1
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Smith SS. The bisulfite reaction with cytosine and genomic DNA structure. Anal Biochem 2024; 691:115532. [PMID: 38609028 DOI: 10.1016/j.ab.2024.115532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 02/19/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024]
Abstract
The bisulfite reaction with native DNA has been extensively employed in the detection of non-B DNA structures that can form spontaneously in DNA. These sequences are dynamic in that they can adopt both normal Watson-Crick paired B-DNA or unusual structures like the Triplex, G-Quadruplex, i-motif and Cruciform or Hairpin. Considerable evidence now suggests that these dynamic sequences play roles in both epigenetics and mutagenesis. The bisulfite reaction with native DNA offers a key approach to their detection. In this application whole cells, isolated nuclei or isolated DNA are treated with bisulfite under non-denaturing conditions in order to detect bisulfite accessible regions DNA that are associated with these structures. Here I review the stereochemistry of the bisulfite reaction, the electronic structure of its DNA cytosine substrates and its application in the detection of unusual structures in native DNA.
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Affiliation(s)
- Steven S Smith
- Department of Stem Cell Biology and Regenerative Medicine, Beckman Research Institute of the City of Hope, Duarte, CA, USA.
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2
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Lai Q, Wan Y, Zhang Y, Huang Y, Tang Q, Chen M, Li Q, Ma K, Xiao P, Luo C, Zhuang X. Hypomethylation-associated LINC00987 downregulation induced lung adenocarcinoma progression by inhibiting the phosphorylation-mediated degradation of SND1. Mol Carcinog 2024; 63:1260-1274. [PMID: 38607240 DOI: 10.1002/mc.23722] [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: 02/02/2024] [Revised: 02/27/2024] [Accepted: 03/25/2024] [Indexed: 04/13/2024]
Abstract
DNA methylation, an epigenetic regulatory mechanism dictating gene transcription, plays a critical role in the occurrence and development of cancer. However, the molecular underpinnings of LINC00987 methylation in the regulation of lung adenocarcinoma (LUAD) remain elusive. This study investigated LINC00987 expression in LUAD patients through analysis of The Cancer Genome Atlas data sets. Quantitative real-time polymerase chain reaction (RT-qPCR) and fluorescence in situ hybridization assays were used to assess LINC00987 expression in LUAD. The bisulfite genomic sequence PCR (BSP) assay was used to determine the methylation levels of the LINC00987 promoter. The interaction between LINC00987 and SND1 was elucidated via immunoprecipitation and RNA pull-down assays. The functional significance of LINC00987 and SND1 in Calu-3 and NCI-H1688 cells was evaluated in vitro through CCK-8, EdU, Transwell, flow cytometry, and vasculogenic mimicry (VM) tube formation assays. LINC00987 expression decreased in LUAD concomitant with hypermethylation of the promoter region, while hypomethylation of the LINC00987 promoter in LUAD tissues correlated with tumor progression. Treatment with 5-Aza-CdR augmented LINC00987 expression and inhibited tumor growth. Mechanistically, LINC00987 overexpression impeded LUAD progression and VM through direct binding with SND1, thereby facilitating its phosphorylation and subsequent degradation. Additionally, overexpression of SND1 counteracted the adverse effects of LINC00987 downregulation on cell proliferation, apoptosis, cell migration, invasion, and VM in LUAD in vitro. In conclusion, this pioneering study focuses on the expression and function of LINC00987 and reveals that hypermethylation of the LINC00987 gene may contribute to LUAD progression. LINC00987 has emerged as a potential tumor suppressor gene in tumorigenesis through its binding with SND1 to facilitate its phosphorylation and subsequent degradation.
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Affiliation(s)
- Qi Lai
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yulin Wan
- Medical Department, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yingqian Zhang
- Laboratory of Nonhuman Primate Disease Modeling Research, West China Hospital, Sichuan University, Chengdu, China
| | - Yingzhao Huang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qiuyue Tang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Mei Chen
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qian Li
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Ke Ma
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Ping Xiao
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Cheng Luo
- Department of Radiation Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Xiang Zhuang
- Department of Thoracic Surgery, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
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3
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Grätz C, Schuster M, Brandes F, Meidert AS, Kirchner B, Reithmair M, Schelling G, Pfaffl MW. A pipeline for the development and analysis of extracellular vesicle-based transcriptomic biomarkers in molecular diagnostics. Mol Aspects Med 2024; 97:101269. [PMID: 38552453 DOI: 10.1016/j.mam.2024.101269] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/17/2024] [Indexed: 06/12/2024]
Abstract
Extracellular vesicles are shed by every cell type and can be found in any biofluid. They contain different molecules that can be utilized as biomarkers, including several RNA species which they protect from degradation. Here, we present a pipeline for the development and analysis of extracellular vesicle-associated transcriptomic biomarkers that our group has successfully applied multiple times. We highlight the key steps of the pipeline and give particular emphasis to the necessary quality control checkpoints, which are linked to numerous available guidelines that should be considered along the workflow. Our pipeline starts with patient recruitment and continues with blood sampling and processing. The purification and characterization of extracellular vesicles is explained in detail, as well as the isolation and quality control of extracellular vesicle-associated RNA. We point out the possible pitfalls during library preparation and RNA sequencing and present multiple bioinformatic tools to pinpoint biomarker signature candidates from the sequencing data. Finally, considerations and pitfalls during the validation of the biomarker signature using RT-qPCR will be elaborated.
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Affiliation(s)
- Christian Grätz
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
| | - Martina Schuster
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Florian Brandes
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Agnes S Meidert
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Benedikt Kirchner
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany; Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Marlene Reithmair
- Institute of Human Genetics, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Gustav Schelling
- Department of Anesthesiology, University Hospital, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Michael W Pfaffl
- Department of Animal Physiology and Immunology, School of Life Sciences, Technical University of Munich, Freising, Germany.
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4
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Sel FA, Oğuz FS. Can novel methods replace the gold standard chimerism method after allogeneic hematopoietic stem cell transplantation? Ann Hematol 2024; 103:1035-1047. [PMID: 37801085 DOI: 10.1007/s00277-023-05448-3] [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: 12/15/2022] [Accepted: 09/07/2023] [Indexed: 10/07/2023]
Abstract
After hematopoietic stem cell transplantation, chimerism assay is a useful approach to monitor the success of the transplant and to select the appropriate treatment strategy, such as donor leukocyte infusion or immunosuppressive drug dosage. Short tandem repeat PCR is the method that has been accepted as the gold standard for chimerism. However, it has not yet been sufficient to detect mixed chimerism in patients with minimal residual disease. Simultaneously, recent years have been marked by developing sensitive, high-throughput, and accurate molecular genetic assays. These novel methods have subsequently been adapted for the analysis of post-transplant chimerism. In this review, we discuss the technical features of both novel and conventional gold standard chimerism assays. We also discuss their advantages and disadvantages.
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Affiliation(s)
- Figen Abatay Sel
- Department of Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey.
- Institute of Graduate Studies in Health Science, Istanbul University, Istanbul, Turkey.
| | - Fatma Savran Oğuz
- Department of Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
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5
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Zhang H, Liu L, Li M. Mini-review of DNA Methylation Detection Techniques and Their Potential Applications in Disease Diagnosis, Prognosis, and Treatment. ACS Sens 2024; 9:1089-1103. [PMID: 38365574 DOI: 10.1021/acssensors.3c02328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2024]
Abstract
DNA methylation is the dominant epigenetic mechanism for regulating gene expression in mammals, playing crucial roles in development, differentiation, and tissue homeostasis. Aberrations in DNA methylation are closely associated with the potential onset of various diseases. Consequently, numerous DNA methylation detection techniques have been successively developed. These methods not only facilitate the exploration of disease mechanisms but also hold significant promise for the development of diagnostic and prognostic strategies. In this Perspective, we present a comprehensive overview of commonly employed DNA methylation detection techniques as well as biosensing based on their underlying analytical techniques. For its medical applications, we begin by examining the pathogenesis of different diseases and then proceed to discuss how relevant technologies are applied in the context of these specific medical conditions. Additionally, we briefly discuss the current limitations of these techniques and highlight future challenges in advancing methylation detection and analysis methodologies.
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Affiliation(s)
- Huaming Zhang
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
| | - Lei Liu
- Institute for Advanced Materials, School of Materials Science and Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Min Li
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China
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6
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Wang B, Wang M, Lin Y, Zhao J, Gu H, Li X. Circulating tumor DNA methylation: a promising clinical tool for cancer diagnosis and management. Clin Chem Lab Med 2024; 0:cclm-2023-1327. [PMID: 38443752 DOI: 10.1515/cclm-2023-1327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/19/2024] [Indexed: 03/07/2024]
Abstract
Cancer continues to pose significant challenges to the medical community. Early detection, accurate molecular profiling, and adequate assessment of treatment response are critical factors in improving the quality of life and survival of cancer patients. Accumulating evidence shows that circulating tumor DNA (ctDNA) shed by tumors into the peripheral blood preserves the genetic and epigenetic information of primary tumors. Notably, DNA methylation, an essential and stable epigenetic modification, exhibits both cancer- and tissue-specific patterns. As a result, ctDNA methylation has emerged as a promising molecular marker for noninvasive testing in cancer clinics. In this review, we summarize the existing techniques for ctDNA methylation detection, describe the current research status of ctDNA methylation, and present the potential applications of ctDNA-based assays in the clinic. The insights presented in this article could serve as a roadmap for future research and clinical applications of ctDNA methylation.
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Affiliation(s)
- Binliang Wang
- Department of Respiratory Medicine, Huangyan Hospital Affiliated to Wenzhou Medical University, Taizhou, P.R. China
| | - Meng Wang
- Institute of Health Education, Hangzhou Center for Disease Control and Prevention, Hangzhou, P.R. China
| | - Ya Lin
- Zhejiang University of Chinese Medicine, Hangzhou, P.R. China
| | - Jinlan Zhao
- Scientific Research Department, Zhejiang Shengting Medical Company, Hangzhou, P.R. China
| | - Hongcang Gu
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, P.R. China
- Anhui Province Key Laboratory of Medical Physics and Technology, Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Science, Hefei, P.R. China
| | - Xiangjuan Li
- Department of Gynaecology, Hangzhou Obstetrics and Gynecology Hospital, Hangzhou, P.R. China
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Zhang L, Li J. Unlocking the secrets: the power of methylation-based cfDNA detection of tissue damage in organ systems. Clin Epigenetics 2023; 15:168. [PMID: 37858233 PMCID: PMC10588141 DOI: 10.1186/s13148-023-01585-8] [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: 06/08/2023] [Accepted: 10/11/2023] [Indexed: 10/21/2023] Open
Abstract
BACKGROUND Detecting organ and tissue damage is essential for early diagnosis, treatment decisions, and monitoring disease progression. Methylation-based assays offer a promising approach, as DNA methylation patterns can change in response to tissue damage. These assays have potential applications in early detection, monitoring disease progression, evaluating treatment efficacy, and assessing organ viability for transplantation. cfDNA released into the bloodstream upon tissue or organ injury can serve as a biomarker for damage. The epigenetic state of cfDNA, including DNA methylation patterns, can provide insights into the extent of tissue and organ damage. CONTENT Firstly, this review highlights DNA methylation as an extensively studied epigenetic modification that plays a pivotal role in processes such as cell growth, differentiation, and disease development. It then presents a variety of highly precise 5-mC methylation detection techniques that serve as powerful tools for gaining profound insights into epigenetic alterations linked with tissue damage. Subsequently, the review delves into the mechanisms underlying DNA methylation changes in organ and tissue damage, encompassing inflammation, oxidative stress, and DNA damage repair mechanisms. Next, it addresses the current research status of cfDNA methylation in the detection of specific organ tissues and organ damage. Finally, it provides an overview of the multiple steps involved in identifying specific methylation markers associated with tissue and organ damage for clinical trials. This review will explore the mechanisms and current state of research on cfDNA methylation-based assay detecting organ and tissue damage, the underlying mechanisms, and potential applications in clinical practice.
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Affiliation(s)
- Lijing Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, People's Republic of China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, No. 1 Dahua Road, Dongdan, Beijing, 100730, People's Republic of China.
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing Hospital, Beijing, People's Republic of China.
- Beijing Engineering Research Center of Laboratory Medicine, Beijing, People's Republic of China.
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8
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Jiang HH, Xing SW, Tang X, Chen Y, Lin K, He LW, Lin MB, Tang EJ. Novel multiplex stool-based assay for the detection of early-stage colon cancer in a Chinese population. World J Gastroenterol 2022; 28:2705-2732. [PMID: 35979157 PMCID: PMC9260868 DOI: 10.3748/wjg.v28.i24.2705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/14/2022] [Accepted: 05/14/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Stool DNA (sDNA) methylation analysis is a promising, noninvasive approach for colorectal cancer screening; however, reliable biomarkers for detecting early-stage colon cancer (ECC) are lacking, particularly in the Chinese population.
AIM To identify a novel stool-based assay that can improve the effectiveness of ECC screening.
METHODS A blinded case-control study was performed using archived stool samples from 125 ECC patients, and 125 control subjects with normal colonoscopy. The cohort was randomly divided into training and test sets at a 1.5:1 ratio. Targeted bisulfite sequencing (TBSeq) was conducted on five pairs of preoperative and postop-erative sDNA samples from ECC patients to identify DNA methylation biomarkers, which were validated using pyrosequencing. By logistic regression analysis, a multiplex stool-based assay was developed in the training set, and the detection performance was further assessed in the test set and combined set. The χ2 test was used to investigate the association of detection sensitivity with clinico-pathological features.
RESULTS Following TBSeq, three hypermethylated cytosine-guanine sites were selected as biomarkers, including paired box 8, Ras-association domain family 1 and secreted frizzled-related protein 2, which differed between the groups and were involved in important cancer pathways. An sDNA panel containing the three biomarkers was constructed with a logistic model. Receiver operating characteristic (ROC) analysis revealed that this panel was superior to the fecal immunochemical test (FIT) or serum carcinoembryonic antigen for the detection of ECC. We further found that the combination of the sDNA panel with FIT could improve the screening effectiveness. In the combined set, the sensitivity, specificity and area under the ROC curve for this multiplex assay were 80.0%, 93.6% and 0.918, respectively, and the performance remained excellent in the subgroup analysis by tumor stage. In addition, the detection sensitivity did not differ with tumor site, tumor stage, histological differentiation, age or sex, but was significantly higher in T4 than in T1-3 stage tumors (P = 0.041).
CONCLUSION We identified a novel multiplex stool-based assay combining sDNA methylation biomarkers and FIT, which could detect ECC with high sensitivity and specificity throughout the colon, showing a promising application perspective.
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Affiliation(s)
- Hui-Hong Jiang
- Department of General Surgery, Yangpu Hospital, Tongji University, Shanghai 200090, China
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai 200090, China
| | - Si-Wei Xing
- Department of Urology, Ruijin Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200025, China
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University, Shanghai 200090, China
| | - Xuan Tang
- Department of General Surgery, Yangpu Hospital, Tongji University, Shanghai 200090, China
| | - Ying Chen
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai 200090, China
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University, Shanghai 200090, China
| | - Kang Lin
- Department of General Surgery, Yangpu Hospital, Tongji University, Shanghai 200090, China
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University, Shanghai 200090, China
| | - Lu-Wei He
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai 200090, China
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University, Shanghai 200090, China
| | - Mou-Bin Lin
- Department of General Surgery, Yangpu Hospital, Tongji University, Shanghai 200090, China
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai 200090, China
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University, Shanghai 200090, China
| | - Er-Jiang Tang
- Institute of Gastrointestinal Surgery and Translational Medicine, Tongji University School of Medicine, Shanghai 200090, China
- Center for Clinical Research and Translational Medicine, Yangpu Hospital, Tongji University, Shanghai 200090, China
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Wang LJ, Han Q, Qiu JG, Zhang CY. Cooperative In Situ Assembly of G-Quadruplex DNAzyme Nanowires for One-Step Sensing of CpG Methylation in Human Genomes. NANO LETTERS 2022; 22:347-354. [PMID: 34931851 DOI: 10.1021/acs.nanolett.1c03969] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
CpG methylation is one the most predominant epigenetic modification that has been recognized as a molecular-level biomarker for various human diseases. Taking advantage of methylation-dependent cleavage and encoding flexibility in nucleic acid functions and structures, we demonstrate the cooperative in situ assembly of G-quadruplex DNAzyme nanowires for one-step sensing of CpG methylation in human genomes. This nanodevice displays good specificity and high sensitivity with a limit of detection (LOD) of 0.565 aM in vitro and 1 cell in vivo. It can distinguish 0.001% CpG methylation level from excess unmethylated DNA, quantify different CpG methylation targets from diverse human cancer cells, and even discriminate CpG methylation expressions between lung tumor and precancerous tissues. Importantly, this nanodevice can be performed isothermally in one step within 2 h in a label-free manner without any bisulfite conversion, fluorescence tagging, and PCR amplification process, providing a new platform for genomic methylation-related clinical diagnosis and biomedical research.
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Affiliation(s)
- Li-Juan Wang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
- School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189, China
| | - Qian Han
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
| | - Jian-Ge Qiu
- Academy of Medical Sciences, Zhengzhou University, Zhengzhou, Henan 450000, China
| | - Chun-Yang Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Shandong Normal University, Jinan 250014, China
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10
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Sharma M, Verma RK, Kumar S, Kumar V. Computational challenges in detection of cancer using cell-free DNA methylation. Comput Struct Biotechnol J 2021; 20:26-39. [PMID: 34976309 PMCID: PMC8669313 DOI: 10.1016/j.csbj.2021.12.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 12/02/2021] [Accepted: 12/02/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-free DNA(cfDNA) methylation profiling is considered promising and potentially reliable for liquid biopsy to study progress of diseases and develop reliable and consistent diagnostic and prognostic biomarkers. There are several different mechanisms responsible for the release of cfDNA in blood plasma, and henceforth it can provide information regarding dynamic changes in the human body. Due to the fragmented nature, low concentration of cfDNA, and high background noise, there are several challenges in its analysis for regular use in diagnosis of cancer. Such challenges in the analysis of the methylation profile of cfDNA are further aggravated due to heterogeneity, biomarker sensitivity, platform biases, and batch effects. This review delineates the origin of cfDNA methylation, its profiling, and associated computational problems in analysis for diagnosis. Here we also contemplate upon the multi-marker approach to handle the scenario of cancer heterogeneity and explore the utility of markers for 5hmC based cfDNA methylation pattern. Further, we provide a critical overview of deconvolution and machine learning methods for cfDNA methylation analysis. Our review of current methods reveals the potential for further improvement in analysis strategies for detecting early cancer using cfDNA methylation.
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Key Words
- Cancer heterogeneity
- Cell free DNA
- Computation
- DMP, Differentially methylated base position
- DMR, Differentially methylated regions
- Diagnosis
- HELP-seq, HpaII-tiny fragment Enrichment by Ligation-mediated PCR sequencing
- MBD-seq, Methyl-CpG Binding Domain Protein Capture Sequencing
- MCTA-seq, Methylated CpG tandems amplification and sequencing
- MSCC, Methylation Sensitive Cut Counting
- MSRE, methylation sensitive restriction enzymes
- MeDIP-seq, Methylated DNA Immunoprecipitation Sequencing
- RRBS, Reduced-Representation Bisulfite Sequencing
- WGBS, Whole Genome Bisulfite Sequencing
- cfDNA, cell free DNA
- ctDNA, circulating tumor DNA
- dPCR, digital polymerase chain reaction
- ddMCP, droplet digital methylation-specific PCR
- ddPCR, droplet digital polymerase chain reaction
- scCGI, methylated CGIs at single cell level
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Affiliation(s)
- Madhu Sharma
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Rohit Kumar Verma
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
| | - Sunil Kumar
- Department of Surgical oncology, All India Institute of Medical sciences, New Delhi 110029, India
| | - Vibhor Kumar
- Department for Computational Biology, Indraprastha Institute of Information Technology, Delhi 110020, India
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11
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Foox J, Nordlund J, Lalancette C, Gong T, Lacey M, Lent S, Langhorst BW, Ponnaluri VKC, Williams L, Padmanabhan KR, Cavalcante R, Lundmark A, Butler D, Mozsary C, Gurvitch J, Greally JM, Suzuki M, Menor M, Nasu M, Alonso A, Sheridan C, Scherer A, Bruinsma S, Golda G, Muszynska A, Łabaj PP, Campbell MA, Wos F, Raine A, Liljedahl U, Axelsson T, Wang C, Chen Z, Yang Z, Li J, Yang X, Wang H, Melnick A, Guo S, Blume A, Franke V, Ibanez de Caceres I, Rodriguez-Antolin C, Rosas R, Davis JW, Ishii J, Megherbi DB, Xiao W, Liao W, Xu J, Hong H, Ning B, Tong W, Akalin A, Wang Y, Deng Y, Mason CE. The SEQC2 epigenomics quality control (EpiQC) study. Genome Biol 2021; 22:332. [PMID: 34872606 PMCID: PMC8650396 DOI: 10.1186/s13059-021-02529-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 10/28/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cytosine modifications in DNA such as 5-methylcytosine (5mC) underlie a broad range of developmental processes, maintain cellular lineage specification, and can define or stratify types of cancer and other diseases. However, the wide variety of approaches available to interrogate these modifications has created a need for harmonized materials, methods, and rigorous benchmarking to improve genome-wide methylome sequencing applications in clinical and basic research. Here, we present a multi-platform assessment and cross-validated resource for epigenetics research from the FDA's Epigenomics Quality Control Group. RESULTS Each sample is processed in multiple replicates by three whole-genome bisulfite sequencing (WGBS) protocols (TruSeq DNA methylation, Accel-NGS MethylSeq, and SPLAT), oxidative bisulfite sequencing (TrueMethyl), enzymatic deamination method (EMSeq), targeted methylation sequencing (Illumina Methyl Capture EPIC), single-molecule long-read nanopore sequencing from Oxford Nanopore Technologies, and 850k Illumina methylation arrays. After rigorous quality assessment and comparison to Illumina EPIC methylation microarrays and testing on a range of algorithms (Bismark, BitmapperBS, bwa-meth, and BitMapperBS), we find overall high concordance between assays, but also differences in efficiency of read mapping, CpG capture, coverage, and platform performance, and variable performance across 26 microarray normalization algorithms. CONCLUSIONS The data provided herein can guide the use of these DNA reference materials in epigenomics research, as well as provide best practices for experimental design in future studies. By leveraging seven human cell lines that are designated as publicly available reference materials, these data can be used as a baseline to advance epigenomics research.
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Affiliation(s)
- Jonathan Foox
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA
| | - Jessica Nordlund
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Claudia Lalancette
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Ting Gong
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | | | - Samantha Lent
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | | | | | | | - Raymond Cavalcante
- BRCF Epigenomics Core, University of Michigan Medicine, Ann Arbor, MI, 48109, USA
| | - Anders Lundmark
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Daniel Butler
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Christopher Mozsary
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Justin Gurvitch
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - John M Greally
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Albert Einstein College of Medicine, Bronx, NY, 10461, USA
| | - Mark Menor
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Masaki Nasu
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA
| | - Alicia Alonso
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Caroline Sheridan
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
- Division of Hematology/Oncology, Department of Medicine, Epigenomics Core Facility, Weill Cornell Medicine, New York, NY, USA
| | - Andreas Scherer
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | | | - Gosia Golda
- Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Krakow, Poland
| | - Agata Muszynska
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | - Paweł P Łabaj
- Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland
| | | | - Frank Wos
- New York Genome Center, New York, NY, 10013, USA
| | - Amanda Raine
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Ulrika Liljedahl
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Tomas Axelsson
- Department of Medical Sciences and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
| | - Charles Wang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhong Chen
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
| | - Zhaowei Yang
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Jing Li
- Center for Genomics, School of Medicine, Loma Linda University, Loma Linda, CA, 92350, USA
- Department of Allergy and Clinical Immunology, State Key Laboratory of Respiratory Disease, Guangzhou Institute of Respiratory Health, the First Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Xiaopeng Yang
- Department of Neurology, The Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Hongwei Wang
- Development of Medicine, the University of Chicago, Chicago, IL, 60637, USA
| | - Ari Melnick
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA
| | - Shang Guo
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China
| | - Alexander Blume
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Vedran Franke
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Inmaculada Ibanez de Caceres
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Carlos Rodriguez-Antolin
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Rocio Rosas
- EATRIS ERIC- European Infrastructure for Translational Medicine, De Boelelaan 1118, 1081, HZ, Amsterdam, The Netherlands
- Cancer Epigenetics Laboratory, INGEMM, IdiPAZ, Madrid, Spain
| | - Justin Wade Davis
- AbbVie Genomics Research Center, 1 N. Waukegan Rd, North Chicago, IL, 60036, USA
| | | | - Dalila B Megherbi
- CMINDS Research Center, Francis College of Engineering, University of Massachusetts Lowell, Lowell, MA, 01854, USA
| | - Wenming Xiao
- Center for Devices and Radiological Health, Food and Drug Administration, 10903 New Hampshire Ave, Silver Spring, MD, 20993, USA
| | - Will Liao
- New York Genome Center, New York, NY, 10013, USA
| | - Joshua Xu
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Huixiao Hong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Baitang Ning
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Weida Tong
- Division of Bioinformatics and Biostatistics, National Center for Toxicological Research, Food and Drug Administration, 3900 NCTR Road, Jefferson, AR, 72079, USA
| | - Altuna Akalin
- Bioinformatics and Omics Data Science Platform, Berlin Institute for Medical Systems Biology, Max Delbrueck Center for Molecular Medicine, Berlin, Germany
| | - Yunliang Wang
- Department of Neurology, the Second Affiliated Hospital of Zhengzhou University, Zhengzhou, 450014, China.
| | - Youping Deng
- Department of Quantitative Health Sciences, University of Hawaii John A. Burns School of Medicine, Honolulu, HI, 96813, USA.
| | - Christopher E Mason
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York, USA.
- The HRH Prince Alwaleed Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, Weill Cornell Medicine, New York, New York, USA.
- The Feil Family Brain and Mind Research Institute, New York, New York, USA.
- The WorldQuant Initiative for Quantitative Prediction, Weill Cornell Medicine, New York, NY, USA.
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12
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Wei S, Tao J, Xu J, Chen X, Wang Z, Zhang N, Zuo L, Jia Z, Chen H, Sun H, Yan Y, Zhang M, Lv H, Kong F, Duan L, Ma Y, Liao M, Xu L, Feng R, Liu G, Project TEWAS, Jiang Y. Ten Years of EWAS. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2100727. [PMID: 34382344 PMCID: PMC8529436 DOI: 10.1002/advs.202100727] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 05/11/2021] [Indexed: 06/13/2023]
Abstract
Epigenome-wide association study (EWAS) has been applied to analyze DNA methylation variation in complex diseases for a decade, and epigenome as a research target has gradually become a hot topic of current studies. The DNA methylation microarrays, next-generation, and third-generation sequencing technologies have prepared a high-quality platform for EWAS. Here, the progress of EWAS research is reviewed, its contributions to clinical applications, and mainly describe the achievements of four typical diseases. Finally, the challenges encountered by EWAS and make bold predictions for its future development are presented.
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Affiliation(s)
- Siyu Wei
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Junxian Tao
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Jing Xu
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Xingyu Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhaoyang Wang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Nan Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Lijiao Zuo
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Zhe Jia
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Haiyan Chen
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongmei Sun
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Yubo Yan
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Mingming Zhang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Hongchao Lv
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
| | - Fanwu Kong
- The EWAS ProjectHarbinChina
- Department of NephrologyThe Second Affiliated HospitalHarbin Medical UniversityHarbin150001China
| | - Lian Duan
- The EWAS ProjectHarbinChina
- The First Affiliated Hospital of Wenzhou Medical UniversityWenzhou325000China
| | - Ye Ma
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
| | - Mingzhi Liao
- The EWAS ProjectHarbinChina
- College of Life SciencesNorthwest A&F UniversityYanglingShanxi712100China
| | - Liangde Xu
- The EWAS ProjectHarbinChina
- School of Biomedical EngineeringWenzhou Medical UniversityWenzhou325035China
| | - Rennan Feng
- The EWAS ProjectHarbinChina
- Department of Nutrition and Food HygienePublic Health CollegeHarbin Medical UniversityHarbin150081China
| | - Guiyou Liu
- The EWAS ProjectHarbinChina
- Beijing Institute for Brain DisordersCapital Medical UniversityBeijing100069China
| | | | - Yongshuai Jiang
- College of Bioinformatics Science and TechnologyHarbin Medical UniversityHarbin150081China
- The EWAS ProjectHarbinChina
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13
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Wajda A, Sivitskaya L, Paradowska-Gorycka A. Application of NGS Technology in Understanding the Pathology of Autoimmune Diseases. J Clin Med 2021; 10:3334. [PMID: 34362117 PMCID: PMC8348854 DOI: 10.3390/jcm10153334] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 07/26/2021] [Indexed: 11/16/2022] Open
Abstract
NGS technologies have transformed clinical diagnostics and broadly used from neonatal emergencies to adult conditions where the diagnosis cannot be made based on clinical symptoms. Autoimmune diseases reveal complicate molecular background and traditional methods could not fully capture them. Certainly, NGS technologies meet the needs of modern exploratory research, diagnostic and pharmacotherapy. Therefore, the main purpose of this review was to briefly present the application of NGS technology used in recent years in the understanding of autoimmune diseases paying particular attention to autoimmune connective tissue diseases. The main issues are presented in four parts: (a) panels, whole-genome and -exome sequencing (WGS and WES) in diagnostic, (b) Human leukocyte antigens (HLA) as a diagnostic tool, (c) RNAseq, (d) microRNA and (f) microbiome. Although all these areas of research are extensive, it seems that epigenetic impact on the development of systemic autoimmune diseases will set trends for future studies on this area.
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Affiliation(s)
- Anna Wajda
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
| | - Larysa Sivitskaya
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, 220072 Minsk, Belarus
| | - Agnieszka Paradowska-Gorycka
- Department of Molecular Biology, National Institute of Geriatrics, Rheumatology and Rehabilitation, 02-637 Warsaw, Poland
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14
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Wang X, Zhou S, Chu C, Yang M, Huo D, Hou C. Dual Methylation-Sensitive Restriction Endonucleases Coupling with an RPA-Assisted CRISPR/Cas13a System (DESCS) for Highly Sensitive Analysis of DNA Methylation and Its Application for Point-of-Care Detection. ACS Sens 2021; 6:2419-2428. [PMID: 34019391 DOI: 10.1021/acssensors.1c00674] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-performance detection of DNA methylation possesses great significance for the diagnosis and therapy of cancer. Herein, for the first time, we present a digestion strategy based on dual methylation-sensitive restriction endonucleases coupling with a recombinase polymerase amplification (RPA)-assisted CRISPR/Cas13a system (DESCS) for accurate and sensitive determination of site-specific DNA methylation. This dual methylation-sensitive restriction endonuclease system selectively digests the unmethylated target but exhibits no response to methylated DNA. Therefore, the intact methylated DNA target triggers the RPA reaction for rapid signal amplification. In contrast, the digested unmethylated target initiates no RPA reaction. RPA products with a T7 promoter can execute the T7 transcription in the presence of T7 RNA polymerase to generate a large number of single-stranded RNA (ssRNA). This ssRNA can be recognized by CRISPR/Cas13a to induce the ssRNase activity of Cas13a, showing the indiscriminate cleavage of the collateral FQ reporter to release the fluorescence signal. With such a design, by combining the unique features of dual methylation-sensitive restriction endonucleases with RPA-assisted CRISPR/Cas13a, the DESCS system not only presents the rapid and powerful signal amplification for the determination of methylated DNA with ultrahigh sensitivity but also effectively eliminates the false positive influences from incomplete digestion of the unmethylated target. More importantly, 0.01% methylation level can be effectively distinguished with the existence of excess unmethylated DNA. In addition, the DESCS assay is integrated into the lateral flow biosensor (LFB) for the point-of-care determination of DNA methylation. In view of the superiorities in high sensitivity, outstanding selectivity, and ease of operation, the DESCS system will provide a reliable assay for site-specific analysis of methylation.
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Affiliation(s)
- Xianfeng Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Chengxiang Chu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
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15
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DNA methylation studies in cattle. J Appl Genet 2021; 62:121-136. [PMID: 33400132 DOI: 10.1007/s13353-020-00604-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 10/23/2020] [Accepted: 12/22/2020] [Indexed: 12/12/2022]
Abstract
Investigation of the role of epigenetics in cattle breeding is gaining importance. DNA methylation represents an epigenetic modification which is essential for genomic stability and maintenance of development. Recently, DNA methylation research in cattle has intensified. The studies focus on the definition of methylomes in various organs and tissues in relation to the expression of genes underlying economically important traits, and explore methylome changes under developmental, environmental, disease, and diet influences. The investigations further characterize the methylation patterns of gametes in connection with their quality, and study methylome alterations in the developing naturally or assisted produced zygotes, embryos, and fetuses, considering their viability. A wide array of technologies developed for accurate and precise analysis of DNA methylation patterns is employed for both single-gene and genome-wide studies. Overall, the research is directed towards the identification of single methylation markers or their combinations which may be useful in the selection and breeding of animals to ensure cattle improvement.
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16
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Milan T, Celton M, Lagacé K, Roques É, Safa-Tahar-Henni S, Bresson E, Bergeron A, Hebert J, Meshinchi S, Cellot S, Barabé F, Wilhelm BT. Epigenetic changes in human model KMT2A leukemias highlight early events during leukemogenesis. Haematologica 2020; 107:86-99. [PMID: 33375773 PMCID: PMC8719083 DOI: 10.3324/haematol.2020.271619] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Indexed: 11/26/2022] Open
Abstract
Chromosomal translocations involving the KMT2A gene are among the most common genetic alterations found in pediatric acute myeloid leukemias although the molecular mechanisms that initiate the disease remain incompletely defined. To elucidate these initiating events we used a human model system of acute myeloid leukemia driven by the KMT2A-MLLT3 (KM3) fusion. More specifically, we investigated changes in DNA methylation, histone modifications, and chromatin accessibility at each stage of our model system and correlated these with expression changes. We observed the development of a pronounced hypomethyl - ation phenotype in the early stages of leukemic transformation after KM3 addition along with loss of expression of stem-cell-associated genes and skewed expression of other genes, such as S100A8/9, implicated in leukemogenesis. In addition, early increases in the expression of the lysine demethylase KDM4B was functionally linked to these expression changes as well as other key transcription factors. Remarkably, our ATAC-sequencing data showed that there were relatively few leukemia-specific changes and that the vast majority corresponded to open chromatin regions and transcription factor clusters previously observed in other cell types. Integration of the gene expression and epigenetic changes revealed that the adenylate cyclase gene ADCY9 is an essential gene in KM3-acute myeloid leukemia, and suggested the potential for autocrine signaling through the chemokine receptor CCR1 and CCL23 ligand. Collectively, our results suggest that KM3 induces subtle changes in the epigenome while co-opting the normal transcriptional machinery to drive leukemogenesis.
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Affiliation(s)
- Thomas Milan
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Magalie Celton
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Karine Lagacé
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Élodie Roques
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Safia Safa-Tahar-Henni
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC
| | - Eva Bresson
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec - Université Laval, Québec City, QC, Canada; CHU de Québec - Université Laval - Hôpital Enfant-Jésus; Québec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC
| | - Anne Bergeron
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec - Université Laval, Québec City, QC, Canada; CHU de Québec - Université Laval - Hôpital Enfant-Jésus; Québec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC
| | - Josée Hebert
- Division of Hematology-Oncology and Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC
| | - Soheil Meshinchi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sonia Cellot
- Department of pediatrics, division of Hematology, Ste-Justine Hospital, Montréal, QC
| | - Frédéric Barabé
- Centre de recherche en infectiologie du CHUL, Centre de recherche du CHU de Québec - Université Laval, Québec City, QC, Canada; CHU de Québec - Université Laval - Hôpital Enfant-Jésus; Québec City, QC, Canada; Department of Medicine, Université Laval, Quebec City, QC
| | - Brian T Wilhelm
- Laboratory for High Throughput Biology, Institute for Research in Immunology and Cancer, Montréal, QC, Canada; Department of Medicine, Université de Montréal, Montréal, QC.
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17
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Lin N, Liu J, Castle J, Wan J, Shendre A, Liu Y, Wang C, He C. Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray. Epigenetics 2020; 16:754-769. [PMID: 33048617 PMCID: PMC8216193 DOI: 10.1080/15592294.2020.1827703] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there was high concordance in methylation levels between the two platforms (Pearson correlation r = 0.98, P < 0.0001). However, we observed that TruSeq EPIC measurements provided a wider dynamic range and likely a higher quantitative sensitivity for CpGs that were either hypo- or hyper-methylated (β close to 0 or 1, respectively). In addition, when comparing different breast tissue types TruSeq EPIC identified more differentially methylated CpGs than EPIC-array, not only out of additional sites interrogated by TruSeq EPIC alone, but also out of common sites interrogated by both platforms. Our results suggest that both platforms show high reproducibility and reliability in genome-wide DNA methylation profiling, while TruSeq EPIC had a significant improvement over EPIC-array regarding genomic resolution and coverage. The wider dynamic range and likely higher precision of the estimates by the TruSeq EPIC may lead to the identification of novel differentially methylated markers that are associated with disease risk.
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Affiliation(s)
- Nan Lin
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Jinpeng Liu
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - James Castle
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Jun Wan
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Aditi Shendre
- Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA
| | - Yunlong Liu
- Department of Medical & Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Chi Wang
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA
| | - Chunyan He
- The Cancer Prevention and Control Research Program, University of Kentucky Markey Cancer Center, Lexington, KY, USA.,Department of Internal Medicine, Division of Medical Oncology, College of Medicine, University of Kentucky, Lexington, KY, USA
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18
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Weiser DA, West-Szymanski DC, Fraint E, Weiner S, Rivas MA, Zhao CWT, He C, Applebaum MA. Progress toward liquid biopsies in pediatric solid tumors. Cancer Metastasis Rev 2020; 38:553-571. [PMID: 31836951 DOI: 10.1007/s10555-019-09825-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Pediatric solid tumors have long been known to shed tumor cells, DNA, RNA, and proteins into the blood. Recent technological advances have allowed for improved capture and analysis of these typically scant circulating materials. Efforts are ongoing to develop "liquid biopsy" assays as minimally invasive tools to address diagnostic, prognostic, and disease monitoring needs in childhood cancer care. Applying these highly sensitive technologies to serial liquid biopsies is expected to advance understanding of tumor biology, heterogeneity, and evolution over the course of therapy, thus opening new avenues for personalized therapy. In this review, we outline the latest technologies available for liquid biopsies and describe the methods, pitfalls, and benefits of the assays that are being developed for children with extracranial solid tumors. We discuss what has been learned in several of the most common pediatric solid tumors including neuroblastoma, sarcoma, Wilms tumor, and hepatoblastoma and highlight promising future directions for the field.
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Affiliation(s)
- Daniel A Weiser
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | | | - Ellen Fraint
- Department of Pediatrics, Albert Einstein College of Medicine and Children's Hospital at Montefiore, Bronx, NY, USA
| | - Shoshana Weiner
- Department of Pediatrics, Weill Cornell Medical Center, New York, NY, USA
| | - Marco A Rivas
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Carolyn W T Zhao
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA
| | - Chuan He
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL, USA.,Howard Hughes Medical Institute, The University of Chicago, Chicago, IL, USA
| | - Mark A Applebaum
- Department of Pediatrics, The University of Chicago, 900 E. 57th St., KCBD 5116, Chicago, IL, 60637, USA.
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19
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Jiang H, Ou Z, He Y, Yu M, Wu S, Li G, Zhu J, Zhang R, Wang J, Zheng L, Zhang X, Hao W, He L, Gu X, Quan Q, Zhang E, Luo H, Wei W, Li Z, Zang G, Zhang C, Poon T, Zhang D, Ziyar I, Zhang RZ, Li O, Cheng L, Shimizu T, Cui X, Zhu JK, Sun X, Zhang K. DNA methylation markers in the diagnosis and prognosis of common leukemias. Signal Transduct Target Ther 2020; 5:3. [PMID: 32296024 PMCID: PMC6959291 DOI: 10.1038/s41392-019-0090-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 09/26/2019] [Accepted: 10/20/2019] [Indexed: 12/12/2022] Open
Abstract
The ability to identify a specific type of leukemia using minimally invasive biopsies holds great promise to improve the diagnosis, treatment selection, and prognosis prediction of patients. Using genome-wide methylation profiling and machine learning methods, we investigated the utility of CpG methylation status to differentiate blood from patients with acute lymphocytic leukemia (ALL) or acute myelogenous leukemia (AML) from normal blood. We established a CpG methylation panel that can distinguish ALL and AML blood from normal blood as well as ALL blood from AML blood with high sensitivity and specificity. We then developed a methylation-based survival classifier with 23 CpGs for ALL and 20 CpGs for AML that could successfully divide patients into high-risk and low-risk groups, with significant differences in clinical outcome in each leukemia type. Together, these findings demonstrate that methylation profiles can be highly sensitive and specific in the accurate diagnosis of ALL and AML, with implications for the prediction of prognosis and treatment selection.
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Affiliation(s)
- Hua Jiang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Zhiying Ou
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Yingyi He
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Meixing Yu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Shaoqing Wu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Gen Li
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jie Zhu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Ru Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Jiayi Wang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Lianghong Zheng
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Xiaohong Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Wenge Hao
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Liya He
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Xiaoqiong Gu
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Qingli Quan
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Edward Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Huiyan Luo
- State Key Laboratory of Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Wei Wei
- State Key Laboratory of Oncology, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Zhihuan Li
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Guangxi Zang
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Charlotte Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Tina Poon
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Daniel Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China
| | - Ian Ziyar
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Run-Ze Zhang
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Oulan Li
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Linhai Cheng
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Taylor Shimizu
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China
| | - Xinping Cui
- Department of Statistics and Institute for Integrative Genome Biology, University of California Riverside, Riverside, CA, 92521, USA
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai, 210602, China
| | - Xin Sun
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
| | - Kang Zhang
- Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China.
- Guangzhou Regenerative Medicine and Health Guangdong Laboratory, Guangzhou, 510005, China.
- Faculty of Medicine, Macau University of Science and Technology, Taipa, Macau, China.
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20
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Di Paolo A, Arrigoni E, Luci G, Cucchiara F, Danesi R, Galimberti S. Precision Medicine in Lymphoma by Innovative Instrumental Platforms. Front Oncol 2019; 9:1417. [PMID: 31921674 PMCID: PMC6928138 DOI: 10.3389/fonc.2019.01417] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 11/28/2019] [Indexed: 12/13/2022] Open
Abstract
In recent years, many efforts have been addressed to the growing field of precision medicine in order to offer individual treatments to every patient on the basis of his/her genetic background. Formerly adopted to achieve new disease classifications as it is still done, innovative platforms, such as microarrays, genome-wide association studies (GWAS), and next generation sequencing (NGS), have made the progress in pharmacogenetics faster and cheaper than previously expected. Several studies in lymphoma patients have demonstrated that these platforms can be used to identify biomarkers predictive of drug efficacy and tolerability, discovering new possible druggable proteins. Indeed, GWAS and NGS allow the investigation of the human genome, finding interesting associations with putative or unexpected targets, which in turns may represent new therapeutic possibilities. Importantly, some objective difficulties have initially hampered the translation of findings in clinical routines, such as the poor quantity/quality of genetic material or the paucity of targets that could be investigated at the same time. At present, some of these technical issues have been partially solved. Furthermore, these analyses are growing in parallel with the development of bioinformatics and its capabilities to manage and analyze big data. Because of pharmacogenetic markers may become important during drug development, regulatory authorities (i.e., EMA, FDA) are preparing ad hoc guidelines and recommendations to include the evaluation of genetic markers in clinical trials. Concerns and difficulties for the adoption of genetic testing in routine are still present, as well as affordability, reliability and the poor confidence of some patients for these tests. However, genetic testing based on predictive markers may offers many advantages to caregivers and patients and their introduction in clinical routine is justified.
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Affiliation(s)
- Antonello Di Paolo
- Section of Pharmacology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Unit of Clinical Pharmacology and Pharmacogenetics, Pisa University Hospital, Pisa, Italy
| | - Elena Arrigoni
- Section of Pharmacology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Giacomo Luci
- Section of Pharmacology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Federico Cucchiara
- Section of Pharmacology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - Romano Danesi
- Section of Pharmacology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Unit of Clinical Pharmacology and Pharmacogenetics, Pisa University Hospital, Pisa, Italy
| | - Sara Galimberti
- Section of Hematology, Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy.,Unit of Hematology, Pisa University Hospital, Pisa, Italy
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21
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Zhang S, Huang J, Lu J, Liu M, Li Y, Fang L, Huang H, Huang J, Mo F, Zheng J. A novel fluorescent biosensor based on dendritic DNA nanostructure in combination with ligase reaction for ultrasensitive detection of DNA methylation. J Nanobiotechnology 2019; 17:121. [PMID: 31812164 PMCID: PMC6898925 DOI: 10.1186/s12951-019-0552-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Accepted: 11/25/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND DNA methylation detection is indispensable for the diagnosis and prognosis of various diseases including malignancies. Hence, it is crucial to develop a simple, sensitive, and specific detection strategy. METHODS A novel fluorescent biosensor was developed based on a simple dual signal amplification strategy using functional dendritic DNA nanostructure and signal-enriching polystyrene microbeads in combination with ligase detection reaction (LDR). Dendritic DNA self-assembled from Y-DNA and X-DNA through enzyme-free DNA catalysis of a hairpin structure, which was prevented from unwinding at high temperature by adding psoralen. Then dendritic DNA polymer labeled with fluorescent dye Cy5 was ligated with reporter probe into a conjugate. Avidin-labeled polystyrene microbeads were specifically bound to biotin-labeled capture probe, and hybridized with target sequence and dendritic DNA. LDR was triggered by adding Taq ligase. When methylated cytosine existed, the capture probe and reporter probe labeled with fluorescent dye perfectly matched the target sequence, forming a stable duplex to generate a fluorescence signal. However, after bisulfite treatment, unmethylated cytosine was converted into uracil, resulting in a single base mismatch. No fluorescence signal was detected due to the absence of duplex. RESULTS The obtained dendritic DNA polymer had a large volume. This method was time-saving and low-cost. Under the optimal experimental conditions using avidin-labeled polystyrene microbeads, the fluorescence signal was amplified more obviously, and DNA methylation was quantified ultrasensitively and selectively. The detection range of this sensor was 10-15 to 10-7 M, and the limit of detection reached as low as 0.4 fM. The constructed biosensor was also successfully used to analyze actual samples. CONCLUSION This strategy has ultrasensitivity and high specificity for DNA methylation quantification, without requiring complex processes such as PCR and enzymatic digestion, which is thus of great value in tumor diagnosis and biomedical research.
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Affiliation(s)
- Shu Zhang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.,Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China.,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jian Huang
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Jingrun Lu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Min Liu
- Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Yan Li
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Lichao Fang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Hui Huang
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China
| | - Jianjun Huang
- Department of Breast Surgery, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Fei Mo
- Department of Basic Clinical Laboratory Medicine, School of Clinical Laboratory Science, Guizhou Medical University, Guiyang, 550004, China. .,Center for Clinical Laboratories, Affiliated Hospital of Guizhou Medical University, Guiyang, 550004, China.
| | - Junsong Zheng
- Department of Clinical and Military Laboratory Medicine, College of Medical Laboratory Science, Army Medical University, Chongqing, 400038, China.
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22
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Liu H, Luo J, Fang L, Huang H, Deng J, Huang J, Zhang S, Li Y, Zheng J. An electrochemical strategy with tetrahedron rolling circle amplification for ultrasensitive detection of DNA methylation. Biosens Bioelectron 2018; 121:47-53. [DOI: 10.1016/j.bios.2018.07.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/23/2018] [Accepted: 07/25/2018] [Indexed: 12/20/2022]
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23
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Zhong L, Liu Y, Wang K, He Z, Gong Z, Zhao Z, Yang Y, Gao X, Li F, Wu H, Zhang S, Chen L. Biomarkers: paving stones on the road towards the personalized precision medicine for oral squamous cell carcinoma. BMC Cancer 2018; 18:911. [PMID: 30241505 PMCID: PMC6151070 DOI: 10.1186/s12885-018-4806-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 09/06/2018] [Indexed: 12/20/2022] Open
Abstract
Traditional therapeutics have encountered a bottleneck caused by diagnosis delay and subjective and unreliable assessment. Biomarkers can overcome this bottleneck and guide us toward personalized precision medicine for oral squamous cell carcinoma. To achieve this, it is important to efficiently and accurately screen out specific biomarkers from among the huge number of molecules. Progress in omics-based high-throughput technology has laid a solid foundation for biomarker discovery. With credible and systemic biomarker models, more precise and personalized diagnosis and assessment would be achieved and patients would be more likely to be cured and have a higher quality of life. However, this is not straightforward owing to the complexity of molecules involved in tumorigenesis. In this context, there is a need to focus on tumor heterogeneity and homogeneity, which are discussed in detail. In this review, we aim to provide an understanding of biomarker discovery and application for precision medicine of oral squamous cell carcinoma, and have a strong belief that biomarker will pave the road toward future precision medicine.
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Affiliation(s)
- Liang Zhong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Yutong Liu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Kai Wang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Zhijing He
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Zhaojian Gong
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Zhili Zhao
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Yaocheng Yang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Xiaofei Gao
- Department of Dermatology, Hunan Key Laboratory of Medical Epigenomics, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Fangjie Li
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Hanjiang Wu
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China
| | - Sheng Zhang
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.
| | - Lin Chen
- Department of Oral and Maxillofacial Surgery, The Second Xiangya Hospital, Central South University, Changsha, 410011, People's Republic of China.
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24
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Liu L, Toung JM, Jassowicz AF, Vijayaraghavan R, Kang H, Zhang R, Kruglyak KM, Huang HJ, Hinoue T, Shen H, Salathia NS, Hong DS, Naing A, Subbiah V, Piha-Paul SA, Bibikova M, Granger G, Barnes B, Shen R, Gutekunst K, Fu S, Tsimberidou AM, Lu C, Eng C, Moulder SL, Kopetz ES, Amaria RN, Meric-Bernstam F, Laird PW, Fan JB, Janku F. Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification. Ann Oncol 2018; 29:1445-1453. [PMID: 29635542 PMCID: PMC6005020 DOI: 10.1093/annonc/mdy119] [Citation(s) in RCA: 82] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Background Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis. Patients and methods We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes. Results Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016). Conclusions Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.
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Affiliation(s)
- L Liu
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
| | - J M Toung
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A F Jassowicz
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Vijayaraghavan
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Kang
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Zhang
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K M Kruglyak
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H J Huang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - T Hinoue
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - H Shen
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - N S Salathia
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - D S Hong
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A Naing
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - V Subbiah
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S A Piha-Paul
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - M Bibikova
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - G Granger
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - B Barnes
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R Shen
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - K Gutekunst
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S Fu
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - A M Tsimberidou
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Lu
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - C Eng
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - S L Moulder
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - E S Kopetz
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - R N Amaria
- Department of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA
| | - P W Laird
- Van Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - J-B Fan
- Illumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA
| | - F Janku
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
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Pirih N, Kunej T. An Updated Taxonomy and a Graphical Summary Tool for Optimal Classification and Comprehension of Omics Research. ACTA ACUST UNITED AC 2018; 22:337-353. [DOI: 10.1089/omi.2017.0186] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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26
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Häkkinen A, Alkodsi A, Facciotto C, Zhang K, Kaipio K, Leppä S, Carpén O, Grénman S, Hynninen J, Hietanen S, Lehtonen R, Hautaniemi S. Identifying differentially methylated sites in samples with varying tumor purity. Bioinformatics 2018; 34:3078-3085. [DOI: 10.1093/bioinformatics/bty310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 04/17/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Antti Häkkinen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Amjad Alkodsi
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Chiara Facciotto
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kaiyang Zhang
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Katja Kaipio
- Department of Pathology and Forensic Medicine, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Sirpa Leppä
- Department of Oncology, Helsinki University Central Hospital, Helsinki, Finland
| | - Olli Carpén
- Department of Pathology, Medicum, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
- Research Programs Unit, Genome-Scale Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Pathology, Institute of Biomedicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Seija Grénman
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Johanna Hynninen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Sakari Hietanen
- Department of Obstetrics and Gynecology, University of Turku and Turku University Hospital, Turku, Finland
| | - Rainer Lehtonen
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Sampsa Hautaniemi
- Research Programs Unit, Genome-Scale Biology, Medicum and Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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27
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Lee JR, Ryu DS, Park SJ, Choe SH, Cho HM, Lee SR, Kim SU, Kim YH, Huh JW. Successful application of human-based methyl capture sequencing for methylome analysis in non-human primate models. BMC Genomics 2018; 19:267. [PMID: 29669513 PMCID: PMC5907189 DOI: 10.1186/s12864-018-4666-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 04/12/2018] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND The characterization of genomic or epigenomic variation in human and animal models could provide important insight into pathophysiological mechanisms of various diseases, and lead to new developments in disease diagnosis and clinical intervention. The African green monkey (AGM; Chlorocebus aethiops) and cynomolgus monkey (CM; Macaca fascicularis) have long been considered important animal models in biomedical research. However, non-human primate-specific methods applicable to epigenomic analyses in AGM and CM are lacking. The recent development of methyl-capture sequencing (MC-seq) has an unprecedented advantage of cost-effectiveness, and further allows for extending the methylome coverage compared to conventional sequencing approaches. RESULTS Here, we used a human probe-designed MC-seq method to assay DNA methylation in DNA obtained from 13 CM and three AGM blood samples. To effectively adapt the human probe-designed target region for methylome analysis in non-human primates, we redefined the target regions, focusing on regulatory regions and intragenic regions with consideration of interspecific sequence homology and promoter region variation. Methyl-capture efficiency was controlled by the sequence identity between the captured probes based on the human reference genome and the AGM and CM genome sequences, respectively. Using reasonable guidelines, 56 and 62% of the human-based capture probes could be effectively mapped for DNA methylome profiling in the AGM and CM genome, respectively, according to numeric global statistics. In particular, our method could cover up to 89 and 87% of the regulatory regions of the AGM and CM genome, respectively. CONCLUSIONS Use of human-based MC-seq methods provides an attractive, cost-effective approach for the methylome profiling of non-human primates at the single-base resolution level.
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Affiliation(s)
- Ja-Rang Lee
- Primate Resource Center, Korea Research Institute of Bioscience and Biotechnology, Jeongeup, 56216, Republic of Korea
| | - Dong-Sung Ryu
- Theragen Etex Bio Institute, Suwon, Republic of Korea
| | - Sang-Je Park
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea
| | - Se-Hee Choe
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Hyeon-Mu Cho
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sang-Rae Lee
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Sun-Uk Kim
- Futuristic Animal Resource and Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea.,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Young-Hyun Kim
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
| | - Jae-Won Huh
- National Primate Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju, 28116, Republic of Korea. .,Department of Functional Genomics, KRIBB School of Bioscience, Korea University of Science and Technology (UST), Daejeon, 34113, Republic of Korea.
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28
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Abstract
Background Methylation is a common modification of DNA. It has been a very important and hot topic to study the correlation between methylation and diseases in medical science. Because of the special process with bisulfite treatment, traditional mapping tools do not work well with such methylation experimental reads. Traditional aligners are not designed for mapping bisulfite-treated reads, where the un-methylated ‘C’s are converted to ‘T’s. Results In this paper, we develop a reliable and visual tool, named VAliBS, for mapping bisulfate sequences to a genome reference. VAliBS works well even on large scale data or high noise data. By comparing with other state-of-the-art tools (BisMark, BSMAP, BS-Seeker2), VAliBS can improve the accuracy of bisulfite mapping. Moreover, VAliBS is a visual tool which makes its operations more easily and the alignment results are shown with colored marks which makes it easier to be read. VAliBS provides fast and accurate mapping of bisulfite-converted reads, and a friendly window system to visualize the detail of mapping of each read. Conclusions VAliBS works well on both simulated data and real data. It can be useful in DNA methylation research. VALiBS implements an X-Window user interface where the methylation positions are visual and the operations are friendly.
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Affiliation(s)
- Min Li
- School of Information Science and Engineering, Central South University, Changsha, 410083, China
| | - Ping Huang
- School of Information Science and Engineering, Central South University, Changsha, 410083, China
| | - Xiaodong Yan
- School of Information Science and Engineering, Central South University, Changsha, 410083, China
| | - Jianxin Wang
- School of Information Science and Engineering, Central South University, Changsha, 410083, China.
| | - Yi Pan
- School of Information Science and Engineering, Central South University, Changsha, 410083, China. .,Department of Computer Science, Georgia State University, Atlanta, GA, 30302-4110, USA.
| | - Fang-Xiang Wu
- School of Information Science and Engineering, Central South University, Changsha, 410083, China.,Division of Biomedical Engineering and Department of Mechanical Engineering, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada
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29
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Aiba T, Saito T, Hayashi A, Sato S, Yunokawa H, Maruyama T, Fujibuchi W, Kurita H, Tohyama C, Ohsako S. Methylated site display (MSD)-AFLP, a sensitive and affordable method for analysis of CpG methylation profiles. BMC Mol Biol 2017; 18:7. [PMID: 28279161 PMCID: PMC5345256 DOI: 10.1186/s12867-017-0083-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Accepted: 03/02/2017] [Indexed: 02/22/2023] Open
Abstract
Background It has been pointed out that environmental factors or chemicals can cause diseases that are developmental in origin. To detect abnormal epigenetic alterations in DNA methylation, convenient and cost-effective methods are required for such research, in which multiple samples are processed simultaneously. We here present methylated site display (MSD), a unique technique for the preparation of DNA libraries. By combining it with amplified fragment length polymorphism (AFLP) analysis, we developed a new method, MSD-AFLP. Results Methylated site display libraries consist of only DNAs derived from DNA fragments that are CpG methylated at the 5′ end in the original genomic DNA sample. To test the effectiveness of this method, CpG methylation levels in liver, kidney, and hippocampal tissues of mice were compared to examine if MSD-AFLP can detect subtle differences in the levels of tissue-specific differentially methylated CpGs. As a result, many CpG sites suspected to be tissue-specific differentially methylated were detected. Nucleotide sequences adjacent to these methyl-CpG sites were identified and we determined the methylation level by methylation-sensitive restriction endonuclease (MSRE)-PCR analysis to confirm the accuracy of AFLP analysis. The differences of the methylation level among tissues were almost identical among these methods. By MSD-AFLP analysis, we detected many CpGs showing less than 5% statistically significant tissue-specific difference and less than 10% degree of variability. Additionally, MSD-AFLP analysis could be used to identify CpG methylation sites in other organisms including humans. Conclusion MSD-AFLP analysis can potentially be used to measure slight changes in CpG methylation level. Regarding the remarkable precision, sensitivity, and throughput of MSD-AFLP analysis studies, this method will be advantageous in a variety of epigenetics-based research. Electronic supplementary material The online version of this article (doi:10.1186/s12867-017-0083-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Toshiki Aiba
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Toshiyuki Saito
- Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan.
| | - Akiko Hayashi
- Department of Radiation Effects Research, National Institutes for Quantum and Radiological Science and Technology, 4-9-1 Anagawa, Inage-ku, Chiba, 263-8555, Japan
| | - Shinji Sato
- Maze, Inc., 1-2-17 Sennincho, Hachioji-shi, Tokyo, 193-0835, Japan
| | | | - Toru Maruyama
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan.,Department of Life Science & Medical Bioscience, Graduate School of Advanced Science & Engineering, Waseda University, Tokyo, Japan
| | - Wataru Fujibuchi
- Center for iPS Cell Research and Application, Kyoto University, 53 Kawahara-cho, Shogoin, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Hisaka Kurita
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Laboratory of Medical Therapeutics and Molecular Therapeutics, Gifu Pharmaceutical University, Gifu, Japan
| | - Chiharu Tohyama
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - Seiichiroh Ohsako
- Laboratory of Environmental Health Sciences, Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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30
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Pirih N, Kunej T. Toward a Taxonomy for Multi-Omics Science? Terminology Development for Whole Genome Study Approaches by Omics Technology and Hierarchy. ACTA ACUST UNITED AC 2017; 21:1-16. [DOI: 10.1089/omi.2016.0144] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Nina Pirih
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
| | - Tanja Kunej
- Department of Animal Science, Biotechnical Faculty, University of Ljubljana, Domzale, Slovenia
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31
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Sina AAI, Foster MT, Korbie D, Carrascosa LG, Shiddiky MJA, Gao J, Dey S, Trau M. A multiplex microplatform for the detection of multiple DNA methylation events using gold–DNA affinity. Analyst 2017; 142:3573-3578. [DOI: 10.1039/c7an00611j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We report a new multiplexed strategy for the electrochemical detection of regional DNA methylation across multiple regions.
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Affiliation(s)
- Abu Ali Ibn Sina
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Matthew Thomas Foster
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Darren Korbie
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Laura G. Carrascosa
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Muhammad J. A. Shiddiky
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Jing Gao
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Shuvashis Dey
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
| | - Matt Trau
- Australian Institute for Bioengineering and Nanotechnology (AIBN)
- The University of Queensland
- Brisbane
- Australia
- School of Chemistry and Molecular Biosciences
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32
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Pechalrieu D, Etievant C, Arimondo PB. DNA methyltransferase inhibitors in cancer: From pharmacology to translational studies. Biochem Pharmacol 2016; 129:1-13. [PMID: 27956110 DOI: 10.1016/j.bcp.2016.12.004] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 12/07/2016] [Indexed: 12/31/2022]
Abstract
DNA methylation is a mammalian epigenetic mark that participates to define where and when genes are expressed, both in normal cells and in the context of diseases. Like other epigenetic marks, it is reversible and can be modulated by chemical agents. Because it plays an important role in cancer by silencing certain genes, such as tumour suppressor genes, it is a promising therapeutic target. Two compounds are already approved to treat haematological cancers, and many efforts have been carried out to discover new molecules that inhibit DNA methyltransferases, the enzymes responsible for DNA methylation. Here, we analyse the molecular mechanisms and cellular pharmacology of these inhibitors, pointing out the necessity for new pharmacological models and paradigms. The parameters of pharmacological responses need to be redefined: the aim is cellular reprogramming rather than general cytotoxicity. Thus, "epigenetic" rather than cytotoxic dosages are defined. Another issue is the delay of the response: cellular reprogramming can take several generations to produce observable phenotypes. Is this compatible with laboratory scale experiments? Finally, it is important to consider the specificity for cancer cells compared to normal cells and the appearance of resistance. We also discuss different techniques that are used and the selection of pharmacological models.
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Affiliation(s)
- Dany Pechalrieu
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Chantal Etievant
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France
| | - Paola B Arimondo
- Unité de Service et de Recherche CNRS-Pierre Fabre USR3388, CNRS FRE3600, ETaC, Epigenetic Targeting of Cancer, Toulouse, France.
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33
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Jeong HM, Lee S, Chae H, Kim R, Kwon MJ, Oh E, Choi YL, Kim S, Shin YK. Efficiency of methylated DNA immunoprecipitation bisulphite sequencing for whole-genome DNA methylation analysis. Epigenomics 2016; 8:1061-77. [PMID: 27266718 DOI: 10.2217/epi-2016-0038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
AIMS We compared four common methods for measuring DNA methylation levels and recommended the most efficient method in terms of cost and coverage. MATERIALS & METHODS The DNA methylation status of liver and stomach tissues was profiled using four different methods, whole-genome bisulphite sequencing (WG-BS), targeted bisulphite sequencing (Targeted-BS), methylated DNA immunoprecipitation sequencing (MeDIP-seq) and methylated DNA immunoprecipitation bisulphite sequencing (MeDIP-BS). We calculated DNA methylation levels using each method and compared the results. RESULTS MeDIP-BS yielded the most similar DNA methylation profile to WG-BS, with 20 times less data, suggesting remarkable cost savings and coverage efficiency compared with the other methods. CONCLUSION MeDIP-BS is a practical cost-effective method for analyzing whole-genome DNA methylation that is highly accurate at base-pair resolution.
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Affiliation(s)
- Hae Min Jeong
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
| | - Sangseon Lee
- School of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea
| | - Heejoon Chae
- Computer Science Department, School of Informatics & Computing, Indiana University, Bloomington, IN, USA
| | - RyongNam Kim
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea
| | - Mi Jeong Kwon
- College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea
| | - Ensel Oh
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Yoon-La Choi
- Department of Pathology & Translational Genomics, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea.,Department of Health Sciences & Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea.,Laboratory of Cancer Genomics & Molecular Pathology, Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Republic of Korea
| | - Sun Kim
- Department of Computer Science & Engineering, Seoul National University, Seoul, Republic of Korea.,Bioinformatics Institute, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea
| | - Young Kee Shin
- Department of Pharmacy, College of Pharmacy, Seoul National University, Seoul, Republic of Korea.,Tumor Microenvironment Global Core Research Center, Seoul National University, Seoul, Republic of Korea.,Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, Republic of Korea.,The Center for Anti-Cancer Companion Diagnostics, School of Biological Science, Institutes of Entrepreneurial BioConvergence, Seoul National University, Seoul, Republic of Korea.,Research Institute of Pharmaceutical Sciences, College of Pharmacy, Seoul National University, Seoul, Republic of Korea
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34
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Taegtmeyer H, Young ME, Lopaschuk GD, Abel ED, Brunengraber H, Darley-Usmar V, Des Rosiers C, Gerszten R, Glatz JF, Griffin JL, Gropler RJ, Holzhuetter HG, Kizer JR, Lewandowski ED, Malloy CR, Neubauer S, Peterson LR, Portman MA, Recchia FA, Van Eyk JE, Wang TJ. Assessing Cardiac Metabolism: A Scientific Statement From the American Heart Association. Circ Res 2016; 118:1659-701. [PMID: 27012580 DOI: 10.1161/res.0000000000000097] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In a complex system of interrelated reactions, the heart converts chemical energy to mechanical energy. Energy transfer is achieved through coordinated activation of enzymes, ion channels, and contractile elements, as well as structural and membrane proteins. The heart's needs for energy are difficult to overestimate. At a time when the cardiovascular research community is discovering a plethora of new molecular methods to assess cardiac metabolism, the methods remain scattered in the literature. The present statement on "Assessing Cardiac Metabolism" seeks to provide a collective and curated resource on methods and models used to investigate established and emerging aspects of cardiac metabolism. Some of those methods are refinements of classic biochemical tools, whereas most others are recent additions from the powerful tools of molecular biology. The aim of this statement is to be useful to many and to do justice to a dynamic field of great complexity.
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35
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Devall M, Roubroeks J, Mill J, Weedon M, Lunnon K. Epigenetic regulation of mitochondrial function in neurodegenerative disease: New insights from advances in genomic technologies. Neurosci Lett 2016; 625:47-55. [PMID: 26876477 DOI: 10.1016/j.neulet.2016.02.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Revised: 02/04/2016] [Accepted: 02/05/2016] [Indexed: 10/22/2022]
Abstract
The field of mitochondrial epigenetics has received increased attention in recent years and changes in mitochondrial DNA (mtDNA) methylation has been implicated in a number of diseases, including neurodegenerative diseases such as amyotrophic lateral sclerosis. However, current publications have been limited by the use of global or targeted methods of measuring DNA methylation. In this review, we discuss current findings in mitochondrial epigenetics as well as its potential role as a regulator of mitochondria within the brain. Finally, we summarize the current technologies best suited to capturing mtDNA methylation, and how a move towards whole epigenome sequencing of mtDNA may help to advance our current understanding of the field.
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Affiliation(s)
- Matthew Devall
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Janou Roubroeks
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK; Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHENS), Maastricht University, Maastricht, The Netherlands
| | - Jonathan Mill
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK; Institute of Psychiatry, Psychology & Neuroscience (IoPPN), King's College London, De Crespigny Park, London, UK
| | - Michael Weedon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK
| | - Katie Lunnon
- Institute of Clinical and Biomedical Science, University of Exeter Medical School, University of Exeter, Devon, UK.
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36
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Shinjo K, Kondo Y. Targeting cancer epigenetics: Linking basic biology to clinical medicine. Adv Drug Deliv Rev 2015; 95:56-64. [PMID: 26494398 DOI: 10.1016/j.addr.2015.10.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 09/23/2015] [Accepted: 10/09/2015] [Indexed: 02/06/2023]
Abstract
Recent studies provide compelling evidence that epigenetic dysregulation is involved in almost every step of tumor development and progression. Differences in tumor behavior, which ultimately reflects clinical outcome, can be explained by variations in gene expression patterns generated by epigenetic mechanisms, such as DNA methylation. Therefore, epigenetic abnormalities are considered potential biomarkers and therapeutic targets. DNA methylation is stable at certain specific loci in cancer cells and predominantly reflects the characteristic clinicopathological features. Thus, it is an ideal biomarker for cancer screening, classification and prognostic purposes. Epigenetic treatment for cancers is based on the pharmacologic targeting of various core transcriptional programs that sustains cancer cell identity. Therefore, targeting aberrant epigenetic modifiers may be effective for multiple processes compared with using a selective inhibitor of aberrant single signaling pathway. This review provides an overview of the epigenetic alterations in human cancers and discusses about novel therapeutic strategies targeting epigenetic alterations.
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Affiliation(s)
- Keiko Shinjo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan
| | - Yutaka Kondo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, 1 Kawasumi, Mizuho-cho, Mizuho-ku, Nagoya 467-8601, Japan.
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37
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Bernstein DL, Kameswaran V, Le Lay JE, Sheaffer KL, Kaestner KH. The BisPCR(2) method for targeted bisulfite sequencing. Epigenetics Chromatin 2015; 8:27. [PMID: 26236400 PMCID: PMC4522100 DOI: 10.1186/s13072-015-0020-x] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2015] [Accepted: 07/23/2015] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND DNA methylation has emerged as an important regulator of development and disease, necessitating the design of more efficient and cost-effective methods for detecting and quantifying this epigenetic modification. Next-generation sequencing (NGS) techniques offer single base resolution of CpG methylation levels with high statistical significance, but are also high cost if performed genome-wide. Here, we describe a simplified targeted bisulfite sequencing approach in which DNA sequencing libraries are prepared following sodium bisulfite conversion and two rounds of PCR for target enrichment and sample barcoding, termed BisPCR(2). RESULTS We have applied the BisPCR(2) technique to validate differential methylation at several type 2 diabetes risk loci identified in genome-wide studies of human islets. We confirmed some previous findings while not others, in addition to identifying novel differentially methylated CpGs at these genes of interest, due to the much higher depth of sequencing coverage in BisPCR(2) compared to prior array-based approaches. CONCLUSION This study presents a robust, efficient, and cost-effective technique for targeted bisulfite NGS, and illustrates its utility by reanalysis of prior findings from genome-wide studies.
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Affiliation(s)
- Diana L Bernstein
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Vasumathi Kameswaran
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - John E Le Lay
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Karyn L Sheaffer
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
| | - Klaus H Kaestner
- Department of Genetics and Institute for Diabetes, Obesity, and Metabolism, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd., Philadelphia, PA 19104 USA
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38
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How-Kit A, Daunay A, Mazaleyrat N, Busato F, Daviaud C, Teyssier E, Deleuze JF, Gallusci P, Tost J. Accurate CpG and non-CpG cytosine methylation analysis by high-throughput locus-specific pyrosequencing in plants. PLANT MOLECULAR BIOLOGY 2015; 88:471-485. [PMID: 26072424 DOI: 10.1007/s11103-015-0336-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Accepted: 05/25/2015] [Indexed: 06/04/2023]
Abstract
Pyrosequencing permits accurate quantification of DNA methylation of specific regions where the proportions of the C/T polymorphism induced by sodium bisulfite treatment of DNA reflects the DNA methylation level. The commercially available high-throughput locus-specific pyrosequencing instruments allow for the simultaneous analysis of 96 samples, but restrict the DNA methylation analysis to CpG dinucleotide sites, which can be limiting in many biological systems. In contrast to mammals where DNA methylation occurs nearly exclusively on CpG dinucleotides, plants genomes harbor DNA methylation also in other sequence contexts including CHG and CHH motives, which cannot be evaluated by these pyrosequencing instruments due to software limitations. Here, we present a complete pipeline for accurate CpG and non-CpG cytosine methylation analysis at single base-resolution using high-throughput locus-specific pyrosequencing. The devised approach includes the design and validation of PCR amplification on bisulfite-treated DNA and pyrosequencing assays as well as the quantification of the methylation level at every cytosine from the raw peak intensities of the Pyrograms by two newly developed Visual Basic Applications. Our method presents accurate and reproducible results as exemplified by the cytosine methylation analysis of the promoter regions of two Tomato genes (NOR and CNR) encoding transcription regulators of fruit ripening during different stages of fruit development. Our results confirmed a significant and temporally coordinated loss of DNA methylation on specific cytosines during the early stages of fruit development in both promoters as previously shown by WGBS. The manuscript describes thus the first high-throughput locus-specific DNA methylation analysis in plants using pyrosequencing.
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Affiliation(s)
- Alexandre How-Kit
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 75010, Paris, France,
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39
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Lin P, Forêt S, Wilson SR, Burden CJ. Estimation of the methylation pattern distribution from deep sequencing data. BMC Bioinformatics 2015; 16:145. [PMID: 25943746 PMCID: PMC4428226 DOI: 10.1186/s12859-015-0600-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 04/17/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Bisulphite sequencing enables the detection of cytosine methylation. The sequence of the methylation states of cytosines on any given read forms a methylation pattern that carries substantially more information than merely studying the average methylation level at individual positions. In order to understand better the complexity of DNA methylation landscapes in biological samples, it is important to study the diversity of these methylation patterns. However, the accurate quantification of methylation patterns is subject to sequencing errors and spurious signals due to incomplete bisulphite conversion of cytosines. RESULTS A statistical model is developed which accounts for the distribution of DNA methylation patterns at any given locus. The model incorporates the effects of sequencing errors and spurious reads, and enables estimation of the true underlying distribution of methylation patterns. CONCLUSIONS Calculation of the estimated distribution over methylation patterns is implemented in the R Bioconductor package MPFE. Source code and documentation of the package are also available for download at http://bioconductor.org/packages/3.0/bioc/html/MPFE.html .
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Affiliation(s)
- Peijie Lin
- Mathematical Sciences Institute, Australian National University, Canberra, ACT 2601, Australia.
| | - Sylvain Forêt
- Research School of Biology, Australian National University, Canberra, ACT 2601, Australia.
| | - Susan R Wilson
- Mathematical Sciences Institute, Australian National University, Canberra, ACT 2601, Australia. .,School of Mathematics and Statistics, University of New South Wales, 2052, NSW, Sydney, Australia.
| | - Conrad J Burden
- Mathematical Sciences Institute, Australian National University, Canberra, ACT 2601, Australia.
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40
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Marzese DM, Hoon DS. Emerging technologies for studying DNA methylation for the molecular diagnosis of cancer. Expert Rev Mol Diagn 2015; 15:647-64. [PMID: 25797072 DOI: 10.1586/14737159.2015.1027194] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is an epigenetic mechanism that plays a key role in regulating gene expression and other functions. Although this modification is seen in different sequence contexts, the most frequently detected DNA methylation in mammals involves cytosine-guanine dinucleotides. Pathological alterations in DNA methylation patterns are described in a variety of human diseases, including cancer. Unlike genetic changes, DNA methylation is heavily influenced by subtle modifications in the cellular microenvironment. In all cancers, aberrant DNA methylation is involved in the alteration of a large number of oncological pathways with relevant theranostic utility. Several technologies for DNA methylation mapping have been developed recently and successfully applied in cancer studies. The scope of these technologies varies from assessing a single cytosine-guanine locus to genome-wide distribution of DNA methylation. Here, we review the strengths and weaknesses of these approaches in the context of clinical utility for the molecular diagnosis of human cancers.
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Affiliation(s)
- Diego M Marzese
- Department of Molecular Oncology, Saint John's Health Center, John Wayne Cancer Institute, 2200 Santa Monica Blvd, Santa Monica, CA 90404, USA
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41
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Yamamoto H, Imai K. Microsatellite instability: an update. Arch Toxicol 2015; 89:899-921. [PMID: 25701956 DOI: 10.1007/s00204-015-1474-0] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 02/09/2015] [Indexed: 02/08/2023]
Abstract
Deficient DNA mismatch repair (MMR) results in a strong mutator phenotype known as microsatellite instability (MSI), which is a hallmark of Lynch syndrome-associated cancers. MSI is characterized by length alterations within simple repeated sequences that are called microsatellites. Lynch syndrome is primarily caused by mutations in the MMR genes, mainly MLH1 and MSH2, and less frequently in MSH6, and rarely PMS2, and large genomic rearrangements account for 5-20 % of all mutations. Germ line hemiallelic methylations of MLH1 or MSH2 are termed as epimutations and have been identified as causative of Lynch syndrome. Moreover, germ line 3' deletions of EPCAM gene is involved in MSH2 methylation. MSI is also observed in about 15 % of sporadic colorectal cancer (CRC), gastric cancer (GC), and endometrial cancer (EC), and at lower frequencies in other cancers, often in association with hypermethylation of the MLH1 gene. Trimethylation of histone H3 on Lys36 (H3K36 me3) is an epigenetic histone mark that was required for DNA MMR in vivo. Thus, mutations in the H3K36 trimethyltransferase SETD2 have been reported as a potential cause of MSI. Genetic, epigenetic, and transcriptomic differences have been identified between cancers with and without MSI. Recent comprehensive molecular characterizations of CRC, EC, and GC by The Cancer Genome Atlas indicate that MSI+ cancers are distinct biological entities. The BRAF V600E mutation is specifically associated with sporadic MSI+ CRCs with methylated MLH1, but is not associated with Lynch syndrome-related CRCs. Accumulating evidence indicates a role of interactions between MSI and microRNA (miRNA) in the pathogenesis of MSI-positive (MSI+) cancer. As another new mechanism underlying MSI, overexpression of miR-155 or miR-21 has been shown to downregulate the expression of the MMR genes. Gene targets of frameshift mutations caused by MSI are involved in various cellular functions, including DNA repair (MSH3 and MSH6), cell signaling (TGFBR2 and ACVR2A), apoptosis (BAX), epigenetic regulation (HDAC2 and ARID1A), and miRNA processing (TARBP2 and XPO5), and a subset of MSI+ CRCs reportedly shows the mutated miRNA machinery phenotype. Moreover, microsatellite repeats in miRNA genes, such as hsa-miR-1273c, may be novel MSI targets for CRC, and mutations in noncoding regulatory regions of MRE11, BAX (BaxΔ2), and HSP110 (HSP110ΔE9) may affect the efficiency of chemotherapy. Thus, analyses of MSI and its related molecular alterations in cancers are increasingly relevant in clinical settings, and MSI is a useful screening marker for identifying patients with Lynch syndrome and a prognostic factor for chemotherapeutic interventions. In this review, we summarize recent advances in the pathogenesis of MSI and focus on genome-wide analyses that indicate the potential use of MSI and related alterations as biomarkers and novel therapeutic targets.
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Affiliation(s)
- Hiroyuki Yamamoto
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, 216-8511, Japan,
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Miura F, Ito T. Highly sensitive targeted methylome sequencing by post-bisulfite adaptor tagging. DNA Res 2015; 22:13-8. [PMID: 25324297 PMCID: PMC4379973 DOI: 10.1093/dnares/dsu034] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 09/24/2014] [Indexed: 12/02/2022] Open
Abstract
The current gold standard method for methylome analysis is whole-genome bisulfite sequencing (WGBS), but its cost is substantial, especially for the purpose of multi-sample comparison of large methylomes. Shotgun bisulfite sequencing of target-enriched DNA, or targeted methylome sequencing (TMS), can be a flexible, cost-effective alternative to WGBS. However, the current TMS protocol requires a considerable amount of input DNA and hence is hardly applicable to samples of limited quantity. Here we report a method to overcome this limitation by using post-bisulfite adaptor tagging (PBAT), in which adaptor tagging is conducted after bisulfite treatment to circumvent bisulfite-induced loss of intact sequencing templates, thereby enabling TMS of a 100-fold smaller amount of input DNA with far fewer cycles of polymerase chain reaction than in the current protocol. We thus expect that the PBAT-mediated TMS will serve as an invaluable method in epigenomics.
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Affiliation(s)
- Fumihito Miura
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Higashi-ku, Fukuoka 812-8582, Japan Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Higashi-ku, Fukuoka 812-8582, Japan
| | - Takashi Ito
- Department of Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo 113-0033, Japan Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Higashi-ku, Fukuoka 812-8582, Japan Department of Biochemistry, Kyushu University Graduate School of Medical Sciences, Higashi-ku, Fukuoka 812-8582, Japan
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Abstract
Cytosine methylation in DNA constitutes an important epigenetic layer of transcriptional and regulatory control in many eukaryotes. Profiling DNA methylation across the genome is critical to understanding the influence of epigenetics in normal biology and disease, such as cancer. Genome-wide analyses such as arrays and next-generation sequencing (NGS) technologies have been used to assess large fractions of the methylome at a single-base-pair resolution. However, the range of DNA methylation profiling techniques can make selecting the appropriate protocol a challenge. This chapter discusses the advantages and disadvantages of various methylome detection approaches to assess which is appropriate for the question at hand. Here, we focus on four prominent genome-wide approaches: whole-genome bisulfite sequencing (WGBS); methyl-binding domain capture sequencing (MBDCap-Seq); reduced-representation-bisulfite-sequencing (RRBS); and Infinium Methylation450 BeadChips (450 K, Illumina). We discuss some of the requirements, merits, and challenges that should be considered when choosing a methylome technology to ensure that it will be informative. In addition, we show how genome-wide methylation detection arrays and high-throughput sequencing have provided immense insight into ovarian cancer-specific methylation signatures that may serve as diagnostic biomarkers or predict patient response to epigenetic therapy.
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Sina AAI, Carrascosa LG, Palanisamy R, Rauf S, Shiddiky MJA, Trau M. Methylsorb: A Simple Method for Quantifying DNA Methylation Using DNA–Gold Affinity Interactions. Anal Chem 2014; 86:10179-85. [DOI: 10.1021/ac502214z] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Abu Ali Ibn Sina
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Laura G. Carrascosa
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Ramkumar Palanisamy
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Sakandar Rauf
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Muhammad J. A. Shiddiky
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
| | - Matt Trau
- Centre
for Personalised Nanomedicine, Australian Institute for Bioengineering
and Nanotechnology (AIBN), The University of Queensland, Corner College and Cooper
Roads (Building 75), Brisbane QLD 4072, Australia
- School
of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, Queensland QLD
4072, Australia
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Comparative analysis of human mitochondrial methylomes shows distinct patterns of epigenetic regulation in mitochondria. Mitochondrion 2014; 18:58-62. [DOI: 10.1016/j.mito.2014.07.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Revised: 06/16/2014] [Accepted: 07/15/2014] [Indexed: 11/18/2022]
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46
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Dysregulated transcriptional and post-translational control of DNA methyltransferases in cancer. Cell Biosci 2014; 4:46. [PMID: 25949795 PMCID: PMC4422219 DOI: 10.1186/2045-3701-4-46] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 07/01/2014] [Indexed: 01/29/2023] Open
Abstract
Cancer is a leading cause of death worldwide. Aberrant promoter hypermethylation of CpG islands associated with tumor suppressor genes can lead to transcriptional silencing and result in tumorigenesis. DNA methyltransferases (DNMTs) are the enzymes responsible for DNA methylation and have been reported to be over-expressed in various cancers. This review highlights the current status of transcriptional and post-translational regulation of the DNMT expression and activity with a focus on dysregulation involved in tumorigenesis. The transcriptional up-regulation of DNMT gene expression can be induced by Ras-c-Jun signaling pathway, Sp1 and Sp3 zinc finger proteins and virus oncoproteins. Transcriptional repression on DNMT genes has also been reported for p53, RB and FOXO3a transcriptional regulators and corepressors. In addition, the low expressions of microRNAs 29 family, 143, 148a and 152 are associated with DNMTs overexpression in various cancers. Several important post-translational modifications including acetylation and phosphorylation have been reported to mediate protein stability and activity of the DNMTs especially DNMT1. In this review, we also discuss drugs targeting DNMT protein expression and activation for therapeutic strategy against cancer.
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Yao Y, Des Marais TL, Costa M. Chromatin Memory in the Development of Human Cancers. GENE TECHNOLOGY 2014; 3:114. [PMID: 25606572 PMCID: PMC4297643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Cancer is a complex disease with acquired genomic and epigenomic alterations that affect cell proliferation, viability and invasiveness. Almost all the epigenetic mechanisms including cytosine methylation and hydroxymethylation, chromatin remodeling and non-coding RNAs have been found associate with carcinogenesis and cancer specific expression profile. Altered histone modification as an epigenetic hallmark is frequently found in tumors. Understanding the epigenetic alterations induced by carcinogens or infectious agents may help us understand early epigenetic changes prior to the development of cancer. In this review, we focus on chromatin remodeling and the associated histone modifiers in the development of cancer; the application of these modifiers as a cancer therapy target in different clinical trial phases is also discussed.
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Affiliation(s)
- Yixin Yao
- Department of Environmental Medicine New York University, New York, USA,Corresponding author: Yixin Yao, Department of Environmental Medicine, New York University, New York, USA; Tel: 845-731-3517;
| | | | - Max Costa
- Department of Environmental Medicine New York University, New York, USA,Department of Biochemistry and Molecular Pharmacology, New York University Langone Medical Center, Tuxedo, New York, USA
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Ten years of next-generation sequencing technology. Trends Genet 2014; 30:418-26. [PMID: 25108476 DOI: 10.1016/j.tig.2014.07.001] [Citation(s) in RCA: 847] [Impact Index Per Article: 84.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Revised: 07/08/2014] [Accepted: 07/09/2014] [Indexed: 02/06/2023]
Abstract
Ten years ago next-generation sequencing (NGS) technologies appeared on the market. During the past decade, tremendous progress has been made in terms of speed, read length, and throughput, along with a sharp reduction in per-base cost. Together, these advances democratized NGS and paved the way for the development of a large number of novel NGS applications in basic science as well as in translational research areas such as clinical diagnostics, agrigenomics, and forensic science. Here we provide an overview of the evolution of NGS and discuss the most significant improvements in sequencing technologies and library preparation protocols. We also explore the current landscape of NGS applications and provide a perspective for future developments.
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Couldrey C, Cave V. Assessing DNA methylation levels in animals: choosing the right tool for the job. Anim Genet 2014; 45 Suppl 1:15-24. [PMID: 24990588 DOI: 10.1111/age.12186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2013] [Indexed: 12/16/2022]
Abstract
Selection of agricultural animals for improved performance based on genetics has seen significant progress made over the past few decades. Further improvements are likely by combining genetic selection with epigenetic selection or manipulation. However, before this can be undertaken, an understanding of epigenetic mechanisms is required, and this can be obtained only by precise and accurate analysis of epigenetic patterns. Even when one only considers a single epigenetic modification such as DNA methylation, the last 10 years have seen a wide array of technologies developed. For scientists whose primary training is in a field other than epigenetics, the choices can be confusing, and it can be challenging to determine which technology is best for the task at hand. There are many factors to take into consideration before beginning analysis of DNA methylation in animals. It is crucial that the most appropriate tools are selected to ensure that the best possible results are achieved. This review provides an overview of the most common methods of analysing DNA methylation in animals, when they are appropriate, what resolution of information they can provide and what their limitations are.
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Affiliation(s)
- Christine Couldrey
- Animal Productivity, AgResearch Ruakura Research Centre, 10 Bisley Road, Hamilton, 3214, New Zealand
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Yamamoto H, Watanabe Y, Maehata T, Morita R, Yoshida Y, Oikawa R, Ishigooka S, Ozawa SI, Matsuo Y, Hosoya K, Yamashita M, Taniguchi H, Nosho K, Suzuki H, Yasuda H, Shinomura Y, Itoh F. An updated review of gastric cancer in the next-generation sequencing era: Insights from bench to bedside and vice versa. World J Gastroenterol 2014; 20:3927-3937. [PMID: 24744582 PMCID: PMC3983448 DOI: 10.3748/wjg.v20.i14.3927] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2013] [Revised: 01/15/2014] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
Gastric cancer (GC) is one of the most common malignancies and remains the second leading cause of cancer-related death worldwide. There is an increasing understanding of the roles that genetic and epigenetic alterations play in GCs. Recent studies using next-generation sequencing (NGS) have revealed a number of potential cancer-driving genes in GC. Whole-exome sequencing of GC has identified recurrent somatic mutations in the chromatin remodeling gene ARID1A and alterations in the cell adhesion gene FAT4, a member of the cadherin gene family. Mutations in chromatin remodeling genes (ARID1A, MLL3 and MLL) have been found in 47% of GCs. Whole-genome sequencing and whole-transcriptome sequencing analyses have also discovered novel alterations in GC. Recent studies of cancer epigenetics have revealed widespread alterations in genes involved in the epigenetic machinery, such as DNA methylation, histone modifications, nucleosome positioning, noncoding RNAs and microRNAs. Recent advances in molecular research on GC have resulted in the introduction of new diagnostic and therapeutic strategies into clinical settings. The anti-human epidermal growth receptor 2 (HER2) antibody trastuzumab has led to an era of personalized therapy in GC. In addition, ramucirumab, a monoclonal antibody targeting vascular endothelial growth factor receptor (VEGFR)-2, is the first biological treatment that showed survival benefits as a single-agent therapy in patients with advanced GC who progressed after first-line chemotherapy. Using NGS to systematically identify gene alterations in GC is a promising approach with remarkable potential for investigating the pathogenesis of GC and identifying novel therapeutic targets, as well as useful biomarkers. In this review, we will summarize the recent advances in the understanding of the molecular pathogenesis of GC, focusing on the potential use of these genetic and epigenetic alterations as diagnostic biomarkers and novel therapeutic targets.
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