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Zhang W, Li X, Yu U, Huang X, Wang H, Lu Y, Liu S, Zhang J. Genome-wide methylation and gene-expression analyses in thalassemia. Aging (Albany NY) 2024; 16:11591-11605. [PMID: 39133159 PMCID: PMC11346785 DOI: 10.18632/aging.206037] [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: 12/05/2023] [Accepted: 07/11/2024] [Indexed: 08/13/2024]
Abstract
Thalassemia is the most common autosomal genetic disorder in humans. The pathogenesis of thalassemia is principally due to the deletion or mutation of globin genes that then leads to disorders in globin-chain synthesis, and its predominant clinical manifestations include chronic forms of hemolytic anemia. However, research on the epigenetics and underlying pathogenesis of thalassemia is in its nascency and not yet been systematically realized. In this study, we compared the results of RNA-seq and the whole-genome bisulfite sequencing (WGBS) on 22 peripheral blood samples from 14 thalassemic patients and eight healthy individuals revealed a genome-wide methylation landscape of differentially methylated regions (DMRs). And functional-enrichment analysis revealed the enriched biological pathways with respect to the differentially expressed genes (DEGs) and differentially methylated genes (DMGs) to include hematopoietic lineage, glucose metabolism, and ribosome. To further analyze the interaction between the transcriptome and methylome, we implemented a comprehensive analysis of overlaps between DEGs and DMGs, and observed that biological processes significantly enriched the immune-related genes (i.e., our hypermethylated and down-regulated gene group). Hypermethylated and hypomethylated regions of thalassemia-related genes exhibited different distribution patterns. We thus, further identified and validated thalassemia-associated DMGs and DEGs by multi-omics integrative analyses of DNA methylation and transcriptomics data, and provided a comprehensive genomic map of thalassemia that will facilitate the exploration of the epigenetics mechanisms and pathogenesis underlying thalassemia.
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Affiliation(s)
- Wei Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
- Shenzhen Key Laboratory of Cardiovascular Health and Precision Medicine, School of Public Health and Emergency Management, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Xiaokang Li
- Center for Reproductive Medicine, University of Hongkong-Shenzhen Hospital, Shenzhen 518053, Guangdong, China
| | - Uet Yu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong, China
| | - Xin Huang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Hongmei Wang
- Department of Infectious Diseases, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong, China
| | - Yi Lu
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
| | - Sixi Liu
- Department of Hematology and Oncology, Shenzhen Children’s Hospital, Shenzhen 518038, Guangdong, China
| | - Jian Zhang
- School of Medicine, Southern University of Science and Technology, Shenzhen 518055, Guangdong, China
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2
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Wei Y, Dong S, Zhu Y, Zhao Y, Wu C, Zhu Y, Li K, Xu Y. DNA co-methylation analysis of lincRNAs across nine cancer types reveals novel potential epigenetic biomarkers in cancer. Epigenomics 2019; 11:1177-1190. [PMID: 31347388 DOI: 10.2217/epi-2018-0138] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Aim: The potential functions and prognostic value of lincRNAs with co-methylation events are explored in 9 cancer types. Materials & methods: Here, we evaluated the co-methylation events in promoter and gene-body regions between two lincRNAs across 9 cancer types by constructing a systematic biological framework. Results: The co-methylation events in both promoter and gene-body regions tended to be highly cancer specific. Patient samples could be separated by tumor and normal types according to the eigengenes of universal co-methylation clusters. Functional enrichment results revealed the lincRNAs that brought promoter and gene-body co-methylation events that affected cancer progress through participating in different pathways and could serve as potential prognostic biomarkers. Conclusion: The study provides new insight into the epigenetic regulation in cancer and leads to a potential new direction for epigenetic biomarker discovery.
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Affiliation(s)
- Yunzhen Wei
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China.,School of Life Science, Faculty of Science, The Chinese University of Hong Kong, PR China
| | - Siyao Dong
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yanjiao Zhu
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yichuan Zhao
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Cheng Wu
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yinling Zhu
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Kun Li
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
| | - Yan Xu
- College of Bioinformatics Science & Technology, Harbin Medical University, Harbin 150081, PR China
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3
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Moinova HR, LaFramboise T, Lutterbaugh JD, Chandar AK, Dumot J, Faulx A, Brock W, De la Cruz Cabrera O, Guda K, Barnholtz-Sloan JS, Iyer PG, Canto MI, Wang JS, Shaheen NJ, Thota PN, Willis JE, Chak A, Markowitz SD. Identifying DNA methylation biomarkers for non-endoscopic detection of Barrett's esophagus. Sci Transl Med 2019; 10:10/424/eaao5848. [PMID: 29343623 DOI: 10.1126/scitranslmed.aao5848] [Citation(s) in RCA: 102] [Impact Index Per Article: 20.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 11/08/2017] [Indexed: 12/17/2022]
Abstract
We report a biomarker-based non-endoscopic method for detecting Barrett's esophagus (BE) based on detecting methylated DNAs retrieved via a swallowable balloon-based esophageal sampling device. BE is the precursor of, and a major recognized risk factor for, developing esophageal adenocarcinoma. Endoscopy, the current standard for BE detection, is not cost-effective for population screening. We performed genome-wide screening to ascertain regions targeted for recurrent aberrant cytosine methylation in BE, identifying high-frequency methylation within the CCNA1 locus. We tested CCNA1 DNA methylation as a BE biomarker in cytology brushings of the distal esophagus from 173 individuals with or without BE. CCNA1 DNA methylation demonstrated an area under the curve of 0.95 for discriminating BE-related metaplasia and neoplasia cases versus normal individuals, performing identically to methylation of VIM DNA, an established BE biomarker. When combined, the resulting two biomarker panel was 95% sensitive and 91% specific. These results were replicated in an independent validation cohort of 149 individuals who were assayed using the same cutoff values for test positivity established in the training population. To progress toward non-endoscopic esophageal screening, we engineered a well-tolerated, swallowable, encapsulated balloon device able to selectively sample the distal esophagus within 5 min. In balloon samples from 86 individuals, tests of CCNA1 plus VIM DNA methylation detected BE metaplasia with 90.3% sensitivity and 91.7% specificity. Combining the balloon sampling device with molecular assays of CCNA1 plus VIM DNA methylation enables an efficient, well-tolerated, sensitive, and specific method of screening at-risk populations for BE.
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Affiliation(s)
- Helen R Moinova
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Thomas LaFramboise
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - James D Lutterbaugh
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Apoorva Krishna Chandar
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - John Dumot
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Ashley Faulx
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Wendy Brock
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | | | - Kishore Guda
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Jill S Barnholtz-Sloan
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Prasad G Iyer
- Barrett's Esophagus Unit, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN 55905, USA
| | - Marcia I Canto
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins Medical Institutions, Baltimore, MD 21205, USA
| | - Jean S Wang
- Division of Gastroenterology, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110, USA
| | - Nicholas J Shaheen
- Center for Esophageal Diseases and Swallowing, Division of Gastroenterology and Hepatology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Prashanti N Thota
- Digestive Disease and Surgery Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Joseph E Willis
- Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA. .,Department of Pathology, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Amitabh Chak
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
| | - Sanford D Markowitz
- Department of Medicine, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA. .,Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, OH 44106, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA.,University Hospitals Seidman Cancer Center, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA
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Jamal S, Goyal S, Shanker A, Grover A. Integrating network, sequence and functional features using machine learning approaches towards identification of novel Alzheimer genes. BMC Genomics 2016; 17:807. [PMID: 27756223 PMCID: PMC5070370 DOI: 10.1186/s12864-016-3108-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/20/2016] [Indexed: 01/01/2023] Open
Abstract
Background Alzheimer’s disease (AD) is a complex progressive neurodegenerative disorder commonly characterized by short term memory loss. Presently no effective therapeutic treatments exist that can completely cure this disease. The cause of Alzheimer’s is still unclear, however one of the other major factors involved in AD pathogenesis are the genetic factors and around 70 % risk of the disease is assumed to be due to the large number of genes involved. Although genetic association studies have revealed a number of potential AD susceptibility genes, there still exists a need for identification of unidentified AD-associated genes and therapeutic targets to have better understanding of the disease-causing mechanisms of Alzheimer’s towards development of effective AD therapeutics. Results In the present study, we have used machine learning approach to identify candidate AD associated genes by integrating topological properties of the genes from the protein-protein interaction networks, sequence features and functional annotations. We also used molecular docking approach and screened already known anti-Alzheimer drugs against the novel predicted probable targets of AD and observed that an investigational drug, AL-108, had high affinity for majority of the possible therapeutic targets. Furthermore, we performed molecular dynamics simulations and MM/GBSA calculations on the docked complexes to validate our preliminary findings. Conclusions To the best of our knowledge, this is the first comprehensive study of its kind for identification of putative Alzheimer-associated genes using machine learning approaches and we propose that such computational studies can improve our understanding on the core etiology of AD which could lead to the development of effective anti-Alzheimer drugs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3108-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Salma Jamal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.,Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, 304022, India
| | - Sukriti Goyal
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.,Department of Bioscience and Biotechnology, Banasthali University, Tonk, Rajasthan, 304022, India
| | - Asheesh Shanker
- Bioinformatics Programme, Centre for Biological Sciences, Central University of South Bihar, BIT Campus, Patna, Bihar, India
| | - Abhinav Grover
- School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India.
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5
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Li Y, Pearl SA, Jackson SA. Gene Networks in Plant Biology: Approaches in Reconstruction and Analysis. TRENDS IN PLANT SCIENCE 2015; 20:664-675. [PMID: 26440435 DOI: 10.1016/j.tplants.2015.06.013] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2015] [Revised: 06/28/2015] [Accepted: 06/30/2015] [Indexed: 05/25/2023]
Abstract
Even though vast amounts of genome-wide gene expression data have become available in plants, it remains a challenge to effectively mine this information for the discovery of genes and gene networks, for instance those that control agronomically important traits. These networks reflect potential interactions among genes and, therefore, can lead to a systematic understanding of the molecular mechanisms underlying targeted biological processes. We discuss methods to analyze gene networks using gene expression data, specifically focusing on four common statistical approaches used to reconstruct networks: correlation, feature selection in supervised learning, probabilistic graphical model, and meta-prediction. In addition, we discuss the effective use of these methods for acquiring an in-depth understanding of biological systems in plants.
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Affiliation(s)
- Yupeng Li
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602; Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA 30602; Department of Statistics, University of Georgia, 101 Cedar Street, Athens, GA 30602
| | - Stephanie A Pearl
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602
| | - Scott A Jackson
- Center for Applied Genetic Technologies, University of Georgia, 111 Riverbend Road, Athens, GA 30602; Institute of Plant Breeding, Genetics and Genomics, University of Georgia, 111 Riverbend Road, Athens, GA 30602.
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Zhang Y, Zhang J, Liu Z, Liu Y, Tuo S. A network-based approach to identify disease-associated gene modules through integrating DNA methylation and gene expression. Biochem Biophys Res Commun 2015; 465:437-42. [DOI: 10.1016/j.bbrc.2015.08.033] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2015] [Accepted: 08/09/2015] [Indexed: 11/28/2022]
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7
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Liao Q, He W, Liu J, Cen Y, Luo L, Yu C, Li Y, Chen S, Duan S. Identification and functional annotation of lncRNA genes with hypermethylation in colorectal cancer. Gene 2015; 572:259-65. [PMID: 26172871 DOI: 10.1016/j.gene.2015.07.028] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2015] [Revised: 05/28/2015] [Accepted: 07/08/2015] [Indexed: 02/08/2023]
Abstract
Colorectal cancer (CRC) is one of the leading causes of mortality worldwide. DNA methylation is an important epigenetic modification for CRC. Although currently a number of studies about DNA methylation of protein coding genes have been carried out, only a few are about the methylation of genes encoding the long noncoding RNAs (lncRNAs). In this study, we identified 761 lncRNA genes with DNA hypermethylation in CRC using a free MethylCap-seq dataset. Integration of lncRNA expression and methylation datasets showed that the expression of lncRNAs is negatively correlated with DNA methylation (p<0.01). Co-methylation network was also constructed to annotate the functions of unknown lncRNAs. Our results showed that a total of 364 lncRNAs were annotated with at least one GO biological process term. The current data-mining work is likely to provide informative clues for biological researchers to further understand the role of lncRNAs in the development of CRC.
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Affiliation(s)
- Qi Liao
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Weiling He
- Gastrointestinal Surgery Center, The First Affiliated Hospital, Sun Yat-Sen University, Guangzhou, Guangdong 510080, China
| | - Jianfa Liu
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yi Cen
- Yinzhou Branch of Ningbo Public Security Bureau, Ningbo, Zhejiang 315100, China
| | - Liang Luo
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Chengliang Yu
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Yang Li
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Sitong Chen
- Department of Prevention Medicine, School of Medicine, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Shiwei Duan
- Zhejiang Provincial Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China.
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