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Hsu FM, Mohanty RP, Rubbi L, Thompson M, Pickering H, Reed EF, Greenland JR, Schaenman JM, Pellegrini M. An epigenetic human cytomegalovirus infection score predicts viremia risk in seropositive lung transplant recipients. Epigenetics 2024; 19:2408843. [PMID: 39360678 PMCID: PMC11451273 DOI: 10.1080/15592294.2024.2408843] [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: 03/21/2024] [Revised: 08/28/2024] [Accepted: 09/04/2024] [Indexed: 10/04/2024] Open
Abstract
Cytomegalovirus (CMV) infection and reactivation in solid organ transplant (SOT) recipients increases the risk of viremia, graft failure and death. Clinical studies of CMV serostatus indicate that donor positive recipient negative (D+/R-) patients have greater viremia risk than D-/R-. The majority of patients are R+ having intermediate serologic risk. To characterize the long-term impact of CMV infection and assess viremia risk, we sought to measure the effects of CMV on the recipient immune epigenome. Specifically, we profiled DNA methylation in 156 individuals before lung or kidney transplant. We found that the methylome of CMV positive SOT recipients is hyper-methylated at loci associated with neural development and Polycomb group (PcG) protein binding, and hypo-methylated at regions critical for the maturation of lymphocytes. In addition, we developed a machine learning-based model to predict the recipient CMV serostatus after correcting for cell type composition and ancestry. This CMV episcore measured at baseline in R+ individual stratifies viremia risk accurately in the lung transplant cohort, and along with serostatus the CMV episcore could be a potential biomarker for identifying R+ patients at high viremia risk.
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Affiliation(s)
- Fei-Man Hsu
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences – The Collaboratory, University of California Los Angeles, Los Angeles, CA, USA
| | - Rashmi P. Mohanty
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Liudmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Michael Thompson
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
| | - Harry Pickering
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Elaine F. Reed
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - John R. Greenland
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Joanna M. Schaenman
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA
- Institute for Quantitative and Computational Biosciences – The Collaboratory, University of California Los Angeles, Los Angeles, CA, USA
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Liu J, Xie Y, Liu F, Qin W, Yu C. Genetic and vascular risk factors for ischemic stroke and cortical morphometry in individuals without a history of stroke: A UK Biobank observational cohort study. Neuroimage Clin 2024; 44:103683. [PMID: 39395374 DOI: 10.1016/j.nicl.2024.103683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 09/30/2024] [Accepted: 10/03/2024] [Indexed: 10/14/2024]
Abstract
BACKGROUND Stroke risk factors may contribute to cognitive decline and dementia by altering brain tissue integrity. If their effects on brain are nonnegligible, the target regions for stroke rehabilitation with brain stimulation identified by cross-sectional case-control studies may be biased due to the pre-existing brain differences caused by these risk factors. Here, we investigated the effects of stroke risk factors on cortical thickness (CT) and surface area (SA) in individuals without a history of stroke. METHODS In this observational study, we used data from the UK Biobank cohort to explore the effects of polygenic risk score for ischemic stroke (PRSIS), systolic blood pressure (SBP), diastolic blood pressure (DBP), glycated hemoglobin (HbA1c), triglycerides (TG), and low-density lipoprotein (LDL) on CT and SA of 62 cerebral regions. We excluded non-Caucasian participants and participants with missing data, unqualified brain images, or a history of stroke or any other brain diseases. We constructed a multivariate linear regression model for each phenotype to simultaneously test the effect of each factor and interaction between factors. The results were verified by sensitivity analyses of SDP or DBP input and adjusting for body-mass index, high-density lipoprotein cholesterol, or smoking and alcohol intake. By excluding participants with abnormal blood pressure, glucose, or lipid, we tested whether vascular risk factor within normal range also affected cortical phenotypes. To determine clinical relevance of our findings, we also investigated the effects of stroke risk factors and cortical phenotypes on cognitive decline assessed by fluid intelligence score (FIQ) and the mediation of cortical phenotype for the association between stroke risk factor and FIQ. RESULTS The study consisted of 27 120 eligible participants. Stroke risk factors were associated with 16 CT and two SA phenotypes in both main and sensitivity analyses (all p < 0.0004, Bonferroni corrected), which could explain portions of variances (partial R2, median 0.62 % [IQR 0.44-0.75 %] in main analyses) in these phenotypes. Among the 18 cortical phenotypes associated with stroke risk factors, we identified 26 specific predictor-phenotype associations (all p < 0.0026), including the positive associations between PRSIS and SA and between HbA1c and CT, negative associations of SBP and TG with CT, and mixed associations of PRSIS and DBP with CT. Neither LDL nor interactions between risk factors affected cortical phenotypes. Of the 16 associations between vascular risk factors and cortical phenotypes, ten were still significant after excluding participants with abnormal vascular risk assessments and diagnoses. Stroke risk factors were associated with FIQ in all analyses (p < 0.0004; partial R2, range 0.22-0.3 %), of which the associations of PRSIS and SBP with cognitive decline were mediated by CT phenotypes. CONCLUSIONS Stroke risk factors have substantial effects on cortical morphometry and cognitive decline in middle-aged and older people, which should be considered in the prevention of dementia and in the identification of target regions for stroke rehabilitation with brain stimulation.
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Affiliation(s)
- Jiawei Liu
- Department of Radiology, Tianjin Key Lab of Functional Imaging and State Key Laboratory of Experimental Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Yingying Xie
- Department of Radiology, Tianjin Key Lab of Functional Imaging and State Key Laboratory of Experimental Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Feng Liu
- Department of Radiology, Tianjin Key Lab of Functional Imaging and State Key Laboratory of Experimental Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Wen Qin
- Department of Radiology, Tianjin Key Lab of Functional Imaging and State Key Laboratory of Experimental Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China
| | - Chunshui Yu
- Department of Radiology, Tianjin Key Lab of Functional Imaging and State Key Laboratory of Experimental Hematology, Tianjin Medical University General Hospital, Tianjin 300052, China; School of Medical Imaging and Tianjin Key Laboratory of Functional Imaging, Tianjin Medical University, 300203 Tianjin, China.
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3
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Wani AH, Katrinli S, Zhao X, Daskalakis NP, Zannas AS, Aiello AE, Baker DG, Boks MP, Brick LA, Chen CY, Dalvie S, Fortier C, Geuze E, Hayes JP, Kessler RC, King AP, Koen N, Liberzon I, Lori A, Luykx JJ, Maihofer AX, Milberg W, Miller MW, Mufford MS, Nugent NR, Rauch S, Ressler KJ, Risbrough VB, Rutten BPF, Stein DJ, Stein MB, Ursano RJ, Verfaellie MH, Vermetten E, Vinkers CH, Ware EB, Wildman DE, Wolf EJ, Nievergelt CM, Logue MW, Smith AK, Uddin M. Blood-based DNA methylation and exposure risk scores predict PTSD with high accuracy in military and civilian cohorts. BMC Med Genomics 2024; 17:235. [PMID: 39334086 PMCID: PMC11429352 DOI: 10.1186/s12920-024-02002-6] [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: 02/12/2024] [Accepted: 08/29/2024] [Indexed: 09/30/2024] Open
Abstract
BACKGROUND Incorporating genomic data into risk prediction has become an increasingly popular approach for rapid identification of individuals most at risk for complex disorders such as PTSD. Our goal was to develop and validate Methylation Risk Scores (MRS) using machine learning to distinguish individuals who have PTSD from those who do not. METHODS Elastic Net was used to develop three risk score models using a discovery dataset (n = 1226; 314 cases, 912 controls) comprised of 5 diverse cohorts with available blood-derived DNA methylation (DNAm) measured on the Illumina Epic BeadChip. The first risk score, exposure and methylation risk score (eMRS) used cumulative and childhood trauma exposure and DNAm variables; the second, methylation-only risk score (MoRS) was based solely on DNAm data; the third, methylation-only risk scores with adjusted exposure variables (MoRSAE) utilized DNAm data adjusted for the two exposure variables. The potential of these risk scores to predict future PTSD based on pre-deployment data was also assessed. External validation of risk scores was conducted in four independent cohorts. RESULTS The eMRS model showed the highest accuracy (92%), precision (91%), recall (87%), and f1-score (89%) in classifying PTSD using 3730 features. While still highly accurate, the MoRS (accuracy = 89%) using 3728 features and MoRSAE (accuracy = 84%) using 4150 features showed a decline in classification power. eMRS significantly predicted PTSD in one of the four independent cohorts, the BEAR cohort (beta = 0.6839, p=0.006), but not in the remaining three cohorts. Pre-deployment risk scores from all models (eMRS, beta = 1.92; MoRS, beta = 1.99 and MoRSAE, beta = 1.77) displayed a significant (p < 0.001) predictive power for post-deployment PTSD. CONCLUSION The inclusion of exposure variables adds to the predictive power of MRS. Classification-based MRS may be useful in predicting risk of future PTSD in populations with anticipated trauma exposure. As more data become available, including additional molecular, environmental, and psychosocial factors in these scores may enhance their accuracy in predicting PTSD and, relatedly, improve their performance in independent cohorts.
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Affiliation(s)
- Agaz H Wani
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Seyma Katrinli
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
| | - Xiang Zhao
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Nikolaos P Daskalakis
- Broad Institute of MIT and Harvard, Stanley Center for Psychiatric Research, Cambridge, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Center of Excellence in Depression and Anxiety Disorders, McLean Hospital, Belmont, MA, USA
| | - Anthony S Zannas
- University of North Carolina at Chapel Hill, Carolina Stress Initiative, Chapel Hill, NC, USA
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Institute for Trauma Recovery, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Allison E Aiello
- Robert N Butler Columbia Aging Center, Department of Epidemiology, Columbia University, New York, NY, USA
| | - Dewleen G Baker
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
| | - Marco P Boks
- Department of Psychiatry, Brain Center University Medical Center Utrecht, Utrecht, UT, Netherlands
| | - Leslie A Brick
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Chia-Yen Chen
- Biogen Inc., Translational Sciences, Cambridge, MA, USA
| | - Shareefa Dalvie
- Department of Pathology, University of Cape Town, Cape Town, Western Province, South Africa
- Division of Human Genetics, University of Cape Town, Cape Town, Western Province, South Africa
| | - Catherine Fortier
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- VA Boston Healthcare System, TRACTS/GRECC, Boston, MA, USA
| | - Elbert Geuze
- Brain Research and Innovation Centre, Netherlands Ministry of Defence, Utrecht, UT, Netherlands
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, UT, Netherlands
| | - Jasmeet P Hayes
- Department of Psychology, The Ohio State University, Columbus, OH, USA
| | - Ronald C Kessler
- Department of Health Care Policy, Harvard Medical School, Boston, MA, USA
| | - Anthony P King
- The Ohio State University, College of Medicine, Institute for Behavioral Medicine Research, Columbus, OH, USA
| | - Nastassja Koen
- Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, Western Province, South Africa
- University of Cape Town, Neuroscience Institute, Cape Town, Western Province, South Africa
- SA MRC Unit On Risk & Resilience in Mental Disorders, University of Cape Town, Cape Town, Western Province, South Africa
| | - Israel Liberzon
- Department of Psychiatry and Behavioral Sciences, Texas A&M University College of Medicine, Bryan, TX, USA
| | - Adriana Lori
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
| | - Jurjen J Luykx
- Department of Psychiatry, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, UT, Netherlands
- Department of Translational Neuroscience, UMC Utrecht Brain Center Rudolf Magnus, Utrecht, UT, Netherlands
| | - Adam X Maihofer
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | | | - Mark W Miller
- Boston University School of Medicine, Psychiatry, Boston, MA, USA
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
| | - Mary S Mufford
- University of Cape Town, Neuroscience Institute, Cape Town, Western Province, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, Western Province, South Africa
| | - Nicole R Nugent
- Department of Emergency Medicine, Warren Alpert Brown Medical School, Providence, RI, USA
- Department of Pediatrics, Warren Alpert Brown Medical School, Providence, RI, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Brown Medical School, Providence, RI, USA
| | - Sheila Rauch
- Department of Psychiatry & Behavioral Sciences, Emory University, Atlanta, GA, USA
- Joseph Maxwell Cleland Atlanta Veterans Affairs Medical Center, Mental Health Service Line, Atlanta, USA
| | - Kerry J Ressler
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- McLean Hospital, Belmont, MA, USA
| | - Victoria B Risbrough
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Bart P F Rutten
- School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology, Maastricht Universitair Medisch Centrum, Maastricht, Limburg, Netherlands
| | - Dan J Stein
- Department of Psychiatry & Mental Health, University of Cape Town, Cape Town, Western Province, South Africa
- University of Cape Town, Neuroscience Institute, Cape Town, Western Province, South Africa
- SA MRC Unit On Risk & Resilience in Mental Disorders, University of Cape Town, Cape Town, Western Province, South Africa
| | - Murray B Stein
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Psychiatry Service, San Diego, CA, USA
- School of Public Health, University of California San Diego, La Jolla, CA, USA
| | - Robert J Ursano
- Department of Psychiatry, Uniformed Services University, Bethesda, MD, USA
| | - Mieke H Verfaellie
- Department of Psychiatry, Boston University School of Medicine, Boston, MA, USA
- VA Boston Healthcare System, Memory Disorders Research Center, Boston, MA, USA
| | - Eric Vermetten
- Department of Psychiatry, Leiden University Medical Center, Leiden, ZH, Netherlands
- Department of Psychiatry, New York University School of Medicine, New York, NY, USA
| | - Christiaan H Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program, Amsterdam, Holland, Netherlands
- Department of Anatomy and Neurosciences, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, Holland, Netherlands
- Department of Psychiatry, Amsterdam UMC Location Vrije Universiteit Amsterdam, Amsterdam, Holland, Netherlands
| | - Erin B Ware
- Survey Research Center, University of Michigan, Institute for Social Research, Ann Arbor, MI, USA
| | - Derek E Wildman
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA
| | - Erika J Wolf
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
- Department of Psychiatry, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, La Jolla, CA, USA
- Veterans Affairs San Diego Healthcare System, Center of Excellence for Stress and Mental Health, San Diego, CA, USA
- Veterans Affairs San Diego Healthcare System, Research Service, San Diego, CA, USA
| | - Mark W Logue
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- VA Boston Healthcare System, National Center for PTSD, Boston, MA, USA
- Boston University School of Medicine, Psychiatry, Biomedical Genetics, Boston, MA, USA
| | - Alicia K Smith
- Department of Gynecology and Obstetrics, Emory University, Atlanta, GA, USA
- Department of Psychiatry and Behavioral Sciences, Emory University, Atlanta, GA, USA
- Department of Human Genetics, Emory University, Atlanta, GA, USA
| | - Monica Uddin
- Genomics Program, College of Public Health, University of South Florida, Tampa, FL, USA.
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Nam Y, Kim J, Jung SH, Woerner J, Suh EH, Lee DG, Shivakumar M, Lee ME, Kim D. Harnessing Artificial Intelligence in Multimodal Omics Data Integration: Paving the Path for the Next Frontier in Precision Medicine. Annu Rev Biomed Data Sci 2024; 7:225-250. [PMID: 38768397 DOI: 10.1146/annurev-biodatasci-102523-103801] [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] [Indexed: 05/22/2024]
Abstract
The integration of multiomics data with detailed phenotypic insights from electronic health records marks a paradigm shift in biomedical research, offering unparalleled holistic views into health and disease pathways. This review delineates the current landscape of multimodal omics data integration, emphasizing its transformative potential in generating a comprehensive understanding of complex biological systems. We explore robust methodologies for data integration, ranging from concatenation-based to transformation-based and network-based strategies, designed to harness the intricate nuances of diverse data types. Our discussion extends from incorporating large-scale population biobanks to dissecting high-dimensional omics layers at the single-cell level. The review underscores the emerging role of large language models in artificial intelligence, anticipating their influence as a near-future pivot in data integration approaches. Highlighting both achievements and hurdles, we advocate for a concerted effort toward sophisticated integration models, fortifying the foundation for groundbreaking discoveries in precision medicine.
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Affiliation(s)
- Yonghyun Nam
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Jaesik Kim
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Sang-Hyuk Jung
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Jakob Woerner
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Erica H Suh
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Dong-Gi Lee
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Manu Shivakumar
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Matthew E Lee
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Dokyoon Kim
- Institute for Biomedical Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biostatistics, Epidemiology and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
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Ahn S, Sung Y, Song W. Machine Learning-Based Identification of Diagnostic Biomarkers for Korean Male Sarcopenia Through Integrative DNA Methylation and Methylation Risk Score: From the Korean Genomic Epidemiology Study (KoGES). J Korean Med Sci 2024; 39:e200. [PMID: 38978487 PMCID: PMC11231442 DOI: 10.3346/jkms.2024.39.e200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 05/21/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Sarcopenia, characterized by a progressive decline in muscle mass, strength, and function, is primarily attributable to aging. DNA methylation, influenced by both genetic predispositions and environmental exposures, plays a significant role in sarcopenia occurrence. This study employed machine learning (ML) methods to identify differentially methylated probes (DMPs) capable of diagnosing sarcopenia in middle-aged individuals. We also investigated the relationship between muscle strength, muscle mass, age, and sarcopenia risk as reflected in methylation profiles. METHODS Data from 509 male participants in the urban cohort of the Korean Genome Epidemiology Study_Health Examinee study were categorized into quartile groups based on the sarcopenia criteria for appendicular skeletal muscle index (ASMI) and handgrip strength (HG). To identify diagnostic biomarkers for sarcopenia, we used recursive feature elimination with cross validation (RFECV), to pinpoint DMPs significantly associated with sarcopenia. An ensemble model, leveraging majority voting, was utilized for evaluation. Furthermore, a methylation risk score (MRS) was calculated, and its correlation with muscle strength, function, and age was assessed using likelihood ratio analysis and multinomial logistic regression. RESULTS Participants were classified into two groups based on quartile thresholds: sarcopenia (n = 37) with ASMI and HG in the lowest quartile, and normal ranges (n = 48) in the highest. In total, 238 DMPs were identified and eight probes were selected using RFECV. These DMPs were used to build an ensemble model with robust diagnostic capabilities for sarcopenia, as evidenced by an area under the receiver operating characteristic curve of 0.94. Based on eight probes, the MRS was calculated and then validated by analyzing age, HG, and ASMI among the control group (n = 424). Age was positively correlated with high MRS (coefficient, 1.2494; odds ratio [OR], 3.4882), whereas ASMI and HG were negatively correlated with high MRS (ASMI coefficient, -0.4275; OR, 0.6521; HG coefficient, -0.3116; OR, 0.7323). CONCLUSION Overall, this study identified key epigenetic markers of sarcopenia in Korean males and developed a ML model with high diagnostic accuracy for sarcopenia. The MRS also revealed significant correlations between these markers and age, HG, and ASMI. These findings suggest that both diagnostic models and the MRS can play an important role in managing sarcopenia in middle-aged populations.
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Affiliation(s)
- Seohyun Ahn
- Health and Exercise Science Laboratory, Institute of Sport Science, Department of Physical Education, Seoul National University, Seoul, Korea
| | - Yunho Sung
- Health and Exercise Science Laboratory, Institute of Sport Science, Department of Physical Education, Seoul National University, Seoul, Korea
| | - Wook Song
- Health and Exercise Science Laboratory, Institute of Sport Science, Department of Physical Education, Seoul National University, Seoul, Korea
- Institute on Aging, Seoul National University, Seoul, Korea.
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Chen BH, Zhou W. mLiftOver: harmonizing data across Infinium DNA methylation platforms. Bioinformatics 2024; 40:btae423. [PMID: 38963309 PMCID: PMC11233119 DOI: 10.1093/bioinformatics/btae423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2024] [Revised: 06/07/2024] [Accepted: 07/03/2024] [Indexed: 07/05/2024] Open
Abstract
MOTIVATION Infinium DNA methylation BeadChips are widely used for genome-wide DNA methylation profiling at the population scale. Recent updates to probe content and naming conventions in the EPIC version 2 (EPICv2) arrays have complicated integrating new data with previous Infinium array platforms, such as the MethylationEPIC (EPIC) and the HumanMethylation450 (HM450) BeadChip. RESULTS We present mLiftOver, a user-friendly tool that harmonizes probe ID, methylation level, and signal intensity data across different Infinium platforms. It manages probe replicates, missing data imputation, and platform-specific bias for accurate data conversion. We validated the tool by applying HM450-based cancer classifiers to EPICv2 cancer data, achieving high accuracy. Additionally, we successfully integrated EPICv2 healthy tissue data with legacy HM450 data for tissue identity analysis and produced consistent copy number profiles in cancer cells. AVAILABILITY AND IMPLEMENTATION mLiftOver is implemented R and available in the Bioconductor package SeSAMe (version 1.21.13+): https://bioconductor.org/packages/release/bioc/html/sesame.html. Analysis of EPIC and EPICv2 platform-specific bias and high-confidence mapping is available at https://github.com/zhou-lab/InfiniumAnnotationV1/raw/main/Anno/EPICv2/EPICv2ToEPIC_conversion.tsv.gz. The source code is available at https://github.com/zwdzwd/sesame/blob/devel/R/mLiftOver.R under the MIT license.
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Affiliation(s)
- Brian H Chen
- California Pacific Medical Center Research Institute, Sutter Health, San Francisco, CA 94143, United States
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, Philadelphia, PA, 19104, United States
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, United States
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7
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Chen Z, Satake E, Pezzolesi MG, Md Dom ZI, Stucki D, Kobayashi H, Syreeni A, Johnson AT, Wu X, Dahlström EH, King JB, Groop PH, Rich SS, Sandholm N, Krolewski AS, Natarajan R. Integrated analysis of blood DNA methylation, genetic variants, circulating proteins, microRNAs, and kidney failure in type 1 diabetes. Sci Transl Med 2024; 16:eadj3385. [PMID: 38776390 DOI: 10.1126/scitranslmed.adj3385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024]
Abstract
Variation in DNA methylation (DNAmet) in white blood cells and other cells/tissues has been implicated in the etiology of progressive diabetic kidney disease (DKD). However, the specific mechanisms linking DNAmet variation in blood cells with risk of kidney failure (KF) and utility of measuring blood cell DNAmet in personalized medicine are not clear. We measured blood cell DNAmet in 277 individuals with type 1 diabetes and DKD using Illumina EPIC arrays; 51% of the cohort developed KF during 7 to 20 years of follow-up. Our epigenome-wide analysis identified DNAmet at 17 CpGs (5'-cytosine-phosphate-guanine-3' loci) associated with risk of KF independent of major clinical risk factors. DNAmet at these KF-associated CpGs remained stable over a median period of 4.7 years. Furthermore, DNAmet variations at seven KF-associated CpGs were strongly associated with multiple genetic variants at seven genomic regions, suggesting a strong genetic influence on DNAmet. The effects of DNAmet variations at the KF-associated CpGs on risk of KF were partially mediated by multiple KF-associated circulating proteins and KF-associated circulating miRNAs. A prediction model for risk of KF was developed by adding blood cell DNAmet at eight selected KF-associated CpGs to the clinical model. This updated model significantly improved prediction performance (c-statistic = 0.93) versus the clinical model (c-statistic = 0.85) at P = 6.62 × 10-14. In conclusion, our multiomics study provides insights into mechanisms through which variation of DNAmet may affect KF development and shows that blood cell DNAmet at certain CpGs can improve risk prediction for KF in T1D.
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Affiliation(s)
- Zhuo Chen
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Eiichiro Satake
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Marcus G Pezzolesi
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Zaipul I Md Dom
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Devorah Stucki
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Hiroki Kobayashi
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
- Division of Nephrology, Hypertension, and Endocrinology, Nihon University School of Medicine, Tokyo, Japan
| | - Anna Syreeni
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Adam T Johnson
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Xiwei Wu
- Department of Computational and Quantitative Medicine, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
- Integrative Genomics Core, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Emma H Dahlström
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Jaxon B King
- Department of Internal Medicine, Division of Nephrology and Hypertension, University of Utah School of Medicine, Salt Lake City, UT 84132, USA
| | - Per-Henrik Groop
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Stephen S Rich
- Center for Public Health Genomics and Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Niina Sandholm
- Folkhälsan Research Center, Helsinki, 00290, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, 00290, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, 00290, Finland
| | - Andrzej S Krolewski
- Section on Genetics and Epidemiology, Research Division, Joslin Diabetes Center, Boston, MA 02215, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Rama Natarajan
- Department of Diabetes Complications and Metabolism, Arthur Riggs Diabetes and Metabolism Research Institute and Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
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Goldberg DC, Cloud C, Lee SM, Barnes B, Gruber S, Kim E, Pottekat A, Westphal M, McAuliffe L, Majournie E, KalayilManian M, Zhu Q, Tran C, Hansen M, Parker JB, Kohli RM, Porecha R, Renke N, Zhou W. MSA: scalable DNA methylation screening BeadChip for high-throughput trait association studies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.17.594606. [PMID: 38826316 PMCID: PMC11142114 DOI: 10.1101/2024.05.17.594606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The Infinium DNA Methylation BeadChips have significantly contributed to population-scale epigenetics research by enabling epigenome-wide trait association discoveries. Here, we design, describe, and experimentally verify a new iteration of this technology, the Methylation Screening Array (MSA), to focus on human trait screening and discovery. This array utilizes extensive data from previous Infinium platform-based epigenome-wide association studies (EWAS). It incorporates knowledge from the latest single-cell and cell type-resolution whole genome methylome profiles. The MSA is engineered to achieve scalable screening of epigenetics-trait association in an ultra-high sample throughput. Our design encompassed diverse human trait associations, including those with genetic, cellular, environmental, and demographical variables and human diseases such as genetic, neurodegenerative, cardiovascular, infectious, and immune diseases. We comprehensively evaluated this array's reproducibility, accuracy, and capacity for cell-type deconvolution and supporting 5-hydroxymethylation profiling in diverse human tissues. Our first atlas data using this platform uncovered the complex chromatin and tissue contexts of DNA modification variations and genetic variants linked to human phenotypes.
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Affiliation(s)
- David C Goldberg
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Cameron Cloud
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | - Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | - Elliot Kim
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
| | | | | | | | | | | | | | | | | | - Jared B Parker
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | | | | | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children’s Hospital of Philadelphia, PA, 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
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9
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Davyson E, Shen X, Huider F, Adams M, Borges K, McCartney D, Barker L, Van Dongen J, Boomsma D, Weihs A, Grabe H, Kühn L, Teumer A, Völzke H, Zhu T, Kaprio J, Ollikainen M, David FS, Meinert S, Stein F, Forstner AJ, Dannlowski U, Kircher T, Tapuc A, Czamara D, Binder EB, Brückl T, Kwong A, Yousefi P, Wong C, Arseneault L, Fisher HL, Mill J, Cox S, Redmond P, Russ TC, van den Oord E, Aberg KA, Penninx B, Marioni RE, Wray NR, McIntosh AM. Antidepressant Exposure and DNA Methylation: Insights from a Methylome-Wide Association Study. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.01.24306640. [PMID: 38746357 PMCID: PMC11092700 DOI: 10.1101/2024.05.01.24306640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Importance Understanding antidepressant mechanisms could help design more effective and tolerated treatments. Objective Identify DNA methylation (DNAm) changes associated with antidepressant exposure. Design Case-control methylome-wide association studies (MWAS) of antidepressant exposure were performed from blood samples collected between 2006-2011 in Generation Scotland (GS). The summary statistics were tested for enrichment in specific tissues, gene ontologies and an independent MWAS in the Netherlands Study of Depression and Anxiety (NESDA). A methylation profile score (MPS) was derived and tested for its association with antidepressant exposure in eight independent cohorts, alongside prospective data from GS. Setting Cohorts; GS, NESDA, FTC, SHIP-Trend, FOR2107, LBC1936, MARS-UniDep, ALSPAC, E-Risk, and NTR. Participants Participants with DNAm data and self-report/prescription derived antidepressant exposure. Main Outcomes and Measures Whole-blood DNAm levels were assayed by the EPIC/450K Illumina array (9 studies, N exposed = 661, N unexposed = 9,575) alongside MBD-Seq in NESDA (N exposed = 398, N unexposed = 414). Antidepressant exposure was measured by self- report and/or antidepressant prescriptions. Results The self-report MWAS (N = 16,536, N exposed = 1,508, mean age = 48, 59% female) and the prescription-derived MWAS (N = 7,951, N exposed = 861, mean age = 47, 59% female), found hypermethylation at seven and four DNAm sites (p < 9.42x10 -8 ), respectively. The top locus was cg26277237 ( KANK1, p self-report = 9.3x10 -13 , p prescription = 6.1x10 -3 ). The self-report MWAS found a differentially methylated region, mapping to DGUOK-AS1 ( p adj = 5.0x10 -3 ) alongside significant enrichment for genes expressed in the amygdala, the "synaptic vesicle membrane" gene ontology and the top 1% of CpGs from the NESDA MWAS (OR = 1.39, p < 0.042). The MPS was associated with antidepressant exposure in meta-analysed data from external cohorts (N studies = 9, N = 10,236, N exposed = 661, f3 = 0.196, p < 1x10 -4 ). Conclusions and Relevance Antidepressant exposure is associated with changes in DNAm across different cohorts. Further investigation into these changes could inform on new targets for antidepressant treatments. 3 Key Points Question: Is antidepressant exposure associated with differential whole blood DNA methylation?Findings: In this methylome-wide association study of 16,536 adults across Scotland, antidepressant exposure was significantly associated with hypermethylation at CpGs mapping to KANK1 and DGUOK-AS1. A methylation profile score trained on this sample was significantly associated with antidepressant exposure (pooled f3 [95%CI]=0.196 [0.105, 0.288], p < 1x10 -4 ) in a meta-analysis of external datasets. Meaning: Antidepressant exposure is associated with hypermethylation at KANK1 and DGUOK-AS1 , which have roles in mitochondrial metabolism and neurite outgrowth. If replicated in future studies, targeting these genes could inform the design of more effective and better tolerated treatments for depression.
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10
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Lee SM, Loo C, Prasasya R, Bartolomei M, Kohli R, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. Nucleic Acids Res 2024; 52:e38. [PMID: 38407446 PMCID: PMC11040145 DOI: 10.1093/nar/gkae127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 01/29/2024] [Accepted: 02/10/2024] [Indexed: 02/27/2024] Open
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection P-value calculation achieved higher sensitivities for low-input datasets and was validated in over 100 000 public diverse methylome profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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Affiliation(s)
- Sol Moe Lee
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
| | - Christian E Loo
- Graduate Group in Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Rexxi D Prasasya
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Marisa S Bartolomei
- Department of Cell and Developmental Biology, Epigenetics Institute, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA 19104, USA
| | - Rahul M Kohli
- Department of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wanding Zhou
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, PA 19104, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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11
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Bunyavanich S, Becker PM, Altman MC, Lasky-Su J, Ober C, Zengler K, Berdyshev E, Bonneau R, Chatila T, Chatterjee N, Chung KF, Cutcliffe C, Davidson W, Dong G, Fang G, Fulkerson P, Himes BE, Liang L, Mathias RA, Ogino S, Petrosino J, Price ND, Schadt E, Schofield J, Seibold MA, Steen H, Wheatley L, Zhang H, Togias A, Hasegawa K. Analytical challenges in omics research on asthma and allergy: A National Institute of Allergy and Infectious Diseases workshop. J Allergy Clin Immunol 2024; 153:954-968. [PMID: 38295882 PMCID: PMC10999353 DOI: 10.1016/j.jaci.2024.01.014] [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: 12/13/2023] [Revised: 01/19/2024] [Accepted: 01/24/2024] [Indexed: 02/29/2024]
Abstract
Studies of asthma and allergy are generating increasing volumes of omics data for analysis and interpretation. The National Institute of Allergy and Infectious Diseases (NIAID) assembled a workshop comprising investigators studying asthma and allergic diseases using omics approaches, omics investigators from outside the field, and NIAID medical and scientific officers to discuss the following areas in asthma and allergy research: genomics, epigenomics, transcriptomics, microbiomics, metabolomics, proteomics, lipidomics, integrative omics, systems biology, and causal inference. Current states of the art, present challenges, novel and emerging strategies, and priorities for progress were presented and discussed for each area. This workshop report summarizes the major points and conclusions from this NIAID workshop. As a group, the investigators underscored the imperatives for rigorous analytic frameworks, integration of different omics data types, cross-disciplinary interaction, strategies for overcoming current limitations, and the overarching goal to improve scientific understanding and care of asthma and allergic diseases.
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Affiliation(s)
| | - Patrice M Becker
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Jessica Lasky-Su
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | | | - Talal Chatila
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | | | | | | | - Wendy Davidson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Dong
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Gang Fang
- Icahn School of Medicine at Mount Sinai, New York, NY
| | - Patricia Fulkerson
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | | | - Liming Liang
- Harvard T. H. Chan School of Public Health, Boston, Mass
| | | | - Shuji Ogino
- Brigham & Women's Hospital and Harvard Medical School, Boston, Mass; Harvard T. H. Chan School of Public Health, Boston, Mass; Broad Institute of MIT and Harvard, Boston, Mass
| | | | | | - Eric Schadt
- Icahn School of Medicine at Mount Sinai, New York, NY
| | | | - Max A Seibold
- National Jewish Health, Denver, Colo; University of Colorado School of Medicine, Aurora, Colo
| | - Hanno Steen
- Boston Children's Hospital and Harvard Medical School, Boston, Mass
| | - Lisa Wheatley
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Hongmei Zhang
- School of Public Health, University of Memphis, Memphis, Tenn
| | - Alkis Togias
- National Institute of Allergy and Infectious Diseases, National Institutes of Health, Rockville, Md
| | - Kohei Hasegawa
- Massachusetts General Hospital and Harvard Medical School, Boston, Mass
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12
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Nishitani S, Smith AK, Tomoda A, Fujisawa TX. Data science using the human epigenome for predicting multifactorial diseases and symptoms. Epigenomics 2024; 16:273-276. [PMID: 38312014 DOI: 10.2217/epi-2023-0321] [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] [Indexed: 02/06/2024] Open
Abstract
Tweetable abstract This article reviews machine learning models that leverages epigenomic data for predicting multifactorial diseases and symptoms as well as how such models can be utilized to explore new research questions.
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Affiliation(s)
- Shota Nishitani
- Research Center for Child Mental Development, University of Fukui, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, & University of Fukui, Osaka, 565-0871, Japan
- Life Science Innovation Center, School of Medical Sciences, University of Fukui, Fukui, 910-8507, Japan
| | - Alicia K Smith
- Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Akemi Tomoda
- Research Center for Child Mental Development, University of Fukui, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, & University of Fukui, Osaka, 565-0871, Japan
- Life Science Innovation Center, School of Medical Sciences, University of Fukui, Fukui, 910-8507, Japan
- Department of Child & Adolescent Psychological Medicine, University of Fukui Hospital, Fukui, 910-1193, Japan
| | - Takashi X Fujisawa
- Research Center for Child Mental Development, University of Fukui, Fukui, 910-1193, Japan
- Division of Developmental Higher Brain Functions, United Graduate School of Child Development, Osaka University, Kanazawa University, Hamamatsu University School of Medicine, Chiba University, & University of Fukui, Osaka, 565-0871, Japan
- Life Science Innovation Center, School of Medical Sciences, University of Fukui, Fukui, 910-8507, Japan
- Gynecology & Obstetrics, Emory University School of Medicine, Atlanta, GA 30322, USA
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13
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Wani A, Katrinli S, Zhao X, Daskalakis N, Zannas A, Aiello A, Baker D, Boks M, Brick L, Chen CY, Dalvie S, Fortier C, Geuze E, Hayes J, Kessler R, King A, Koen N, Liberzon I, Lori A, Luykx J, Maihofer A, Milberg W, Miller M, Mufford M, Nugent N, Rauch S, Ressler K, Risbrough V, Rutten B, Stein D, Stein M, Ursano R, Verfaellie M, Ware E, Wildman D, Wolf E, Nievergelt C, Logue M, Smith A, Uddin M, Vermetten E, Vinkers C. Blood-based DNA methylation and exposure risk scores predict PTSD with high accuracy in military and civilian cohorts. RESEARCH SQUARE 2024:rs.3.rs-3952163. [PMID: 38410438 PMCID: PMC10896387 DOI: 10.21203/rs.3.rs-3952163/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: 02/28/2024]
Abstract
Background Incorporating genomic data into risk prediction has become an increasingly useful approach for rapid identification of individuals most at risk for complex disorders such as PTSD. Our goal was to develop and validate Methylation Risk Scores (MRS) using machine learning to distinguish individuals who have PTSD from those who do not. Methods Elastic Net was used to develop three risk score models using a discovery dataset (n = 1226; 314 cases, 912 controls) comprised of 5 diverse cohorts with available blood-derived DNA methylation (DNAm) measured on the Illumina Epic BeadChip. The first risk score, exposure and methylation risk score (eMRS) used cumulative and childhood trauma exposure and DNAm variables; the second, methylation-only risk score (MoRS) was based solely on DNAm data; the third, methylation-only risk scores with adjusted exposure variables (MoRSAE) utilized DNAm data adjusted for the two exposure variables. The potential of these risk scores to predict future PTSD based on pre-deployment data was also assessed. External validation of risk scores was conducted in four independent cohorts. Results The eMRS model showed the highest accuracy (92%), precision (91%), recall (87%), and f1-score (89%) in classifying PTSD using 3730 features. While still highly accurate, the MoRS (accuracy = 89%) using 3728 features and MoRSAE (accuracy = 84%) using 4150 features showed a decline in classification power. eMRS significantly predicted PTSD in one of the four independent cohorts, the BEAR cohort (beta = 0.6839, p-0.003), but not in the remaining three cohorts. Pre-deployment risk scores from all models (eMRS, beta = 1.92; MoRS, beta = 1.99 and MoRSAE, beta = 1.77) displayed a significant (p < 0.001) predictive power for post-deployment PTSD. Conclusion Results, especially those from the eMRS, reinforce earlier findings that methylation and trauma are interconnected and can be leveraged to increase the correct classification of those with vs. without PTSD. Moreover, our models can potentially be a valuable tool in predicting the future risk of developing PTSD. As more data become available, including additional molecular, environmental, and psychosocial factors in these scores may enhance their accuracy in predicting the condition and, relatedly, improve their performance in independent cohorts.
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Affiliation(s)
- Agaz Wani
- University of South Florida College of Public Health, Genomics Program
| | - Seyma Katrinli
- Emory University Department of Gynecology and Obstetrics
| | - Xiang Zhao
- Boston University School of Public Health
| | | | - Anthony Zannas
- University of North Carolina at Chapel Hill, Carolina Stress Initiative
| | - Allison Aiello
- Robert N Butler Columbia Aging Center, Columbia University
| | - Dewleen Baker
- University of California San Diego, Department of Psychiatry
| | - Marco Boks
- Brain Center University Medical Center Utrecht, Department of Psychiatry
| | | | | | | | | | - Elbert Geuze
- Netherlands Ministry of Defence, Brain Research and Innovation Centre
| | | | - Ronald Kessler
- Harvard Medical School, Department of Health Care Policy
| | - Anthony King
- The Ohio State University, College of Medicine, Institute for Behavioral Medicine Research
| | - Nastassja Koen
- University of Cape Town, Department of Psychiatry & Mental Health
| | - Israel Liberzon
- Texas A&M University College of Medicine, Department of Psychiatry and Behavioral Sciences
| | - Adriana Lori
- Emory University, Department of Psychiatry and Behavioral Sciences
| | - Jurjen Luykx
- UMC Utrecht Brain Center Rudolf Magnus, Department of Psychiatry
| | | | | | - Mark Miller
- Boston University School of Medicine, Psychiatry
| | | | - Nicole Nugent
- Alpert Brown Medical School, Department of Emergency Medicine
| | - Sheila Rauch
- Emory University, Department of Psychiatry & Behavioral Sciences
| | | | | | - Bart Rutten
- Maastricht Universitair Medisch Centrum, School for Mental Health and Neuroscience, Department of Psychiatry and Neuropsychology
| | - Dan Stein
- University of Cape Town, Department of Psychiatry & Mental Health
| | - Murrary Stein
- University of California San Diego, Department of Psychiatry
| | - Robert Ursano
- Uniformed Services University, Department of Psychiatry
| | | | - Erin Ware
- University of Michigan, Population Studies Center
| | - Derek Wildman
- University of South Florida College of Public Health, Genomics Program
| | - Erika Wolf
- VA Boston Healthcare System, National Center for PTSD
| | | | - Mark Logue
- Boston University School of Public Health
| | - Alicia Smith
- Emory University Department of Gynecology and Obstetrics
| | - Monica Uddin
- University of South Florida College of Public Health, Genomics Program
| | - Eric Vermetten
- Leiden University Medical Center, Department of Psychiatry
| | - Christiaan Vinkers
- Amsterdam Neuroscience, Mood, Anxiety, Psychosis, Sleep & Stress Program
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14
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Linares-Pineda TM, Fragoso-Bargas N, Picón MJ, Molina-Vega M, Jenum AK, Sletner L, Lee-Ødegård S, Opsahl JO, Moen GH, Qvigstad E, Prasad RB, Birkeland KI, Morcillo S, Sommer C. DNA methylation risk score for type 2 diabetes is associated with gestational diabetes. Cardiovasc Diabetol 2024; 23:68. [PMID: 38350951 PMCID: PMC10865541 DOI: 10.1186/s12933-024-02151-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 02/02/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND Gestational diabetes mellitus (GDM) and type 2 diabetes mellitus (T2DM) share many pathophysiological factors including genetics, but whether epigenetic marks are shared is unknown. We aimed to test whether a DNA methylation risk score (MRS) for T2DM was associated with GDM across ancestry and GDM criteria. METHODS In two independent pregnancy cohorts, EPIPREG (n = 480) and EPIDG (n = 32), DNA methylation in peripheral blood leukocytes was measured at a gestational age of 28 ± 2. We constructed an MRS in EPIPREG and EPIDG based on CpG hits from a published epigenome-wide association study (EWAS) of T2DM. RESULTS With mixed models logistic regression of EPIPREG and EPIDG, MRS for T2DM was associated with GDM: odd ratio (OR)[95% CI]: 1.3 [1.1-1.8], P = 0.002 for the unadjusted model, and 1.4 [1.1-1.7], P = 0.00014 for a model adjusted by age, pre-pregnant BMI, family history of diabetes and smoking status. Also, we found 6 CpGs through a meta-analysis (cg14020176, cg22650271, cg14870271, cg27243685, cg06378491, cg25130381) associated with GDM, and some of their methylation quantitative loci (mQTLs) were related to T2DM and GDM. CONCLUSION For the first time, we show that DNA methylation marks for T2DM are also associated with GDM, suggesting shared epigenetic mechanisms between GDM and T2DM.
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Affiliation(s)
- Teresa M Linares-Pineda
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
- Department of Biochemistry and Molecular Biology 2, University of Granada, Granada, Spain
- Centre for Biomedical Research Network on Obesity Physiopathology and Nutrition (CIBEROBN), Madrid, Spain
| | - Nicolas Fragoso-Bargas
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Mohn Center for Diabetes Precision Medicine, Department of Clinical Science, University of Bergen, Bergen, Norway
| | - María José Picón
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
| | - Maria Molina-Vega
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
| | - Anne Karen Jenum
- General Practice Research Unit (AFE), Department of General Practice, Institute of Health and Society, University of Oslo, Oslo, Norway
| | - Line Sletner
- Department of Pediatric and Adolescents Medicine, Akershus University Hospital, Lørenskog, Norway
| | - Sindre Lee-Ødegård
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Julia O Opsahl
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Haukeland University Hospital, Bergen, Norway
| | - Gunn-Helen Moen
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Institute of Molecular Bioscience, The University of Queensland, Brisbane, Australia
- K. G Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Trondheim, Norway
- Population Health Science, Bristol Medical School, University of Bristol, Bristol, UK
- Frazer Institute, The University of Queensland, Woolloongabba, QLD, 4102, Australia
| | - Elisabeth Qvigstad
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Rashmi B Prasad
- Lund University Diabetes Centre, Malmo, Sweden
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Kåre I Birkeland
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway
- Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sonsoles Morcillo
- Department of Endocrinology and Nutrition, Instituto de Investigación Biomédica Málaga (IBIMA)- Plataforma Bionand, University Hospital Virgen de la Victoria, Málaga, Spain
- Centre for Biomedical Research Network on Obesity Physiopathology and Nutrition (CIBEROBN), Madrid, Spain
| | - Christine Sommer
- Department of Endocrinology, Morbid Obesity and Preventive Medicine, Oslo University Hospital, Oslo, 0424, Norway.
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Viola TW, Danzer C, Mardini V, Szobot C, Chrusciel JH, Stertz L, Schmitz JM, Walss-Bass C, Fries GR, Grassi-Oliveira R. Prenatal cocaine exposure and its influence on pediatric epigenetic clocks and epigenetic scores in humans. Sci Rep 2024; 14:1946. [PMID: 38253635 PMCID: PMC10803757 DOI: 10.1038/s41598-024-52433-5] [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: 10/09/2023] [Accepted: 01/18/2024] [Indexed: 01/24/2024] Open
Abstract
The investigation of the effects of prenatal cocaine exposure (PCE) on offspring has been inconsistent, with few studies investigating biological outcomes in humans. We profiled genome-wide DNA methylation (DNAm) of umbilical cord blood (UCB) from newborns with (n = 35) and without (n = 47) PCE. We used DNAm data to (1) assess pediatric epigenetic clocks at birth and (2) to estimate epigenetic scores (ES) for lifetime disorders. We generated gestational epigenetic age estimates (DNAmGA) based on Knight and Bohlin epigenetic clocks. We also investigated the association between DNAmGA and UCB serum brain-derived neurotrophic factor (BDNF) levels. Considering the large-scale DNAm data availability and existing evidence regarding PCE as a risk for health problems later in life, we generated ES for tobacco smoking, psychosis, autism, diabetes, and obesity. A gene ontology (GO) analysis on the CpGs included in the ES with group differences was performed. PCE was associated with lower DNAmGA in newborns, and this effect remained significant when controlling for potential confounders, such as blood cell type composition predicted by DNAm and obstetric data. DNAmGA was negatively correlated with BDNF levels in the serum of UCB. Higher tobacco smoking, psychosis, and diabetes ES were found in the PCE group. The GO analysis revealed GABAergic synapses as a potential pathway altered by PCE. Our findings of decelerated DNAmGA and ES for adverse phenotypes associated with PCE, suggest that the effects of gestational cocaine exposure on the epigenetic landscape of human newborns are detectable at birth.
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Affiliation(s)
- Thiago Wendt Viola
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Christina Danzer
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 11, A701-129, 8200, Aarhus, Denmark
| | - Victor Mardini
- Clinical Hospital of Porto Alegre, Porto Alegre, RS, Brazil
| | - Claudia Szobot
- Clinical Hospital of Porto Alegre, Porto Alegre, RS, Brazil
| | - João Henrique Chrusciel
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil
| | - Laura Stertz
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Joy M Schmitz
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Consuelo Walss-Bass
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Gabriel R Fries
- Faillace Department of Psychiatry and Behavioral Sciences, Translational Psychiatry Program, The University of Texas Health Science Center at Houston, Houston, USA
| | - Rodrigo Grassi-Oliveira
- School of Medicine, Developmental Cognitive Neuroscience Lab, Pontifical Catholic University of Rio Grande Do Sul (PUCRS), Porto Alegre, RS, Brazil.
- Translational Neuropsychiatry Unit, Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 11, A701-129, 8200, Aarhus, Denmark.
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16
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Arehart CH, Sterrett JD, Garris RL, Quispe-Pilco RE, Gignoux CR, Evans LM, Stanislawski MA. Poly-omic risk scores predict inflammatory bowel disease diagnosis. mSystems 2024; 9:e0067723. [PMID: 38095449 PMCID: PMC10805030 DOI: 10.1128/msystems.00677-23] [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: 07/26/2023] [Accepted: 11/02/2023] [Indexed: 01/11/2024] Open
Abstract
Inflammatory bowel disease (IBD) is characterized by complex etiology and a disrupted colonic ecosystem. We provide a framework for the analysis of multi-omic data, which we apply to study the gut ecosystem in IBD. Specifically, we train and validate models using data on the metagenome, metatranscriptome, virome, and metabolome from the Human Microbiome Project 2 IBD multi-omic database, with 1,785 repeated samples from 130 individuals (103 cases and 27 controls). After splitting the participants into training and testing groups, we used mixed-effects least absolute shrinkage and selection operator regression to select features for each omic. These features, with demographic covariates, were used to generate separate single-omic prediction scores. All four single-omic scores were then combined into a final regression to assess the relative importance of the individual omics and the predictive benefits when considered together. We identified several species, pathways, and metabolites known to be associated with IBD risk, and we explored the connections between data sets. Individually, metabolomic and viromic scores were more predictive than metagenomics or metatranscriptomics, and when all four scores were combined, we predicted disease diagnosis with a Nagelkerke's R2 of 0.46 and an area under the curve of 0.80 (95% confidence interval: 0.63, 0.98). Our work supports that some single-omic models for complex traits are more predictive than others, that incorporating multiple omic data sets may improve prediction, and that each omic data type provides a combination of unique and redundant information. This modeling framework can be extended to other complex traits and multi-omic data sets.IMPORTANCEComplex traits are characterized by many biological and environmental factors, such that multi-omic data sets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each omic data set in single-omic versus multi-omic models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple omic data types to disentangle complex disease etiologies and biological signatures.
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Affiliation(s)
- Christopher H. Arehart
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| | - John D. Sterrett
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Integrative Physiology, University of Colorado, Boulder, Colorado, USA
| | - Rosanna L. Garris
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Biochemistry, University of Colorado, Boulder, Colorado, USA
| | - Ruth E. Quispe-Pilco
- Interdisciplinary Quantitative Biology PhD Program, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Christopher R. Gignoux
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Luke M. Evans
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
- Institute for Behavioral Genetics, University of Colorado, Boulder, Colorado, USA
| | - Maggie A. Stanislawski
- Department of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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17
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Chen J, Gatev E, Everson T, Conneely KN, Koen N, Epstein MP, Kobor MS, Zar HJ, Stein DJ, Hüls A. Pruning and thresholding approach for methylation risk scores in multi-ancestry populations. Epigenetics 2023; 18:2187172. [PMID: 36908043 PMCID: PMC10026878 DOI: 10.1080/15592294.2023.2187172] [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] [Indexed: 03/14/2023] Open
Abstract
Recent efforts have focused on developing methylation risk scores (MRS), a weighted sum of the individual's DNA methylation (DNAm) values of pre-selected CpG sites. Most of the current MRS approaches that utilize Epigenome-wide association studies (EWAS) summary statistics only include genome-wide significant CpG sites and do not consider co-methylation. New methods that relax the p-value threshold to include more CpG sites and account for the inter-correlation of DNAm might improve the predictive performance of MRS. We paired informed co-methylation pruning with P-value thresholding to generate pruning and thresholding (P+T) MRS and evaluated its performance among multi-ancestry populations. Through simulation studies and real data analyses, we demonstrated that pruning provides an improvement over simple thresholding methods for prediction of phenotypes. We demonstrated that European-derived summary statistics can be used to develop P+T MRS among other populations such as African populations. However, the prediction accuracy of P+T MRS may differ across multi-ancestry population due to environmental/cultural/social differences.
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Affiliation(s)
- Junyu Chen
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
| | - Evan Gatev
- Institute of Molecular Biology "Acad. Roumen Tsanev", Sofia, Bulgaria
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - Todd Everson
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Karen N Conneely
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA USA
| | - Nastassja Koen
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Michael P Epstein
- Department of Human Genetics, School of Medicine, Emory University, Atlanta, GA USA
| | - Michael S Kobor
- Department of Medical Genetics, University of British Columbia, Vancouver, Canada
- BC Children's Hospital Research Institute, Vancouver, Canada
- Centre for Molecular Medicine and Therapeutics, Vancouver, Canada
| | - Heather J Zar
- Department of Pediatrics and Child Health, Red Cross War Memorial Children's Hospital, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Child and Adolescent Health, University of Cape Town, Cape Town, South Africa
| | - Dan J Stein
- Neuroscience Institute, University of Cape Town, Cape Town, South Africa
- Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
- South African Medical Research Council (SAMRC) Unit on Risk and Resilience in Mental Disorders, University of Cape Town, Cape Town, South Africa
| | - Anke Hüls
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA USA
- Gangarosa Department of Environmental Health, Rollins School of Public Health, Emory University, Atlanta, Georgia
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18
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Lee SM, Loo CE, Prasasya RD, Bartolomei MS, Kohli RM, Zhou W. Low-input and single-cell methods for Infinium DNA methylation BeadChips. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.18.558252. [PMID: 37786695 PMCID: PMC10541608 DOI: 10.1101/2023.09.18.558252] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The Infinium BeadChip is the most widely used DNA methylome assay technology for population-scale epigenome profiling. However, the standard workflow requires over 200 ng of input DNA, hindering its application to small cell-number samples, such as primordial germ cells. We developed experimental and analysis workflows to extend this technology to suboptimal input DNA conditions, including ultra-low input down to single cells. DNA preamplification significantly enhanced detection rates to over 50% in five-cell samples and ∼25% in single cells. Enzymatic conversion also substantially improved data quality. Computationally, we developed a method to model the background signal's influence on the DNA methylation level readings. The modified detection p -values calculation achieved higher sensitivities for low-input datasets and was validated in over 100,000 public datasets with diverse methylation profiles. We employed the optimized workflow to query the demethylation dynamics in mouse primordial germ cells available at low cell numbers. Our data revealed nuanced chromatin states, sex disparities, and the role of DNA methylation in transposable element regulation during germ cell development. Collectively, we present comprehensive experimental and computational solutions to extend this widely used methylation assay technology to applications with limited DNA.
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19
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Colicino E, Fiorito G. DNA methylation-based biomarkers for cardiometabolic-related traits and their importance for risk stratification. CURRENT OPINION IN EPIDEMIOLOGY AND PUBLIC HEALTH 2023; 2:25-31. [PMID: 38601732 PMCID: PMC11003758 DOI: 10.1097/pxh.0000000000000020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/12/2024]
Abstract
Recent findings The prevalence of cardiometabolic syndrome in adults is increasing worldwide, highlighting the importance of biomarkers for individuals' classification based on their health status. Although cardiometabolic risk scores and diagnostic criteria have been developed aggregating adverse health effects of individual conditions on the overall syndrome, none of them has gained unanimous acceptance. Therefore, novel molecular biomarkers have been developed to better understand the risk, onset and progression of both individual conditions and the overall cardiometabolic syndrome. Summary Consistent associations between whole blood DNA methylation (DNAm) levels at several single genomic (i.e. CpG) sites and both individual and aggregated cardiometabolic conditions supported the creation of second-generation DNAm-based cardiometabolic-related biomarkers. These biomarkers linearly combine individual DNAm levels from key CpG sites, selected by a two-step machine learning procedures. They can be used, even retrospectively, in populations with extant whole blood DNAm levels and without observed cardiometabolic phenotypes. Purpose of review Here we offer an overview of the second-generation DNAm-based cardiometabolic biomarkers, discussing methodological advancements and implications on the interpretation and generalizability of the findings. We finally emphasize the contribution of DNAm-based biomarkers for risk stratification beyond traditional factors and discuss limitations and future directions of the field.
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Affiliation(s)
- Elena Colicino
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
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20
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Sandholm N, Dahlström EH, Groop PH. Genetic and epigenetic background of diabetic kidney disease. Front Endocrinol (Lausanne) 2023; 14:1163001. [PMID: 37324271 PMCID: PMC10262849 DOI: 10.3389/fendo.2023.1163001] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/10/2023] [Indexed: 06/17/2023] Open
Abstract
Diabetic kidney disease (DKD) is a severe diabetic complication that affects up to half of the individuals with diabetes. Elevated blood glucose levels are a key underlying cause of DKD, but DKD is a complex multifactorial disease, which takes years to develop. Family studies have shown that inherited factors also contribute to the risk of the disease. During the last decade, genome-wide association studies (GWASs) have emerged as a powerful tool to identify genetic risk factors for DKD. In recent years, the GWASs have acquired larger number of participants, leading to increased statistical power to detect more genetic risk factors. In addition, whole-exome and whole-genome sequencing studies are emerging, aiming to identify rare genetic risk factors for DKD, as well as epigenome-wide association studies, investigating DNA methylation in relation to DKD. This article aims to review the identified genetic and epigenetic risk factors for DKD.
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Affiliation(s)
- Niina Sandholm
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Emma H. Dahlström
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Per-Henrik Groop
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland
- Department of Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Research Program for Clinical and Molecular Metabolism, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
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21
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Chi C, Solomon O, Shiboski C, Taylor KE, Quach H, Quach D, Barcellos LF, Criswell LA. Identification of Sjögren's syndrome patient subgroups by clustering of labial salivary gland DNA methylation profiles. PLoS One 2023; 18:e0281891. [PMID: 36862625 PMCID: PMC9980741 DOI: 10.1371/journal.pone.0281891] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 02/02/2023] [Indexed: 03/03/2023] Open
Abstract
Heterogeneity in Sjögren's syndrome (SS), increasingly called Sjögren's disease, suggests the presence of disease subtypes, which poses a major challenge for the diagnosis, management, and treatment of this autoimmune disorder. Previous work distinguished patient subgroups based on clinical symptoms, but it is not clear to what extent symptoms reflect underlying pathobiology. The purpose of this study was to discover clinical meaningful subtypes of SS based on genome-wide DNA methylation data. We performed a cluster analysis of genome-wide DNA methylation data from labial salivary gland (LSG) tissue collected from 64 SS cases and 67 non-cases. Specifically, hierarchical clustering was performed on low dimensional embeddings of DNA methylation data extracted from a variational autoencoder to uncover unknown heterogeneity. Clustering revealed clinically severe and mild subgroups of SS. Differential methylation analysis revealed that hypomethylation at the MHC and hypermethylation at other genome regions characterize the epigenetic differences between these SS subgroups. Epigenetic profiling of LSGs in SS yields new insights into mechanisms underlying disease heterogeneity. The methylation patterns at differentially methylated CpGs are different in SS subgroups and support the role of epigenetic contributions to the heterogeneity in SS. Biomarker data derived from epigenetic profiling could be explored in future iterations of the classification criteria for defining SS subgroups.
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Affiliation(s)
- Calvin Chi
- Division of Computing, Center for Computational Biology, Data Science and Society, University of California Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Olivia Solomon
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Caroline Shiboski
- Department of Orofacial Sciences, School of Dentistry, University of California San Francisco, San Francisco, California, United States of America
| | - Kimberly E. Taylor
- Department of Medicine, Russell/Engleman Rheumatology Research Center, University of California San Francisco, San Francisco, California, United States of America
| | - Hong Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Diana Quach
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Lisa F. Barcellos
- Division of Computing, Center for Computational Biology, Data Science and Society, University of California Berkeley, Berkeley, California, United States of America
- Genetic Epidemiology and Genomics Laboratory, School of Public Health, University of California Berkeley, Berkeley, California, United States of America
| | - Lindsey A. Criswell
- Genomics of Autoimmune Rheumatic Disease Section, National Human Genome Research Institute, National Institute of Health, Bethesda, Maryland, United States of America
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22
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Nabais MF, Gadd DA, Hannon E, Mill J, McRae AF, Wray NR. An overview of DNA methylation-derived trait score methods and applications. Genome Biol 2023; 24:28. [PMID: 36797751 PMCID: PMC9936670 DOI: 10.1186/s13059-023-02855-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 01/17/2023] [Indexed: 02/18/2023] Open
Abstract
Microarray technology has been used to measure genome-wide DNA methylation in thousands of individuals. These studies typically test the associations between individual DNA methylation sites ("probes") and complex traits or diseases. The results can be used to generate methylation profile scores (MPS) to predict outcomes in independent data sets. Although there are many parallels between MPS and polygenic (risk) scores (PGS), there are key differences. Here, we review motivations, methods, and applications of DNA methylation-based trait prediction, with a focus on common diseases. We contrast MPS with PGS, highlighting where assumptions made in genetic modeling may not hold in epigenetic data.
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Affiliation(s)
- Marta F Nabais
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Eilis Hannon
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Jonathan Mill
- University of Exeter Medical School, RILD Building, RD&E Hospital Wonford, Barrack Road, Exeter, EX2 5DW, UK
| | - Allan F McRae
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Naomi R Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, 4072, Australia.
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23
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Lu AKM, Lin JJ, Tseng HH, Wang XY, Jang FL, Chen PS, Huang CC, Hsieh S, Lin SH. DNA methylation signature aberration as potential biomarkers in treatment-resistant schizophrenia: Constructing a methylation risk score using a machine learning method. J Psychiatr Res 2023; 157:57-65. [PMID: 36442407 DOI: 10.1016/j.jpsychires.2022.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/08/2022] [Accepted: 11/12/2022] [Indexed: 11/18/2022]
Abstract
Treatment-resistant schizophrenia (TRS) is defined as a non-response to at least two trials of antipsychotic medication with an adequate dose and duration. We aimed to evaluate the discriminant abilities of DNA methylation probes and methylation risk score between treatment-resistant schizophrenia and non-treatment-resistant schizophrenia. This study recruited 96 schizophrenia patients (TRS and non-TRS) and 56 healthy controls (HC). Participants were divided into a discovery set and a validation set. In the discovery set, we conducted genome-wide methylation analysis (human MethylationEPIC 850K BeadChip) on the subject's blood DNA and discriminated significant methylation signatures, then verified these methylation signatures in the validation set. Based on genome-wide scans of TRS versus non-TRS, thirteen differentially methylated probes were identified at FDR <0.05 and >20% differences in DNA methylation β-values. Next, we selected six probes within gene coding regions (LOC404266, LOXL2, CERK, CHMP7, and SLC17A9) to conduct verification in the validation set using quantitative methylation-specific PCR (qMSP). These six methylation probes showed satisfactory discrimination between TRS patients and non-TRS patients, with an AUC ranging from 0.83 to 0.92, accuracy ranging from 77.8% to 87.3%, sensitivity ranging from 80% to 90%, and specificity ranging from 65.6% to 85%. This methylation risk score model showed satisfactory discrimination between TRS patients and non-TRS patients, with an accuracy of 88.3%. These findings support that methylation signatures may be used as an indicator of TRS vulnerability and provide a model for the clinical use of methylation to identify TRS.
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Affiliation(s)
- Andrew Ke-Ming Lu
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jin-Jia Lin
- Department of Psychiatry, Chi Mei Medical Center, Tainan, Taiwan
| | - Huai-Hsuan Tseng
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Xin-Yu Wang
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Fong-Lin Jang
- Department of Psychiatry, Chi Mei Medical Center, Tainan, Taiwan
| | - Po-See Chen
- Department of Psychiatry, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Behavioral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Chun Huang
- Department of Psychiatry, National Cheng Kung University Hospital, Dou-Liou Branch, Yunlin, Taiwan
| | - Shulan Hsieh
- Department of Psychology, College of Social Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Hsiang Lin
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Public Health, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Biostatistics Consulting Center, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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24
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Cappozzo A, McCrory C, Robinson O, Freni Sterrantino A, Sacerdote C, Krogh V, Panico S, Tumino R, Iacoviello L, Ricceri F, Sieri S, Chiodini P, McKay GJ, McKnight AJ, Kee F, Young IS, McGuinness B, Crimmins EM, Arpawong TE, Kenny RA, O'Halloran A, Polidoro S, Solinas G, Vineis P, Ieva F, Fiorito G. A blood DNA methylation biomarker for predicting short-term risk of cardiovascular events. Clin Epigenetics 2022; 14:121. [PMID: 36175966 PMCID: PMC9521011 DOI: 10.1186/s13148-022-01341-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/13/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Recent evidence highlights the epidemiological value of blood DNA methylation (DNAm) as surrogate biomarker for exposure to risk factors for non-communicable diseases (NCD). DNAm surrogate of exposures predicts diseases and longevity better than self-reported or measured exposures in many cases. Consequently, disease prediction models based on blood DNAm surrogates may outperform current state-of-the-art prediction models. This study aims to develop novel DNAm surrogates for cardiovascular diseases (CVD) risk factors and develop a composite biomarker predictive of CVD risk. We compared the prediction performance of our newly developed risk score with the state-of-the-art DNAm risk scores for cardiovascular diseases, the 'next-generation' epigenetic clock DNAmGrimAge, and the prediction model based on traditional risk factors SCORE2. RESULTS Using data from the EPIC Italy cohort, we derived novel DNAm surrogates for BMI, blood pressure, fasting glucose and insulin, cholesterol, triglycerides, and coagulation biomarkers. We validated them in four independent data sets from Europe and the USA. Further, we derived a DNAmCVDscore predictive of the time-to-CVD event as a combination of several DNAm surrogates. ROC curve analyses show that DNAmCVDscore outperforms previously developed DNAm scores for CVD risk and SCORE2 for short-term CVD risk. Interestingly, the performance of DNAmGrimAge and DNAmCVDscore was comparable (slightly lower for DNAmGrimAge, although the differences were not statistically significant). CONCLUSIONS We described novel DNAm surrogates for CVD risk factors useful for future molecular epidemiology research, and we described a blood DNAm-based composite biomarker, DNAmCVDscore, predictive of short-term cardiovascular events. Our results highlight the usefulness of DNAm surrogate biomarkers of risk factors in epigenetic epidemiology to identify high-risk populations. In addition, we provide further evidence on the effectiveness of prediction models based on DNAm surrogates and discuss methodological aspects for further improvements. Finally, our results encourage testing this approach for other NCD diseases by training and developing DNAm surrogates for disease-specific risk factors and exposures.
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Affiliation(s)
- Andrea Cappozzo
- MOX - Laboratory for Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milan, Italy
| | - Cathal McCrory
- Department of Medical Gerontology, Trinity College Dublin, Dublin, Ireland
| | - Oliver Robinson
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Anna Freni Sterrantino
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
- The Alan Turing Institute, London, UK
| | - Carlotta Sacerdote
- Unit of Cancer Epidemiology, Città della Salute e della Scienza University-Hospital, Turin, Italy
| | - Vittorio Krogh
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Salvatore Panico
- Department of Clinical Medicine and Surgery, University of Naples Federico II, Naples, Italy
| | - Rosario Tumino
- Association for Epidemiology Research, AIRE ONLYS, Ragusa, Italy
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS NEUROMED, Pozzilli, Italy
- Department of Medicine and Surgery, Research Center in Epidemiology and Preventive Medicine (EPIMED), Turin, Italy
| | - Fulvio Ricceri
- Epidemiology Unit, Regional Health Service TO3, Grugliasco, Italy
- Department of Clinical and Biological Sciences, Centre for Biostatistics, Epidemiology, and Public Health (C-BEPH), University of Turin, Turin, Italy
| | - Sabina Sieri
- Fondazione IRCCS - Istituto Nazionale dei Tumori, Milan, Italy
| | - Paolo Chiodini
- Department of Mental, Physical Health and Preventive Medicine, University of Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Gareth J McKay
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | | | - Frank Kee
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | - Ian S Young
- Centre for Public Health, Queen's University Belfast, Belfast, UK
| | | | - Eileen M Crimmins
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Thalida Em Arpawong
- Leonard Davis School of Gerontology, University of Southern California, Los Angeles, CA, USA
| | - Rose Anne Kenny
- Department of Medical Gerontology, Trinity College Dublin, Dublin, Ireland
| | - Aisling O'Halloran
- Department of Medical Gerontology, Trinity College Dublin, Dublin, Ireland
| | | | - Giuliana Solinas
- Laboratory Biostatistics, Department of Biomedical Sciences, University of Sassari, Via Padre Manzella 4, Sassari, Italy
| | - Paolo Vineis
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Francesca Ieva
- MOX - Laboratory for Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milan, Italy
- CHDS - Health Data Science Center, Human Technopole, Milan, Italy
| | - Giovanni Fiorito
- Department of Medical Gerontology, Trinity College Dublin, Dublin, Ireland.
- MRC-PHE Centre for Environment and Health, Imperial College London, London, UK.
- Laboratory Biostatistics, Department of Biomedical Sciences, University of Sassari, Via Padre Manzella 4, Sassari, Italy.
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