanda Schäfer Hackenhaar
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
| | - Maria Josefsson
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
- Department of Statistics, USBE, Umeå University, Umeå, Sweden
- Center for Ageing and Demographic Research, Umeå University, Umeå, Sweden
| | | | - Mattias Landfors
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Karolina Kauppi
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Tenielle Porter
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Lidija Milicic
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Simon M. Laws
- Centre for Precision Health, Edith Cowan University, Joondalup, WA, Australia
- Collaborative Genomics and Translation Group, School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
- Curtin Medical School, Curtin University, Bentley, WA, Australia
| | - Magnus Hultdin
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
| | - Rolf Adolfsson
- Department of Clinical Sciences, Umeå University, Umeå, Sweden
| | - Sofie Degerman
- Department of Medical Biosciences, Pathology, Umeå University, Umeå, Sweden
- Department of Clinical Microbiology, Umeå University, Umeå, Sweden
| | - Sara Pudas
- Department of Integrative Medical Biology, Umeå University, Umeå, Sweden
- Umeå Center for Functional Brain Imaging, Umeå University, Umeå, Sweden
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24
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Liu M, Liu R, Wang R, Ba Y, Yu F, Deng Q, Huang H. Lead-induced neurodevelopmental lesion and epigenetic landscape: Implication in neurological disorders. J Appl Toxicol 2022. [PMID: 36433892 DOI: 10.1002/jat.4419] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Revised: 11/20/2022] [Accepted: 11/20/2022] [Indexed: 11/27/2022]
Abstract
Lead (Pb) was implicated in multiple genotoxic, neuroepigenotoxic, and chromosomal-toxic mechanisms and interacted with varying synaptic plasticity pathways, likely underpinning previous reports of links between Pb and cognitive impairment. Epigenetic changes have emerged as a promising biomarker for neurological disorders, including cognitive disorders, Alzheimer's disease (AD), and Parkinson's disease (PD). In the present review, special attention is paid to neural epigenetic features and mechanisms that can alter gene expression patterns upon environmental Pb exposure in rodents, primates, and zebrafish. Epigenetic modifications have also been discussed in population studies and cell experiment. Further, we explore growing evidence of potential linkage between Pb-induced disruption of regulatory pathway and neurodevelopmental and neurological disorders both in vivo and in vitro. These findings uncover how epigenome in neurons facilitates the development and function of the brain in response to Pb insult.
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Affiliation(s)
- Mengchen Liu
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Rundong Liu
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Ruike Wang
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Yue Ba
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Fangfang Yu
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Qihong Deng
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
| | - Hui Huang
- Department of Environmental Health, College of Public Health, Zhengzhou University, Zhengzhou, Henan province, 450001, China
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25
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Chen L, Saykin AJ, Yao B, Zhao F. Multi-task deep autoencoder to predict Alzheimer's disease progression using temporal DNA methylation data in peripheral blood. Comput Struct Biotechnol J 2022; 20:5761-5774. [PMID: 36756173 PMCID: PMC9619306 DOI: 10.1016/j.csbj.2022.10.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/10/2022] [Accepted: 10/11/2022] [Indexed: 11/03/2022] Open
Abstract
Traditional approaches for diagnosing Alzheimer's disease (AD) such as brain imaging and cerebrospinal fluid are invasive and expensive. It is desirable to develop a useful diagnostic tool by exploiting biomarkers obtained from peripheral tissues due to their noninvasive and easily accessible characteristics. However, the capacity of using DNA methylation data in peripheral blood for predicting AD progression is rarely known. It is also challenging to develop an efficient prediction model considering the complex and high-dimensional DNA methylation data in a longitudinal study. Here, we develop two multi-task deep autoencoders, which are based on the convolutional autoencoder and long short-term memory autoencoder to learn the compressed feature representation by jointly minimizing the reconstruction error and maximizing the prediction accuracy. By benchmarking on longitudinal DNA methylation data collected from the peripheral blood in Alzheimer's Disease Neuroimaging Initiative, we demonstrate that the proposed multi-task deep autoencoders outperform state-of-the-art machine learning approaches for both predicting AD progression and reconstructing the temporal DNA methylation profiles. In addition, the proposed multi-task deep autoencoders can predict AD progression accurately using only the historical DNA methylation data and the performance is further improved by including all temporal DNA methylation data. Availability:: https://github.com/lichen-lab/MTAE.
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Affiliation(s)
- Li Chen
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Bing Yao
- Department of Human Genetics, Emory University, Atlanta, GA 30322, United States
| | - Fengdi Zhao
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States
| | - Alzheimer’s Disease Neuroimaging Initiative (ADNI)
- Department of Biostatistics, University of Florida, Gainesville, FL 32603, United States
- Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN 46202, United States
- Department of Human Genetics, Emory University, Atlanta, GA 30322, United States
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26
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Baloni P, Arnold M, Buitrago L, Nho K, Moreno H, Huynh K, Brauner B, Louie G, Kueider-Paisley A, Suhre K, Saykin AJ, Ekroos K, Meikle PJ, Hood L, Price ND, Doraiswamy PM, Funk CC, Hernández AI, Kastenmüller G, Baillie R, Han X, Kaddurah-Daouk R. Multi-Omic analyses characterize the ceramide/sphingomyelin pathway as a therapeutic target in Alzheimer's disease. Commun Biol 2022; 5:1074. [PMID: 36209301 PMCID: PMC9547905 DOI: 10.1038/s42003-022-04011-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 09/20/2022] [Indexed: 11/09/2022] Open
Abstract
Dysregulation of sphingomyelin and ceramide metabolism have been implicated in Alzheimer's disease. Genome-wide and transcriptome-wide association studies have identified various genes and genetic variants in lipid metabolism that are associated with Alzheimer's disease. However, the molecular mechanisms of sphingomyelin and ceramide disruption remain to be determined. We focus on the sphingolipid pathway and carry out multi-omics analyses to identify central and peripheral metabolic changes in Alzheimer's patients, correlating them to imaging features. Our multi-omics approach is based on (a) 2114 human post-mortem brain transcriptomics to identify differentially expressed genes; (b) in silico metabolic flux analysis on context-specific metabolic networks identified differential reaction fluxes; (c) multimodal neuroimaging analysis on 1576 participants to associate genetic variants in sphingomyelin pathway with Alzheimer's disease pathogenesis; (d) plasma metabolomic and lipidomic analysis to identify associations of lipid species with dysregulation in Alzheimer's; and (e) metabolite genome-wide association studies to define receptors within the pathway as a potential drug target. We validate our hypothesis in amyloidogenic APP/PS1 mice and show prolonged exposure to fingolimod alleviated synaptic plasticity and cognitive impairment in mice. Our integrative multi-omics approach identifies potential targets in the sphingomyelin pathway and suggests modulators of S1P metabolism as possible candidates for Alzheimer's disease treatment.
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Affiliation(s)
- Priyanka Baloni
- Institute for Systems Biology, Seattle, WA, USA
- School of Health Sciences, Purdue University, West Lafayette, IN, USA
| | - Matthias Arnold
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
| | - Luna Buitrago
- Department of Neurology/Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Kwangsik Nho
- Indiana Alzheimer's Disease Research Center and Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Herman Moreno
- Department of Neurology/Pharmacology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Kevin Huynh
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Barbara Brauner
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | - Gregory Louie
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
| | - Alexandra Kueider-Paisley
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
| | - Karsten Suhre
- Department of Physiology and Biophysics, Weill Cornell Medicine-Qatar, Education City, PO 24144, Doha, Qatar
| | - Andrew J Saykin
- Indiana Alzheimer's Disease Research Center and Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Kim Ekroos
- Lipidomics Consulting Ltd., Esbo, Finland
| | - Peter J Meikle
- Metabolomics Laboratory, Baker Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, USA
| | | | - P Murali Doraiswamy
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA
| | - Cory C Funk
- Institute for Systems Biology, Seattle, WA, USA
| | - A Iván Hernández
- Department of Pathology, SUNY Downstate Medical Center, Brooklyn, NY, USA
| | - Gabi Kastenmüller
- Institute of Computational Biology, Helmholtz Zentrum München - German Research Center for Environmental Health, Neuherberg, Germany
| | | | - Xianlin Han
- University of Texas Health Science Center at San Antonio, San Antonio, TX, USA.
| | - Rima Kaddurah-Daouk
- Department of Psychiatry and Behavioral Sciences, Duke University School of Medicine, Durham, Durham, NC, USA.
- Department of Medicine, Duke University, Durham, NC, USA.
- Duke Institute of Brain Sciences, Duke University, Durham, NC, USA.
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27
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Migliore L, Coppedè F. Gene-environment interactions in Alzheimer disease: the emerging role of epigenetics. Nat Rev Neurol 2022; 18:643-660. [PMID: 36180553 DOI: 10.1038/s41582-022-00714-w] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
Abstract
With the exception of a few monogenic forms, Alzheimer disease (AD) has a complex aetiology that is likely to involve multiple susceptibility genes and environmental factors. The role of environmental factors is difficult to determine and, until a few years ago, the molecular mechanisms underlying gene-environment (G × E) interactions in AD were largely unknown. Here, we review evidence that has emerged over the past two decades to explain how environmental factors, such as diet, lifestyle, alcohol, smoking and pollutants, might interact with the human genome. In particular, we discuss how various environmental AD risk factors can induce epigenetic modifications of key AD-related genes and pathways and consider how epigenetic mechanisms could contribute to the effects of oxidative stress on AD onset. Studies on early-life exposures are helping to uncover critical time windows of sensitivity to epigenetic influences from environmental factors, thereby laying the foundations for future primary preventative approaches. We conclude that epigenetic modifications need to be considered when assessing G × E interactions in AD.
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Affiliation(s)
- Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy. .,Department of Laboratory Medicine, Pisa University Hospital, Pisa, Italy.
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy
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28
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Shireby G, Dempster EL, Policicchio S, Smith RG, Pishva E, Chioza B, Davies JP, Burrage J, Lunnon K, Seiler Vellame D, Love S, Thomas A, Brookes K, Morgan K, Francis P, Hannon E, Mill J. DNA methylation signatures of Alzheimer's disease neuropathology in the cortex are primarily driven by variation in non-neuronal cell-types. Nat Commun 2022; 13:5620. [PMID: 36153390 PMCID: PMC9509387 DOI: 10.1038/s41467-022-33394-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disease characterized by the progressive accumulation of amyloid-beta and neurofibrillary tangles of tau in the neocortex. We profiled DNA methylation in two regions of the cortex from 631 donors, performing an epigenome-wide association study of multiple measures of AD neuropathology. We meta-analyzed our results with those from previous studies of DNA methylation in AD cortex (total n = 2013 donors), identifying 334 cortical differentially methylated positions (DMPs) associated with AD pathology including methylomic variation at loci not previously implicated in dementia. We subsequently profiled DNA methylation in NeuN+ (neuronal-enriched), SOX10+ (oligodendrocyte-enriched) and NeuN-/SOX10- (microglia- and astrocyte-enriched) nuclei, finding that the majority of DMPs identified in 'bulk' cortex tissue reflect DNA methylation differences occurring in non-neuronal cells. Our study highlights the power of utilizing multiple measures of neuropathology to identify epigenetic signatures of AD and the importance of characterizing disease-associated variation in purified cell-types.
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Affiliation(s)
- Gemma Shireby
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Emma L Dempster
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Stefania Policicchio
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Rebecca G Smith
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Barry Chioza
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan P Davies
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Joe Burrage
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Katie Lunnon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Dorothea Seiler Vellame
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Seth Love
- Dementia Research Group, University of Bristol Medical School (Translational Health Sciences), Bristol, UK
| | - Alan Thomas
- Translational and Clinical Research Institute, Newcastle University, Newcastle Upon Tyne, UK
| | - Keeley Brookes
- Biosciences, School of Science & Technology, Nottingham Trent University, Nottingham, UK
| | - Kevin Morgan
- Human Genetics, School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Paul Francis
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
- Wolfson Centre for Age-Related Diseases, King's College London, London, UK
| | - Eilis Hannon
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Jonathan Mill
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, University of Exeter, Exeter, UK.
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C. Silva T, Zhang W, Young JI, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Distinct sex-specific DNA methylation differences in Alzheimer's disease. Alzheimers Res Ther 2022; 14:133. [PMID: 36109771 PMCID: PMC9479371 DOI: 10.1186/s13195-022-01070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/30/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Sex is increasingly recognized as a significant factor contributing to the biological and clinical heterogeneity in AD. There is also growing evidence for the prominent role of DNA methylation (DNAm) in Alzheimer's disease (AD). METHODS We studied sex-specific DNA methylation differences in the blood samples of AD subjects compared to cognitively normal subjects, by performing sex-specific meta-analyses of two large blood-based epigenome-wide association studies (ADNI and AIBL), which included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males). Within each dataset, we used two complementary analytical strategies, a sex-stratified analysis that examined methylation to AD associations in male and female samples separately, and a methylation-by-sex interaction analysis that compared the magnitude of these associations between different sexes. After adjusting for age, estimated immune cell type proportions, batch effects, and correcting for inflation, the inverse-variance fixed-effects meta-analysis model was used to identify the most consistent DNAm differences across datasets. In addition, we also evaluated the performance of the sex-specific methylation-based risk prediction models for AD diagnosis using an independent external dataset. RESULTS In the sex-stratified analysis, we identified 2 CpGs, mapped to the PRRC2A and RPS8 genes, significantly associated with AD in females at a 5% false discovery rate, and an additional 25 significant CpGs (21 in females, 4 in males) at P-value < 1×10-5. In methylation-by-sex interaction analysis, we identified 5 significant CpGs at P-value < 10-5. Out-of-sample validations using the AddNeuroMed dataset showed in females, the best logistic prediction model included age, estimated immune cell-type proportions, and methylation risk scores (MRS) computed from 9 of the 23 CpGs identified in AD vs. CN analysis that are also available in AddNeuroMed dataset (AUC = 0.74, 95% CI: 0.65-0.83). In males, the best logistic prediction model included only age and MRS computed from 2 of the 5 CpGs identified in methylation-by-sex interaction analysis that are also available in the AddNeuroMed dataset (AUC = 0.70, 95% CI: 0.56-0.82). CONCLUSIONS Overall, our results show that the DNA methylation differences in AD are largely distinct between males and females. Our best-performing sex-specific methylation-based prediction model in females performed better than that for males and additionally included estimated cell-type proportions. The significant discriminatory classification of AD samples with our methylation-based prediction models demonstrates that sex-specific DNA methylation could be a predictive biomarker for AD. As sex is a strong factor underlying phenotypic variability in AD, the results of our study are particularly relevant for a better understanding of the epigenetic architecture that underlie AD and for promoting precision medicine in AD.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Wei Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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C. Silva T, Young JI, Zhang L, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Cross-tissue analysis of blood and brain epigenome-wide association studies in Alzheimer's disease. Nat Commun 2022; 13:4852. [PMID: 35982059 PMCID: PMC9388493 DOI: 10.1038/s41467-022-32475-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 08/01/2022] [Indexed: 01/17/2023] Open
Abstract
To better understand DNA methylation in Alzheimer's disease (AD) from both mechanistic and biomarker perspectives, we performed an epigenome-wide meta-analysis of blood DNA methylation in two large independent blood-based studies in AD, the ADNI and AIBL studies, and identified 5 CpGs, mapped to the SPIDR, CDH6 genes, and intergenic regions, that are significantly associated with AD diagnosis. A cross-tissue analysis that combined these blood DNA methylation datasets with four brain methylation datasets prioritized 97 CpGs and 10 genomic regions that are significantly associated with both AD neuropathology and AD diagnosis. An out-of-sample validation using the AddNeuroMed dataset showed the best performing logistic regression model includes age, sex, immune cell type proportions, and methylation risk score based on prioritized CpGs in cross-tissue analysis (AUC = 0.696, 95% CI: 0.616 - 0.770, P-value = 2.78 × 10-5). Our study offers new insights into epigenetics in AD and provides a valuable resource for future AD biomarker discovery.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lanyu Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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31
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Villa C, Stoccoro A. Epigenetic Peripheral Biomarkers for Early Diagnosis of Alzheimer’s Disease. Genes (Basel) 2022; 13:genes13081308. [PMID: 35893045 PMCID: PMC9332601 DOI: 10.3390/genes13081308] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Revised: 07/20/2022] [Accepted: 07/20/2022] [Indexed: 11/16/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disorder and represents the leading cause of cognitive impairment and dementia in older individuals throughout the world. The main hallmarks of AD include brain atrophy, extracellular deposition of insoluble amyloid-β (Aβ) plaques, and the intracellular aggregation of protein tau in neurofibrillary tangles. These pathological modifications start many years prior to clinical manifestations of disease and the spectrum of AD progresses along a continuum from preclinical to clinical phases. Therefore, identifying specific biomarkers for detecting AD at early stages greatly improves clinical management. However, stable and non-invasive biomarkers are not currently available for the early detection of the disease. In the search for more reliable biomarkers, epigenetic mechanisms, able to mediate the interaction between the genome and the environment, are emerging as important players in AD pathogenesis. Herein, we discuss altered epigenetic signatures in blood as potential peripheral biomarkers for the early detection of AD in order to help diagnosis and improve therapy.
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Affiliation(s)
- Chiara Villa
- School of Medicine and Surgery, University of Milano-Bicocca, 20900 Monza, Italy
- Correspondence: ; Tel.: +39-02-6448-8138
| | - Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, Medical School, University of Pisa, 56126 Pisa, Italy;
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32
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Stoccoro A, Baldacci F, Ceravolo R, Giampietri L, Tognoni G, Siciliano G, Migliore L, Coppedè F. Increase in Mitochondrial D-Loop Region Methylation Levels in Mild Cognitive Impairment Individuals. Int J Mol Sci 2022; 23:ijms23105393. [PMID: 35628202 PMCID: PMC9142993 DOI: 10.3390/ijms23105393] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 05/04/2022] [Accepted: 05/10/2022] [Indexed: 12/25/2022] Open
Abstract
Methylation levels of the mitochondrial displacement loop (D-loop) region have been reported to be altered in the brain and blood of Alzheimer’s disease (AD) patients. Moreover, a dynamic D-loop methylation pattern was observed in the brain of transgenic AD mice along with disease progression. However, investigations on the blood cells of AD patients in the prodromal phases of the disease have not been performed so far. The aim of this study was to analyze D-loop methylation levels by means of the MS-HRM technique in the peripheral blood cells of 14 mild cognitive impairment (MCI) patients, 18 early stage AD patients, 70 advanced stage AD patients, and 105 healthy control subjects. We found higher D-loop methylation levels in MCI patients than in control subjects and AD patients. Moreover, higher D-loop methylation levels were observed in control subjects than in AD patients in advanced stages of the disease, but not in those at early stages. The present pilot study shows that peripheral D-loop methylation levels differ in patients at different stages of AD pathology, suggesting that further studies deserve to be performed in order to validate the usefulness of D-loop methylation analysis as a peripheral biomarker for the early detection of AD.
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Affiliation(s)
- Andrea Stoccoro
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy;
- Correspondence: (A.S.); (F.C.); Tel.: +39-0502-218549 (A.S.); +39-0502-218544 (F.C.)
| | - Filippo Baldacci
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (R.C.); (L.G.); (G.T.); (G.S.)
| | - Roberto Ceravolo
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (R.C.); (L.G.); (G.T.); (G.S.)
| | - Linda Giampietri
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (R.C.); (L.G.); (G.T.); (G.S.)
| | - Gloria Tognoni
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (R.C.); (L.G.); (G.T.); (G.S.)
| | - Gabriele Siciliano
- Department of Clinical and Experimental Medicine, University of Pisa, 56126 Pisa, Italy; (F.B.); (R.C.); (L.G.); (G.T.); (G.S.)
| | - Lucia Migliore
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy;
| | - Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126 Pisa, Italy;
- Correspondence: (A.S.); (F.C.); Tel.: +39-0502-218549 (A.S.); +39-0502-218544 (F.C.)
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Weber CJ, Carrillo MC, Jagust W, Jack CR, Shaw LM, Trojanowski JQ, Saykin AJ, Beckett LA, Sur C, Rao NP, Mendez PC, Black SE, Li K, Iwatsubo T, Chang C, Sosa AL, Rowe CC, Perrin RJ, Morris JC, Healan AM, Hall SE, Weiner MW. The Worldwide Alzheimer's Disease Neuroimaging Initiative: ADNI-3 updates and global perspectives. ALZHEIMER'S & DEMENTIA (NEW YORK, N. Y.) 2021; 7:e12226. [PMID: 35005206 PMCID: PMC8719344 DOI: 10.1002/trc2.12226] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/05/2021] [Indexed: 11/06/2022]
Abstract
The Worldwide Alzheimer's Disease Neuroimaging Initiative (WW-ADNI) is a collaborative effort to investigate imaging and biofluid markers that can inform Alzheimer's disease treatment trials. It is a public-private partnership that spans North America, Argentina, Australia, Canada, China, Japan, Korea, Mexico, and Taiwan. In 2004, ADNI researchers began a naturalistic, longitudinal study that continues today around the globe. Through several successive phases (ADNI-1, ADNI-GO, ADNI-2, and ADNI-3), the study has fueled amyloid and tau phenotyping and refined neuroimaging methodologies. WW-ADNI researchers have successfully standardized analyses and openly share data without embargo, providing a rich data set for other investigators. On August 26, 2020, the Alzheimer's Association convened WW-ADNI researchers who shared updates from ADNI-3 and their vision for ADNI-4.
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Affiliation(s)
| | | | - William Jagust
- School of Public Health and Helen Wills Neuroscience InstituteUniversity of California BerkeleyBerkeleyCaliforniaUSA
| | | | - Leslie M. Shaw
- Department of Pathology and Laboratory MedicinePerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - John Q. Trojanowski
- Department of Pathology and Laboratory MedicinePerelman School of MedicineInstitute on AgingPerelman School of MedicineAlzheimer's Disease Core Center, Perelman School of MedicineUdall Parkinson's Research CenterPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPennsylvaniaUSA
| | - Andrew J. Saykin
- Department of Radiology and Imaging Sciences and the Indiana Alzheimer's Disease Research CenterDepartment of Medical and Molecular GeneticsIndiana University School of MedicineIndianapolisIndianaUSA
| | - Laurel A. Beckett
- Division of BiostatisticsDepartment of Public Health SciencesUniversity of CaliforniaDavisCaliforniaUSA
| | - Cyrille Sur
- Merck Research LaboratoriesMerckKenilworthNew JerseyUSA
| | - Naren P. Rao
- Department of PsychiatryNational Institute of Mental Health and NeurosciencesBengaluruKarnatakaIndia
| | | | - Sandra E. Black
- Department of Medicine (Neurology)Hurvitz Brain Sciences ProgramCanadian Partnership for Stroke Recovery, and LC Campbell Cognitive Neurology Research UnitHurvitz Brain Sciences Research ProgramSunnybrook Research InstituteSunnybrook Health Sciences CentreUniversity of TorontoTorontoCanada
| | - Kuncheng Li
- Department of RadiologyXuanwu Hospital of Capital Medical UniversityBeijingChina
| | - Takeshi Iwatsubo
- Department of NeuropathologyGraduate School of MedicineThe University of TokyoTokyoJapan
| | - Chiung‐Chih Chang
- Department of General Neurology and Institute for Translational Research in BiomedicineKaohsiung Chang Gung Memorial HospitalChang Gung University College of MedicineKaohsiungTaiwan
| | - Ana Luisa Sosa
- National Institute of Neurology and Neurosurgery of MexicoMexico CityMexico
| | - Christopher C. Rowe
- Department of Molecular Imaging and TherapyAustin Health and Florey Department of Neuroscience and Mental HealthUniversity of MelbourneMelbourneVictoriaAustralia
| | - Richard J. Perrin
- Charles F. and Joanne Knight Alzheimer Disease Research CenterDepartment of Pathology and ImmunologyDepartment of NeurologyWashington University School of MedicineSaint LouisMissouriUSA
| | - John C. Morris
- Charles F. and Joanne Knight Alzheimer Disease Research CenterDepartment of NeurologyWashington University School of MedicineSaint LouisMissouriUSA
| | | | | | - Michael W. Weiner
- Department of Veterans Affairs Medical CenterCenter for Imaging of Neurodegenerative DiseasesDepartment of RadiologyDepartment of MedicineDepartment of PsychiatryDepartment of NeurologyUniversity of CaliforniaSan FranciscoCaliforniaUSA
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Song W, Wang W, Liu Z, Cai W, Yu S, Zhao M, Lin GN. A Comprehensive Evaluation of Cross-Omics Blood-Based Biomarkers for Neuropsychiatric Disorders. J Pers Med 2021; 11:1247. [PMID: 34945719 PMCID: PMC8703948 DOI: 10.3390/jpm11121247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/22/2021] [Accepted: 11/23/2021] [Indexed: 12/03/2022] Open
Abstract
The identification of peripheral multi-omics biomarkers of brain disorders has long been hindered by insufficient sample size and confounder influence. This study aimed to compare biomarker potential for different molecules and diseases. We leveraged summary statistics of five blood quantitative trait loci studies (N = 1980 to 22,609) and genome-wide association studies (N = 9725 to 500,199) from 14 different brain disorders, such as Schizophrenia (SCZ) and Alzheimer's Disease (AD). We applied summary-based and two-sample Mendelian Randomization to estimate the associations between blood molecules and brain disorders. We identified 524 RNA, 807 methylation sites, 29 proteins, seven cytokines, and 22 metabolites having a significant association with at least one of 14 brain disorders. Simulation analyses indicated that a cross-omics combination of biomarkers had better performance for most disorders, and different disorders could associate with different omics. We identified an 11-methylation-site model for SCZ diagnosis (Area Under Curve, AUC = 0.74) by analyzing selected candidate markers in published datasets (total N = 6098). Moreover, we constructed an 18-methylation-sites model that could predict the prognosis of elders with mild cognitive impairment (hazard ratio = 2.32). We provided an association landscape between blood cross-omic biomarkers and 14 brain disorders as well as a suggestion guide for future clinical discovery and application.
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Affiliation(s)
- Weichen Song
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Weidi Wang
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Zhe Liu
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Wenxiang Cai
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
| | - Shunying Yu
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, China; (S.Y.); (M.Z.)
| | - Min Zhao
- Shanghai Key Laboratory of Psychotic Disorders, Shanghai 200030, China; (S.Y.); (M.Z.)
| | - Guan Ning Lin
- School of Biomedical Engineering, Shanghai Jiao Tong University, Shanghai 200030, China; (W.S.); (W.W.); (Z.L.); (W.C.)
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35
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Li QS, Vasanthakumar A, Davis JW, Idler KB, Nho K, Waring JF, Saykin AJ. Association of peripheral blood DNA methylation level with Alzheimer's disease progression. Clin Epigenetics 2021; 13:191. [PMID: 34654479 PMCID: PMC8518178 DOI: 10.1186/s13148-021-01179-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Identifying biomarkers associated with Alzheimer’s disease (AD) progression may enable patient enrichment and improve clinical trial designs. Epigenome-wide association studies have revealed correlations between DNA methylation at cytosine-phosphate-guanine (CpG) sites and AD pathology and diagnosis. Here, we report relationships between peripheral blood DNA methylation profiles measured using Infinium® MethylationEPIC BeadChip and AD progression in participants from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) cohort. Results The rate of cognitive decline from initial DNA sampling visit to subsequent visits was estimated by the slopes of the modified Preclinical Alzheimer Cognitive Composite (mPACC; mPACCdigit and mPACCtrailsB) and Clinical Dementia Rating Scale Sum of Boxes (CDR-SB) plots using robust linear regression in cognitively normal (CN) participants and patients with mild cognitive impairment (MCI), respectively. In addition, diagnosis conversion status was assessed using a dichotomized endpoint. Two CpG sites were significantly associated with the slope of mPACC in CN participants (P < 5.79 × 10−8 [Bonferroni correction threshold]); cg00386386 was associated with the slope of mPACCdigit, and cg09422696 annotated to RP11-661A12.5 was associated with the slope of CDR-SB. No significant CpG sites associated with diagnosis conversion status were identified. Genes involved in cognition and learning were enriched. A total of 19, 13, and 5 differentially methylated regions (DMRs) associated with the slopes of mPACCtrailsB, mPACCdigit, and CDR-SB, respectively, were identified by both comb-p and DMRcate algorithms; these included DMRs annotated to HOXA4. Furthermore, 5 and 19 DMRs were associated with conversion status in CN and MCI participants, respectively. The most significant DMR was annotated to the AD-associated gene PM20D1 (chr1: 205,818,956 to 205,820,014 [13 probes], Sidak-corrected P = 7.74 × 10−24), which was associated with both the slope of CDR-SB and the MCI conversion status. Conclusion Candidate CpG sites and regions in peripheral blood were identified as associated with the rate of cognitive decline in participants in the ADNI cohort. While we did not identify a single CpG site with sufficient clinical utility to be used by itself due to the observed effect size, a biosignature composed of DNA methylation changes may have utility as a prognostic biomarker for AD progression. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01179-2.
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Affiliation(s)
- Qingqin S Li
- Neuroscience, Janssen Research and Development, LLC, 1125 Trenton-Harbourton Road, Titusville, NJ, 08560, USA.
| | | | - Justin W Davis
- Genomics Research Center, AbbVie, North Chicago, IL, USA
| | | | - Kwangsik Nho
- Indiana Alzheimer's Disease Research Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
| | | | - Andrew J Saykin
- Indiana Alzheimer's Disease Research Center, Department of Radiology and Imaging Sciences, Indiana University School of Medicine, Indianapolis, IN, USA
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36
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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37
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Xu S, Zhang X, Liu C, Liu Q, Chai H, Luo Y, Li S. Role of Mitochondria in Neurodegenerative Diseases: From an Epigenetic Perspective. Front Cell Dev Biol 2021; 9:688789. [PMID: 34513831 PMCID: PMC8429841 DOI: 10.3389/fcell.2021.688789] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/10/2021] [Indexed: 12/18/2022] Open
Abstract
Mitochondria, the centers of energy metabolism, have been shown to participate in epigenetic regulation of neurodegenerative diseases. Epigenetic modification of nuclear genes encoding mitochondrial proteins has an impact on mitochondria homeostasis, including mitochondrial biogenesis, and quality, which plays role in the pathogenesis of neurodegenerative diseases like Alzheimer’s disease, Parkinson’s disease, Huntington’s disease, and amyotrophic lateral sclerosis. On the other hand, intermediate metabolites regulated by mitochondria such as acetyl-CoA and NAD+, in turn, may regulate nuclear epigenome as the substrate for acetylation and a cofactor of deacetylation, respectively. Thus, mitochondria are involved in epigenetic regulation through bidirectional communication between mitochondria and nuclear, which may provide a new strategy for neurodegenerative diseases treatment. In addition, emerging evidence has suggested that the abnormal modification of mitochondria DNA contributes to disease development through mitochondria dysfunction. In this review, we provide an overview of how mitochondria are involved in epigenetic regulation and discuss the mechanisms of mitochondria in regulation of neurodegenerative diseases from epigenetic perspective.
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Affiliation(s)
- Sutong Xu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Zhang
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Chenming Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Qiulu Liu
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Huazhen Chai
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yuping Luo
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Siguang Li
- Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopedic Department of Tongji Hospital, Tongji University School of Medicine, Shanghai, China.,Stem Cell Translational Research Center, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
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38
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Xu M, Zhu J, Liu XD, Luo MY, Xu NJ. Roles of physical exercise in neurodegeneration: reversal of epigenetic clock. Transl Neurodegener 2021; 10:30. [PMID: 34389067 PMCID: PMC8361623 DOI: 10.1186/s40035-021-00254-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/29/2021] [Indexed: 12/17/2022] Open
Abstract
The epigenetic clock is defined by the DNA methylation (DNAm) level and has been extensively applied to distinguish biological age from chronological age. Aging-related neurodegeneration is associated with epigenetic alteration, which determines the status of diseases. In recent years, extensive research has shown that physical exercise (PE) can affect the DNAm level, implying a reversal of the epigenetic clock in neurodegeneration. PE also regulates brain plasticity, neuroinflammation, and molecular signaling cascades associated with epigenetics. This review summarizes the effects of PE on neurodegenerative diseases via both general and disease-specific DNAm mechanisms, and discusses epigenetic modifications that alleviate the pathological symptoms of these diseases. This may lead to probing of the underpinnings of neurodegenerative disorders and provide valuable therapeutic references for cognitive and motor dysfunction.
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Affiliation(s)
- Miao Xu
- Department of Anatomy, Histology and Embryology, Kunming Medical University, Kunming, 650500, China.,Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - JiaYi Zhu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Xian-Dong Liu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.,Department of Neurology and Institute of Neurology, Rui Jin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Ming-Ying Luo
- Department of Anatomy, Histology and Embryology, Kunming Medical University, Kunming, 650500, China
| | - Nan-Jie Xu
- Collaborative Innovation Center for Brain Science, Department of Anatomy and Physiology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Shanghai Key Laboratory of Reproductive Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
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39
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Coppedè F. One-carbon epigenetics and redox biology of neurodegeneration. Free Radic Biol Med 2021; 170:19-33. [PMID: 33307166 DOI: 10.1016/j.freeradbiomed.2020.12.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 12/12/2022]
Abstract
One-carbon metabolism provides the methyl groups for both DNA and histone tail methylation reactions, two of the main epigenetic processes that tightly regulate the chromatin structure and gene expression levels. Several enzymes involved in one-carbon metabolism, as well as several epigenetic enzymes, are regulated by intracellular metabolites and redox cofactors, but their expression levels are in turn regulated by epigenetic modifications, in such a way that metabolism and gene expression reciprocally regulate each other to maintain homeostasis and regulate cell growth, survival, differentiation and response to environmental stimuli. Increasing evidence highlights the contribution of impaired one-carbon metabolism and epigenetic modifications in neurodegeneration. This article provides an overview of DNA and histone tail methylation changes in major neurodegenerative disorders, namely Alzheimer's disease, Parkinson's disease and amyotrophic lateral sclerosis, discussing the contribution of oxidative stress and impaired one-carbon and redox metabolism to their onset and progression.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Via Roma 55, 56126, Pisa, Italy.
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40
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Coppedè F. Epigenetic regulation in Alzheimer's disease: is it a potential therapeutic target? Expert Opin Ther Targets 2021; 25:283-298. [PMID: 33843425 DOI: 10.1080/14728222.2021.1916469] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Introduction: Alzheimer's disease (AD) is the most common neurodegenerative disorder and the primary form of dementia in the elderly. Changes in DNA methylation and post-translational modifications of histone tails are increasingly observed in AD tissues, and likely contribute to disease onset and progression. The reversibility of these epigenetic marks offers the potential for therapeutic interventions.Areas covered: After a concise and updated overview of DNA methylation and post-translational modifications of histone tails in AD tissues, this review provides an overview of the animal and cell culture studies investigating the potential of targeting these modifications to attenuate AD-like features. PubMed was searched for relevant literature between 2003 and 2021.Expert opinion: Methyl donor compounds and drugs acting on histone tail modifications attenuated the AD-like features and improved cognition in several transgenic AD mice; however, there are concerns about safety and tolerability for long-term treatment in humans. The challenges will be to take advantage of recent epigenome-wide investigations to identify the principal targets for future interventions, and to design novel, selective and safer agents. Natural compounds exerting epigenetic properties could represent a promising opportunity to delay disease onset in middle-aged individuals at increased AD risk.
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Affiliation(s)
- Fabio Coppedè
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa, Pisa, Italy.,Interdepartmental Research Center Nutrafood "Nutraceuticals and Food for Health", University of Pisa, Pisa, Italy
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41
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Association between methylation of BIN1 promoter in peripheral blood and preclinical Alzheimer's disease. Transl Psychiatry 2021; 11:89. [PMID: 33531457 PMCID: PMC7854626 DOI: 10.1038/s41398-021-01218-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 12/28/2020] [Accepted: 01/12/2021] [Indexed: 11/08/2022] Open
Abstract
The bridging integrator 1 (BIN1) gene is the second most important susceptibility gene for late-onset Alzheimer's disease (LOAD) after apolipoprotein E (APOE) gene. To explore whether the BIN1 methylation in peripheral blood changed in the early stage of LOAD, we included 814 participants (484 cognitively normal participants [CN] and 330 participants with subjective cognitive decline [SCD]) from the Chinese Alzheimer's Biomarker and LifestylE (CABLE) database. Then we tested associations of methylation of BIN1 promoter in peripheral blood with the susceptibility for preclinical AD or early changes of cerebrospinal fluid (CSF) AD-related biomarkers. Results showed that SCD participants with significant AD biological characteristics had lower methylation levels of BIN1 promoter, even after correcting for covariates. Hypomethylation of BIN1 promoter were associated with decreased CSF Aβ42 (p = 0.0008), as well as increased p-tau/Aβ42 (p = 0.0001) and t-tau/Aβ42 (p < 0.0001) in total participants. Subgroup analysis showed that the above associations only remained in the SCD subgroup. In addition, hypomethylation of BIN1 promoter was also accompanied by increased CSF p-tau (p = 0.0028) and t-tau (p = 0.0130) in the SCD subgroup, which was independent of CSF Aβ42. Finally, above associations were still significant after correcting single nucleotide polymorphic sites (SNPs) and interaction of APOE ɛ4 status. Our study is the first to find a robust association between hypomethylation of BIN1 promoter in peripheral blood and preclinical AD. This provides new evidence for the involvement of BIN1 in AD, and may contribute to the discovery of new therapeutic targets for AD.
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Philibert R, Mills JA, Long JD, Salisbury SE, Comellas A, Gerke A, Dawes K, Vander Weg M, Hoffman EA. The Reversion of cg05575921 Methylation in Smoking Cessation: A Potential Tool for Incentivizing Healthy Aging. Genes (Basel) 2020; 11:E1415. [PMID: 33260961 PMCID: PMC7760261 DOI: 10.3390/genes11121415] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Revised: 11/18/2020] [Accepted: 11/24/2020] [Indexed: 02/06/2023] Open
Abstract
Smoking is the largest preventable cause of mortality and the largest environmental driver of epigenetic aging. Contingency management-based strategies can be used to treat smoking but require objective methods of verifying quitting status. Prior studies have suggested that cg05575921 methylation reverts as a function of smoking cessation, but that it can be used to verify the success of smoking cessation has not been unequivocally demonstrated. To test whether methylation can be used to verify cessation, we determined monthly cg05575921 levels in a group of 67 self-reported smokers undergoing biochemically monitored contingency management-based smoking cessation therapy, as part of a lung imaging protocol. A total of 20 subjects in this protocol completed three months of cotinine verified smoking cessation. In these 20 quitters, the reversion of cg05575921 methylation was dependent on their initial smoking intensity, with methylation levels in the heaviest smokers reverting to an average of 0.12% per day over the 3-month treatment period. In addition, we found suggestive evidence that some individuals may have embellished their smoking history to gain entry to the study. Given the prominent effect of smoking on longevity, we conclude that DNA methylation may be a useful tool for guiding and incentivizing contingency management-based approaches for smoking cessation.
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Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
- Behavioral Diagnostics LLC, Coralville, IA 52241, USA
| | - James A. Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
| | - Jeffrey D. Long
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
- Department of Biostatistics, University of Iowa, Iowa City, IA 52242, USA
| | - Sue Ellen Salisbury
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA; (S.E.S.); (E.A.H.)
| | - Alejandro Comellas
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.C.); (A.G.); (M.V.W.)
| | - Alicia Gerke
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.C.); (A.G.); (M.V.W.)
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA 52242, USA; (J.A.M.); (J.D.L.); (K.D.)
- Molecular Medicine Program, University of Iowa, Iowa City, IA 52242, USA
| | - Mark Vander Weg
- Department of Internal Medicine, University of Iowa, Iowa City, IA 52242, USA; (A.C.); (A.G.); (M.V.W.)
- Center for Access & Delivery Research and Evaluation, Iowa City VA Health Care System, Iowa City, IA 52242, USA
| | - Eric A. Hoffman
- Department of Radiology, University of Iowa, Iowa City, IA 52242, USA; (S.E.S.); (E.A.H.)
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Philibert R, Long JD, Mills JA, Beach SRH, Gibbons FX, Gerrard M, Simons R, Pinho PB, Ingle D, Dawes K, Dogan T, Dogan M. A simple, rapid, interpretable, actionable and implementable digital PCR based mortality index. Epigenetics 2020; 16:1135-1149. [PMID: 33138668 DOI: 10.1080/15592294.2020.1841874] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Mortality assessments are conducted for both civil and commercial purposes. Recent advances in epigenetics have resulted in DNA methylation tools to assess risk and aid in this task. However, widely available array-based algorithms are not readily translatable into clinical tools and do not provide a good foundation for clinical recommendations. Further, recent work shows evidence of heritability and possible racial bias in these indices. Using a publicly available array data set, the Framingham Heart Study (FHS), we develop and test a five-locus mortality-risk algorithm using only previously validated methylation biomarkers that have been shown to be free of racial bias, and that provide specific assessments of smoking, alcohol consumption, diabetes and heart disease. We show that a model using age, sex and methylation measurements at these five loci outperforms the 513 probe Levine index and approximates the predictive power of the 1030 probe GrimAge index. We then show each of the five loci in our algorithm can be assessed using a more powerful, reference-free digital PCR approach, further demonstrating that it is readily clinically translatable. Finally, we show the loci do not reflect ethnically specific variation. We conclude that this algorithm is a simple, yet powerful tool for assessing mortality risk. We further suggest that the output from this or similarly derived algorithms using either array or digital PCR can be used to provide powerful feedback to patients, guide recommendations for additional medical assessments, and help monitor the effect of public health prevention interventions.
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Affiliation(s)
- Robert Philibert
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.,Behavioral Diagnostics LLC, Coralville, IA, USA
| | - Jeffrey D Long
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.,Department of Biostatistics, University of Iowa, Iowa City, IA, USA
| | - James A Mills
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - S R H Beach
- Center for Family Research, University of Georgia, Athens, GA USA
| | | | - Meg Gerrard
- Department of Psychology, University of Connecticut, Storrs, CT, USA
| | - Ron Simons
- Department of Sociology, University of Georgia, Athens, GA, USA
| | | | - Douglas Ingle
- Association of Home Office Underwriters, Washington, DC, USA
| | - Kelsey Dawes
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA
| | - Timur Dogan
- Behavioral Diagnostics LLC, Coralville, IA, USA.,Cardio Diagnostics Inc, Coralville, IA, USA
| | - Meeshanthini Dogan
- Department of Psychiatry, University of Iowa, Iowa City, IA, USA.,Behavioral Diagnostics LLC, Coralville, IA, USA.,Cardio Diagnostics Inc, Coralville, IA, USA
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44
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Exploring Beyond the DNA Sequence: A Review of Epigenomic Studies of DNA and Histone Modifications in Dementia. CURRENT GENETIC MEDICINE REPORTS 2020. [DOI: 10.1007/s40142-020-00190-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Abstract
Purpose of Review
Although genome-scale studies have identified many genetic variants associated with dementia, these do not account for all of disease incidence and so recently attention has turned to studying mechanisms of genome regulation. Epigenetic processes such as modifications to the DNA and histones alter transcriptional activity and have been hypothesized to be involved in the etiology of dementia. Here, we review the growing body of literature on dementia epigenomics, with a focus on novel discoveries, current limitations, and future directions for the field.
Recent Findings
It is through advances in genomic technology that large-scale quantification of epigenetic modifications is now possible in dementia. Most of the literature in the field has primarily focussed on exploring DNA modifications, namely DNA methylation, in postmortem brain samples from individuals with Alzheimer’s disease. However, recent studies have now begun to explore other epigenetic marks, such as histone modifications, investigating these signatures in both the brain and blood, and in a range of other dementias.
Summary
There is still a demand for more epigenomic studies to be conducted in the dementia field, particularly those assessing chromatin dynamics and a broader range of histone modifications. The field faces limitations in sample accessibility with many studies lacking power. Furthermore, the frequent use of heterogeneous bulk tissue containing multiple cell types further hinders data interpretation. Looking to the future, multi-omic studies, integrating many different epigenetic marks, with matched genetic, transcriptomic, and proteomic data, will be vital, particularly when undertaken in isolated cell populations, or ideally at the level of the single cell. Ultimately these studies could identify novel dysfunctional pathways and biomarkers for disease, which could lead to new therapeutic avenues.
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Imbimbo BP, Ippati S, Watling M. Should drug discovery scientists still embrace the amyloid hypothesis for Alzheimer's disease or should they be looking elsewhere? Expert Opin Drug Discov 2020; 15:1241-1251. [PMID: 32686970 DOI: 10.1080/17460441.2020.1793755] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Alzheimer's Disease (AD) represents a large and growing challenge to patients, carers and healthcare systems, yet extensive efforts to develop therapeutics to modify its course have been met with repeated failure in recent decades. Although the evident presence of accumulated β-amyloid (Aβ) in AD brains has singled it out as an obvious therapeutic target, the effective reduction of plaque load or soluble Aβ by numerous drug candidates has not produced commensurate clinical benefits - calling into question the Aβ cascade hypothesis of AD. A similar path is now unfolding in the pursuit of therapeutics targeting hyperphosphorylated tau-comprised neurofibrillary tangles. AREAS COVERED This perspective reviews the basis of the Aβ cascade hypothesis of AD and how clinical trials of anti-Aβ drugs have failed to support it, and reflects upon the early findings suggesting that a similar path is being followed with therapeutics targeting tau. Other potential approaches to identifying therapeutics for AD are explored herein. EXPERT OPINION The relevance of the Aβ cascade hypothesis to the development of therapeutics for AD appears disproven. Drugs targeting tau appear to be suffering the same fate but may yet produce better results. Alternative approaches are being pursued, some of them with initial small-scale, but promising, results.
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Affiliation(s)
| | - Stefania Ippati
- Experimental Imaging Center, San Raffaele Scientific Institute , Milano, Italy
| | - Mark Watling
- CNS & Pain Department, Transcrip Partners LLP Reading , Berkshire, United Kingdom of Great Britain and Northern Ireland
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