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Lee NY, Hum M, Tan GP, Seah AC, Ong PY, Kin PT, Lim CW, Samol J, Tan NC, Law HY, Tan MH, Lee SC, Ang P, Lee ASG. Machine learning unveils an immune-related DNA methylation profile in germline DNA from breast cancer patients. Clin Epigenetics 2024; 16:66. [PMID: 38750495 PMCID: PMC11094860 DOI: 10.1186/s13148-024-01674-2] [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: 12/11/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
BACKGROUND There is an unmet need for precise biomarkers for early non-invasive breast cancer detection. Here, we aimed to identify blood-based DNA methylation biomarkers that are associated with breast cancer. METHODS DNA methylation profiling was performed for 524 Asian Chinese individuals, comprising 256 breast cancer patients and 268 age-matched healthy controls, using the Infinium MethylationEPIC array. Feature selection was applied to 649,688 CpG sites in the training set. Predictive models were built by training three machine learning models, with performance evaluated on an independent test set. Enrichment analysis to identify transcription factors binding to regions associated with the selected CpG sites and pathway analysis for genes located nearby were conducted. RESULTS A methylation profile comprising 51 CpGs was identified that effectively distinguishes breast cancer patients from healthy controls achieving an AUC of 0.823 on an independent test set. Notably, it outperformed all four previously reported breast cancer-associated methylation profiles. Enrichment analysis revealed enrichment of genomic loci associated with the binding of immune modulating AP-1 transcription factors, while pathway analysis of nearby genes showed an overrepresentation of immune-related pathways. CONCLUSION This study has identified a breast cancer-associated methylation profile that is immune-related to potential for early cancer detection.
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Affiliation(s)
- Ning Yuan Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore
| | - Melissa Hum
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore
| | - Guek Peng Tan
- DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, 100 Bukit Timah Rd, Singapore, 229899, Singapore
| | - Ai Choo Seah
- SingHealth Polyclinics, 167 Jalan Bukit Merah Connection One (Tower 5), Singapore, 150167, Singapore
| | - Pei-Yi Ong
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - Patricia T Kin
- SingHealth Polyclinics, 167 Jalan Bukit Merah Connection One (Tower 5), Singapore, 150167, Singapore
| | - Chia Wei Lim
- Department of Personalised Medicine, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
| | - Jens Samol
- Medical Oncology Department, Tan Tock Seng Hospital, 11 Jalan Tan Tock Seng, Singapore, 308433, Singapore
- Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Ngiap Chuan Tan
- SingHealth Polyclinics, 167 Jalan Bukit Merah Connection One (Tower 5), Singapore, 150167, Singapore
- SingHealth Duke-NUS Family Medicine Academic Clinical Programme, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Hai-Yang Law
- DNA Diagnostic and Research Laboratory, KK Women's and Children's Hospital, 100 Bukit Timah Rd, Singapore, 229899, Singapore
| | - Min-Han Tan
- Lucence Diagnostics Pte Ltd, 211 Henderson Road, Singapore, 159552, Singapore
| | - Soo-Chin Lee
- Department of Hematology-Oncology, National University Cancer Institute, Singapore (NCIS), National University Health System, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
- Department of Medicine, Yong Loo Lin School of Medicine, National University of Singapore, 10 Medical Dr, Singapore, 117597, Singapore
- Cancer Science Institute, Singapore (CSI), National University of Singapore, 14 Medical Dr, Singapore, 117599, Singapore
| | - Peter Ang
- Oncocare Cancer Centre, Gleneagles Medical Centre, 6 Napier Road, Singapore, 258499, Singapore
| | - Ann S G Lee
- Division of Cellular and Molecular Research, National Cancer Centre Singapore, 30 Hospital Boulevard, Singapore, 168583, Republic of Singapore.
- SingHealth Duke-NUS Oncology Academic Clinical Programme (ONCO ACP), Duke-NUS Graduate Medical School, 8 College Road, Singapore, 169857, Singapore.
- Department of Physiology, Yong Loo Lin School of Medicine, National University of Singapore, 2 Medical Drive, Singapore, 117593, Singapore.
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Dong H, Sun Y, Nie L, Cui A, Zhao P, Leung WK, Wang Q. Metabolic memory: mechanisms and diseases. Signal Transduct Target Ther 2024; 9:38. [PMID: 38413567 PMCID: PMC10899265 DOI: 10.1038/s41392-024-01755-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/18/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024] Open
Abstract
Metabolic diseases and their complications impose health and economic burdens worldwide. Evidence from past experimental studies and clinical trials suggests our body may have the ability to remember the past metabolic environment, such as hyperglycemia or hyperlipidemia, thus leading to chronic inflammatory disorders and other diseases even after the elimination of these metabolic environments. The long-term effects of that aberrant metabolism on the body have been summarized as metabolic memory and are found to assume a crucial role in states of health and disease. Multiple molecular mechanisms collectively participate in metabolic memory management, resulting in different cellular alterations as well as tissue and organ dysfunctions, culminating in disease progression and even affecting offspring. The elucidation and expansion of the concept of metabolic memory provides more comprehensive insight into pathogenic mechanisms underlying metabolic diseases and complications and promises to be a new target in disease detection and management. Here, we retrace the history of relevant research on metabolic memory and summarize its salient characteristics. We provide a detailed discussion of the mechanisms by which metabolic memory may be involved in disease development at molecular, cellular, and organ levels, with emphasis on the impact of epigenetic modulations. Finally, we present some of the pivotal findings arguing in favor of targeting metabolic memory to develop therapeutic strategies for metabolic diseases and provide the latest reflections on the consequences of metabolic memory as well as their implications for human health and diseases.
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Affiliation(s)
- Hao Dong
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Yuezhang Sun
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Lulingxiao Nie
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Aimin Cui
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China
| | - Pengfei Zhao
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Wai Keung Leung
- Periodontology and Implant Dentistry Division, Faculty of Dentistry, The University of Hong Kong, Hong Kong, China
| | - Qi Wang
- State Key Laboratory of Oral Diseases & National Center for Stomatology & National Clinical Research Center for Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
- Department of Prosthodontics, West China Hospital of Stomatology, Sichuan University, Chengdu, China.
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3
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Fujii R, Ando Y, Yamada H, Tsuboi Y, Munetsuna E, Yamazaki M, Mizuno G, Maeda K, Ohashi K, Ishikawa H, Watanabe M, Imaeda N, Goto C, Wakai K, Hashimoto S, Suzuki K. Integration of methylation quantitative trait loci (mQTL) on dietary intake on DNA methylation levels: an example of n-3 PUFA and ABCA1 gene. Eur J Clin Nutr 2023; 77:881-887. [PMID: 37542202 DOI: 10.1038/s41430-023-01315-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 07/18/2023] [Accepted: 07/18/2023] [Indexed: 08/06/2023]
Abstract
BACKGROUND Epigenetic studies have reported relationships between dietary nutrient intake and methylation levels. However, genetic variants that may affect DNA methylation (DNAm) pattern, called methylation quantitative loci (mQTL), are usually overlooked in these analyses. We investigated whether mQTL change the relationship between dietary nutrient intake and leukocyte DNAm levels with an example of estimated fatty acid intake and ATP-binding cassette transporter A1 (ABCA1). METHODS A cross-sectional study on 231 participants (108 men, mean age: 62.7 y) without clinical history of cancer and no prescriptions for dyslipidemia. We measured leukocyte DNAm levels of 8 CpG sites within ABCA1 gene by pyrosequencing method and used mean methylation levels for statistical analysis. TaqMan assay was used for genotyping a genetic variant of ABCA1 (rs1800976). Dietary fatty acid intake was estimated with a validated food frequency questionnaire and adjusted for total energy intake by using residual methods. RESULTS Mean ABCA1 DNAm levels were 5% lower with the number of minor alleles in rs1800976 (CC, 40.6%; CG, 35.9%; GG, 30.6%). Higher dietary n-3 PUFA intake was associated with lower ABCA1 DNAm levels (1st (ref) vs. 4th, β [95% CI]: -2.52 [-4.77, -0.28]). After controlling for rs180076, the association between dietary n-3 PUFA intake and ABCA1 DNAm levels was attenuated, but still showed an independent association (1st (ref) vs. 4th, β [95% CI]: -2.00 [-3.84, -0.18]). The interaction of mQTL and dietary n-3 PUFA intake on DNAm levels was not significant. CONCLUSIONS This result suggested that dietary n-3 PUFA intake would be an independent predictor of DNAm levels in ABCA1 gene after adjusting for individual genetic background. Considering mQTL need to broaden into other genes and nutrients for deeper understanding of DNA methylation, which can contribute to personalized nutritional intervention.
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Affiliation(s)
- Ryosuke Fujii
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
- Institute for Biomedicine (affiliated to the University of Lübeck), Eurac Research, Via Alessandro Volta 21, Bolzano/Bozen, Italy
| | - Yoshitaka Ando
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Hiroya Yamada
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Yoshiki Tsuboi
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Eiji Munetsuna
- Department of Biochemistry, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Mirai Yamazaki
- Department of Medical Technology, Kagawa Prefectural University of Health Sciences, 281-1 Hara, Mure-cho, Takamatsu, Japan
| | - Genki Mizuno
- Department of Medical Technology, Tokyo University of Technology School of Health Sciences, 5-23-22 Nishi-Kamata, Ota-ku, Japan
| | - Keisuke Maeda
- Department of Clinical Physiology, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Koji Ohashi
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Hiroaki Ishikawa
- Department of Informative Clinical Medicine, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Mami Watanabe
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Nahomi Imaeda
- Department of Nutrition, Faculty of Wellness, Shigakkan University, 55 Nakoyama, Yokonemachi, Obu, Japan
| | - Chiho Goto
- Department of Health and Nutrition, Nagoya Bunri University, 365 Maeda, Inazawa-city, Inazawa, Japan
| | - Kenji Wakai
- Department of Preventive Medicine, Nagoya University Graduate School of Medicine, 65 Tsurumai-cho, Showa-ku, Nagoya, Japan
| | - Shuji Hashimoto
- Department of Hygiene, Fujita Health University School of Medicine, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan
| | - Koji Suzuki
- Department of Preventive Medical Sciences, Fujita Health University School of Medical Sciences, 1-98 Dengakugakubo, Kutsukake-cho, Toyoake, Japan.
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Aurich S, Müller L, Kovacs P, Keller M. Implication of DNA methylation during lifestyle mediated weight loss. Front Endocrinol (Lausanne) 2023; 14:1181002. [PMID: 37614712 PMCID: PMC10442821 DOI: 10.3389/fendo.2023.1181002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/18/2023] [Indexed: 08/25/2023] Open
Abstract
Over the past 50 years, the number of overweight/obese people increased significantly, making obesity a global public health challenge. Apart from rare monogenic forms, obesity is a multifactorial disease, most likely resulting from a concerted interaction of genetic, epigenetic and environmental factors. Although recent studies opened new avenues in elucidating the complex genetics behind obesity, the biological mechanisms contributing to individual's risk to become obese are not yet fully understood. Non-genetic factors such as eating behaviour or physical activity are strong contributing factors for the onset of obesity. These factors may interact with genetic predispositions most likely via epigenetic mechanisms. Epigenome-wide association studies or methylome-wide association studies are measuring DNA methylation at single CpGs across thousands of genes and capture associations to obesity phenotypes such as BMI. However, they only represent a snapshot in the complex biological network and cannot distinguish between causes and consequences. Intervention studies are therefore a suitable method to control for confounding factors and to avoid possible sources of bias. In particular, intervention studies documenting changes in obesity-associated epigenetic markers during lifestyle driven weight loss, make an important contribution to a better understanding of epigenetic reprogramming in obesity. To investigate the impact of lifestyle in obesity state specific DNA methylation, especially concerning the development of new strategies for prevention and individual therapy, we reviewed 19 most recent human intervention studies. In summary, this review highlights the huge potential of targeted interventions to alter disease-associated epigenetic patterns. However, there is an urgent need for further robust and larger studies to identify the specific DNA methylation biomarkers which influence obesity.
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Affiliation(s)
- Samantha Aurich
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
| | - Luise Müller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
| | - Peter Kovacs
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Deutsches Zentrum für Diabetesforschung e.V., Neuherberg, Germany
| | - Maria Keller
- Medical Department III - Endocrinology, Nephrology, Rheumatology, University of Leipzig Medical Center, Leipzig, Germany
- Helmholtz Institute for Metabolic, Obesity and Vascular Research (HI-MAG) of the Helmholtz Center Munich at the University of Leipzig and University Hospital Leipzig, Leipzig, Germany
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5
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Xing W, Gao W, Zhao Z, Xu X, Bu H, Su H, Mao G, Chen J. Dietary flavonoids intake contributes to delay biological aging process: analysis from NHANES dataset. J Transl Med 2023; 21:492. [PMID: 37480074 PMCID: PMC10362762 DOI: 10.1186/s12967-023-04321-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 07/01/2023] [Indexed: 07/23/2023] Open
Abstract
BACKGROUND Diet may influence biological aging and the discrepancy (∆age) between a subject's biological age (BA) and chronological age (CA). We aimed to investigate the correlation of dietary flavonoids with the ∆age of organs (heart, kidney, liver) and the whole body. METHOD A total of 3193 United States adults were extracted from the National Health and Nutrition Examination Survey (NHANES) in 2007-2008 and 2017-2018. Dietary flavonoids intake was assessed using 24-h dietary recall method. Multiple linear regression analysis was performed to evaluate the association of dietary flavonoids intake with the ∆age of organs (heart, kidney, liver) and the whole body. BA was computed based on circulating biomarkers, and the resulting ∆age was tested as an outcome in linear regression analysis. RESULTS The ∆age of the whole body, heart, and liver was inversely associated with higher flavonoids intake (the whole body ∆age β = - 0.58, cardiovascular ∆age β = - 0.96, liver ∆age β = - 3.19) after adjustment for variables. However, higher flavonoids intake positively related to renal ∆age (β = 0.40) in participants with chronic kidney disease (CKD). Associations were influenced by population characteristics, such as age, health behavior, or chronic diseases. Anthocyanidins, isoflavones and flavones had the strongest inverse associations between the whole body ∆age and cardiovascular ∆age among all the flavonoids subclasses. CONCLUSION Flavonoids intake positively contributes to delaying the biological aging process, especially in the heart, and liver organ, which may be beneficial for reducing the long-term risk of cardiovascular or liver disease.
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Affiliation(s)
- Wenmin Xing
- Department of Geriatrics, Zhejiang Provincial Key Laboratory of Geriatrics, Zhejiang Hospital, No. 1229, Gudun Road, 310013, Hangzhou, China
| | - Wenyan Gao
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
| | - Zhenlei Zhao
- Department of Geriatrics, Zhejiang Provincial Key Laboratory of Geriatrics, Zhejiang Hospital, No. 1229, Gudun Road, 310013, Hangzhou, China
| | - Xiaogang Xu
- Department of Geriatrics, Zhejiang Provincial Key Laboratory of Geriatrics, Zhejiang Hospital, No. 1229, Gudun Road, 310013, Hangzhou, China
| | - Hongyan Bu
- School of Pharmacy, Hangzhou Medical College, Hangzhou, China
| | - Huili Su
- Department of Geriatrics, Zhejiang Provincial Key Laboratory of Geriatrics, Zhejiang Hospital, No. 1229, Gudun Road, 310013, Hangzhou, China.
| | - Genxiang Mao
- Department of Geriatrics, Zhejiang Provincial Key Laboratory of Geriatrics, Zhejiang Hospital, No. 1229, Gudun Road, 310013, Hangzhou, China.
| | - Jun Chen
- Department of Geriatrics, Zhejiang Provincial Key Laboratory of Geriatrics, Zhejiang Hospital, No. 1229, Gudun Road, 310013, Hangzhou, China.
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Restoring Epigenetic Reprogramming with Diet and Exercise to Improve Health-Related Metabolic Diseases. Biomolecules 2023; 13:biom13020318. [PMID: 36830687 PMCID: PMC9953584 DOI: 10.3390/biom13020318] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 01/30/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
Epigenetic reprogramming predicts the long-term functional health effects of health-related metabolic disease. This epigenetic reprogramming is activated by exogenous or endogenous insults, leading to altered healthy and different disease states. The epigenetic and environmental changes involve a roadmap of epigenetic networking, such as dietary components and exercise on epigenetic imprinting and restoring epigenome patterns laid down during embryonic development, which are paramount to establishing youthful cell type and health. Nutrition and exercise are among the most well-known environmental epigenetic factors influencing the proper developmental and functional lifestyle, with potential beneficial or detrimental effects on health status. The diet and exercise strategies applied from conception could represent an innovative epigenetic target for preventing and treating human diseases. Here, we describe the potential role of diet and exercise as therapeutic epigenetic strategies for health and diseases, highlighting putative future perspectives in this field.
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Ghemrawi M, Tejero NF, Duncan G, McCord B. Pyrosequencing: Current forensic methodology and future applications-a review. Electrophoresis 2023; 44:298-312. [PMID: 36168852 DOI: 10.1002/elps.202200177] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 02/01/2023]
Abstract
The recent development of small, single-amplicon-based benchtop systems for pyrosequencing has opened up a host of novel procedures for applications in forensic science. Pyrosequencing is a sequencing by synthesis technique, based on chemiluminescent inorganic pyrophosphate detection. This review explains the pyrosequencing workflow and illustrates the step-by-step chemistry, followed by a description of the assay design and factors to keep in mind for an exemplary assay. Existing and potential forensic applications are highlighted using this technology. Current applications include identifying species, identifying bodily fluids, and determining smoking status. We also review progress in potential applications for the future, including research on distinguishing monozygotic twins, detecting alcohol and drug abuse, and other phenotypic characteristics such as diet and body mass index. Overall, the versatility of the pyrosequencing technologies renders it a useful tool in forensic genomics.
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Affiliation(s)
- Mirna Ghemrawi
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - Nicole Fernandez Tejero
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
| | - George Duncan
- Halmos College of Natural Sciences and Oceanography, Nova Southeastern University, Dania Beach, Florida, USA
| | - Bruce McCord
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida, USA
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Domingo-Relloso A, Gribble MO, Riffo-Campos AL, Haack K, Cole SA, Tellez-Plaza M, Umans JG, Fretts AM, Zhang Y, Fallin MD, Navas-Acien A, Everson TM. Epigenetics of type 2 diabetes and diabetes-related outcomes in the Strong Heart Study. Clin Epigenetics 2022; 14:177. [PMID: 36529747 PMCID: PMC9759920 DOI: 10.1186/s13148-022-01392-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 11/30/2022] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND The prevalence of type 2 diabetes has dramatically increased in the past years. Increasing evidence supports that blood DNA methylation, the best studied epigenetic mark, is related to diabetes risk. Few prospective studies, however, are available. We studied the association of blood DNA methylation with diabetes in the Strong Heart Study. We used limma, Iterative Sure Independence Screening and Cox regression to study the association of blood DNA methylation with fasting glucose, HOMA-IR and incident type 2 diabetes among 1312 American Indians from the Strong Heart Study. DNA methylation was measured using Illumina's MethylationEPIC beadchip. We also assessed the biological relevance of our findings using bioinformatics analyses. RESULTS Among the 358 differentially methylated positions (DMPs) that were cross-sectionally associated either with fasting glucose or HOMA-IR, 49 were prospectively associated with incident type 2 diabetes, although no DMPs remained significant after multiple comparisons correction. Multiple of the top DMPs were annotated to genes with relevant functions for diabetes including SREBF1, associated with obesity, type 2 diabetes and insulin sensitivity; ABCG1, involved in cholesterol and phospholipids transport; and HDAC1, of the HDAC family. (HDAC inhibitors have been proposed as an emerging treatment for diabetes and its complications.) CONCLUSIONS: Our results suggest that differences in peripheral blood DNA methylation are related to cross-sectional markers of glucose metabolism and insulin activity. While some of these DMPs were modestly associated with prospective incident type 2 diabetes, they did not survive multiple testing. Common DMPs with diabetes epigenome-wide association studies from other populations suggest a partially common epigenomic signature of glucose and insulin activity.
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Affiliation(s)
- Arce Domingo-Relloso
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain.
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA.
- Department of Statistics and Operations Research, University of Valencia, Valencia, Spain.
| | - Matthew O Gribble
- Department of Epidemiology, University of Alabama at Birmingham School of Public Health, Birmingham, AL, USA
| | - Angela L Riffo-Campos
- Millennium Nucleus On Sociomedicine (SocioMed) and Vicerrectoría Académica, Universidad de La Frontera, Temuco, Chile
- Department of Computer Science, ETSE, University of Valencia, Valencia, Spain
| | - Karin Haack
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Shelley A Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX, USA
| | - Maria Tellez-Plaza
- Department of Chronic Diseases Epidemiology, National Center for Epidemiology, Carlos III Health Institute, Madrid, Spain
| | - Jason G Umans
- MedStar Health Research Institute, Hyattsville, MD, USA
- Georgetown-Howard Universities Center for Clinical and Translational Science, Washington, DC, USA
| | - Amanda M Fretts
- Department of Epidemiology, Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
| | - Ying Zhang
- Department of Biostatistics and Epidemiology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK, USA
| | - M Daniele Fallin
- Emory University Rollins School of Public Health, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
| | - Ana Navas-Acien
- Department of Environmental Health Sciences, Columbia University Mailman School of Public Health, New York, NY, USA
| | - Todd M Everson
- Gangarosa Department of Environmental Health, Emory University Rollins School of Public Health, Atlanta, GA, USA
- Department of Epidemiology, Emory University Rollins School of Public Health, Atlanta, GA, USA
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9
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Gevaert AB, Wood N, Boen JRA, Davos CH, Hansen D, Hanssen H, Krenning G, Moholdt T, Osto E, Paneni F, Pedretti RFE, Plösch T, Simonenko M, Bowen TS. Epigenetics in the primary and secondary prevention of cardiovascular disease: influence of exercise and nutrition. Eur J Prev Cardiol 2022; 29:2183-2199. [PMID: 35989414 DOI: 10.1093/eurjpc/zwac179] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 07/29/2022] [Accepted: 08/16/2022] [Indexed: 01/11/2023]
Abstract
Increasing evidence links changes in epigenetic systems, such as DNA methylation, histone modification, and non-coding RNA expression, to the occurrence of cardiovascular disease (CVD). These epigenetic modifications can change genetic function under influence of exogenous stimuli and can be transferred to next generations, providing a potential mechanism for inheritance of behavioural intervention effects. The benefits of exercise and nutritional interventions in the primary and secondary prevention of CVD are well established, but the mechanisms are not completely understood. In this review, we describe the acute and chronic epigenetic effects of physical activity and dietary changes. We propose exercise and nutrition as potential triggers of epigenetic signals, promoting the reshaping of transcriptional programmes with effects on CVD phenotypes. Finally, we highlight recent developments in epigenetic therapeutics with implications for primary and secondary CVD prevention.
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Affiliation(s)
- Andreas B Gevaert
- Research Group Cardiovascular Diseases, GENCOR Department, University of Antwerp, Campus Drie Eiken D.T.228, Universiteitsplein 1, Antwerp 2610, Belgium.,Department of Cardiology, Antwerp University Hospital (UZA), Edegem, Belgium
| | - Nathanael Wood
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Jente R A Boen
- Research Group Cardiovascular Diseases, GENCOR Department, University of Antwerp, Campus Drie Eiken D.T.228, Universiteitsplein 1, Antwerp 2610, Belgium
| | - Constantinos H Davos
- Cardiovascular Research Laboratory, Biomedical Research Foundation, Academy of Athens, Athens, Greece
| | - Dominique Hansen
- Department of Cardiology, Heart Center Hasselt, Jessa Hospital, Hasselt, Belgium.,BIOMED-REVAL-Rehabilitation Research Centre, Faculty of Rehabilitation Sciences, Hasselt University, Hasselt, Belgium
| | - Henner Hanssen
- Department of Sport, Exercise and Health, Sports and Exercise Medicine, Faculty of Medicine, University of Basel, Basel, Switzerland
| | - Guido Krenning
- Laboratory for Cardiovascular Regenerative Medicine, Department of Pathology and Medical Biology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Trine Moholdt
- Department of Circulation and Medical Imaging, Faculty of Medicine and Health Sciences, Norwegian Institute of Science and Technology (NTNU), Trondheim, Norway.,Department of Women's Health, St Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Elena Osto
- Institute of Clinical Chemistry, University and University Hospital Zurich, Zurich, Switzerland.,University Heart Center, University Hospital Zurich, Zurich, Switzerland.,Laboratory of Translational Nutrition Biology, Swiss Federal Institute of Technology (ETH), Zurich, Switzerland
| | - Francesco Paneni
- University Heart Center, University Hospital Zurich, Zurich, Switzerland.,Center for Molecular Cardiology, University of Zurich, Zurich, Switzerland.,Department of Research and Education, University Hospital Zurich, Zurich, Switzerland
| | - Roberto F E Pedretti
- Cardiovascular Department, IRCCS MultiMedica, Care and Research Institute, Milan, Italy
| | - Torsten Plösch
- Department of Obstetrics and Gynaecology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.,Perinatal Neurobiology, Department of Human Medicine, School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Maria Simonenko
- Physiology Research and Blood Circulation Department, Cardiopulmonary Exercise Test SRL, Federal State Budgetary Institution, 'V.A. Almazov National Medical Research Centre' of the Ministry of Health of the Russian Federation, Saint-Petersburg, Russian Federation
| | - T Scott Bowen
- School of Biomedical Sciences, Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
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10
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Sokolowska KE, Maciejewska-Markiewicz D, Bińkowski J, Palma J, Taryma-Leśniak O, Kozlowska-Petriczko K, Borowski K, Baśkiewicz-Hałasa M, Hawryłkowicz V, Załęcka P, Ufnal M, Strapagiel D, Jarczak J, Skonieczna-Żydecka K, Ryterska K, Machaliński B, Wojdacz TK, Stachowska E. Identified in blood diet-related methylation changes stratify liver biopsies of NAFLD patients according to fibrosis grade. Clin Epigenetics 2022; 14:157. [PMID: 36447285 PMCID: PMC9710135 DOI: 10.1186/s13148-022-01377-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/15/2022] [Indexed: 12/05/2022] Open
Abstract
BACKGROUND High caloric diet and lack of physical activity are considered main causes of NAFLD, and a change in the diet is still the only effective treatment of this disease. However, molecular mechanism of the effectiveness of diet change in treatment of NAFLD is poorly understood. We aimed to assess the involvement of epigenetic mechanisms of gene expression regulation in treatment of NAFLD. Eighteen participants with medium- to high-grade steatosis were recruited and trained to follow the Mediterranean diet modified to include fibre supplements. At three timepoints (baseline, after 30 and 60 days), we evaluated adherence to the diet and measured a number of physiological parameters such as anthropometry, blood and stool biochemistry, liver steatosis and stiffness. We also collected whole blood samples for genome-wide methylation profiling and histone acetylation assessment. RESULTS The diet change resulted in a decrease in liver steatosis along with statistically significant, but a minor change in BMI and weight of our study participants. The epigenetic profiling of blood cells identified significant genome-wide changes of methylation and acetylation with the former not involving regions directly regulating gene expression. Most importantly, we were able to show that identified blood methylation changes occur also in liver cells of NAFLD patients and the machine learning-based classifier that we build on those methylation changes was able to predict the stage of liver fibrosis with ROC AUC = 0.9834. CONCLUSION Methylomes of blood cells from NAFLD patients display a number of changes that are most likely a consequence of unhealthy diet, and the diet change appears to reverse those epigenetic changes. Moreover, the methylation status at CpG sites undergoing diet-related methylation change in blood cells stratifies liver biopsies from NAFLD patients according to fibrosis grade.
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Affiliation(s)
- Katarzyna Ewa Sokolowska
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Dominika Maciejewska-Markiewicz
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Jan Bińkowski
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Joanna Palma
- grid.107950.a0000 0001 1411 4349Department of Biochemical Sciences, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Olga Taryma-Leśniak
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Katarzyna Kozlowska-Petriczko
- grid.107950.a0000 0001 1411 4349Translational Medicine Group, Pomeranian Medical University, 70-204 Szczecin, Poland ,Department of Gastroenterology and Internal Medicine, SPWSZ Hospital, 71-455 Szczecin, Poland
| | - Konrad Borowski
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Magdalena Baśkiewicz-Hałasa
- grid.107950.a0000 0001 1411 4349Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Viktoria Hawryłkowicz
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Patrycja Załęcka
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Marcin Ufnal
- grid.13339.3b0000000113287408Department of Experimental Physiology and Pathophysiology, Laboratory of Centre for Preclinical Research, Medical University of Warsaw, 02-097 Warsaw, Poland
| | - Dominik Strapagiel
- grid.10789.370000 0000 9730 2769Biobank Laboratory, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland
| | - Justyna Jarczak
- grid.10789.370000 0000 9730 2769Biobank Laboratory, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, 90-237 Lodz, Poland ,grid.413454.30000 0001 1958 0162Laboratory of Molecular Basis of Behavior, Nencki Institute of Experimental Biology, Polish Academy of Science, Warsaw, Poland
| | - Karolina Skonieczna-Żydecka
- grid.107950.a0000 0001 1411 4349Department of Biochemical Sciences, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Karina Ryterska
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
| | - Bogusław Machaliński
- grid.107950.a0000 0001 1411 4349Department of General Pathology, Pomeranian Medical University, 70-111 Szczecin, Poland
| | - Tomasz Kazimierz Wojdacz
- grid.107950.a0000 0001 1411 4349Independent Clinical Epigenetics Laboratory, Pomeranian Medical University, Unii Lubelskiej 1, 71-252 Szczecin, Poland
| | - Ewa Stachowska
- grid.107950.a0000 0001 1411 4349Department of Human Nutrition and Metabolomics, Pomeranian Medical University, 71-460 Szczecin, Poland
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11
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Liu Y, He L, Wang W. Systematic assessment of microRNAs associated with lung cancer and physical exercise. Front Oncol 2022; 12:917667. [PMID: 36110941 PMCID: PMC9468783 DOI: 10.3389/fonc.2022.917667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 08/08/2022] [Indexed: 12/24/2022] Open
Abstract
It has long been evident that physical exercise reduces the risk of cancer and improves treatment efficacy in tumor patients, particularly in lung cancer (LC). Several molecular mechanisms have been reported, but the mechanisms related to microRNAs (miRNAs) are not well understood. MiRNAs modulated various basic biological processes by negatively regulating gene expression and can be transmitted between cells as signaling molecules. Recent studies have shown that miRNAs are actively released into the circulation during exercise, and are deeply involved in cancer pathology. Hence, the role of exercise intervention in LC treatment may be further understood by identifying miRNAs associated with LC and physical activity. Here, miRNAs expression datasets related to LC and exercise were collected to screen altered miRNAs. Further bioinformatic approaches were performed to analyze the value of the selected miRNAs. The results identified 42 marker miRNAs in LC, of which three core-miRNAs (has-miR-195, has-miR-26b, and has-miR-126) were co-regulated by exercise and cancer, mainly involved in cell cycle and immunity. Our study supports the idea that using exercise intervention as adjuvant therapy for LC patients. These core-miRNAs, which are down-regulated in cancer but elevated by exercise, may act as suppressors in LC and serve as non-invasive biomarkers for cancer prevention.
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Affiliation(s)
- Yang Liu
- Department of Central Laboratory, The First People’s Hospital of Huzhou, First Affiliated Hospital of Huzhou University, Huzhou, China
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- *Correspondence: Yang Liu,
| | - Libo He
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Wang Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
- Department of Medicine, Nanchang Medical College, Nanchang, China
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12
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Woldeamanuel YW, Shrivastava S, Vila-Pueyo M. Editorial: Lifestyle modifications to manage migraine. Front Neurol 2022; 13:966424. [PMID: 36105771 PMCID: PMC9465452 DOI: 10.3389/fneur.2022.966424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 06/27/2022] [Indexed: 11/17/2022] Open
Affiliation(s)
- Yohannes W. Woldeamanuel
- Division of Headache & Facial Pain, Department of Neurology & Neurological Sciences, Stanford University School of Medicine, Stanford, CA, United States
- *Correspondence: Yohannes W. Woldeamanuel
| | | | - Marta Vila-Pueyo
- Headache and Neurological Pain Research Group, Department of Medicine, Vall d'Hebron Research Institute, Universitat Autònoma de Barcelona, Barcelona, Spain
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13
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Thompson M, Hill BL, Rakocz N, Chiang JN, Geschwind D, Sankararaman S, Hofer I, Cannesson M, Zaitlen N, Halperin E. Methylation risk scores are associated with a collection of phenotypes within electronic health record systems. NPJ Genom Med 2022; 7:50. [PMID: 36008412 PMCID: PMC9411568 DOI: 10.1038/s41525-022-00320-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 07/18/2022] [Indexed: 12/20/2022] Open
Abstract
Inference of clinical phenotypes is a fundamental task in precision medicine, and has therefore been heavily investigated in recent years in the context of electronic health records (EHR) using a large arsenal of machine learning techniques, as well as in the context of genetics using polygenic risk scores (PRS). In this work, we considered the epigenetic analog of PRS, methylation risk scores (MRS), a linear combination of methylation states. We measured methylation across a large cohort (n = 831) of diverse samples in the UCLA Health biobank, for which both genetic and complete EHR data are available. We constructed MRS for 607 phenotypes spanning diagnoses, clinical lab tests, and medication prescriptions. When added to a baseline set of predictive features, MRS significantly improved the imputation of 139 outcomes, whereas the PRS improved only 22 (median improvement for methylation 10.74%, 141.52%, and 15.46% in medications, labs, and diagnosis codes, respectively, whereas genotypes only improved the labs at a median increase of 18.42%). We added significant MRS to state-of-the-art EHR imputation methods that leverage the entire set of medical records, and found that including MRS as a medical feature in the algorithm significantly improves EHR imputation in 37% of lab tests examined (median R2 increase 47.6%). Finally, we replicated several MRS in multiple external studies of methylation (minimum p-value of 2.72 × 10−7) and replicated 22 of 30 tested MRS internally in two separate cohorts of different ethnicity. Our publicly available results and weights show promise for methylation risk scores as clinical and scientific tools.
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Affiliation(s)
- Mike Thompson
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
| | - Brian L Hill
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.
| | - Nadav Rakocz
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA
| | - Jeffrey N Chiang
- Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Daniel Geschwind
- Institute of Precision Health, University of California Los Angeles, Los Angeles, CA, USA
| | - Sriram Sankararaman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA.,Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA.,Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA
| | - Ira Hofer
- Department of Anesthesiology and Perioperative Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Maxime Cannesson
- Department of Anesthesiology and Perioperative Medicine, University of California Los Angeles, Los Angeles, CA, USA
| | - Noah Zaitlen
- Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Eran Halperin
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Computational Medicine, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Human Genetics, University of California Los Angeles, Los Angeles, CA, USA. .,Department of Anesthesiology and Perioperative Medicine, University of California Los Angeles, Los Angeles, CA, USA.
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14
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Gim JA. A Genomic Information Management System for Maintaining Healthy Genomic States and Application of Genomic Big Data in Clinical Research. Int J Mol Sci 2022; 23:5963. [PMID: 35682641 PMCID: PMC9180925 DOI: 10.3390/ijms23115963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 05/22/2022] [Accepted: 05/25/2022] [Indexed: 01/19/2023] Open
Abstract
Improvements in next-generation sequencing (NGS) technology and computer systems have enabled personalized therapies based on genomic information. Recently, health management strategies using genomics and big data have been developed for application in medicine and public health science. In this review, I first discuss the development of a genomic information management system (GIMS) to maintain a highly detailed health record and detect diseases by collecting the genomic information of one individual over time. Maintaining a health record and detecting abnormal genomic states are important; thus, the development of a GIMS is necessary. Based on the current research status, open public data, and databases, I discuss the possibility of a GIMS for clinical use. I also discuss how the analysis of genomic information as big data can be applied for clinical and research purposes. Tremendous volumes of genomic information are being generated, and the development of methods for the collection, cleansing, storing, indexing, and serving must progress under legal regulation. Genetic information is a type of personal information and is covered under privacy protection; here, I examine the regulations on the use of genetic information in different countries. This review provides useful insights for scientists and clinicians who wish to use genomic information for healthy aging and personalized medicine.
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Affiliation(s)
- Jeong-An Gim
- Medical Science Research Center, College of Medicine, Korea University Guro Hospital, Seoul 08308, Korea
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15
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Bordoni L, Malinowska AM, Petracci I, Szwengiel A, Gabbianelli R, Chmurzynska A. Diet, Trimethylamine Metabolism, and Mitochondrial DNA: An Observational Study. Mol Nutr Food Res 2022; 66:e2200003. [PMID: 35490412 DOI: 10.1002/mnfr.202200003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 04/14/2022] [Indexed: 12/11/2022]
Abstract
SCOPE Mitochondrial DNA copy number (mtDNAcn) and its methylation level in the D-loop area have been correlated with metabolic health and are suggested to vary in response to environmental stimuli, including diet. Circulating levels of trimethylamine-n-oxide (TMAO), which is an oxidative derivative of the trimethylamine (TMA) produced by the gut microbiome from dietary precursors, have been associated with chronic diseases and are suggested to have an impact on mitochondrial dynamics. This study is aimed to investigate the relationship between diet, TMA, TMAO, and mtDNAcn, as well as DNA methylation. METHODS AND RESULTS Two hundred subjects with extreme (healthy and unhealthy) dietary patterns are recruited. Dietary records are collected to assess their nutrient intake and diets' quality (Healthy Eating Index). Blood levels of TMA and TMAO, circulating levels of TMA precursors and their dietary intakes are measured. MtDNAcn, nuclear DNA methylation long interspersed nuclear element 1 (LINE-1), and strand-specific D-loop methylation levels are assessed. There is no association between dietary patterns and mtDNAcn. The TMAO/TMA ratio is negatively correlated with d-loop methylation levels but positively with mtDNAcn. CONCLUSIONS These findings suggest a potential association between TMA metabolism and mitochondrial dynamics (and mtDNA), indicating a new avenue for further research.
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Affiliation(s)
- Laura Bordoni
- Unit of Molecular Biology and Nutrigenomics, School of Pharmacy, University of Camerino, Camerino, 62032, MC, Italy
| | - Anna M Malinowska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, 60-624, Poland
| | - Irene Petracci
- School of Advanced Studies, University of Camerino, Camerino, 62032, MC, Italy
| | - Artur Szwengiel
- Department of Food Technology of Plant Origin, Poznań University of Life Sciences, Poznań, 60-624, Poland
| | - Rosita Gabbianelli
- Unit of Molecular Biology and Nutrigenomics, School of Pharmacy, University of Camerino, Camerino, 62032, MC, Italy
| | - Agata Chmurzynska
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Poznań, 60-624, Poland
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16
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Obesity-Associated Differentially Methylated Regions in Colon Cancer. J Pers Med 2022; 12:jpm12050660. [PMID: 35629083 PMCID: PMC9142939 DOI: 10.3390/jpm12050660] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Obesity with adiposity is a common disorder in modern days, influenced by environmental factors such as eating and lifestyle habits and affecting the epigenetics of adipose-based gene regulations and metabolic pathways in colorectal cancer (CRC). We compared epigenetic changes of differentially methylated regions (DMR) of genes in colon tissues of 225 colon cancer cases (154 non-obese and 71 obese) and 15 healthy non-obese controls by accessing The Cancer Genome Atlas (TCGA) data. We applied machine-learning-based analytics including generalized regression (GR) as a confirmatory validation model to identify the factors that could contribute to DMRs impacting colon cancer to enhance prediction accuracy. We found that age was a significant predictor in obese cancer patients, both alone (p = 0.003) and interacting with hypomethylated DMRs of ZBTB46, a tumor suppressor gene (p = 0.008). DMRs of three additional genes: HIST1H3I (p = 0.001), an oncogene with a hypomethylated DMR in the promoter region; SRGAP2C (p = 0.006), a tumor suppressor gene with a hypermethylated DMR in the promoter region; and NFATC4 (p = 0.006), an adipocyte differentiating oncogene with a hypermethylated DMR in an intron region, are also significant predictors of cancer in obese patients, independent of age. The genes affected by these DMR could be potential novel biomarkers of colon cancer in obese patients for cancer prevention and progression.
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17
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Mediterranean diet and other dietary patterns in association with biological aging in the moli-sani study cohort. Clin Nutr 2022; 41:1025-1033. [DOI: 10.1016/j.clnu.2022.02.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 02/17/2022] [Accepted: 02/28/2022] [Indexed: 02/07/2023]
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18
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A dry immersion model of microgravity modulates platelet phenotype, miRNA signature, and circulating plasma protein biomarker profile. Sci Rep 2021; 11:21906. [PMID: 34753989 PMCID: PMC8578674 DOI: 10.1038/s41598-021-01335-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/26/2021] [Indexed: 11/08/2022] Open
Abstract
Ground based research modalities of microgravity have been proposed as innovative methods to investigate the aetiology of chronic age-related conditions such as cardiovascular disease. Dry Immersion (DI), has been effectively used to interrogate the sequelae of physical inactivity (PI) and microgravity on multiple physiological systems. Herein we look at the causa et effectus of 3-day DI on platelet phenotype, and correlate with both miRomic and circulating biomarker expression. The miRomic profile of platelets is reflective of phenotype, which itself is sensitive and malleable to the exposome, undergoing responsive transitions in order to fulfil platelets role in thrombosis and haemostasis. Heterogeneous platelet subpopulations circulate at any given time, with varying degrees of sensitivity to activation. Employing a DI model, we investigate the effect of acute PI on platelet function in 12 healthy males. 3-day DI resulted in a significant increase in platelet count, plateletcrit, platelet adhesion, aggregation, and a modest elevation of platelet reactivity index (PRI). We identified 15 protein biomarkers and 22 miRNA whose expression levels were altered after DI. A 3-day DI model of microgravity/physical inactivity induced a prothrombotic platelet phenotype with an unique platelet miRNA signature, increased platelet count and plateletcrit. This correlated with a unique circulating protein biomarker signature. Taken together, these findings highlight platelets as sensitive adaptive sentinels and functional biomarkers of epigenetic drift within the cardiovascular compartment.
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19
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Saito T, Whatmore P, Taylor JF, Fernandes JM, Adam AC, Tocher DR, Espe M, Skjærven KH. Micronutrient supplementation affects transcriptional and epigenetic regulation of lipid metabolism in a dose-dependent manner. Epigenetics 2021; 16:1217-1234. [PMID: 33315488 PMCID: PMC8813078 DOI: 10.1080/15592294.2020.1859867] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/15/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Micronutrients (vitamins and minerals) have been less well studied compared to macronutrients (fats, proteins, and carbohydrates) although they play important roles in growth, metabolism, and maintenance of tissues. Hence, there is growing interest to understand the influence of micronutrients across various aspects in nutritional research. In the last two decades, aquaculture feeds have been shifted to containing more plant-based materials to meet the increasing demand and maintain the sustainability in the industry. A recent whole life cycle feeding trial of Atlantic salmon (Salmo salar) with graded levels of micronutrient packages has concluded that the levels of several B-vitamins and microminerals need to be increased from the current recommendation levels for optimal growth and fish welfare when plant-based diets are used. Here, we show the effect of micronutrient supplementation on hepatic transcriptional and epigenetic regulation in a dose dependent manner. . Specifically, our aim is to reveal the mechanisms of altered cell metabolism, which results in improved growth performance by micronutrient surpluses, at gene expression and DNA methylation levels. Our results strongly indicate that micronutrient supplementation suppresses gene expression in lipid metabolism in a dose-dependent manner and broadly affects DNA methylation in cell-adhesion and cell-signalling. In particular, it increases DNA methylation levels on the acetyl-CoA carboxylase alpha promoter in a concentration-dependent manner, which further suggests that acetyl-CoA carboxylase alpha is an upstream epigenetic regulator controlling its downstream lipid biosynthesis activities. This study demonstrates a comprehensive analysis to reveal an important role of micronutrients in lipid metabolism through epigenetic control of gene expression.
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Affiliation(s)
- Takaya Saito
- Feed and Nutrition, Institute of Marine Research, Bergen, Norway
| | - Paul Whatmore
- Feed and Nutrition, Institute of Marine Research, Bergen, Norway
| | - John F. Taylor
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Scotland, UK
| | | | - Anne-Catrin Adam
- Feed and Nutrition, Institute of Marine Research, Bergen, Norway
| | - Douglas R. Tocher
- Institute of Aquaculture, Faculty of Natural Sciences, University of Stirling, Scotland, UK
| | - Marit Espe
- Feed and Nutrition, Institute of Marine Research, Bergen, Norway
| | - Kaja H. Skjærven
- Feed and Nutrition, Institute of Marine Research, Bergen, Norway
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20
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Shields RK, Dudley-Javoroski S. Epigenetics and the International Classification of Functioning, Disability and Health Model: Bridging Nature, Nurture, and Patient-Centered Population Health. Phys Ther 2021; 102:6413906. [PMID: 34718813 PMCID: PMC9432474 DOI: 10.1093/ptj/pzab247] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 08/10/2021] [Accepted: 09/23/2021] [Indexed: 11/13/2022]
Abstract
Epigenetic processes enable environmental inputs such as diet, exercise, and health behaviors to reversibly tag DNA with chemical "marks" that increase or decrease the expression of an individual's genetic template. Over time, epigenetic adaptations enable the effects of healthy or unhealthy stresses to become stably expressed in the tissue of an organism, with important consequences for health and disease. New research indicates that seemingly non-biological factors such as social stress, poverty, and childhood hardship initiate epigenetic adaptations in gene pathways that govern inflammation and immunity, two of the greatest contributors to chronic diseases such as diabetes and obesity. Epigenetic processes therefore provide a biological bridge between the genome-an individual's genetic inheritance-and the Social Determinants of Health-the conditions in which they are born, grow, live, work, and age. This Perspective paper argues that physical therapy clinicians, researchers, and educators can use the theoretical framework provided by the International Classification of Functioning, Disability, and Health (ICF model) to harmonize new discoveries from both public health research and medically focused genomic research. The ICF model likewise captures the essential role played by physical activity and exercise, which initiate powerful and widespread epigenetic adaptations that promote health and functioning. In this proposed framework, epigenetic processes transduce the effects of the social determinants of health and behaviors such as exercise into stable biological adaptations that affect an individual's daily activities and their participation in social roles. By harmonizing "nature" and "nurture," physical therapists can approach patient care with a more integrated perspective, capitalizing on novel discoveries in precision medicine, rehabilitation science, and in population-level research. As the experts in physical activity and exercise, physical therapists are ideally positioned to drive progress in the new era of patient-centered population health care.
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Affiliation(s)
| | - Shauna Dudley-Javoroski
- Department of Physical Therapy and Rehabilitation Science, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
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21
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DNA Methylation and Type 2 Diabetes: Novel Biomarkers for Risk Assessment? Int J Mol Sci 2021; 22:ijms222111652. [PMID: 34769081 PMCID: PMC8584054 DOI: 10.3390/ijms222111652] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/25/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Diabetes is a severe threat to global health. Almost 500 million people live with diabetes worldwide. Most of them have type 2 diabetes (T2D). T2D patients are at risk of developing severe and life-threatening complications, leading to an increased need for medical care and reduced quality of life. Improved care for people with T2D is essential. Actions aiming at identifying undiagnosed diabetes and at preventing diabetes in those at high risk are needed as well. To this end, biomarker discovery and validation of risk assessment for T2D are critical. Alterations of DNA methylation have recently helped to better understand T2D pathophysiology by explaining differences among endophenotypes of diabetic patients in tissues. Recent evidence further suggests that variations of DNA methylation might contribute to the risk of T2D even more significantly than genetic variability and might represent a valuable tool to predict T2D risk. In this review, we focus on recent information on the contribution of DNA methylation to the risk and the pathogenesis of T2D. We discuss the limitations of these studies and provide evidence supporting the potential for clinical application of DNA methylation marks to predict the risk and progression of T2D.
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Esposito S, Gialluisi A, Costanzo S, Di Castelnuovo A, Ruggiero E, De Curtis A, Persichillo M, Cerletti C, Donati MB, de Gaetano G, Iacoviello L, Bonaccio M. Dietary Polyphenol Intake Is Associated with Biological Aging, a Novel Predictor of Cardiovascular Disease: Cross-Sectional Findings from the Moli-Sani Study. Nutrients 2021; 13:1701. [PMID: 34067821 PMCID: PMC8157169 DOI: 10.3390/nu13051701] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 05/12/2021] [Accepted: 05/12/2021] [Indexed: 12/11/2022] Open
Abstract
Biological aging, or the discrepancy between biological and chronological age of a subject (Δage), has been associated with a polyphenol-rich Mediterranean diet and represents a new, robust indicator of cardiovascular disease risk. We aimed to disentangle the relationship of dietary polyphenols and total antioxidant capacity with Δage in a cohort of Italians. A cross-sectional analysis was performed on a sub-cohort of 4592 subjects (aged ≥ 35 y; 51.8% women) from the Moli-sani Study (2005-2010). Food intake was recorded by a 188-item food-frequency questionnaire. The polyphenol antioxidant content (PAC)-score was constructed to assess the total dietary content of polyphenols. Total antioxidant capacity was measured in foods by these assays: trolox equivalent antioxidant capacity (TEAC), total radical-trapping antioxidant parameter (TRAP) and ferric reducing-antioxidant power (FRAP). A deep neural network, based on 36 circulating biomarkers, was used to compute biological age and the resulting Δage, which was tested as outcome in multivariable-adjusted linear regressions. Δage was inversely associated with the PAC-score (β = -0.31; 95%CI -0.39, -0.24) but not with total antioxidant capacity of the diet. A diet rich in polyphenols, by positively contributing to deceleration of the biological aging process, may exert beneficial effects on the long-term risk of cardiovascular disease and possibly of bone health.
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Affiliation(s)
- Simona Esposito
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Simona Costanzo
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | | | - Emilia Ruggiero
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Amalia De Curtis
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Mariarosaria Persichillo
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Chiara Cerletti
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Maria Benedetta Donati
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Giovanni de Gaetano
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
| | - Licia Iacoviello
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
- Department of Medicine and Surgery, Research Center in Epidemiology and Preventive Medicine (EPIMED), University of Insubria, 21100 Varese-Como, Italy
| | - Marialaura Bonaccio
- Department of Epidemiology and Prevention, IRCCS Neuromed, via dell’Elettronica, 86077 Pozzilli, Italy; (S.E.); (A.G.); (S.C.); (E.R.); (A.D.C.); (M.P.); (C.C.); (M.B.D.); (G.d.G.); (M.B.)
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Zhang X, Asllanaj E, Amiri M, Portilla-Fernandez E, Bramer WM, Nano J, Voortman T, Pan Q, Ghanbari M. Deciphering the role of epigenetic modifications in fatty liver disease: A systematic review. Eur J Clin Invest 2021; 51:e13479. [PMID: 33350463 PMCID: PMC8243926 DOI: 10.1111/eci.13479] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Accepted: 12/17/2020] [Indexed: 02/06/2023]
Abstract
BACKGROUND Fatty liver disease (FLD), primarily nonalcoholic fatty liver disease (NAFLD), is the most common liver disorder that affects a quarter of the global population. NAFLD is a spectrum of disease ranging from simple steatosis to nonalcoholic steatohepatitis, which is associated with increased risk of developing liver cancer. Given that the pathogenic mechanisms of fatty liver remain largely elusive, it is important to further investigate potential underlying mechanisms including epigenetic modifications. Here, we performed a systematic review of human epigenetic studies on FLD presence. METHODS Five bibliographic databases were screened until 28 August 2020. We included cross-sectional, case-control and cohort studies in humans that examined the association of epigenetic modifications including global, candidate or epigenome-wide methylation of DNA, noncoding RNAs and histone modifications with FLD. RESULTS In total 36 articles, based on 33 unique studies, consisting of 12 112 participants met the inclusion criteria. Among these, two recent epigenome-wide association studies conducted among large population-based cohorts have reported the association between cg06690548 (SLC7A11) and FLD. Moreover, several studies have demonstrated the association between microRNAs (miRNAs) and FLD, in which miR-122, miR-34a and miR-192 were recognized as the most relevant miRNAs as biomarkers for FLD. We did not find any studies examining histone modifications in relation to FLD. CONCLUSIONS Cumulative evidence suggests a link between epigenetic mechanisms, specifically DNA methylation and miRNAs, and FLD. Further efforts should investigate the molecular pathways by which these epigenetic markers may regulate FLD and also the potential role of histone modifications in FLD.
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Affiliation(s)
- Xiaofang Zhang
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eralda Asllanaj
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands.,Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Masoud Amiri
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Eliana Portilla-Fernandez
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Wichor M Bramer
- Medical Library, Erasmus MC, Erasmus University Medical Centre, Rotterdam, the Netherlands
| | - Jana Nano
- Institute of Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany.,German Diabetes Center, München-Neuherberg, Germany
| | - Trudy Voortman
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Qiuwei Pan
- Department of Gastroenterology and Hepatology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
| | - Mohsen Ghanbari
- Department of Epidemiology, Erasmus MC, Erasmus University Medical Center, Rotterdam, the Netherlands
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Traversi D, Pulliero A, Izzotti A, Franchitti E, Iacoviello L, Gianfagna F, Gialluisi A, Izzi B, Agodi A, Barchitta M, Calabrò GE, Hoxhaj I, Sassano M, Sbrogiò LG, Del Sole A, Marchiori F, Pitini E, Migliara G, Marzuillo C, De Vito C, Tamburro M, Sammarco ML, Ripabelli G, Villari P, Boccia S. Precision Medicine and Public Health: New Challenges for Effective and Sustainable Health. J Pers Med 2021; 11:135. [PMID: 33669364 PMCID: PMC7920275 DOI: 10.3390/jpm11020135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 02/11/2021] [Accepted: 02/14/2021] [Indexed: 02/06/2023] Open
Abstract
The development of high-throughput omics technologies represents an unmissable opportunity for evidence-based prevention of adverse effects on human health. However, the applicability and access to multi-omics tests are limited. In Italy, this is due to the rapid increase of knowledge and the high levels of skill and economic investment initially necessary. The fields of human genetics and public health have highlighted the relevance of an implementation strategy at a national level in Italy, including integration in sanitary regulations and governance instruments. In this review, the emerging field of public health genomics is discussed, including the polygenic scores approach, epigenetic modulation, nutrigenomics, and microbiomes implications. Moreover, the Italian state of implementation is presented. The omics sciences have important implications for the prevention of both communicable and noncommunicable diseases, especially because they can be used to assess the health status during the whole course of life. An effective population health gain is possible if omics tools are implemented for each person after a preliminary assessment of effectiveness in the medium to long term.
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Affiliation(s)
- Deborah Traversi
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Alessandra Pulliero
- Department of Health Sciences School of Medicine, University of Genoa, 16132 Genova, Italy;
| | - Alberto Izzotti
- Department of Experimental Medicine, University of Genoa, 16132 Genova, Italy;
- IRCCS Ospedale Policlinico San Martino, 161632 Genova, Italy
| | - Elena Franchitti
- Department of Public Health and Pediatrics, University of Torino, Piazza Polonia 94, 10126 Torino, Italy;
| | - Licia Iacoviello
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Francesco Gianfagna
- Research Center in Epidemiology and Preventive Medicine (EPIMED), Department of Medicine and Surgery, University of Insubria, 21100 Varese, Italy; (L.I.); (F.G.)
- Mediterranea Cardiocentro, 80122 Napoli, Italy
| | - Alessandro Gialluisi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Benedetta Izzi
- Department of Epidemiology and Prevention, IRCCS NEUROMED, 86077 Pozzilli, Italy; (A.G.); (B.I.)
| | - Antonella Agodi
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Martina Barchitta
- Department of Medical and Surgical Sciences and Advanced Technologies “GF Ingrassia”, University of Catania, 95123 Catania, Italy; (A.A.); (M.B.)
| | - Giovanna Elisa Calabrò
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Ilda Hoxhaj
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Michele Sassano
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
| | - Luca Gino Sbrogiò
- Dipartimento di Prevenzione, Az. ULSS3 Serenissima, 30174 Venezia, Italy;
| | | | | | - Erica Pitini
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Giuseppe Migliara
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Carolina Marzuillo
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Corrado De Vito
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Manuela Tamburro
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Giancarlo Ripabelli
- Department of Medicine and Health Sciences “Vincenzo Tiberio”, University of Molise, 86100 Campobasso, Italy; (M.T.); (M.L.S.); (G.R.)
| | - Paolo Villari
- Department of Public Health and Infectious Diseases, Sapienza University of Rome, 00185 Roma, Italy; (E.P.); (G.M.); (C.M.); (C.D.V.); (P.V.)
| | - Stefania Boccia
- Section of Hygiene, University Department of Life Sciences and Public Health, Università Cattolica del Sacro Cuore, 00168 Roma, Italy; (G.E.C.); (I.H.); (M.S.); (S.B.)
- Department of Woman and Child Health and Public Health-Public Health Area, Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Roma, Italy
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Ayurveda and Epigenetics. ACTA ACUST UNITED AC 2020; 56:medicina56120687. [PMID: 33322263 PMCID: PMC7763202 DOI: 10.3390/medicina56120687] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 11/30/2020] [Accepted: 12/08/2020] [Indexed: 12/13/2022]
Abstract
Ayurveda is a comprehensive, natural health care system that originated in the ancient Vedic times of India. Epigenetics refers to the external modification of DNA that turns genes on and off, affecting gene expression. This occurs without changes in the basic structure of the DNA. This gene expression can have transgenerational effects. The major factors that cause epigenetic changes are lifestyle and behavior, diet and digestion, stress, and environmental factors. Ayurveda addresses these factors, thereby affecting the Deha (body) Prakriti (psychophysiological constitution), which corresponds to the phenotype, and indirectly the Janma (birth) Prakriti, which corresponds to the genotype. Thus, it is proposed that epigenetics is an important mechanism of Ayurveda. This correlation and understanding will lead to better communication and understanding with the current medical system, and lead to better integration of both sciences in the management of optimal health. In addition, research on Ayurvedic modalities affecting gene expression will further increase correlation and understanding between the current medical system and Ayurveda.
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Cronjé HT, Elliott HR, Nienaber-Rousseau C, Pieters M. Leveraging the urban-rural divide for epigenetic research. Epigenomics 2020; 12:1071-1081. [PMID: 32657149 DOI: 10.2217/epi-2020-0049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Urbanization coincides with a complex change in environmental exposure and a rapid increase in noncommunicable diseases (NCDs). Epigenetics, including DNA methylation (DNAm), is thought to mediate part of the association between genetic/environmental exposure and NCDs. The urban-rural divide provides a unique opportunity to investigate the effect of the combined presence of multiple forms of environmental exposure on DNAm and the related increase in disease risk. This review evaluates the ability of three epidemiological study designs (migration, income-comparative and urban-rural designs) to investigate the role of DNAm in the association between urbanization and the rise in NCD prevalence. We also discuss the ability of each study design to address the gaps in the current literature, including the complex methylation-mediated risk attributable to the cluster of forms of exposure characterizing urban and rural living, while providing a platform for developing countries to leverage their demographic discrepancies in future research ventures.
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Affiliation(s)
- Héléne T Cronjé
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Hannah R Elliott
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol BS8 2BN, UK.,Population Health Sciences, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Cornelie Nienaber-Rousseau
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
| | - Marlien Pieters
- Centre of Excellence for Nutrition, North-West University, Potchefstroom Campus, Potchefstroom, 2520, North-West Province, South Africa
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Dimauro I, Paronetto MP, Caporossi D. Exercise, redox homeostasis and the epigenetic landscape. Redox Biol 2020; 35:101477. [PMID: 32127290 PMCID: PMC7284912 DOI: 10.1016/j.redox.2020.101477] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/12/2020] [Accepted: 02/23/2020] [Indexed: 02/07/2023] Open
Abstract
Physical exercise represents one of the strongest physiological stimuli capable to induce functional and structural modifications in all biological systems. Indeed, beside the traditional genetic mechanisms, physical exercise can modulate gene expression through epigenetic modifications, namely DNA methylation, post-translational histone modification and non-coding RNA transcripts. Initially considered as merely damaging molecules, it is now well recognized that both reactive oxygen (ROS) and nitrogen species (RNS) produced under voluntary exercise play an important role as regulatory mediators in signaling processes. While robust scientific evidences highlight the role of exercise-associated redox modifications in modulating gene expression through the genetic machinery, the understanding of their specific impact on epigenomic profile is still at an early stage. This review will provide an overview of the role of ROS and RNS in modulating the epigenetic landscape in the context of exercise-related adaptations. Physical exercise can modulate gene expression through epigenetic modifications. Epigenetic regulation of ROS/RNS generating, sensing and neutralizing enzymes can impact the cellular levels of ROS and RNS. ROS might act as modulators of epigenetic machinery, interfering with DNA methylation, hPTMs and ncRNAs expression. Redox homeostasis might hold a relevant role in the epigenetic landscape modulating exercise-related adaptations.
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Affiliation(s)
- Ivan Dimauro
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy
| | - Maria Paola Paronetto
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy; Laboratory of Cellular and Molecular Neurobiology, IRCCS Fondazione Santa Lucia, Via Del Fosso di Fiorano, Rome, Italy
| | - Daniela Caporossi
- Unit of Biology and Genetics of Movement, Department of Movement, Human and Health Sciences, University of Rome Foro Italico, Piazza Lauro de Bosis 15, 00135, Rome, Italy.
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