1
|
Xiong X, Chen H, Zhang Q, Liu Y, Xu C. Uncovering the roles of DNA hemi-methylation in transcriptional regulation using MspJI-assisted hemi-methylation sequencing. Nucleic Acids Res 2024; 52:e24. [PMID: 38261991 PMCID: PMC10954476 DOI: 10.1093/nar/gkae023] [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: 08/31/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024] Open
Abstract
Hemi-methylated cytosine dyads widely occur on mammalian genomic DNA, and can be stably inherited across cell divisions, serving as potential epigenetic marks. Previous identification of hemi-methylation relied on harsh bisulfite treatment, leading to extensive DNA degradation and loss of methylation information. Here we introduce Mhemi-seq, a bisulfite-free strategy, to efficiently resolve methylation status of cytosine dyads into unmethylation, strand-specific hemi-methylation, or full-methylation. Mhemi-seq reproduces methylomes from bisulfite-based sequencing (BS-seq & hpBS-seq), including the asymmetric hemi-methylation enrichment flanking CTCF motifs. By avoiding base conversion, Mhemi-seq resolves allele-specific methylation and associated imprinted gene expression more efficiently than BS-seq. Furthermore, we reveal an inhibitory role of hemi-methylation in gene expression and transcription factor (TF)-DNA binding, and some displays a similar extent of inhibition as full-methylation. Finally, we uncover new hemi-methylation patterns within Alu retrotransposon elements. Collectively, Mhemi-seq can accelerate the identification of DNA hemi-methylation and facilitate its integration into the chromatin environment for future studies.
Collapse
Affiliation(s)
- Xiong Xiong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Hengye Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
| | - Qifan Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangying Liu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chenhuan Xu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| |
Collapse
|
2
|
Walsh JR, Sun G, Balan J, Hardcastle J, Vollenweider J, Jerde C, Rumilla K, Koellner C, Koleilat A, Hasadsri L, Kipp B, Jenkinson G, Klee E. A supervised learning method for classifying methylation disorders. BMC Bioinformatics 2024; 25:66. [PMID: 38347515 PMCID: PMC10863277 DOI: 10.1186/s12859-024-05673-1] [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] [Received: 09/20/2023] [Accepted: 01/24/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND DNA methylation is one of the most stable and well-characterized epigenetic alterations in humans. Accordingly, it has already found clinical utility as a molecular biomarker in a variety of disease contexts. Existing methods for clinical diagnosis of methylation-related disorders focus on outlier detection in a small number of CpG sites using standardized cutoffs which differentiate healthy from abnormal methylation levels. The standardized cutoff values used in these methods do not take into account methylation patterns which are known to differ between the sexes and with age. RESULTS Here we profile genome-wide DNA methylation from blood samples drawn from within a cohort composed of healthy controls of different age and sex alongside patients with Prader-Willi syndrome (PWS), Beckwith-Wiedemann syndrome, Fragile-X syndrome, Angelman syndrome, and Silver-Russell syndrome. We propose a Generalized Additive Model to perform age and sex adjusted outlier analysis of around 700,000 CpG sites throughout the human genome. Utilizing z-scores among the cohort for each site, we deployed an ensemble based machine learning pipeline and achieved a combined prediction accuracy of 0.96 (Binomial 95% Confidence Interval 0.868[Formula: see text]0.995). CONCLUSION We demonstrate a method for age and sex adjusted outlier detection of differentially methylated loci based on a large cohort of healthy individuals. We present a custom machine learning pipeline utilizing this outlier analysis to classify samples for potential methylation associated congenital disorders. These methods are able to achieve high accuracy when used with machine learning methods to classify abnormal methylation patterns.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Alaa Koleilat
- Department of Molecular and Medical Genetics, Oregon Health and Science University, Portland, OR, USA
| | | | | | | | | |
Collapse
|
3
|
Jiraboonsri S, Hemvipat P, Kamolratanakul S, Bhummaphan N, Siritientong T, Kitkumthorn N, Mutirangura A, Meevassana J. CpG methylation changes in Alu repetitive sequences in normal aging due to diastolic hypertension in human dermal fibroblasts from the facial area. Biomed Rep 2024; 20:5. [PMID: 38222864 PMCID: PMC10784876 DOI: 10.3892/br.2023.1693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 11/02/2023] [Indexed: 01/16/2024] Open
Abstract
Aging fibroblasts, an important factor contributing to skin aging, are affected by numerous mechanisms, including alterations in DNA methylation and age-related diseases. The current study aimed to investigate the role of Alu methylation in aging fibroblasts and hypertension. The Alu methylation levels in dermal fibroblasts obtained from patients of different ages and blood pressure status were analyzed using the combined bisulfite restriction analysis technique. An inverse correlation was observed between Alu methylation in dermal fibroblasts and patient age. Dermal fibroblasts from the high-normal diastolic blood pressure group had higher Alu methylation levels compared with those from the normal group. The findings of the present study suggest that Alu methylation alterations can be observed with chronological aging and hypertension, and are a potential aging marker or therapeutic target.
Collapse
Affiliation(s)
- Suvinai Jiraboonsri
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Panicha Hemvipat
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Supitcha Kamolratanakul
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok 10400, Thailand
| | - Narumol Bhummaphan
- College of Public Health Sciences, Chulalongkorn University, Bangkok 10330, Thailand
| | - Tippawan Siritientong
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
| | - Apiwat Mutirangura
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Jiraroch Meevassana
- Center of Excellence in Burn and Wound Care, Chulalongkorn University, Bangkok 10330, Thailand
- Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| |
Collapse
|
4
|
Ng JWY, Felix JF, Olson DM. A novel approach to risk exposure and epigenetics-the use of multidimensional context to gain insights into the early origins of cardiometabolic and neurocognitive health. BMC Med 2023; 21:466. [PMID: 38012757 PMCID: PMC10683259 DOI: 10.1186/s12916-023-03168-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: 02/02/2023] [Accepted: 11/09/2023] [Indexed: 11/29/2023] Open
Abstract
BACKGROUND Each mother-child dyad represents a unique combination of genetic and environmental factors. This constellation of variables impacts the expression of countless genes. Numerous studies have uncovered changes in DNA methylation (DNAm), a form of epigenetic regulation, in offspring related to maternal risk factors. How these changes work together to link maternal-child risks to childhood cardiometabolic and neurocognitive traits remains unknown. This question is a key research priority as such traits predispose to future non-communicable diseases (NCDs). We propose viewing risk and the genome through a multidimensional lens to identify common DNAm patterns shared among diverse risk profiles. METHODS We identified multifactorial Maternal Risk Profiles (MRPs) generated from population-based data (n = 15,454, Avon Longitudinal Study of Parents and Children (ALSPAC)). Using cord blood HumanMethylation450 BeadChip data, we identified genome-wide patterns of DNAm that co-vary with these MRPs. We tested the prospective relation of these DNAm patterns (n = 914) to future outcomes using decision tree analysis. We then tested the reproducibility of these patterns in (1) DNAm data at age 7 and 17 years within the same cohort (n = 973 and 974, respectively) and (2) cord DNAm in an independent cohort, the Generation R Study (n = 686). RESULTS We identified twenty MRP-related DNAm patterns at birth in ALSPAC. Four were prospectively related to cardiometabolic and/or neurocognitive childhood outcomes. These patterns were replicated in DNAm data from blood collected at later ages. Three of these patterns were externally validated in cord DNAm data in Generation R. Compared to previous literature, DNAm patterns exhibited novel spatial distribution across the genome that intersects with chromatin functional and tissue-specific signatures. CONCLUSIONS To our knowledge, we are the first to leverage multifactorial population-wide data to detect patterns of variability in DNAm. This context-based approach decreases biases stemming from overreliance on specific samples or variables. We discovered molecular patterns demonstrating prospective and replicable relations to complex traits. Moreover, results suggest that patterns harbour a genome-wide organisation specific to chromatin regulation and target tissues. These preliminary findings warrant further investigation to better reflect the reality of human context in molecular studies of NCDs.
Collapse
Affiliation(s)
- Jane W Y Ng
- Department of Pediatrics, Cummings School of Medicine, University of Calgary, 28 Oki Drive NW, Calgary, AB, T3B 6A8, Canada
| | - Janine F Felix
- The Generation F Study Group, Erasmus MC University Medical Center Rotterdam, Postbus, 2040, 3000 CA, Rotterdam, The Netherlands
- Department of Pediatrics, Erasmus MC University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - David M Olson
- Departments of Obstetrics and Gynecology, Physiology, and Pediatrics, Faculty of Medicine and Dentistry, University of Alberta, 220 HMRC, Edmonton, AB, T6G2S2, Canada.
| |
Collapse
|
5
|
Deng Z, Ji Y, Han B, Tan Z, Ren Y, Gao J, Chen N, Ma C, Zhang Y, Yao Y, Lu H, Huang H, Xu M, Chen L, Zheng L, Gu J, Xiong D, Zhao J, Gu J, Chen Z, Wang K. Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network. Genome Med 2023; 15:93. [PMID: 37936230 PMCID: PMC10631027 DOI: 10.1186/s13073-023-01238-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 09/26/2023] [Indexed: 11/09/2023] Open
Abstract
BACKGROUND Early detection of hepatocellular carcinoma (HCC) is important in order to improve patient prognosis and survival rate. Methylation sequencing combined with neural networks to identify cell-free DNA (cfDNA) carrying aberrant methylation offers an appealing and non-invasive approach for HCC detection. However, some limitations exist in traditional methylation detection technologies and models, which may impede their performance in the read-level detection of HCC. METHODS We developed a low DNA damage and high-fidelity methylation detection method called No End-repair Enzymatic Methyl-seq (NEEM-seq). We further developed a read-level neural detection model called DeepTrace that can better identify HCC-derived sequencing reads through a pre-trained and fine-tuned neural network. After pre-training on 11 million reads from NEEM-seq, DeepTrace was fine-tuned using 1.2 million HCC-derived reads from tumor tissue DNA after noise reduction, and 2.7 million non-tumor reads from non-tumor cfDNA. We validated the model using data from 130 individuals with cfDNA whole-genome NEEM-seq at around 1.6X depth. RESULTS NEEM-seq overcomes the drawbacks of traditional enzymatic methylation sequencing methods by avoiding the introduction of unmethylation errors in cfDNA. DeepTrace outperformed other models in identifying HCC-derived reads and detecting HCC individuals. Based on the whole-genome NEEM-seq data of cfDNA, our model showed high accuracy of 96.2%, sensitivity of 93.6%, and specificity of 98.5% in the validation cohort consisting of 62 HCC patients, 48 liver disease patients, and 20 healthy individuals. In the early stage of HCC (BCLC 0/A and TNM I), the sensitivity of DeepTrace was 89.6 and 89.5% respectively, outperforming Alpha Fetoprotein (AFP) which showed much lower sensitivity in both BCLC 0/A (50.5%) and TNM I (44.7%). CONCLUSIONS By combining high-fidelity methylation data from NEEM-seq with the DeepTrace model, our method has great potential for HCC early detection with high sensitivity and specificity, making it potentially suitable for clinical applications. DeepTrace: https://github.com/Bamrock/DeepTrace.
Collapse
Affiliation(s)
- Zhenzhong Deng
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongkun Ji
- BamRock Research Department, Suzhou BamRock Biotechnology Ltd., Suzhou, Jiangsu Province, China
| | - Bing Han
- Division of Hepatobiliary and Transplantation Surgery, Department of General Surgery, Nanjing Drum Tower Hospital, the Affiliated Hospital of Medical School, Nanjing University, Nanjing, China
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zhongming Tan
- Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China
| | - Yuqi Ren
- College of Intelligence and Computing, Tianjin University, Tianjin, China
| | - Jinghan Gao
- Department of Software Engineering, Tsinghua University, Beijing, China
| | - Nan Chen
- National Clinical Research Center for Hematologic Diseases, Jiangsu Institute of Hematology, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Cong Ma
- Suzhou Known Biotechnology Ltd, Suzhou, Jiangsu Province, China
| | - Yichi Zhang
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yunhai Yao
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Hong Lu
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Heqing Huang
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China
| | - Midie Xu
- Department of Pathology, Fudan University Shanghai Cancer Center, Shanghai, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Lei Chen
- Department of Pathology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Leizhen Zheng
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianchun Gu
- Department of Oncology, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Deyi Xiong
- College of Intelligence and Computing, Tianjin University, Tianjin, China.
| | - Jianxin Zhao
- Department of Interventional Medicine, the affiliated hospital of infectious diseases of Soochow University, Suzhou, 215131, Jiangsu Province, China.
| | - Jinyang Gu
- Department of Transplantation, Xinhua Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai, China.
- Liver Transplantation Center, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei Province, China.
| | - Zutao Chen
- Infectious Disease Department, the First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China.
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-Infective Medicine, Suzhou, Jiangsu Province, China.
| | - Ke Wang
- Hepatobiliary Center, the First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu Province, China.
| |
Collapse
|
6
|
Gussakovsky D, Booy EP, Brown MJF, McKenna SA. Nuclear SRP9/SRP14 heterodimer transcriptionally regulates 7SL and BC200 RNA expression. RNA (NEW YORK, N.Y.) 2023; 29:1185-1200. [PMID: 37156570 PMCID: PMC10351891 DOI: 10.1261/rna.079649.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 04/21/2023] [Indexed: 05/10/2023]
Abstract
The SRP9/SRP14 heterodimer is a central component of signal recognition particle (SRP) RNA (7SL) processing and Alu retrotransposition. In this study, we sought to establish the role of nuclear SRP9/SRP14 in the transcriptional regulation of 7SL and BC200 RNA. 7SL and BC200 RNA steady-state levels, rate of decay, and transcriptional activity were evaluated under SRP9/SRP14 knockdown conditions. Immunofluorescent imaging, and subcellular fractionation of MCF-7 cells, revealed a distinct nuclear localization for SRP9/SRP14. The relationship between this localization and transcriptional activity at 7SL and BC200 genes was also examined. These findings demonstrate a novel nuclear function of SRP9/SRP14 establishing that this heterodimer transcriptionally regulates 7SL and BC200 RNA expression. We describe a model in which SRP9/SRP14 cotranscriptionally regulate 7SL and BC200 RNA expression. Our model is also a plausible pathway for regulating Alu RNA transcription and is consistent with the hypothesized roles of SRP9/SRP14 transporting 7SL RNA into the nucleolus for posttranscriptional processing, and trafficking of Alu RNA for retrotransposition.
Collapse
Affiliation(s)
- Daniel Gussakovsky
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Evan P Booy
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Mira J F Brown
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| | - Sean A McKenna
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba R3T 2N2, Canada
| |
Collapse
|
7
|
Ravaioli F, Bacalini MG, Giuliani C, Pellegrini C, D’Silva C, De Fanti S, Pirazzini C, Giorgi G, Del Re B. Evaluation of DNA Methylation Profiles of LINE-1, Alu and Ribosomal DNA Repeats in Human Cell Lines Exposed to Radiofrequency Radiation. Int J Mol Sci 2023; 24:9380. [PMID: 37298336 PMCID: PMC10253908 DOI: 10.3390/ijms24119380] [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] [Received: 04/24/2023] [Revised: 05/22/2023] [Accepted: 05/25/2023] [Indexed: 06/12/2023] Open
Abstract
A large body of evidence indicates that environmental agents can induce alterations in DNA methylation (DNAm) profiles. Radiofrequency electromagnetic fields (RF-EMFs) are radiations emitted by everyday devices, which have been classified as "possibly carcinogenic"; however, their biological effects are unclear. As aberrant DNAm of genomic repetitive elements (REs) may promote genomic instability, here, we sought to determine whether exposure to RF-EMFs could affect DNAm of different classes of REs, such as long interspersed nuclear elements-1 (LINE-1), Alu short interspersed nuclear elements and ribosomal repeats. To this purpose, we analysed DNAm profiles of cervical cancer and neuroblastoma cell lines (HeLa, BE(2)C and SH-SY5Y) exposed to 900 MHz GSM-modulated RF-EMF through an Illumina-based targeted deep bisulfite sequencing approach. Our findings showed that radiofrequency exposure did not affect the DNAm of Alu elements in any of the cell lines analysed. Conversely, it influenced DNAm of LINE-1 and ribosomal repeats in terms of both average profiles and organisation of methylated and unmethylated CpG sites, in different ways in each of the three cell lines studied.
Collapse
Affiliation(s)
- Francesco Ravaioli
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Maria Giulia Bacalini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences (BIGEA), University of Bologna, 40126 Bologna, Italy;
| | - Camilla Pellegrini
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara D’Silva
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Sara De Fanti
- IRCCS Istituto Delle Scienze Neurologiche di Bologna, 40139 Bologna, Italy; (F.R.); (M.G.B.); (C.P.); (C.D.); (S.D.F.)
| | - Chiara Pirazzini
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy;
| | - Gianfranco Giorgi
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| | - Brunella Del Re
- Department of Pharmacy and Biotechnology (FABIT), University of Bologna, 40126 Bologna, Italy;
| |
Collapse
|
8
|
Kotsifaki R, Korakakis V, King E, Barbosa O, Maree D, Pantouveris M, Bjerregaard A, Luomajoki J, Wilhelmsen J, Whiteley R. Aspetar clinical practice guideline on rehabilitation after anterior cruciate ligament reconstruction. Br J Sports Med 2023; 57:500-514. [PMID: 36731908 DOI: 10.1136/bjsports-2022-106158] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2023] [Indexed: 02/04/2023]
Abstract
This guideline was developed to inform clinical practice on rehabilitation after anterior cruciate ligament reconstruction (ACLR) and was performed in accordance with the Appraisal of Guidelines for REsearch & Evaluation II (AGREE II) instrument and used the Grading of Recommendations, Assessment, Development and Evaluation (GRADE) approach. A Guideline Development Group systematically searched and reviewed evidence using randomised clinical trials and systematic reviews to evaluate the effectiveness of rehabilitation interventions and guide clinicians and patients on the content of the optimal rehabilitation protocol after ACLR.The guideline targets patients during rehabilitation after ACLR and investigates the effectiveness of the available interventions to the physiotherapist, alone or in combination (eg, exercise, modalities, objective progression criteria). Exercise interventions should be considered the mainstay of ACLR rehabilitation. However, there is little evidence on the dose-response relationship between volume and/or intensity of exercise and outcomes. Physical therapy modalities can be helpful as an adjunct in the early phase of rehabilitation when pain, swelling and limitations in range of motion are present. Adding modalities in the early phase may allow earlier pain-free commencement of exercise rehabilitation. Return to running and return to training/activity are key milestones for rehabilitation after ACLR. However, there is no evidence on which progression or discharge criteria should be used.While there is a very low level of certainty for most components of rehabilitation, most of the recommendations provided in this guideline were agreed to by expert clinicians. This guideline also highlights several new elements of ACLR management not reported previously.
Collapse
Affiliation(s)
- Roula Kotsifaki
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Vasileios Korakakis
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Enda King
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Olivia Barbosa
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Dustin Maree
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Michail Pantouveris
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Andreas Bjerregaard
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Julius Luomajoki
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Jan Wilhelmsen
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| | - Rodney Whiteley
- Rehabilitation Department, Aspetar Orthopaedic and Sports Medicine Hospital, Doha, Qatar
| |
Collapse
|
9
|
Colwell ML, Townsel C, Petroff RL, Goodrich JM, Dolinoy DC. Epigenetics and the Exposome: DNA Methylation as a Proxy for Health Impacts of Prenatal Environmental Exposures. EXPOSOME 2023; 3:osad001. [PMID: 37333730 PMCID: PMC10275510 DOI: 10.1093/exposome/osad001] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The accumulation of every day exposures can impact health across the life course, but our understanding of such exposures is impeded by our ability to delineate the relationship between an individual's early life exposome and later life health effects. Measuring the exposome is challenging. Exposure assessed at a given time point captures a snapshot of the exposome but does not represent the full spectrum of exposures across the life course. In addition, the assessment of early life exposures and their effects is often further challenged by lack of relevant samples and the time gap between exposures and related health outcomes in later life. Epigenetics, specifically DNA methylation, has the potential to overcome these barriers as environmental epigenetic perturbances can be retained through time. In this review, we describe how DNA methylation can be framed in the world of the exposome. We offer three compelling examples of common environmental exposures, including cigarette smoke, the endocrine active compound bisphenol A (BPA), and the metal lead (Pb), to illustrate the application of DNA methylation as a proxy to measure the exposome. We discuss areas for future explorations and current limitations of this approach. Epigenetic profiling is a promising and rapidly developing tool and field of study, offering us a unique and powerful way to assess the early life exposome and its effects across different life stages.
Collapse
Affiliation(s)
- Mathia L. Colwell
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Courtney Townsel
- Department of Obstetrics and Gynecology, University of Michigan School of Medicine, Ann Arbor, MI, USA
| | - Rebekah L. Petroff
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Jaclyn M. Goodrich
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Dana C. Dolinoy
- Department of Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
- Department of Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| |
Collapse
|
10
|
Alfano R, Zugna D, Barros H, Bustamante M, Chatzi L, Ghantous A, Herceg Z, Keski-Rahkonen P, de Kok TM, Nawrot TS, Relton CL, Robinson O, Roumeliotaki T, Scalbert A, Vrijheid M, Vineis P, Richiardi L, Plusquin M. Cord blood epigenome-wide meta-analysis in six European-based child cohorts identifies signatures linked to rapid weight growth. BMC Med 2023; 21:17. [PMID: 36627699 PMCID: PMC9831885 DOI: 10.1186/s12916-022-02685-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/29/2022] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Rapid postnatal growth may result from exposure in utero or early life to adverse conditions and has been associated with diseases later in life and, in particular, with childhood obesity. DNA methylation, interfacing early-life exposures and subsequent diseases, is a possible mechanism underlying early-life programming. METHODS Here, a meta-analysis of Illumina HumanMethylation 450K/EPIC-array associations of cord blood DNA methylation at single CpG sites and CpG genomic regions with rapid weight growth at 1 year of age (defined with reference to WHO growth charts) was conducted in six European-based child cohorts (ALSPAC, ENVIRONAGE, Generation XXI, INMA, Piccolipiù, and RHEA, N = 2003). The association of gestational age acceleration (calculated using the Bohlin epigenetic clock) with rapid weight growth was also explored via meta-analysis. Follow-up analyses of identified DNA methylation signals included prediction of rapid weight growth, mediation of the effect of conventional risk factors on rapid weight growth, integration with transcriptomics and metabolomics, association with overweight in childhood (between 4 and 8 years), and comparison with previous findings. RESULTS Forty-seven CpGs were associated with rapid weight growth at suggestive p-value <1e-05 and, among them, three CpGs (cg14459032, cg25953130 annotated to ARID5B, and cg00049440 annotated to KLF9) passed the genome-wide significance level (p-value <1.25e-07). Sixteen differentially methylated regions (DMRs) were identified as associated with rapid weight growth at false discovery rate (FDR)-adjusted/Siddak p-values < 0.01. Gestational age acceleration was associated with decreasing risk of rapid weight growth (p-value = 9.75e-04). Identified DNA methylation signals slightly increased the prediction of rapid weight growth in addition to conventional risk factors. Among the identified signals, three CpGs partially mediated the effect of gestational age on rapid weight growth. Both CpGs (N=3) and DMRs (N=3) were associated with differential expression of transcripts (N=10 and 7, respectively), including long non-coding RNAs. An AURKC DMR was associated with childhood overweight. We observed enrichment of CpGs previously reported associated with birthweight. CONCLUSIONS Our findings provide evidence of the association between cord blood DNA methylation and rapid weight growth and suggest links with prenatal exposures and association with childhood obesity providing opportunities for early prevention.
Collapse
Affiliation(s)
- Rossella Alfano
- Medical Research Council Centre for Environment and Health, Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Daniela Zugna
- Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Henrique Barros
- Institute of Public Health, University of Porto, Porto, Portugal
| | - Mariona Bustamante
- ISGlobal, Institute of Global Health, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- CIBER Epidemiología y Salud Pública, Madrid, Spain
| | - Leda Chatzi
- Department of Preventive Medicine, University of Southern California, Los Angeles, USA
| | - Akram Ghantous
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Zdenko Herceg
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Pekka Keski-Rahkonen
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Theo M de Kok
- Department of Toxicogenomics, Maastricht University, Maastricht, The Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Caroline L Relton
- Μedical Research Council Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Oliver Robinson
- Medical Research Council Centre for Environment and Health, Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
- Mohn Centre for Children's Health and Well-being, The School of Public Health, Imperial College London, London, UK
| | - Theano Roumeliotaki
- Department of Social Medicine, Faculty of Medicine, University of Crete, Heraklion, Greece
| | - Augustin Scalbert
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Martine Vrijheid
- International Agency for Research on Cancer (IARC), 150 Cours Albert Thomas, 69008, Lyon, France
| | - Paolo Vineis
- Medical Research Council Centre for Environment and Health, Department of Epidemiology and Biostatistics, The School of Public Health, Imperial College London, London, UK
| | - Lorenzo Richiardi
- Department of Medical Sciences, University of Turin and CPO-Piemonte, Turin, Italy
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium.
| |
Collapse
|
11
|
Alfano R, Bijnens E, Langie SAS, Nawrot TS, Reimann B, Vanbrabant K, Wang C, Plusquin M. Epigenome-wide analysis of maternal exposure to green space during gestation and cord blood DNA methylation in the ENVIRONAGE cohort. ENVIRONMENTAL RESEARCH 2023; 216:114828. [PMID: 36400229 PMCID: PMC9760568 DOI: 10.1016/j.envres.2022.114828] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 11/10/2022] [Accepted: 11/14/2022] [Indexed: 06/05/2023]
Abstract
BACKGROUND DNA methylation programming is sensitive to prenatal life environmental influences, but the impact of maternal exposure to green space on newborns DNA methylation has not been studied yet. METHODS We conducted a meta-epigenome-wide association study (EWAS) of maternal exposure to green space during gestation with cord blood DNA methylation in two subsets of the ENVIRONAGE cohort (N = 538). Cord blood DNA methylation was measured by Illumina HumanMethylation 450K in one subset (N = 189) and EPICarray in another (N = 349). High (vegetation height>3 m (m)), low (vegetation height<3 m) and total (including both) high-resolution green space exposures during pregnancy were estimated within 100 m and 1000 m distance around maternal residence. In each subset, we sought cytosine-phosphate-guanine (CpG) sites via linear mixed models adjusted on newborns' sex, ethnicity, gestational age, season at delivery, sampling day, maternal parity, age, smoking, education, and estimated blood cell proportions. EWASs results were meta-analysed via fixed-effects meta-analyses. Differentially methylated regions (DMRs) were identified via ENmix-combp and DMRcate algorithms. Sensitivity analyses were additionally adjusted on PM2.5, distance to major roads, urbanicity and neighborhood income. In the 450K subset, cord blood expression of differentially methylated genes was measured by Agilent microarrays and associated with green space. RESULTS 147 DMRs were identified, 85 of which were still significant upon adjustment for PM2.5, distance to major roads, urbanicity and neighborhood income, including HLA-DRB5, RPTOR, KCNQ1DN, A1BG-AS1, HTR2A, ZNF274, COL11A1 and PRSS36 DMRs. One CpG reached genome-wide significance, while 54 CpGs were suggestive significant (p-values<1e-05). Among them, a CpG, hypermethylated with 100 m buffer total green space, was annotated to PAQR9, whose expression decreased with 1000 m buffer low green space (p-value = 1.45e-05). CONCLUSIONS Our results demonstrate that maternal exposure to green space during pregnancy is associated with cord blood DNA methylation, mainly at loci organized in regions, in genes playing important roles in neurological development (e.g., HTR2A).
Collapse
Affiliation(s)
- Rossella Alfano
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium.
| | - Esmée Bijnens
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Sabine A S Langie
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium; Department of Pharmacology & Toxicology, School for Nutrition and Translational Research in Metabolism (NUTRIM), Maastricht University, Maastricht, the Netherlands
| | - Tim S Nawrot
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium; Department of Public Health, Leuven University (KU Leuven), Leuven, Belgium
| | - Brigitte Reimann
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Kenneth Vanbrabant
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Congrong Wang
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| | - Michelle Plusquin
- Centre for Environmental Sciences, Hasselt University, Agoralaan Building D, 3590, Diepenbeek, Belgium
| |
Collapse
|
12
|
Xu R, Li S, Wu Y, Yue X, Wong EM, Southey MC, Hopper JL, Abramson MJ, Li S, Guo Y. Wildfire-related PM 2.5 and DNA methylation: An Australian twin and family study. ENVIRONMENT INTERNATIONAL 2023; 171:107704. [PMID: 36542997 DOI: 10.1016/j.envint.2022.107704] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 11/24/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Wildfire-related fine particulate matter (PM2.5) has many adverse health impacts, but its impacts on human epigenome are unknown. We aimed to evaluate the associations between long-term exposure to wildfire-related PM2.5 and blood DNA methylation, and whether the associations differ from those with non-wildfire-related PM2.5. METHODS We studied 479 Australian women comprising 132 twin pairs and 215 of their sisters. Blood-derived DNA methylation was measured using the HumanMethylation450 BeadChip array. Data on 3-year (year of blood collection and previous two years) average wildfire-related and non-wildfire-related PM2.5 at 0.01°×0.01° spatial resolution were created by combining information from satellite observations, chemical transport models, and ground-based observations. Exposure data were linked to each participant's home address, assuming the address did not change during the exposure window. For DNA methylation of each cytosine-guanine dinucleotide (CpG), and for global DNA methylation represented by the average of all measured CpGs or CpGs in repetitive elements, we evaluated their associations with wildfire- or non-wildfire-related PM2.5 using a within-sibship analysis controlling for factors shared between siblings and other important covariates. Differentially methylated regions (DMRs) were defined by comb-p and DMRcate. RESULTS The 3-year average wildfire-related PM2.5 (range: 0.3 to 7.6 µg/m3, mean: 1.6 µg/m3) was negatively, but not significantly (p-values greater than 0.05) associated with all seven global DNA methylation measures. There were 26 CpGs and 33 DMRs associated with wildfire-related PM2.5 (Bonferroni adjusted p-value < 0.05) mapped to 47 genes enriched for pathways related to inflammatory regulation and platelet activation. These genes have been related to many human diseases or phenotypes e.g., cancer, mental disorders, diabetes, obesity, asthma, blood pressure. These CpGs, DMRs and enriched pathways did not overlap with the 1 CpG and 7 DMRs associated with non-wildfire-related PM2.5. CONCLUSIONS Long-term exposure to wildfire-related PM2.5 was associated with various blood DNA methylation signatures in Australian women, and these were distinct from those associated with non-wildfire-related PM2.5.
Collapse
Affiliation(s)
- Rongbin Xu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shanshan Li
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Yao Wu
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Xu Yue
- Jiangsu Key Laboratory of Atmospheric Environment Monitoring and Pollution Control, Collaborative Innovation Center of Atmospheric Environment and Equipment Technology, School of Environmental Science and Engineering, Nanjing University of Information Science and Technology, Nanjing, China
| | - Ee Ming Wong
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Melissa C Southey
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Department of Clinical Pathology, Melbourne Medical School, The University of Melbourne, Melbourne, VIC 3010, Australia; Cancer Epidemiology Division, Cancer Council Victoria, VIC 3004, Australia
| | - John L Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Michael J Abramson
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia
| | - Shuai Li
- Precision Medicine, School of Clinical Sciences at Monash Health, Monash University, Clayton, VIC 3800, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, VIC 3010, Australia; Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge CB1 8RN, UK; Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC 3052, Australia
| | - Yuming Guo
- School of Public Health and Preventive Medicine, Monash University, Melbourne, VIC 3004, Australia.
| |
Collapse
|
13
|
DENARIYAKOON SIKRIT, PUTTIPANYALEARS CHAROENCHAI, CHATAMRA KRIS, MUTIRANGURA APIWAT. Breast Cancer Sera Changes in Alu Element Methylation Predict Metastatic Disease Progression. CANCER DIAGNOSIS & PROGNOSIS 2022; 2:731-738. [PMID: 36340456 PMCID: PMC9628142 DOI: 10.21873/cdp.10168] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 09/19/2022] [Indexed: 11/11/2022]
Abstract
BACKGROUND/AIM During metastatic disease development, the cancer-immune system crosstalk induces epigenetic modifications to immune cells, impairing their functions. Recently, Alu elements methylation changes were widely studied in terms of early cancer detection. This study aimed to demonstrate in vitro Alu element methylation changes in peripheral immune cells in a metastatic setting and examine their prognostic values in metastatic breast cancer. MATERIALS AND METHODS Sera from sixteen metastatic cancer patients and sixteen healthy participants were obtained and used to culture normal peripheral immune cells. After 48 h of incubation, the percentage and pattern of Alu element methylation were examined for clinical relevance. RESULTS We found that the Alu element hypomethylation was affected by age in the cancer group. Intriguingly, a decrease in Alu element methylation was found in patients with early progressive disease. Moreover, an increase in unmethylated cytosine (mCuC) loci was related to the poorer prognosis group. Accordingly, the decrease in Alu element methylation and the increase in mCuC loci pattern in peripheral immune cells correlated with poorer prognosis and early progression in metastatic breast cancer. CONCLUSION Alu element hypomethylation in immune cells and their increased mCuC foci were related to the early progression of breast cancer. These warrant the use of Alu element methylation changes for diagnostic and therapeutic purposes in breast cancer.
Collapse
Affiliation(s)
- SIKRIT DENARIYAKOON
- Queen Sirikit Centre for Breast Cancer, The Thai Red Cross Society, Bangkok, Thailand
| | - CHAROENCHAI PUTTIPANYALEARS
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - KRIS CHATAMRA
- Queen Sirikit Centre for Breast Cancer, The Thai Red Cross Society, Bangkok, Thailand
| | - APIWAT MUTIRANGURA
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| |
Collapse
|
14
|
Piao YH, Cui Y, Rami FZ, Li L, Karamikheirabad M, Kang SH, Kim SW, Kim JJ, Lee BJ, Chung YC. Methylome-wide Association Study of Patients with Recent-onset Psychosis. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE 2022; 20:462-473. [PMID: 35879030 PMCID: PMC9329103 DOI: 10.9758/cpn.2022.20.3.462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Revised: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 11/30/2022]
Abstract
Objective Dysregulation of gene expression through epigenetic mechanisms may have a vital role in the pathogenesis of schizophrenia (SZ). In this study, we investigated the association of altered methylation patterns with SZ symptoms and early trauma in patients and healthy controls. Methods The present study was conducted to identify methylation changes in CpG sites in peripheral blood associated with recent-onset (RO) psychosis using methylome-wide analysis. Lifestyle factors, such as smoking, alcohol, exercise, and diet, were controlled. Results We identified 2,912 differentially methylated CpG sites in patients with RO psychosis compared to controls. Most of the genes associated with the top 20 differentially methylated sites had not been reported in previous methylation studies and were involved in apoptosis, autophagy, axonal growth, neuroinflammation, protein folding, etc. The top 15 significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways included the oxytocin signaling pathway, long-term depression pathway, axon guidance, endometrial cancer, long-term potentiation, mitogen-activated protein kinase signaling pathway, and glutamatergic pathway, among others. In the patient group, significant associations of novel methylated genes with early trauma and psychopathology were observed. Conclusion Our results suggest an association of differential DNA methylation with the pathophysiology of psychosis and early trauma. Blood DNA methylation signatures show promise as biomarkers of future psychosis.
Collapse
Affiliation(s)
- Yan-Hong Piao
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Yin Cui
- Shanghai Mental Health Center, Shanghai Jiao Tong University School of Medicine, Shanghai, PR China
| | - Fatima Zahra Rami
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Ling Li
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Maryam Karamikheirabad
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| | - Shi Hyun Kang
- Department of Social Psychiatry and Rehabilitation, National Center for Mental Health, Seoul, Korea
| | - Sung-Wan Kim
- Department of Psychiatry, Chonnam National University Medical School, Gwangju, Korea
| | - Jung Jin Kim
- Department of Psychiatry, The Catholic University of Korea, Seoul St. Mary’s Hospital, Seoul, Korea
| | - Bong Ju Lee
- Department of Psychiatry, Inje University Haeundae Paik Hospital, Inje University College of Medicine, Busan, Korea
| | - Young-Chul Chung
- Department of Psychiatry, Jeonbuk National University Medical School, Jeonju, Korea
- Research Institute of Clinical Medicine of Jeonbuk National University-Biomedical Research Institute of Jeonbuk National University Hospital, Jeonju, Korea
| |
Collapse
|
15
|
Hill C, Avila-Palencia I, Maxwell AP, Hunter RF, McKnight AJ. Harnessing the Full Potential of Multi-Omic Analyses to Advance the Study and Treatment of Chronic Kidney Disease. FRONTIERS IN NEPHROLOGY 2022; 2:923068. [PMID: 37674991 PMCID: PMC10479694 DOI: 10.3389/fneph.2022.923068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Accepted: 05/30/2022] [Indexed: 09/08/2023]
Abstract
Chronic kidney disease (CKD) was the 12th leading cause of death globally in 2017 with the prevalence of CKD estimated at ~9%. Early detection and intervention for CKD may improve patient outcomes, but standard testing approaches even in developed countries do not facilitate identification of patients at high risk of developing CKD, nor those progressing to end-stage kidney disease (ESKD). Recent advances in CKD research are moving towards a more personalised approach for CKD. Heritability for CKD ranges from 30% to 75%, yet identified genetic risk factors account for only a small proportion of the inherited contribution to CKD. More in depth analysis of genomic sequencing data in large cohorts is revealing new genetic risk factors for common diagnoses of CKD and providing novel diagnoses for rare forms of CKD. Multi-omic approaches are now being harnessed to improve our understanding of CKD and explain some of the so-called 'missing heritability'. The most common omic analyses employed for CKD are genomics, epigenomics, transcriptomics, metabolomics, proteomics and phenomics. While each of these omics have been reviewed individually, considering integrated multi-omic analysis offers considerable scope to improve our understanding and treatment of CKD. This narrative review summarises current understanding of multi-omic research alongside recent experimental and analytical approaches, discusses current challenges and future perspectives, and offers new insights for CKD.
Collapse
Affiliation(s)
| | | | | | | | - Amy Jayne McKnight
- Centre for Public Health, Queen’s University Belfast, Belfast, United Kingdom
| |
Collapse
|
16
|
Sankar S, Maruthai K, Zachariah B, Bethou A. Global DNA hypomethylation and the expression profile of DNA methyltransferase genes in late-onset neonatal sepsis. Epigenomics 2022; 14:671-682. [PMID: 35587102 DOI: 10.2217/epi-2022-0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: Infectious organisms tend to cause DNA methylation changes. Thus, this paper aims to study global DNA methylation and the expression of DNA methyltransferase (DNMT) genes in late-onset neonatal sepsis (LONS). Methods: Global and Alu DNA methylation and expression levels of DNMT were performed using 5mc ELISA, methylation-specific PCR and quantitative real-time-PCR, respectively for LONS and controls. Results: Significant hypomethylation of global DNA and Alu DNA methylation and lower expression of DNMT1 and DNMT3a were observed in LONS compared with controls. Receiver operating characteristic analysis of global and Alu DNA methylation showed good discrimination for the identification of LONS. Conclusion: The hypomethylation of global DNA and Alu elements is evident in neonates with LONS. This may be clinically useful for the prognosis of LONS.
Collapse
Affiliation(s)
- Saranya Sankar
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India
| | - Kathirvel Maruthai
- Department of Pediatrics, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India.,Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA 30605, USA
| | - Bobby Zachariah
- Department of Biochemistry, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India
| | - Adhisivam Bethou
- Department of Neonatology, Jawaharlal Institute of Postgraduate Medical Education & Research (JIPMER), Puducherry, 605011, India
| |
Collapse
|
17
|
Global DNA methylation changes in adults with attention deficit-hyperactivity disorder and its comorbidity with bipolar disorder: links with polygenic scores. Mol Psychiatry 2022; 27:2485-2491. [PMID: 35256746 DOI: 10.1038/s41380-022-01493-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 02/05/2022] [Accepted: 02/14/2022] [Indexed: 11/09/2022]
Abstract
Genetic and environmental factors contribute to the etiology of Attention Deficit-Hyperactivity Disorder (ADHD). In this sense, the study of epigenetic mechanisms could contribute to the understanding of the disorder's neurobiology. Global DNA methylation (GMe) evaluated through 5-methylcytosine levels could be a promising epigenetic biomarker to capture long-lasting biological effects in response to environmental and hormonal changes. We conducted the first assessment of GMe levels in subjects with ADHD (n = 394) and its main comorbidities in comparison to populational controls (n = 390). Furthermore, given the high genetic contribution to ADHD (heritability of 80%), polygenic risk scores (PRS) were calculated to verify the genetic contribution to GMe levels in ADHD and the comorbidities associated with GMe levels. The GMe levels observed in patients were lower than controls (P = 1.1e-8), with women being significantly less globally methylated than men (P = 0.002). Regarding comorbidities, the presence of bipolar disorder (BD) among patients with ADHD was associated with higher methylation levels compared to patients with ADHD without BD (P = 0.031). The results did not change when pharmacological treatment was accounted for in the analyses. The ADHD and BD most predictive PRSs were negatively (P = 0.0064) and positively (P = 0.0042) correlated with GMe, respectively. This study is the first to report an association between GMe, ADHD, and its comorbidity with BD and associations between PRSs for specific psychiatric disorders and GMe. Our findings add to previous evidence that GMe may be a relevant piece in the psychiatric disorders' etiological landscape.
Collapse
|
18
|
A Sight of the Diagnostic Value of Aberrant Cell-Free DNA Methylation in Lung Cancer. DISEASE MARKERS 2022; 2022:9619357. [PMID: 35126793 PMCID: PMC8814721 DOI: 10.1155/2022/9619357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 12/12/2021] [Accepted: 12/24/2021] [Indexed: 11/18/2022]
Abstract
Background Lung cancer is one of the most commonly diagnosed cancer worldwide. As one of the liquid biopsy analytes, alternations in cell-free DNA (cfDNA) methylation could function as promising biomarkers for lung cancer detection. Methods In this study, differential methylation analysis was performed to identify candidate markers, and lasso regression with 10-fold cross-validation (CV) was used to establish the diagnostic marker panel. The performance of the binary classifier was evaluated using the receiver operating characteristic (ROC) curve and the precision-recall (PR) curve. Results We identified 4072 differentially methylated regions (DMRs) based on cfDNA methylation data, and then a 10-DMR marker panel was established. The panel achieved an area under the ROC curve (AUROC) of 0.922 and an area under the PR curve (AUPR) of 0.899 in a cfDNA cohort containing 29 lung cancer and 74 normal samples, showing outstanding performance. Besides, the cfDNA-derived markers also performed well in primary tissue datasets, which were more robust than the tissue-derived markers. Conclusion Our study suggested that the 10-DMR marker panel attained high accuracy and robustness and may function as a novel and promising target for lung cancer detection.
Collapse
|
19
|
Hwang T, Kim S, Chowdhury T, Yu HJ, Kim KM, Kang H, Won JK, Park SH, Shin JH, Park CK. Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas. Commun Biol 2022; 5:62. [PMID: 35042936 PMCID: PMC8766575 DOI: 10.1038/s42003-022-03011-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 12/27/2021] [Indexed: 01/09/2023] Open
Abstract
AbstractAlu is a primate-specific repeat element in the human genome and has been increasingly appreciated as a regulatory element in many biological processes. But the appreciation of Alu has been limited in tumorigenesis, especially for brain tumor. To investigate the relevance of Alu to the gliomagenesis, we studied Alu element-associated post-transcriptional processes and the RNA expression of the element by performing RNA-seq for a total of 41 pairs of neurotypical and diverse glioma brain tissues. We find that A-to-I editing and circular RNA levels, as well as Alu RNA expression, are decreased overall in gliomas, compared to normal tissue. Interestingly, grade 2 oligodendrogliomas are least affected in A-to-I editing and circular RNA levels among gliomas, whereas they have a higher proportion of down-regulated Alu subfamilies, compared to the other gliomas. These findings collectively imply a unique pattern of Alu-associated transcriptomes in grade 2 oligodendroglioma, providing an insight to gliomagenesis from the perspective of an evolutionary genetic element.
Collapse
|
20
|
Hernandez-Landero F, Sanchez-Garcia E, Gomez-Crisostomo N, Contreras-Paredes A, Eduardo MA, de la Cruz-Hernandez E. Anthropometric, biochemical, and haematological indicators associated with hyperhomocysteinemia and their relation to global DNA methylation in a young adult population. Epigenetics 2021; 17:1269-1280. [PMID: 34923898 DOI: 10.1080/15592294.2021.2013420] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Increased homocysteine (Hcy) levels have been associated with a higher risk of cardiovascular and neurodegenerative diseases. Passive DNA demethylation has been suggested as one of the mechanisms implicated in the development of these conditions, and most studies have investigated this relationship in older adult populations. Therefore, this study aimed to evaluate the relationship between corporal composition and biochemical and haematological indicators with plasma homocysteine levels and genome-wide methylation (Alu, LINE-1, and SAT2) in a population of healthy young adults (median age, 18 years). We showed that the prevalence of hyperhomocysteinemia was significantly higher in men (18.5%) than in women (6.6%) (P = 0.034). Increased Hcy level was substantially associated with higher levels of body mass index and visceral fat in females, whereas in males, it was significantly associated with reduced red cell distribution width and high-density lipoprotein (HDL) cholesterol (HDL-C) levels and increased low-density lipoprotein/HDL ratio. Hypomethylation of Alu was significantly associated with reduced levels of HDL-C (<40.0 mg dL-1), whereas hypomethylation of LINE-1 and SAT2 was significantly associated with higher levels of skeletal muscle (<39.3%) in males. These results highlight the participation of hormonal factors in regulating Hcy metabolism, primarily in the female population, whereas changes in DNA methylation observed in males might be associated with the consumption of a protein diet with high levels of methionine, independent of increased Hcy levels.
Collapse
Affiliation(s)
- Fernanda Hernandez-Landero
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Erika Sanchez-Garcia
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Nancy Gomez-Crisostomo
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Adriana Contreras-Paredes
- Laboratory of Molecular Biology of Oncogenic Viruses, Unit of Biomedical Research in Cancer, National Cancer Institute - Biomedical Research Institute, National Autonomous University of Mexico, Mexico City, Mexico
| | - Martínez Abundis Eduardo
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| | - Erick de la Cruz-Hernandez
- Laboratory of Research in Metabolic and Infectious Diseases. Multidisciplinary Academic Division of Comalcalco, Juarez Autonomous University of Tabasco, Comalcalco City, Mexico
| |
Collapse
|
21
|
Zhou Q, Guan P, Zhu Z, Cheng S, Zhou C, Wang H, Xu Q, Sung WK, Li G. ASMdb: a comprehensive database for allele-specific DNA methylation in diverse organisms. Nucleic Acids Res 2021; 50:D60-D71. [PMID: 34664666 PMCID: PMC8728259 DOI: 10.1093/nar/gkab937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 09/27/2021] [Accepted: 09/30/2021] [Indexed: 11/18/2022] Open
Abstract
DNA methylation is known to be the most stable epigenetic modification and has been extensively studied in relation to cell differentiation, development, X chromosome inactivation and disease. Allele-specific DNA methylation (ASM) is a well-established mechanism for genomic imprinting and regulates imprinted gene expression. Previous studies have confirmed that certain special regions with ASM are susceptible and closely related to human carcinogenesis and plant development. In addition, recent studies have proven ASM to be an effective tumour marker. However, research on the functions of ASM in diseases and development is still extremely scarce. Here, we collected 4400 BS-Seq datasets and 1598 corresponding RNA-Seq datasets from 47 species, including human and mouse, to establish a comprehensive ASM database. We obtained the data on DNA methylation level, ASM and allele-specific expressed genes (ASEGs) and further analysed the ASM/ASEG distribution patterns of these species. In-depth ASM distribution analysis and differential methylation analysis conducted in nine cancer types showed results consistent with the reported changes in ASM in key tumour genes and revealed several potential ASM tumour-related genes. Finally, integrating these results, we constructed the first well-resourced and comprehensive ASM database for 47 species (ASMdb, www.dna-asmdb.com).
Collapse
Affiliation(s)
- Qiangwei Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Pengpeng Guan
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhixian Zhu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Sheng Cheng
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Cong Zhou
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Huanhuan Wang
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Qian Xu
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| | - Wing-Kin Sung
- Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China.,Department of Computer Science, National University of Singapore, Singapore 117417, Singapore.,Department of Computational and Systems Biology, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Guoliang Li
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, Wuhan 430070, China.,Agricultural Bioinformatics Key Laboratory of Hubei Province, Hubei Engineering Technology Research Center of Agricultural Big Data, 3D Genomics Research Center, College of Informatics, Huazhong Agricultural University, Wuhan 430070, China
| |
Collapse
|
22
|
Lead (Pb) and neurodevelopment: A review on exposure and biomarkers of effect (BDNF, HDL) and susceptibility. Int J Hyg Environ Health 2021; 238:113855. [PMID: 34655857 DOI: 10.1016/j.ijheh.2021.113855] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/29/2021] [Accepted: 10/01/2021] [Indexed: 12/13/2022]
Abstract
Lead (Pb) is a ubiquitous environmental pollutant and a potent toxic compound. Humans are exposed to Pb through inhalation, ingestion, and skin contact via food, water, tobacco smoke, air, dust, and soil. Pb accumulates in bones, brain, liver and kidney. Fetal exposure occurs via transplacental transmission. The most critical health effects are developmental neurotoxicity in infants and cardiovascular effects and nephrotoxicity in adults. Pb exposure has been steadily decreasing over the past decades, but there are few recent exposure data from the general European population; moreover, no safe Pb limit has been set. Sensitive biomarkers of exposure, effect and susceptibility, that reliably and timely indicate Pb-associated toxicity are required to assess human exposure-health relationships in a situation of low to moderate exposure. Therefore, a systematic literature review based on PubMed entries published before July 2019 that addressed Pb exposure and biomarkers of effect and susceptibility, neurodevelopmental toxicity, epigenetic modifications, and transcriptomics was conducted. Finally included were 58 original papers on Pb exposure and 17 studies on biomarkers. The biomarkers that are linked to Pb exposure and neurodevelopment were grouped into effect biomarkers (serum brain-derived neurotrophic factor (BDNF) and serum/saliva cortisol), susceptibility markers (epigenetic markers and gene sequence variants) and other biomarkers (serum high-density lipoprotein (HDL), maternal iron (Fe) and calcium (Ca) status). Serum BDNF and plasma HDL are potential candidates to be further validated as effect markers for routine use in HBM studies of Pb, complemented by markers of Fe and Ca status to also address nutritional interactions related to neurodevelopmental disorders. For several markers, a causal relationship with Pb-induced neurodevelopmental toxicity is likely. Results on BDNF are discussed in relation to Adverse Outcome Pathway (AOP) 13 ("Chronic binding of antagonist to N-methyl-D-aspartate receptors (NMDARs) during brain development induces impairment of learning and memory abilities") of the AOP-Wiki. Further studies are needed to validate sensitive, reliable, and timely effect biomarkers, especially for low to moderate Pb exposure scenarios.
Collapse
|
23
|
Johnson KC, Anderson KJ, Courtois ET, Gujar AD, Barthel FP, Varn FS, Luo D, Seignon M, Yi E, Kim H, Estecio MRH, Zhao D, Tang M, Navin NE, Maurya R, Ngan CY, Verburg N, de Witt Hamer PC, Bulsara K, Samuels ML, Das S, Robson P, Verhaak RGW. Single-cell multimodal glioma analyses identify epigenetic regulators of cellular plasticity and environmental stress response. Nat Genet 2021; 53:1456-1468. [PMID: 34594038 PMCID: PMC8570135 DOI: 10.1038/s41588-021-00926-8] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 07/27/2021] [Indexed: 02/08/2023]
Abstract
Glioma intratumoral heterogeneity enables adaptation to challenging microenvironments and contributes to therapeutic resistance. We integrated 914 single-cell DNA methylomes, 55,284 single-cell transcriptomes and bulk multi-omic profiles across 11 adult IDH mutant or IDH wild-type gliomas to delineate sources of intratumoral heterogeneity. We showed that local DNA methylation disorder is associated with cell-cell DNA methylation differences, is elevated in more aggressive tumors, links with transcriptional disruption and is altered during the environmental stress response. Glioma cells under in vitro hypoxic and irradiation stress increased local DNA methylation disorder and shifted cell states. We identified a positive association between genetic and epigenetic instability that was supported in bulk longitudinally collected DNA methylation data. Increased DNA methylation disorder associated with accelerated disease progression and recurrently selected DNA methylation changes were enriched for environmental stress response pathways. Our work identified an epigenetically facilitated adaptive stress response process and highlights the importance of epigenetic heterogeneity in shaping therapeutic outcomes.
Collapse
Affiliation(s)
- Kevin C. Johnson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,These authors contributed equally,Co-corresponding authors: and
| | - Kevin J. Anderson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,These authors contributed equally
| | - Elise T. Courtois
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Amit D. Gujar
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Floris P. Barthel
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Pathology, Brain Tumor Center Amsterdam, Amsterdam UMC, Vrije Universiteit, Amsterdam, The Netherlands
| | - Frederick S. Varn
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Diane Luo
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Martine Seignon
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Eunhee Yi
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Hoon Kim
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Marcos RH Estecio
- Department of Epigenetics and Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, TX, US
| | - Dacheng Zhao
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Ming Tang
- Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, US
| | - Nicholas E. Navin
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, US
| | - Rahul Maurya
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Chew Yee Ngan
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA
| | - Niels Verburg
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Brain Tumor Center Amsterdam, de Boelelaan 1117, Amsterdam, The Netherlands
| | - Philip C de Witt Hamer
- Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Neurosurgery, Brain Tumor Center Amsterdam, de Boelelaan 1117, Amsterdam, The Netherlands
| | - Ketan Bulsara
- Division of Neurosurgery, The University of Connecticut Health Center, Farmington, CT, US
| | | | - Sunit Das
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for SickKids, University of Toronto.,Institute of Medical Science, University of Toronto.,Division of Neurosurgery, Li Ka Shing Knowledge Institute, St. Michael’s Hospital, University of Toronto
| | - Paul Robson
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Genetics and Genome Sciences, University of Connecticut School of Medicine
| | - Roel GW Verhaak
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, 06032, USA.,Co-corresponding authors: and
| |
Collapse
|
24
|
Martin CA, Vorn R, Schrieber M, Lai C, Yun S, Kim HS, Gill J. Identification of DNA Methylation Changes That Predict Onset of Post-traumatic Stress Disorder and Depression Following Physical Trauma. Front Neurosci 2021; 15:738347. [PMID: 34630024 PMCID: PMC8498101 DOI: 10.3389/fnins.2021.738347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/06/2021] [Indexed: 11/13/2022] Open
Abstract
Post-traumatic stress disorder (PTSD) and major depressive disorder (MDD) are commonly experienced after exposure to highly stressful events, including physical trauma, yet, biological predictors remain elusive. Methylation of DNA may provide key insights, as it likely is reflective of factors that may increase the risk in trauma patients, as DNA methylation is altered by previous stressors. Here, we compared DNA methylation patterns using bisulfite sequencing in patients with a physical trauma that required more than a 24-h hospitalization (n = 33). We then compared DNA methylation in patients who developed and compared the following groups (1) PTSD and MDD; n = 12), (2) MDD (patients with MDD only; n = 12), and (3) control (patients who did not have PTSD or MDD; n = 9), determined by the PTSD Checklist (PCL-5) and Quick Inventory of Depressive Symptomatology (QIDS) at 6-months follow-up. We identified 17 genes with hypermethylated cytosine sites and 2 genes with hypomethylated sites in comparison between PTSD and control group. In comparison between MDD and control group, we identified 12 genes with hypermethylated cytosine sites and 6 genes with hypomethylated sites. Demethylation of these genes altered the CREB signaling pathway in neurons and may represent a promising therapeutic development target for PTSD and MDD. Our findings suggest that epigenetic changes in these gene regions potentially relate to the onset and symptomology of PTSD and MDD and could be used as potential biomarkers in predicting the onset of PTSD or MDD following traumatic events.
Collapse
Affiliation(s)
- Carina A. Martin
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Rany Vorn
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Martin Schrieber
- Division of Trauma, Critical Care and Acute Care Surgery, Oregon Health and Sciences University, Portland, OR, United States
| | - Chen Lai
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Sijung Yun
- Yotta Biomed, Bethesda, MD, United States
| | - Hyung-Suk Kim
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| | - Jessica Gill
- National Institute of Nursing Research, National Institutes of Health, Bethesda, MD, United States
| |
Collapse
|
25
|
Cardelli M, Doorn RV, Larcher L, Donato MD, Piacenza F, Pierpaoli E, Giacconi R, Malavolta M, Rachakonda S, Gruis NA, Molven A, Andresen PA, Pjanova D, van den Oord JJ, Provinciali M, Nagore E, Kumar R. Association of HERV-K and LINE-1 hypomethylation with reduced disease-free survival in melanoma patients. Epigenomics 2020; 12:1689-1706. [PMID: 33125285 DOI: 10.2217/epi-2020-0127] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To evaluate CpG methylation of long interspersed nuclear elements 1 (LINE-1) and human endogenous retrovirus K (HERV-K) retroelements as potential prognostic biomarkers in cutaneous melanoma. Materials & methods: Methylation of HERV-K and LINE-1 retroelements was assessed in resected melanoma tissues from 82 patients ranging in age from 14 to 88 years. In addition, nevi from eight patients were included for comparison with nonmalignant melanocytic lesions. Results: Methylation levels were lower in melanomas than in nevi. HERV-K and LINE-1 methylation were decreased in melanoma patients with clinical parameters associated with adverse prognosis, while they were independent of age and gender. Hypomethylation of HERV-K (but not LINE-1) was an independent predictor of reduced disease-free survival. Conclusion: HERV-K hypomethylation can be a potential independent biomarker of melanoma recurrence.
Collapse
Affiliation(s)
- Maurizio Cardelli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Remco van Doorn
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Lares Larcher
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Michela Di Donato
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Francesco Piacenza
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Elisa Pierpaoli
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Robertina Giacconi
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Marco Malavolta
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Sivaramakrishna Rachakonda
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| | - Nelleke A Gruis
- Department of Dermatology, Leiden University Medical Center, 2300RC Leiden, The Netherlands
| | - Anders Molven
- Gade Laboratory for Pathology, Department of Clinical Medicine, University of Bergen, N-5020 Bergen, Norway.,Department of Pathology, Haukeland University Hospital, N-5021 Bergen, Norway
| | - Per Arne Andresen
- Department of Pathology, Oslo University Hospital, Rikshospitalet, 0424 Oslo, Norway
| | - Dace Pjanova
- Latvian Biomedical Research & Study Centre, LV-1067 Riga, Latvia
| | | | - Mauro Provinciali
- Advanced Technology Center for Aging Research, Scientific Technological Area, IRCCS INRCA, 60121 Ancona, Italy
| | - Eduardo Nagore
- Department of Dermatology, Instituto Valenciano de Oncología, 46009 València, Spain
| | - Rajiv Kumar
- Division of Molecular Genetic Epidemiology, German Cancer Research Center, 69120 Heidelberg, Germany.,Division of Functional Genome Analysis, German Cancer Research Center, 69120 Heidelberg, Germany
| |
Collapse
|
26
|
Wells D, Bitoun E, Moralli D, Zhang G, Hinch A, Jankowska J, Donnelly P, Green C, Myers SR. ZCWPW1 is recruited to recombination hotspots by PRDM9 and is essential for meiotic double strand break repair. eLife 2020; 9:53392. [PMID: 32744506 PMCID: PMC7494361 DOI: 10.7554/elife.53392] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 07/31/2020] [Indexed: 12/13/2022] Open
Abstract
During meiosis, homologous chromosomes pair and recombine, enabling balanced segregation and generating genetic diversity. In many vertebrates, double-strand breaks (DSBs) initiate recombination within hotspots where PRDM9 binds, and deposits H3K4me3 and H3K36me3. However, no protein(s) recognising this unique combination of histone marks have been identified. We identified Zcwpw1, containing H3K4me3 and H3K36me3 recognition domains, as having highly correlated expression with Prdm9. Here, we show that ZCWPW1 has co-evolved with PRDM9 and, in human cells, is strongly and specifically recruited to PRDM9 binding sites, with higher affinity than sites possessing H3K4me3 alone. Surprisingly, ZCWPW1 also recognises CpG dinucleotides. Male Zcwpw1 knockout mice show completely normal DSB positioning, but persistent DMC1 foci, severe DSB repair and synapsis defects, and downstream sterility. Our findings suggest ZCWPW1 recognition of PRDM9-bound sites at DSB hotspots is critical for synapsis, and hence fertility. Sexual reproduction – that is, the combination of sex cells from two different individuals to produce an embryo – is one of the many mechanisms that have evolved to maintain genetic diversity. Most human cells contain 23 pairs of chromosomes, with each chromosome in a pair carrying either a paternal or maternal copy of the same gene. To form an embryo with the right number of chromosomes, each sex cell (the egg or sperm cell) must only contain one chromosome from each pair. Sex cells are produced from parent cells containing two sets of paternal and maternal chromosomes: these cells then divide twice to form four sex cells which contain only one chromosome from each pair. Before the parent cell divides, a process known as ‘recombination’ takes place, which allows chromosomes in a pair to exchange bits of genetic information. This reshuffling ensures that each chromosome in a sex cell is unique. A protein called PRDM9 helps control which sections of genetic information are recombined by modifying proteins attached to the chromosomes, marking them as locations for exchange. The DNA at each of these sites is then broken and repaired using the genetic sequence of the chromosome it is paired with as a template, thus causing the two chromosomes to swap genes. In 2019, a group of researchers found a set of genes in the testis of mice that are expressed at the same time as the gene for PRDM9. This suggested that another protein called ZCWPW1 is likely involved in recombination, but the precise role of this protein was unclear. To answer this question, Wells, Bitoun et al. – including many of the researchers involved in the 2019 study – examined human cells grown in the laboratory to determine where ZCWPW1 binds to in the chromosome. This revealed that ZCWPW1 can be found at the same sites as PRDM9, which is responsible for bringing it there. Furthermore, cells from male mice lacking the gene for ZCWPW1 cannot complete the exchange of genetic information between chromosomes, meaning that the mice are infertile. As such, ZCWPW1 seems to connect location selection by PRDM9 to the DNA repair mechanisms needed for gene exchange between chromosomes. Infertility is a significant issue for humans affecting as many as one in every six couples. Fertility is complex and many of the biological mechanisms involved are not fully understood. This work suggests that both PRDM9 and ZCWPW1 are key to the production of sex cells and may be worth investigating as factors that affect fertility in humans.
Collapse
Affiliation(s)
- Daniel Wells
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Emmanuelle Bitoun
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Daniela Moralli
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Gang Zhang
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Anjali Hinch
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Julia Jankowska
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Peter Donnelly
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| | - Catherine Green
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom
| | - Simon R Myers
- The Wellcome Centre for Human Genetics, Roosevelt Drive, University of Oxford, Oxford, United Kingdom.,Department of Statistics, University of Oxford, Oxford, United Kingdom
| |
Collapse
|
27
|
Zeggar HR, How-Kit A, Daunay A, Bettaieb I, Sahbatou M, Rahal K, Adouni O, Gammoudi A, Douik H, Deleuze JF, Kharrat M. Tumor DNA hypomethylation of LINE-1 is associated with low tumor grade of breast cancer in Tunisian patients. Oncol Lett 2020; 20:1999-2006. [PMID: 32724446 PMCID: PMC7377197 DOI: 10.3892/ol.2020.11745] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Accepted: 05/19/2020] [Indexed: 12/24/2022] Open
Abstract
DNA hypomethylation of long interspersed repetitive DNA retrotransposon (LINE-1) and Alu repeats elements of short interspersed elements family (SINEs) is an early event in carcinogenesis that causes transcriptional activation and leads to chromosomal instability. In the current study, DNA methylation levels of LINE-1 and Alu repeats were analyzed in tumoral tissues of invasive breast cancer in a Tunisian cohort and its association with the clinicopathological features of patients was defined. DNA methylation of LINE-1 and Alu repeats were analyzed using pyrosequencing in 61 invasive breast cancers. Median values observed for DNA methylation of LINE-1 and Alu repeats were considered as the cut-off (59.81 and 18.49%, respectively). The results of the current study demonstrated a positive correlation between DNA methylation levels of LINE-1 and Alu repeats (rho=0.284; P<0.03). DNA hypomethylation of LINE-1 was also indicated to be associated with low grade (P=0.023). To the best of our knowledge, the current study is the first study regarding DNA methylation of LINE-1 and Alu repeats element in breast cancer of the Tunisian population. The results of the current study suggest that, since hypomethylation of LINE-1 is associated with low grade, it could be used as a biomarker for prognosis for patients with breast cancer.
Collapse
Affiliation(s)
- Hayet Radia Zeggar
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Alexandre How-Kit
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Antoine Daunay
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Ilhem Bettaieb
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Mourad Sahbatou
- Laboratoire de Biostatistique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
| | - Khaled Rahal
- Service de Chirurgie Carcinologique, Institut Salah Azaiz de Tunis, 1006 Tunis, Tunisia
| | - Olfa Adouni
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Amor Gammoudi
- Department of Immunohistocytology, Salah Azaïz Cancer Institute, 1006 Tunis, Tunisia
| | - Hayet Douik
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| | - Jean-François Deleuze
- Laboratoire de Génomique, Fondation Jean Dausset-CEPH, Centre d'Etude du Polymorphisme Humain, 75010 Paris, France
- Centre National de Recherche en Génomique Humaine, CEA, Le Commissariat à l'énergie atomique et aux énergies alternatives-Institut François Jacob, 92265 Evry, France
| | - Maher Kharrat
- University of Tunis El Manar, Faculty of Medicine of Tunis, LR99ES10 Human Genetics Laboratory, 1007 Tunis, Tunisia
| |
Collapse
|
28
|
Bain CR, Ziemann M, Kaspi A, Khan AW, Taylor R, Trahair H, Khurana I, Kaipananickal H, Wallace S, El-Osta A, Myles PS, Bozaoglu K. DNA methylation patterns from peripheral blood separate coronary artery disease patients with and without heart failure. ESC Heart Fail 2020; 7:2468-2478. [PMID: 32618141 PMCID: PMC7524212 DOI: 10.1002/ehf2.12810] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 03/11/2020] [Accepted: 05/14/2020] [Indexed: 01/01/2023] Open
Abstract
Aims Natriuretic peptides are useful for diagnosis and prognostication of heart failure of any cause. Now, research aims to discover novel biomarkers that will more specifically define the heart failure phenotype. DNA methylation plays a critical role in the development of cardiovascular disease with the potential to predict fundamental pathogenic processes. There is a lack of data relating DNA methylation in heart failure that specifically focuses on patients with severe multi‐vessel coronary artery disease. To begin to address this, we conducted a pilot study uniquely exploring the utility of powerful whole‐genome methyl‐binding domain‐capture sequencing in a cohort of cardiac surgery patients, matched for the severity of their coronary artery disease, aiming to identify candidate peripheral blood DNA methylation markers of ischaemic cardiomyopathy and heart failure. Methods and results We recruited a cohort of 20 male patients presenting for coronary artery bypass graft surgery with phenotypic extremes of heart failure but who otherwise share a similar coronary ischaemic burden, age, sex, and ethnicity. Methylation profiling in patient blood samples was performed using methyl‐binding domain‐capture sequencing. Differentially methylated regions were validated using targeted bisulfite sequencing. Gene set enrichment analysis was performed to identify differences in methylation at or near gene promoters in certain known Reactome pathways. We detected 567 188 methylation peaks of which our general linear model identified 68 significantly differentially methylated regions in heart failure with a false discovery rate <0.05. Of these regions, 48 occurred within gene bodies and 25 were located near enhancer elements, some within coding genes and some in non‐coding genes. Gene set enrichment analyses identified 103 significantly enriched gene sets (false discovery rate <0.05) in heart failure. Validation analysis of regions with the strongest differential methylation data was performed for two genes: HDAC9 and the uncharacterized miRNA gene MIR3675. Genes of particular interest as novel candidate markers of the heart failure phenotype with reduced methylation were HDAC9, JARID2, and GREM1 and with increased methylation PDSS2. Conclusions We demonstrate the utility of methyl‐binding domain‐capture sequencing to evaluate peripheral blood DNA methylation markers in a cohort of cardiac surgical patients with severe multi‐vessel coronary artery disease and phenotypic extremes of heart failure. The differential methylation status of specific coding genes identified are candidates for larger longitudinal studies. We have further demonstrated the value and feasibility of examining DNA methylation during the perioperative period to highlight biological pathways and processes contributing to complex phenotypes.
Collapse
Affiliation(s)
- Chris R Bain
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Mark Ziemann
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.,School of Life and Environmental Sciences, Faculty of Science, Engineering and Built Environment, Deakin University, Melbourne, VIC, Australia
| | - Antony Kaspi
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | | | - Rachael Taylor
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Hugh Trahair
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia
| | - Ishant Khurana
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Harikrishnan Kaipananickal
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Department of Clinical Pathology, University of Melbourne, Melbourne, VIC, Australia
| | - Sophie Wallace
- Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Assam El-Osta
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia.,Epigenetics in Human Health and Disease Laboratory, Department of Diabetes, Central Clinical School, Monash University, Melbourne, VIC, Australia.,Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, Hong Kong SAR.,Faculty of Health, Department of Technology, Biomedical Laboratory Science, University College Copenhagen, Copenhagen, Denmark
| | - Paul S Myles
- Department of Anaesthesiology and Perioperative Medicine, The Alfred Hospital and Monash University, The Alfred Centre, Level 6, 99 Commercial Road, Melbourne, VIC, 3004, Australia.,Central Clinical School, Faculty of Medicine, Nursing and Health Sciences, Monash University, Melbourne, VIC, Australia
| | - Kiymet Bozaoglu
- Baker IDI Heart and Diabetes Institute, Melbourne, VIC, Australia.,Murdoch Children's Research Institute and Department of Paediatrics, University of Melbourne, Melbourne, VIC, Australia
| |
Collapse
|
29
|
Ye D, Jiang D, Zhang X, Mao Y. Alu Methylation and Risk of Cancer: A Meta-analysis. Am J Med Sci 2020; 359:271-280. [PMID: 32268941 DOI: 10.1016/j.amjms.2020.03.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 01/10/2020] [Accepted: 03/03/2020] [Indexed: 12/19/2022]
Abstract
BACKGROUND The association between Alu methylation and risk of cancer remains uncertain. This meta-analysis was conducted to elucidate this issue. MATERIALS AND METHODS PubMed and Web of Science up to December 31, 2018, and the reference lists of studies, as well as those presented in relevant meta-analyses and reviews were systematically searched. Standardized mean difference (SMD) in Alu methylation level between cases and controls were pooled using random effects model and assessed heterogeneity between strata by stratified factors using meta-regression model. Sensitivity analysis and publication bias test were also conducted. RESULTS Twenty-five articles, including 2719 cases and 3018 controls were included in the meta-analysis. The significant difference in Alu methylation level between cancer cases and controls was greater in tissue (SMD = -1.89, 95% CI: -2.72, -1.05) than blood (SMD = -0.46, 95% CI: -0.82, -0.09), and heterogeneity was found in materials (P = 0.038). In tissue samples, Alu hypomethylation was found in carcinoma (SMD = -2.50, 95% CI: -3.51, -1.48), while not in non-carcinoma. The inverse associations were consistently found in subgroups stratified by data sources and quality score in tissue samples, and publication year was considered to be the potential source of between-study heterogeneity. Moreover, reduced Alu methylation level was found in the European subgroup, detection method of SIRPH and COBRA, and original data source in blood samples. CONCLUSIONS Alu hypomethylation was associated with increased risk of cancer, which could be a potential biomarker for cancer.
Collapse
Affiliation(s)
- Ding Ye
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China
| | - Danjie Jiang
- Ningbo Municipal Center for Disease Control and Prevention, Ningbo, China
| | - Xinhan Zhang
- Department of Epidemiology and Biostatistics, Zhejiang University School of Public Health, Hangzhou, China
| | - Yingying Mao
- Department of Epidemiology and Biostatistics, Zhejiang Chinese Medical University, Hangzhou, China.
| |
Collapse
|
30
|
Martín B, Pappa S, Díez-Villanueva A, Mallona I, Custodio J, Barrero MJ, Peinado MA, Jordà M. Tissue and cancer-specific expression of DIEXF is epigenetically mediated by an Alu repeat. Epigenetics 2020; 15:765-779. [PMID: 32041475 DOI: 10.1080/15592294.2020.1722398] [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: 01/06/2023] Open
Abstract
Alu repeats constitute a major fraction of human genome and for a small subset of them a role in gene regulation has been described. The number of studies focused on the functional characterization of particular Alu elements is very limited. Most Alu elements are DNA methylated and then assumed to lie in repressed chromatin domains. We hypothesize that Alu elements with low or variable DNA methylation are candidates for a functional role. In a genome-wide study in normal and cancer tissues, we pinpointed an Alu repeat (AluSq2) with differential methylation located upstream of the promoter region of the DIEXF gene. DIEXF encodes a highly conserved factor essential for the development of zebrafish digestive tract. To characterize the contribution of the Alu element to the regulation of DIEXF we analysed the epigenetic landscapes of the gene promoter and flanking regions in different cell types and cancers. Alternate epigenetic profiles (DNA methylation and histone modifications) of the AluSq2 element were associated with DIEXF transcript diversity as well as protein levels, while the epigenetic profile of the CpG island associated with the DIEXF promoter remained unchanged. These results suggest that AluSq2 might directly contribute to the regulation of DIEXF transcription and protein expression. Moreover, AluSq2 was DNA hypomethylated in different cancer types, pointing out its putative contribution to DIEXF alteration in cancer and its potential as tumoural biomarker.
Collapse
Affiliation(s)
- Berta Martín
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Stella Pappa
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Anna Díez-Villanueva
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Izaskun Mallona
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Joaquín Custodio
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - María José Barrero
- Center for Regenerative Medicine in Barcelona (CMRB), Avinguda de la Granvia de l'Hospitalet , Barcelona, Spain
| | - Miguel A Peinado
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| | - Mireia Jordà
- Program of Predictive and Personalized Medicine of Cancer, Germans Trias i Pujol Research Institute (PMPPC-IGTP) , Barcelona, Spain
| |
Collapse
|
31
|
Guerrero-Bosagna C. From epigenotype to new genotypes: Relevance of epigenetic mechanisms in the emergence of genomic evolutionary novelty. Semin Cell Dev Biol 2020; 97:86-92. [DOI: 10.1016/j.semcdb.2019.07.006] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 07/08/2019] [Accepted: 07/08/2019] [Indexed: 11/24/2022]
|
32
|
Guarasci F, D'Aquila P, Montesanto A, Corsonello A, Bellizzi D, Passarino G. Individual DNA Methylation Profile is Correlated with Age and can be Targeted to Modulate Healthy Aging and Longevity. Curr Pharm Des 2019; 25:4139-4149. [DOI: 10.2174/1381612825666191112095655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023]
Abstract
:Patterns of DNA methylation, the best characterized epigenetic modification, are modulated by aging. In humans, different studies at both site-specific and genome-wide levels have reported that modifications of DNA methylation are associated with the chronological aging process but also with the quality of aging (or biological aging), providing new perspectives for establishing powerful biomarkers of aging.:In this article, the role of DNA methylation in aging and longevity has been reviewed by analysing literature data about DNA methylation variations occurring during the lifetime in response to environmental factors and genetic background, and their association with the aging process and, in particular, with the quality of aging. Special attention has been devoted to the relationship between nuclear DNA methylation patterns, mitochondrial DNA epigenetic modifications, and longevity. Mitochondrial DNA has recently been reported to modulate global DNA methylation levels of the nuclear genome during the lifetime, and, in spite of the previous belief, it has been found to be the target of methylation modifications.:Analysis of DNA methylation profiles across lifetime shows that a remodeling of the methylome occurs with age and/or with age-related decline. Thus, it can be an excellent biomarker of aging and of the individual decline and frailty status. The knowledge about the mechanisms underlying these modifications is crucial since it might allow the opportunity for targeted treatment to modulate the rate of aging and longevity.
Collapse
Affiliation(s)
- Francesco Guarasci
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Patrizia D'Aquila
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Alberto Montesanto
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Andrea Corsonello
- Unit of Geriatric Pharmacoepidemiology, Scientific Research Institute - Italian National Research Center on Aging (IRCCS INRCA), Cosenza, Italy
| | - Dina Bellizzi
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| | - Giuseppe Passarino
- Department of Biology, Ecology and Earth Science, University of Calabria, 87030 Rende, Italy
| |
Collapse
|
33
|
Nutritional Factors Modulating Alu Methylation in an Italian Sample from The Mark-Age Study Including Offspring of Healthy Nonagenarians. Nutrients 2019; 11:nu11122986. [PMID: 31817660 PMCID: PMC6950565 DOI: 10.3390/nu11122986] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 11/11/2019] [Accepted: 11/29/2019] [Indexed: 12/11/2022] Open
Abstract
Alu hypomethylation promotes genomic instability and is associated with aging and age-related diseases. Dietary factors affect global DNA methylation, leading to changes in genomic stability and gene expression with an impact on longevity and the risk of disease. This preliminary study aims to investigate the relationship between nutritional factors, such as circulating trace elements, lipids and antioxidants, and Alu methylation in elderly subjects and offspring of healthy nonagenarians. Alu DNA methylation was analyzed in sixty RASIG (randomly recruited age-stratified individuals from the general population) and thirty-two GO (GeHA offspring) enrolled in Italy in the framework of the MARK-AGE project. Factor analysis revealed a different clustering between Alu CpG1 and the other CpG sites. RASIG over 65 years showed lower Alu CpG1 methylation than those of GO subjects in the same age class. Moreover, Alu CpG1 methylation was associated with fruit and whole-grain bread consumption, LDL2-Cholesterol and plasma copper. The preserved Alu methylation status in GO, suggests Alu epigenetic changes as a potential marker of aging. Our preliminary investigation shows that Alu methylation may be affected by food rich in fibers and antioxidants, or circulating LDL subfractions and plasma copper.
Collapse
|
34
|
Guo M, Peng Y, Gao A, Du C, Herman JG. Epigenetic heterogeneity in cancer. Biomark Res 2019; 7:23. [PMID: 31695915 PMCID: PMC6824025 DOI: 10.1186/s40364-019-0174-y] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022] Open
Abstract
Phenotypic and functional heterogeneity is one of the hallmarks of human cancers. Tumor genotype variations among tumors within different patients are known as interpatient heterogeneity, and variability among multiple tumors of the same type arising in the same patient is referred to as intra-patient heterogeneity. Subpopulations of cancer cells with distinct phenotypic and molecular features within a tumor are called intratumor heterogeneity (ITH). Since Nowell proposed the clonal evolution of tumor cell populations in 1976, tumor heterogeneity, especially ITH, was actively studied. Research has focused on the genetic basis of cancer, particularly mutational activation of oncogenes or inactivation of tumor-suppressor genes (TSGs). The phenomenon of ITH is commonly explained by Darwinian-like clonal evolution of a single tumor. Despite the monoclonal origin of most cancers, new clones arise during tumor progression due to the continuous acquisition of mutations. It is clear that disruption of the "epigenetic machinery" plays an important role in cancer development. Aberrant epigenetic changes occur more frequently than gene mutations in human cancers. The epigenome is at the intersection of the environment and genome. Epigenetic dysregulation occurs in the earliest stage of cancer. The current trend of epigenetic therapy is to use epigenetic drugs to reverse and/or delay future resistance to cancer therapies. A majority of cancer therapies fail to achieve durable responses, which is often attributed to ITH. Epigenetic therapy may reverse drug resistance in heterogeneous cancer. Complete understanding of genetic and epigenetic heterogeneity may assist in designing combinations of targeted therapies based on molecular information extracted from individual tumors.
Collapse
Affiliation(s)
- Mingzhou Guo
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China.,State Key Laboratory of Esophageal Cancer Prevention and Treatment, 40 Daxue Road, Zhengzhou, Henan 450052 China
| | - Yaojun Peng
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Aiai Gao
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - Chen Du
- 1Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, #28 Fuxing Road, Beijing, 100853 China
| | - James G Herman
- 3The Hillman Cancer Center, University of Pittsburgh Cancer Institute, 5117 Centre Ave., Pittsburgh, PA 15213 USA
| |
Collapse
|
35
|
Zheng Y, Hlady RA, Joyce BT, Robertson KD, He C, Nannini DR, Kibbe WA, Achenbach CJ, Murphy RL, Roberts LR, Hou L. DNA methylation of individual repetitive elements in hepatitis C virus infection-induced hepatocellular carcinoma. Clin Epigenetics 2019; 11:145. [PMID: 31639042 PMCID: PMC6802191 DOI: 10.1186/s13148-019-0733-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 08/29/2019] [Indexed: 02/07/2023] Open
Abstract
Background The two most common repetitive elements (REs) in humans, long interspersed nuclear element-1 (LINE-1) and Alu element (Alu), have been linked to various cancers. Hepatitis C virus (HCV) may cause hepatocellular carcinoma (HCC) by suppressing host defenses, through DNA methylation that controls the mobilization of REs. We aimed to investigate the role of RE methylation in HCV-induced HCC (HCV-HCC). Results We studied methylation of over 30,000 locus-specific REs across the genome in HCC, cirrhotic, and healthy liver tissues obtained by surgical resection. Relative to normal liver tissue, we observed the largest number of differentially methylated REs in HCV-HCC followed by alcohol-induced HCC (EtOH-HCC). After excluding EtOH-HCC-associated RE methylation (FDR < 0.001) and those unable to be validated in The Cancer Genome Atlas (TCGA), we identified 13 hypomethylated REs (11 LINE-1 and 2 Alu) and 2 hypermethylated REs (1 LINE-1 and 1 Alu) in HCV-HCC (FDR < 0.001). A majority of these REs were located in non-coding regions, preferentially enriched with chromatin repressive marks H3K27me3, and positively associated with gene expression (median correlation r = 0.32 across REs). We further constructed an HCV-HCC RE methylation score that distinguished HCV-HCC (lowest score), HCV-cirrhosis, and normal liver (highest score) in a dose-responsive manner (p for trend < 0.001). HCV-cirrhosis had a lower score than EtOH-cirrhosis (p = 0.038) and HCV-HCC had a lower score than EtOH-HCC in TCGA (p = 0.024). Conclusions Our findings indicate that HCV infection is associated with loss of DNA methylation in specific REs, which could implicate molecular mechanisms in liver cancer development. If our findings are validated in larger sample sizes, methylation of these REs may be useful as an early detection biomarker for HCV-HCC and/or a target for prevention of HCC in HCV-positive individuals. Electronic supplementary material The online version of this article (10.1186/s13148-019-0733-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yinan Zheng
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA.
| | - Ryan A Hlady
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Brian T Joyce
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| | - Keith D Robertson
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, USA
| | - Chunyan He
- University of Kentucky Markey Cancer Center, Lexington, KY, USA.,Department of Internal Medicine, Division of Medical Oncology, University of Kentucky, Lexington, KY, USA
| | - Drew R Nannini
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| | - Warren A Kibbe
- Duke Cancer Institute and Duke School of Medicine, Duke University, Durham, NC, USA
| | - Chad J Achenbach
- Center for Global Health, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Robert L Murphy
- Center for Global Health, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA.,Robert H Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Lewis R Roberts
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Lifang Hou
- Center for Global Oncology, Institute for Global Health, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, 680 N. Lake Shore Drive, Suite 1400, Chicago, IL, 60611-4402, USA
| |
Collapse
|
36
|
Sándor S, Kubinyi E. Genetic Pathways of Aging and Their Relevance in the Dog as a Natural Model of Human Aging. Front Genet 2019; 10:948. [PMID: 31681409 PMCID: PMC6813227 DOI: 10.3389/fgene.2019.00948] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 09/05/2019] [Indexed: 12/15/2022] Open
Abstract
Aging research has experienced a burst of scientific efforts in the last decades as the growing ratio of elderly people has begun to pose an increased burden on the healthcare and pension systems of developed countries. Although many breakthroughs have been reported in understanding the cellular mechanisms of aging, the intrinsic and extrinsic factors that contribute to senescence on higher biological levels are still barely understood. The dog, Canis familiaris, has already served as a valuable model of human physiology and disease. The possible role the dog could play in aging research is still an open question, although utilization of dogs may hold great promises as they naturally develop age-related cognitive decline, with behavioral and histological characteristics very similar to those of humans. In this regard, family dogs may possess unmatched potentials as models for investigations on the complex interactions between environmental, behavioral, and genetic factors that determine the course of aging. In this review, we summarize the known genetic pathways in aging and their relevance in dogs, putting emphasis on the yet barely described nature of certain aging pathways in canines. Reasons for highlighting the dog as a future aging and gerontology model are also discussed, ranging from its unique evolutionary path shared with humans, its social skills, and the fact that family dogs live together with their owners, and are being exposed to the same environmental effects.
Collapse
Affiliation(s)
- Sára Sándor
- Department of Ethology, Eötvös Loránd University, Budapest, Hungary
| | | |
Collapse
|
37
|
Ho AMC, Winham SJ, Armasu SM, Blacker CJ, Millischer V, Lavebratt C, Overholser JC, Jurjus GJ, Dieter L, Mahajan G, Rajkowska G, Vallender EJ, Stockmeier CA, Robertson KD, Frye MA, Choi DS, Veldic M. Genome-wide DNA methylomic differences between dorsolateral prefrontal and temporal pole cortices of bipolar disorder. J Psychiatr Res 2019; 117:45-54. [PMID: 31279243 PMCID: PMC6941851 DOI: 10.1016/j.jpsychires.2019.05.030] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/06/2019] [Revised: 04/04/2019] [Accepted: 05/09/2019] [Indexed: 01/07/2023]
Abstract
Dorsolateral prefrontal cortex (DLPFC) and temporal pole (TP) are brain regions that display abnormalities in bipolar disorder (BD) patients. DNA methylation - an epigenetic mechanism both heritable and sensitive to the environment - may be involved in the pathophysiology of BD. To study BD-associated DNA methylomic differences in these brain regions, we extracted genomic DNA from the postmortem tissues of Brodmann Area (BA) 9 (DLPFC) and BA38 (TP) gray matter from 20 BD, ten major depression (MDD), and ten control age-and-sex-matched subjects. Genome-wide methylation levels were measured using the 850 K Illumina MethylationEPIC BeadChip. We detected striking differences between cortical regions, with greater numbers of between-brain-region differentially methylated positions (DMPs; i.e., CpG sites) in all groups, most pronounced in the BD group, and with substantial overlap across groups. The genes of DMPs common to both BD and MDD (hypothetically associated with their common features such as depression) and those distinct to BD (hypothetically associated with BD-specific features such as mania) were enriched in pathways involved in neurodevelopment including axon guidance. Pathways enriched only in the BD-MDD shared list pointed to GABAergic dysregulation, while those enriched in the BD-only list suggested glutamatergic dysregulation and greater impact on synaptogenesis and synaptic plasticity. We further detected group-specific between-brain-region gene expression differences in ODC1, CALY, GALNT2, and GABRD, which contained significant between-brain-region DMPs. In each brain region, no significant DMPs or differentially methylated regions (DMRs) were found between diagnostic groups. In summary, the methylation differences between DLPFC and TP may provide molecular targets for further investigations of genetic and environmental vulnerabilities associated with both unique and common features of various mood disorders and suggest directions of future development of individualized treatment strategies.
Collapse
Affiliation(s)
- Ada M.-C. Ho
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA,Department of Molecular Pharmacology and Experimental
Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Department of Health Science Research, Mayo Clinic,
Rochester, MN, USA
| | | | - Caren J. Blacker
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA
| | - Vincent Millischer
- Department for Molecular Medicine and Surgery (MMK),
Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University
Hospital, Stockholm, Sweden
| | - Catharina Lavebratt
- Department for Molecular Medicine and Surgery (MMK),
Karolinska Institutet, Stockholm, Sweden,Center for Molecular Medicine, Karolinska University
Hospital, Stockholm, Sweden
| | - James C. Overholser
- Department of Psychology, Case Western Reserve University,
Cleveland, OH, USA
| | - George J. Jurjus
- Department of Psychiatry, Case Western Reserve University,
Cleveland, OH, USA,Louis Stokes Cleveland VA Medical Center, Cleveland, OH,
USA
| | - Lesa Dieter
- Department of Psychology, Case Western Reserve University,
Cleveland, OH, USA
| | - Gouri Mahajan
- Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Grazyna Rajkowska
- Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Eric J. Vallender
- Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Craig A. Stockmeier
- Department of Psychiatry, Case Western Reserve University,
Cleveland, OH, USA,Psychiatry and Human Behavior, University of Mississippi
Medical Center, Jackson, MS, USA
| | - Keith D. Robertson
- Department of Molecular Pharmacology and Experimental
Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Mark A. Frye
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA
| | - Doo-Sup Choi
- Department of Psychiatry and Psychology, Mayo Clinic,
Rochester, MN, USA,Department of Molecular Pharmacology and Experimental
Therapeutics, Mayo Clinic, Rochester, MN, USA
| | - Marin Veldic
- Department of Psychiatry and Psychology, Mayo Clinic, Rochester, MN, USA.
| |
Collapse
|
38
|
Li R, Liang F, Li M, Zou D, Sun S, Zhao Y, Zhao W, Bao Y, Xiao J, Zhang Z. MethBank 3.0: a database of DNA methylomes across a variety of species. Nucleic Acids Res 2019; 46:D288-D295. [PMID: 29161430 PMCID: PMC5753180 DOI: 10.1093/nar/gkx1139] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 10/30/2017] [Indexed: 12/11/2022] Open
Abstract
MethBank (http://bigd.big.ac.cn/methbank) is a database that integrates high-quality DNA methylomes across a variety of species and provides an interactive browser for visualization of methylation data. Here, we present an updated implementation of MethBank (version 3.0) by incorporating more DNA methylomes from multiple species and equipping with more enhanced functionalities for data annotation and more friendly web interfaces for data presentation, search and visualization. MethBank 3.0 features large-scale integration of high-quality methylomes, involving 34 consensus reference methylomes derived from a large number of human samples, 336 single-base resolution methylomes from different developmental stages and/or tissues of five plants, and 18 single-base resolution methylomes from gametes and early embryos at multiple stages of two animals. Additionally, it is enhanced by improving the functionalities for data annotation, which accordingly enables systematic identification of methylation sites closely associated with age, sites with constant methylation levels across different ages, differentially methylated promoters, age-specific differentially methylated cytosines/regions, and methylated CpG islands. Moreover, MethBank provides tools to estimate human methylation age online and to identify differentially methylated promoters, respectively. Taken together, MethBank is upgraded with significant improvements and advances over the previous version, which is of great help for deciphering DNA methylation regulatory mechanisms for epigenetic studies.
Collapse
Affiliation(s)
- Rujiao Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Fang Liang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Mengwei Li
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Dong Zou
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Shixiang Sun
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yongbing Zhao
- Lymphocyte Nuclear Biology, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wenming Zhao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yiming Bao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingfa Xiao
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| | - Zhang Zhang
- BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China.,Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200438, China
| |
Collapse
|
39
|
Zhou L, Ng HK, Drautz-Moses DI, Schuster SC, Beck S, Kim C, Chambers JC, Loh M. Systematic evaluation of library preparation methods and sequencing platforms for high-throughput whole genome bisulfite sequencing. Sci Rep 2019; 9:10383. [PMID: 31316107 PMCID: PMC6637168 DOI: 10.1038/s41598-019-46875-5] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 07/05/2019] [Indexed: 01/30/2023] Open
Abstract
Whole genome bisulfite sequencing (WGBS), with its ability to interrogate methylation status at single CpG site resolution epigenome-wide, is a powerful technique for use in molecular experiments. Here, we aim to advance strategies for accurate and efficient WGBS for application in future large-scale epidemiological studies. We systematically compared the performance of three WGBS library preparation methods with low DNA input requirement (Swift Biosciences Accel-NGS, Illumina TruSeq and QIAGEN QIAseq) on two state-of-the-art sequencing platforms (Illumina NovaSeq and HiSeq X), and also assessed concordance between data generated by WGBS and methylation arrays. Swift achieved the highest proportion of CpG sites assayed and effective coverage at 26x (P < 0.001). TruSeq suffered from the highest proportion of PCR duplicates, while QIAseq failed to deliver across all quality metrics. There was little difference in performance between NovaSeq and HiSeq X, with the exception of higher read duplication rate on the NovaSeq (P < 0.05), likely attributable to the higher cluster densities on its flow cells. Systematic biases exist between WGBS and methylation arrays, with lower precision observed for WGBS across the range of depths investigated. To achieve a level of precision broadly comparable to the methylation array, a minimum coverage of 100x is recommended.
Collapse
Affiliation(s)
- Li Zhou
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Hong Kiat Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore
| | - Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Stephan Beck
- University College London Cancer Institute, London, WC1E 6BT, United Kingdom
| | | | - John Campbell Chambers
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore.,Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, United Kingdom.,Department of Cardiology, Ealing Hospital, London North West Healthcare NHS Trust, Southall, UB1 3HW, United Kingdom.,Imperial College Healthcare NHS Trust, London, W12 0HS, United Kingdom
| | - Marie Loh
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 308232, Singapore. .,Department of Epidemiology and Biostatistics, Imperial College London, London, W2 1PG, United Kingdom. .,Translational Laboratory in Genetic Medicine, Agency for Science, Technology and Research (A*STAR), Singapore, 138648, Singapore.
| |
Collapse
|
40
|
The Impact of Caloric Restriction on the Epigenetic Signatures of Aging. Int J Mol Sci 2019; 20:ijms20082022. [PMID: 31022953 PMCID: PMC6515465 DOI: 10.3390/ijms20082022] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Revised: 04/19/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022] Open
Abstract
Aging is characterized by an extensive remodeling of epigenetic patterns, which has been implicated in the physiopathology of age-related diseases. Nutrition plays a significant role in modulating the epigenome, and a growing amount of data indicate that dietary changes can modify the epigenetic marks associated with aging. In this review, we will assess the current advances in the relationship between caloric restriction, a proven anti-aging intervention, and epigenetic signatures of aging. We will specifically discuss the impact of caloric restriction on epigenetic regulation and how some of the favorable effects of caloric restriction on lifespan and healthspan could be mediated by epigenetic modifications.
Collapse
|
41
|
Orsini P, Impera L, Parciante E, Cumbo C, Minervini CF, Minervini A, Zagaria A, Anelli L, Coccaro N, Casieri P, Tota G, Brunetti C, Ricco A, Carluccio P, Specchia G, Albano F. Droplet digital PCR for the quantification of Alu methylation status in hematological malignancies. Diagn Pathol 2018; 13:98. [PMID: 30579366 PMCID: PMC6303857 DOI: 10.1186/s13000-018-0777-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 12/10/2018] [Indexed: 12/14/2022] Open
Abstract
Background Alu repeats, belonging to the Short Interspersed Repetitive Elements (SINEs) class, contain about 25% of CpG sites in the human genome. Alu sequences lie in gene-rich regions, so their methylation is an important transcriptional regulation mechanism. Aberrant Alu methylation has been associated with tumor aggressiveness, and also previously discussed in hematological malignancies, by applying different approaches. Moreover, today different techniques designed to measure global DNA methylation are focused on the methylation level of specific repeat elements. In this work we propose a new method of investigating Alu differential methylation, based on droplet digital PCR (ddPCR) technology. Methods Forty-six patients with hematological neoplasms were included in the study: 30 patients affected by chronic lymphocytic leukemia, 7 patients with myelodysplastic syndromes at intermediate/high risk, according with the International Prognostic Scoring System, and 9 patients with myelomonocytic leukemia. Ten healthy donors were included as controls. Acute promyelocytic leukemia-derived NB4 cell line, either untreated or treated with decitabine (DEC) hypomethylating agent, was also analyzed. DNA samples were investigated for Alu methylation level by digestion of genomic DNA with isoschizomers with differential sensitivity to DNA methylation, followed by ddPCR. Results Using ddPCR, a significant decrease of the global Alu methylation level in DNA extracted from NB4 cells treated with DEC, as compared to untreated cells, was observed. Moreover, comparing the global Alu methylation levels at diagnosis and after azacytidine (AZA) treatment in MDS patients, a statistically significant decrease of Alu sequences methylation after therapy as compared to diagnosis was evident. We also observed a significant decrease of the Alu methylation level in CLL patients compared to HD, and, finally, for CMML patients, a decrease of Alu sequences methylation was observed in patients harboring the SRSF2 hotspot gene mutation c.284C>D. Conclusions In our work, we propose a method to investigate Alu differential methylation based on ddPCR technology. This assay introduces ddPCR as a more sensitive and immediate technique for Alu methylation analysis. To date, this is the first application of ddPCR to study DNA repetitive elements. This approach may be useful to profile patients affected by hematologic malignancies for diagnostic/prognostic purpose. Electronic supplementary material The online version of this article (10.1186/s13000-018-0777-x) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Paola Orsini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Luciana Impera
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Elisa Parciante
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Cosimo Cumbo
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Crescenzio F Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Angela Minervini
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Antonella Zagaria
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Luisa Anelli
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Nicoletta Coccaro
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Paola Casieri
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Giuseppina Tota
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Claudia Brunetti
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Alessandra Ricco
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Paola Carluccio
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Giorgina Specchia
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy
| | - Francesco Albano
- Department of Emergency and Organ Transplantation (D.E.T.O.), Hematology Section, University of Bari, P.zza G. Cesare, 11 70124, Bari, Italy.
| |
Collapse
|
42
|
Saeliw T, Tangsuwansri C, Thongkorn S, Chonchaiya W, Suphapeetiporn K, Mutirangura A, Tencomnao T, Hu VW, Sarachana T. Integrated genome-wide Alu methylation and transcriptome profiling analyses reveal novel epigenetic regulatory networks associated with autism spectrum disorder. Mol Autism 2018; 9:27. [PMID: 29686828 PMCID: PMC5902935 DOI: 10.1186/s13229-018-0213-9] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Accepted: 04/03/2018] [Indexed: 12/20/2022] Open
Abstract
Background Alu elements are a group of repetitive elements that can influence gene expression through CpG residues and transcription factor binding. Altered gene expression and methylation profiles have been reported in various tissues and cell lines from individuals with autism spectrum disorder (ASD). However, the role of Alu elements in ASD remains unclear. We thus investigated whether Alu elements are associated with altered gene expression profiles in ASD. Methods We obtained five blood-based gene expression profiles from the Gene Expression Omnibus database and human Alu-inserted gene lists from the TranspoGene database. Differentially expressed genes (DEGs) in ASD were identified from each study and overlapped with the human Alu-inserted genes. The biological functions and networks of Alu-inserted DEGs were then predicted by Ingenuity Pathway Analysis (IPA). A combined bisulfite restriction analysis of lymphoblastoid cell lines (LCLs) derived from 36 ASD and 20 sex- and age-matched unaffected individuals was performed to assess the global DNA methylation levels within Alu elements, and the Alu expression levels were determined by quantitative RT-PCR. Results In ASD blood or blood-derived cells, 320 Alu-inserted genes were reproducibly differentially expressed. Biological function and pathway analysis showed that these genes were significantly associated with neurodevelopmental disorders and neurological functions involved in ASD etiology. Interestingly, estrogen receptor and androgen signaling pathways implicated in the sex bias of ASD, as well as IL-6 signaling and neuroinflammation signaling pathways, were also highlighted. Alu methylation was not significantly different between the ASD and sex- and age-matched control groups. However, significantly altered Alu methylation patterns were observed in ASD cases sub-grouped based on Autism Diagnostic Interview-Revised scores compared with matched controls. Quantitative RT-PCR analysis of Alu expression also showed significant differences between ASD subgroups. Interestingly, Alu expression was correlated with methylation status in one phenotypic ASD subgroup. Conclusion Alu methylation and expression were altered in LCLs from ASD subgroups. Our findings highlight the association of Alu elements with gene dysregulation in ASD blood samples and warrant further investigation. Moreover, the classification of ASD individuals into subgroups based on phenotypes may be beneficial and could provide insights into the still unknown etiology and the underlying mechanisms of ASD. Electronic supplementary material The online version of this article (10.1186/s13229-018-0213-9) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Thanit Saeliw
- 1M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Chayanin Tangsuwansri
- 1M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Surangrat Thongkorn
- 1M.Sc. Program in Clinical Biochemistry and Molecular Medicine, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, Bangkok, Thailand
| | - Weerasak Chonchaiya
- 2Maximizing Thai Children's Developmental Potential Research Unit, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University and King Chulalongkorn Memorial Hospital, the Thai Red Cross Society, Bangkok, Thailand
| | - Kanya Suphapeetiporn
- 3Center of Excellence for Medical Genetics, Department of Pediatrics, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.,Excellence Center for Medical Genetics, King Chulalongkorn Memorial Hospital, Thai Red Cross Society, Bangkok, Thailand
| | - Apiwat Mutirangura
- 5Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
| | - Tewin Tencomnao
- 6Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand
| | - Valerie W Hu
- 7Department of Biochemistry and Molecular Medicine, The George Washington University School of Medicine and Health Sciences, The George Washington University, Washington, DC USA
| | - Tewarit Sarachana
- 6Age-related Inflammation and Degeneration Research Unit, Department of Clinical Chemistry, Faculty of Allied Health Sciences, Chulalongkorn University, 154 Soi Chula 12, Rama 1 Road, Wangmai, Pathumwan, Bangkok, 10330 Thailand
| |
Collapse
|
43
|
Zheng Y, Joyce BT, Liu L, Zhang Z, Kibbe WA, Zhang W, Hou L. Prediction of genome-wide DNA methylation in repetitive elements. Nucleic Acids Res 2017; 45:8697-8711. [PMID: 28911103 PMCID: PMC5587781 DOI: 10.1093/nar/gkx587] [Citation(s) in RCA: 74] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Accepted: 06/28/2017] [Indexed: 12/16/2022] Open
Abstract
DNA methylation in repetitive elements (RE) suppresses their mobility and maintains genomic stability, and decreases in it are frequently observed in tumor and/or surrogate tissues. Averaging methylation across RE in genome is widely used to quantify global methylation. However, methylation may vary in specific RE and play diverse roles in disease development, thus averaging methylation across RE may lose significant biological information. The ambiguous mapping of short reads by and high cost of current bisulfite sequencing platforms make them impractical for quantifying locus-specific RE methylation. Although microarray-based approaches (particularly Illumina's Infinium methylation arrays) provide cost-effective and robust genome-wide methylation quantification, the number of interrogated CpGs in RE remains limited. We report a random forest-based algorithm (and corresponding R package, REMP) that can accurately predict genome-wide locus-specific RE methylation based on Infinium array profiling data. We validated its prediction performance using alternative sequencing and microarray data. Testing its clinical utility with The Cancer Genome Atlas data demonstrated that our algorithm offers more comprehensively extended locus-specific RE methylation information that can be readily applied to large human studies in a cost-effective manner. Our work has the potential to improve our understanding of the role of global methylation in human diseases, especially cancer.
Collapse
Affiliation(s)
- Yinan Zheng
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Brian T Joyce
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lei Liu
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Zhou Zhang
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA.,Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Warren A Kibbe
- Center for Biomedical Informatics and Information Technology, National Cancer Institute, Rockville, MD 20850, USA
| | - Wei Zhang
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| | - Lifang Hou
- Center for Population Epigenetics, Robert H. Lurie Comprehensive Cancer Center and Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL 60611, USA
| |
Collapse
|
44
|
Saliva as a Blood Alternative for Genome-Wide DNA Methylation Profiling by Methylated DNA Immunoprecipitation (MeDIP) Sequencing. EPIGENOMES 2017. [DOI: 10.3390/epigenomes1030014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
|
45
|
Gianfrancesco O, Bubb VJ, Quinn JP. SVA retrotransposons as potential modulators of neuropeptide gene expression. Neuropeptides 2017; 64:3-7. [PMID: 27743609 PMCID: PMC5529292 DOI: 10.1016/j.npep.2016.09.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/06/2016] [Accepted: 09/06/2016] [Indexed: 12/21/2022]
Abstract
Many facets of human behaviour are likely to have developed in part due to evolutionary changes in the regulation of neuropeptide and other brain-related genes. This has allowed species-specific expression patterns and unique epigenetic modulation in response to our environment, regulating response not only at the molecular level, but also contributing to differences in behaviour between individuals. As such, genetic variants or epigenetic changes that may alter neuropeptide gene expression are predicted to play a role in behavioural conditions and psychiatric illness. It is therefore of interest to identify regulatory elements that have the potential to drive differential gene expression. Retrotransposons are mobile genetic elements that are known to be drivers of genomic diversity, with the ability to alter expression of nearby genes. In particular, the SINE-VNTR-Alu (SVA) class of retrotransposons is specific to hominids, and its appearance and expansion across the genome has been associated with the evolution of numerous behavioural traits, presumably through their ability to confer unique regulatory properties at the site of their insertion. We review the evidence for SVAs as regulatory elements, exploring how polymorphic variation within these repetitive sequences can drive allele specific gene expression, which would be associated with changes in behaviour and disease risk through the alteration of molecular pathways that are central to healthy brain function.
Collapse
Affiliation(s)
- Olympia Gianfrancesco
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, L69 3BX, UK
| | - Vivien J Bubb
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, L69 3BX, UK
| | - John P Quinn
- Department of Molecular and Clinical Pharmacology, Institute of Translational Medicine, The University of Liverpool, Liverpool, L69 3BX, UK.
| |
Collapse
|
46
|
Abstract
Background The studies on CpG islands (CGI) and Alu elements functions, evolution, and distribution in the genome started since the discovery in nineteen eighties (1981, 1986, correspondingly). Their highly skewed genome wide distribution implies the non-random retrotransposition pattern. Besides CGIs in gene promoters, CGIs clusters were observed in the homeobox gene regions and in the macrosatellites, but the whole picture of their distribution specifics was not grasped. Attempts to identify any causative features upon their (genome wide) distribution, such as the DNA context mediated preferred insertion sites of Alu repeats, have been made to ascribe their clusters location. Methods Recent emergence of high resolution 3D map of human genome allowed segregating the genome into the large scale chromatin domains of naturally observable nuclear subcompartments, or Topologically Associated Domains (TADs), designated by spatial chromatin distribution. We utilized the chromatin map to elucidate relations between large scale chromatin state and CpG rich elements landscape. In the course of analysis it was confirmed that genes, Alu and CGI clusters maintain obvious, albeit different in strength, preference for open chromatin. For the first time it was clearly shown that the clusters density of the Alu and CGIs monotonically depend on the chromatin accessibility rate. In particular, the highest density of these elements is found in A1 euchromatin regions characterized by a high density of small length genes replicating in the early S-phase. It implies that these elements mediate (CGIs) or are a side element (Alus) of chromatin accessibility. Results We elucidated that both methylated and non-methylated CGIs display the affinity to chromatin accessibility. As a part of comparative genomics section, we elucidated that the dog’s genome non-canonical structure, outstanding in mammals for its high CGIs abundance compared to gene number, is explained by the presence of dense tandem CGI extended hotspots (500 kb on average) in subtelomeric and pericentromeric regions with highly skewed CG content, and not by CGIs global distribution pattern shift. Conclusions The study underlines the close association of CG-rich elements distribution with the newly introduced large scale chromatin state map, proposing a refined standpoint on interrelation of aforementioned genome elements and the chromatin state. To our expertise, the TAD-associated partition model employed in the study is likely the most substantial one regarding CpG rich clusters distribution among the whole genome chromatin/isochores maps available. Electronic supplementary material The online version of this article (doi:10.1186/s12862-016-0864-0) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Vladimir N Babenko
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia. .,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia.
| | - Irina V Chadaeva
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia
| | - Yuriy L Orlov
- Institute of Cytology and Genetics SB RAS, Lavrentyeva, 10, 630090, Novosibirsk, Russia.,Novosibirsk State University, Pirogova, 2, 630090, Novosibirsk, Russia
| |
Collapse
|
47
|
Jordà M, Díez-Villanueva A, Mallona I, Martín B, Lois S, Barrera V, Esteller M, Vavouri T, Peinado MA. The epigenetic landscape of Alu repeats delineates the structural and functional genomic architecture of colon cancer cells. Genome Res 2016; 27:118-132. [PMID: 27999094 PMCID: PMC5204336 DOI: 10.1101/gr.207522.116] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Accepted: 11/10/2016] [Indexed: 12/16/2022]
Abstract
Cancer cells exhibit multiple epigenetic changes with prominent local DNA hypermethylation and widespread hypomethylation affecting large chromosomal domains. Epigenome studies often disregard the study of repeat elements owing to technical complexity and their undefined role in genome regulation. We have developed NSUMA (Next-generation Sequencing of UnMethylated Alu), a cost-effective approach allowing the unambiguous interrogation of DNA methylation in more than 130,000 individual Alu elements, the most abundant retrotransposon in the human genome. DNA methylation profiles of Alu repeats have been analyzed in colon cancers and normal tissues using NSUMA and whole-genome bisulfite sequencing. Normal cells show a low proportion of unmethylated Alu (1%–4%) that may increase up to 10-fold in cancer cells. In normal cells, unmethylated Alu elements tend to locate in the vicinity of functionally rich regions and display epigenetic features consistent with a direct impact on genome regulation. In cancer cells, Alu repeats are more resistant to hypomethylation than other retroelements. Genome segmentation based on high/low rates of Alu hypomethylation allows the identification of genomic compartments with differential genetic, epigenetic, and transcriptomic features. Alu hypomethylated regions show low transcriptional activity, late DNA replication, and its extent is associated with higher chromosomal instability. Our analysis demonstrates that Alu retroelements contribute to define the epigenetic landscape of normal and cancer cells and provides a unique resource on the epigenetic dynamics of a principal, but largely unexplored, component of the primate genome.
Collapse
Affiliation(s)
- Mireia Jordà
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Anna Díez-Villanueva
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Izaskun Mallona
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Berta Martín
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Sergi Lois
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Víctor Barrera
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| | - Manel Esteller
- Cancer Epigenetics and Biology Program (PEBC), Bellvitge Biomedical Research Institute (IDIBELL), Barcelona 08908, Catalonia, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona 08907, Catalonia, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona 08010, Catalonia, Spain
| | - Tanya Vavouri
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Josep Carreras Leukaemia Research Institute (IJC), Badalona 08916, Catalonia, Spain
| | - Miguel A Peinado
- Germans Trias i Pujol Health Science Research Institute (IGTP), Badalona 08916, Catalonia, Spain.,Institute of Predictive and Personalized Medicine of Cancer (IMPPC), Badalona 08916, Catalonia, Spain
| |
Collapse
|
48
|
Desaulniers D, Cummings-Lorbetskie C, Li N, Xiao GH, Marro L, Khan N, Leingartner K. Sodium bisulfite pyrosequencing revealed that developmental exposure to environmental contaminant mixtures does not affect DNA methylation of DNA repeats in Sprague-Dawley rats. JOURNAL OF TOXICOLOGY AND ENVIRONMENTAL HEALTH. PART A 2016; 80:32-52. [PMID: 27905861 DOI: 10.1080/15287394.2016.1231644] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
Hypomethylation of DNA repeats has been linked to diseases and cancer predisposition. Human studies suggest that higher blood concentrations of environmental contaminants (EC) correlate with levels of hypomethylation of DNA repeats in blood. The objective of this study was to examine the effect of in utero and/or lactational exposure to EC on the methylation of DNA repeats (LINE-1 and identifier element) in Sprague-Dawley rat pups at birth, at postnatal day (PND) 21, and in adulthood (PND78-86). From gestation day 0 to PND20, dams were exposed to a mixture "M" of polychlorinated biphenyls (PCB), pesticides, and methylmercury (MeHg), at 0.5 or 1 mg/kg/d (0.5M and M). At birth, some control (C) and M litters were cross-fostered to create the following in utero/postnatal exposure groups: C/C, M/C, C/M, M/M. Additional dams received 1.8 ng/kg/d of a mixture of aryl-hydrocarbon receptor (AhR) agonists (non-ortho-PCB, PC-dibenzodioxins, and PC-dibenzofurans) without or with 0.5M (0.5MAhR). Measurements of EC residue levels confirmed differences in their accumulation across treatments, age, and tissues. Although induction of hepatic detoxification enzyme activities (cytochrome P-450) demonstrated biological effects of treatments, the assessment of methylation in DNA repeats by sodium bisulfite pyrosequencing of liver, spleen, and thymus samples revealed no marked treatment-related effects but significant tissue- and age-related methylation differences. Further studies are required to determine whether absence of significant observable treatment effects on methylation of DNA repeats in the rat relate to tissue, strain, or species differences.
Collapse
Affiliation(s)
- Daniel Desaulniers
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| | - Cathy Cummings-Lorbetskie
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| | - Nanqin Li
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| | - Gong-Hua Xiao
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| | - Leonora Marro
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| | - Nasrin Khan
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| | - Karen Leingartner
- a Health Canada, Healthy Environments and Consumer Safety Branch, Environmental Health Sciences and Research Bureau , Ottawa , Ontario , Canada
| |
Collapse
|
49
|
Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements. Sci Rep 2016; 6:32207. [PMID: 27573482 PMCID: PMC5004121 DOI: 10.1038/srep32207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 08/03/2016] [Indexed: 12/04/2022] Open
Abstract
Although non-CG methylations are abundant in several mammalian cell types, their biological significance is sparsely characterized. We gathered 51 human and mouse DNA methylomes from brain neurons, embryonic stem cells and induced pluripotent stem cells, primordial germ cells and oocytes. We utilized an unbiased sub-motif prediction method and reported CW as the representative non-CG methylation context, which is distinct from CC methylation in terms of sequence context and genomic distribution. A two-dimensional comparison of non-CG methylations across cell types and species was performed. Unambiguous studies of sequence preferences and genomic region enrichment showed that CW methylation is cell-type specific and is also conserved between humans and mice. In brain neurons, it was found that active long interspersed nuclear element-1 (LINE-1) lacked CW methylations but not CG methylations. Coincidentally, both human Alu and mouse B1 elements preferred high CW methylations at specific loci during their respective evolutionary development. Last, the strand-specific distributions of CW methylations in introns and long interspersed nuclear elements are also cell-type specific and conserved. In summary, our results illustrate that CW methylations are highly conserved among species, are dynamically regulated in each cell type, and are potentially involved in the evolution of transposon elements.
Collapse
|
50
|
Madissoon E, Jouhilahti EM, Vesterlund L, Töhönen V, Krjutškov K, Petropoulous S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J. Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. Sci Rep 2016; 6:28995. [PMID: 27412763 PMCID: PMC4944136 DOI: 10.1038/srep28995] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 01/07/2023] Open
Abstract
PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes, ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB, NOBOX, TPRX1 and TPRX2, were expressed in human preimplantation embryos. In the current study we characterized these PRD-like homeobox genes in depth and studied their functions as transcription factors. We cloned multiple transcript variants from human embryos and showed that the expression of these genes is specific to embryos and pluripotent stem cells. Overexpression of the genes in human embryonic stem cells confirmed their roles as transcription factors as either activators (CPHX1, CPHX2, ARGFX) or repressors (DPRX, DUXA, TPRX2) with distinct targets that could be explained by the amino acid sequence in homeodomain. Some PRD-like homeodomain transcription factors had high concordance of target genes and showed enrichment for both developmentally important gene sets and a 36 bp DNA recognition motif implicated in Embryo Genome Activation (EGA). Our data implicate a role for these previously uncharacterized PRD-like homeodomain proteins in the regulation of human embryo genome activation and preimplantation embryo development.
Collapse
Affiliation(s)
- Elo Madissoon
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | | | - Virpi Töhönen
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kaarel Krjutškov
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Sophie Petropoulous
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Robert Månsson
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | - Shintaro Katayama
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Juha Kere
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| |
Collapse
|