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Dowd S, Sharo C, Abdulmalik O, Elmer J. Optimizing the lyophilization of Lumbricus terrestris erythrocruorin. ARTIFICIAL CELLS, NANOMEDICINE, AND BIOTECHNOLOGY 2024; 52:291-299. [PMID: 38733371 DOI: 10.1080/21691401.2024.2352003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024]
Abstract
Haemorrhagic shock is a leading cause of death worldwide. Blood transfusions can be used to treat patients suffering severe blood loss but donated red blood cells (RBCs) have several limitations that limit their availability and use. To solve the problems associated with donated RBCs, several acellular haemoglobin-based oxygen carriers (HBOCs) have been developed to restore the most important function of blood: oxygen transport. One promising HBOC is the naturally extracellular haemoglobin (i.e. erythrocruorin) of Lumbricus terrestris (LtEc). The goal of this study was to maximise the portability of LtEc by lyophilising it and then testing its stability at elevated temperatures. To prevent oxidation, several cryoprotectants were screened to determine the optimum formulation for lyophilisation that could minimise oxidation of the haem iron and maximise recovery. Furthermore, samples were also deoxygenated prior to storage to decrease auto-oxidation, while resuspension in a solution containing ascorbic acid was shown to partially reduce LtEc that had oxidised during storage (e.g. from 42% Fe3+ to 11% Fe3+). Analysis of the oxygen equilibria and size of the resuspended LtEc showed that the lyophilisation, storage, and resuspension processes did not affect the oxygen transport properties or the structure of the LtEc, even after 6 months of storage at 40 °C. Altogether, these efforts have yielded a shelf-stable LtEc powder that can be stored for long periods at high temperatures, but future animal studies will be necessary to prove that the resuspended product is a safe and effective oxygen transporter in vivo.
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Affiliation(s)
- Sean Dowd
- Department of Chemical & Biological Engineering, Villanova University, Villanova, Pennsylvania, USA
| | - Catherine Sharo
- Department of Chemical & Biological Engineering, Villanova University, Villanova, Pennsylvania, USA
| | - Osheiza Abdulmalik
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Jacob Elmer
- Department of Chemical & Biological Engineering, Villanova University, Villanova, Pennsylvania, USA
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2
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Yang Q, Zhu X, Liu Y, He Z, Xu H, Zheng H, Huang Z, Wang D, Lin X, Guo P, Chen H. Reduced representative methylome profiling of cell-free DNA for breast cancer detection. Clin Epigenetics 2024; 16:33. [PMID: 38414041 PMCID: PMC10898043 DOI: 10.1186/s13148-024-01641-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 02/06/2024] [Indexed: 02/29/2024] Open
Abstract
BACKGROUND Whole-genome methylation sequencing of cfDNA is not cost-effective for tumor detection. Here, we introduce reduced representative methylome profiling (RRMP), which employs restriction enzyme for depletion of AT-rich sequence to achieve enrichment and deep sequencing of CG-rich sequences. METHODS We first verified the ability of RRMP to enrich CG-rich sequences using tumor cell genomic DNA and analyzed differential methylation regions between tumor cells and normal whole blood cells. We then analyzed cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals to detect breast cancer by building machine learning models. RESULTS RRMP captured 81.9% CpG islands and 75.2% gene promoters when sequenced to 10 billion base pairs, with an enrichment efficiency being comparable to RRBS. RRMP allowed us to assess DNA methylation changes between tumor cells and whole blood cells. Applying our approach to cfDNA from 29 breast cancer patients and 27 non-breast cancer individuals, we developed machine learning models that could discriminate between breast cancer and non-breast cancer controls (AUC = 0.85), suggesting possibilities for truly non-invasive cancer detection. CONCLUSIONS We developed a new method to achieve reduced representative methylome profiling of cell-free DNA for tumor detection.
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Affiliation(s)
- Qingmo Yang
- The First Affiliated Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, Fujian, China
| | - Xingqiang Zhu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Yulu Liu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhi He
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Huan Xu
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Hailing Zheng
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Zhiming Huang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Dan Wang
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Xiaofang Lin
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China
| | - Ping Guo
- Xiamen Huazao Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
| | - Hongliang Chen
- Xiamen Vangenes Biotechnology Co., Ltd, Xiamen, 361015, Fujian, China.
- School of Life Sciences, Xiamen University, Xiamen, 361102, Fujian, China.
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3
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An N, Cui L, Yang X. Low RPMB indicates better disease-free survival of adjuvant radiotherapy after radical surgery in thymoma. Am J Transl Res 2023; 15:5457-5468. [PMID: 37692947 PMCID: PMC10492043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 08/09/2023] [Indexed: 09/12/2023]
Abstract
BACKGROUND The current use of adjuvant radiotherapy in thymoma (THYM) following radical surgery is primarily based on clinical factors and is a subject of ongoing debate. METHODS We developed a new biomarker, promotor methylation burden of Deoxyribonucleic acid repair genes (RPMB), to identify patients who may benefit from adjuvant radiotherapy after complete resection in THYM. RPMB quantitatively measures the promoter methylation level of Deoxyribonucleic acid (DNA) repair genes. RESULTS The methylation profile of 124 patients and corresponding clinical data were retrieved from The Cancer Genome Atlas (TCGA) database. The methylation level of DNA repair genes (DRGs) was found to be significantly hypomethylated juxtaposed to other genes across the whole human genome (all P < 0.001). THYM patients with higher RPMB tended to be female (P = 1.114×10-12) and have a more advanced Masaoka stage (P = 0.034). Kaplan-Meier analysis showed that high RPMB could significantly predict a poor disease-free survival (DFS) in THYM patients who received adjuvant radiotherapy after complete resection (HR = 5.750, 95% CI: 1.213-27.251, P = 0.013). Furthermore, Cox regression analysis indicated that RPMB was the only prognostic factor significantly associated with DFS after adjuvant radiotherapy (P = 0.028). CONCLUSIONS Low RPMB may be a potential indicator to identify suitable patients who can benefit from adjuvant radiotherapy in THYM, sparing others from treatment toxicity.
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Affiliation(s)
- Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao UniversityQingdao 266003, Shandong, China
| | - Li Cui
- Department of Oncology, The People’s Hospital of Pingyi CountyLinyi 273399, Shandong, China
| | - Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao UniversityQingdao 266003, Shandong, China
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An N, Yang X. Prediction of disease-free survival of N1/2 non-small cell lung cancer after adjuvant chemotherapy by the biomarker RPMB. Heliyon 2023; 9:e18266. [PMID: 37501955 PMCID: PMC10368914 DOI: 10.1016/j.heliyon.2023.e18266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
No molecular biomarkers have been proven applicable in clinical practice to identify patients who can benefit from adjuvant chemotherapy in non-small cell lung cancer (NSCLC). In this study, we established a biomarker, RPMB, short for promotor methylation burden of DNA repair genes (DRGs), to identify the subgroup of patients who might benefit from adjuvant chemotherapy in NSCLC. Methylation profiles of 828 NSCLC primary tumors and their clinical information were downloaded from The Cancer Genome Atlas (TCGA) database. The RPMB for each patient after radical resection was calculated and its correlation with the prognosis of NSCLC was extensively investigated. DRGs of NSCLC were much more hypomethylated than the other genes (all p<0.001). RPMB was defined as the ratio of methylated DRGs to the total number of all the DRGs. Patients with higher RPMB values tended to be nonsmokers, had adenocarcinoma, were female and had peripheral tumors. Subgroup analysis of forest plot among different clinical factors showed that high RPMB was significantly correlated to better disease-free survival (DFS) in pathologic N-positive patients after adjuvant chemotherapy (HR = 0.404, n = 62, p = 0.034). Notably, more superior DFS was exhibited in high RPMB NSCLCs with N1 nodal stage compared with those with low RPMB values (HR = 0.348, n = 47, p = 0.043). High RPMB might be used as a potential predictor to identify suitable N-positive NSCLC patients who can benefit from adjuvant chemotherapy after radical surgery.
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Affiliation(s)
- Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, China
| | - Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, 266003, China
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Milner JJ, Zadinsky JK, Shiao SPK. Nursing Informatics and Epigenetics: Methodological Considerations for Big Data Analysis. Comput Inform Nurs 2023; 41:369-376. [PMID: 36728378 PMCID: PMC10241417 DOI: 10.1097/cin.0000000000000992] [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: 02/03/2023]
Abstract
Nursing informatics requires an understanding of patient-centered data and clinical workflow, and epigenetic research requires an understanding of data analysis. The purpose of this article is to document the methodology that nursing informatics specialists can use to conduct epigenetic research and subsequently strengthen patient-centered care. A pilot study of a secondary methylation data analysis using The Cancer Genome Atlas data from individuals with colon cancer is utilized to illustrate the methodology. The steps for conducting the study using public and free resources are discussed. These steps include finding a data source; downloading and analyzing differentially methylated regions; annotating differentially methylated region, gene ontology and function analysis; and reporting results. A model of epigenetic testing workflow is provided, as is a list of publicly available data and analysis sources that can be used to conduct epigenetic research.
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Xi Y, Zhang XL, Luo QX, Gan HN, Liu YS, Shao SH, Mao XH. Helicobacter pylori regulates stomach diseases by activating cell pathways and DNA methylation of host cells. Front Cell Dev Biol 2023; 11:1187638. [PMID: 37215092 PMCID: PMC10192871 DOI: 10.3389/fcell.2023.1187638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 04/25/2023] [Indexed: 05/24/2023] Open
Abstract
One of the most prevalent malignant tumors of the digestive tract is gastric cancer (GC). Age, high salt intake, Helicobacter pylori (H. pylori) infection, and a diet deficient in fruits and vegetables are risk factors for the illness. A significant risk factor for gastric cancer is infection with H. pylori. Infecting gastric epithelial cells with virulence agents secreted by H. pylori can cause methylation of tumor genes or carcinogenic signaling pathways to be activated. Regulate downstream genes' aberrant expression, albeit the precise mechanism by which this happens is unclear. Oncogene, oncosuppressor, and other gene modifications, as well as a number of different gene change types, are all directly associated to the carcinogenesis of gastric cancer. In this review, we describe comprehensive H. pylori and its virulence factors, as well as the activation of the NF-κB, MAPK, JAK/STAT signaling pathways, and DNA methylation following infection with host cells via virulence factors, resulting in abnormal gene expression. As a result, host-related proteins are regulated, and gastric cancer progression is influenced. This review provides insight into the H. pylori infection, summarizes a series of relevant papers, discusses the complex signaling pathways underlying molecular mechanisms, and proposes new approach to immunotherapy of this important disease.
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Affiliation(s)
- Yue Xi
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xiao-Li Zhang
- Department of Clinical Laboratory, The Affiliated Yixing Hospital of Jiangsu University, Wuxi, China
| | - Qing-Xin Luo
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Hai-Ning Gan
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Yu-Shi Liu
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Shi-He Shao
- School of Medicine, Jiangsu University, Zhenjiang, China
| | - Xu-Hua Mao
- Department of Clinical Laboratory, The Affiliated Yixing Hospital of Jiangsu University, Wuxi, China
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Agarwal A, Kansal V, Farooqi H, Prasad R, Singh VK. Epigallocatechin Gallate (EGCG), an Active Phenolic Compound of Green Tea, Inhibits Tumor Growth of Head and Neck Cancer Cells by Targeting DNA Hypermethylation. Biomedicines 2023; 11:biomedicines11030789. [PMID: 36979768 PMCID: PMC10045148 DOI: 10.3390/biomedicines11030789] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Revised: 02/24/2023] [Accepted: 03/03/2023] [Indexed: 03/08/2023] Open
Abstract
Head and neck cancers are among the deadliest cancers, ranked sixth globally in rates of high mortality and poor patient prognoses. The prevalence of head and neck squamous cell carcinoma (HNSCC) is associated with smoking and excessive alcohol consumption. Despite several advances in diagnostic and interventional methods, the morbidity of subjects with HNSCC has remained unchanged over the last 30 years. Epigenetic alterations, such as DNA hypermethylation, are commonly associated with several cancers, including HNSCC. Thus, epigenetic changes are considered promising therapeutic targets for chemoprevention. Here, we investigated the effect of EGCG on DNA hypermethylation and the growth of HNSCC. First, we assessed the expression levels of global DNA methylation in HNSCC cells (FaDu and SCC-1) and observed enhanced methylation levels compared with normal human bronchial epithelial cells (NHBE). Treatment of EGCG to HNSCC cells significantly inhibited global DNA hypermethylation by up to 70–80% after 6 days. Inhibition of DNA hypermethylation in HNSCC cells was confirmed by the conversion of 5-methylcytosine (5-mc) into 5-hydroxy methylcytosine (5hmC). DNA methyltransferases regulate DNA methylation. Next, we checked the effect of EGCG on the expression levels of DNA methyltransferases (DNMTs) and DNMT activity. Treatment of EGCG to HNSCC cells significantly reduced DNMT activity to 60% in SCC-1 and 80% in FaDu cells. The protein levels of DNMT3a and DNMT3b were downregulated in both cell lines after EGCG treatment. EGCG treatment to HNSCC cells reactivated tumor suppressors and caused decreased cell proliferation. Our in vivo study demonstrated that administration of EGCG (0.5%, w/w) as a supplement within an AIN76A diet resulted in inhibition of tumor growth in FaDu xenografts in nude mice (80%; p < 0.01) compared with non-EGCG-treated controls. The growth inhibitory effect of dietary EGCG on the HNSCC xenograft tumors was associated with the inhibition of DNMTs and reactivation of silenced tumor suppressors. Together, our study provides evidence that EGCG acts as a DNA demethylating agent and can reactivate epigenetically silenced tumor suppressors to inhibit the growth of HNSCC cells.
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Affiliation(s)
- Anshu Agarwal
- Department of Zoology, Agra College, Dr. Bhimrao Ambedkar University, Agra 282004, India
| | - Vikash Kansal
- Department of Otolaryngology, Emory University, Atlanta, GA 30322, USA
| | - Humaira Farooqi
- Department of Biochemistry, Hamdard University, New Delhi 110062, India
| | - Ram Prasad
- Department of Ophthalmology and Visual Sciences, University of Alabama at Birmingham, Birmingham, AL 35294, USA
- Correspondence: (R.P.); (V.K.S.); Tel.: +1-205-996-8685 (R.P.); +91-9412137516 (V.K.S.); Fax: +1-205-996-8653 (R.P.)
| | - Vijay Kumar Singh
- Department of Zoology, Agra College, Dr. Bhimrao Ambedkar University, Agra 282004, India
- Narain PG Degree College, Shikohabad, Dr. Bhimrao Ambedkar University, Agra 282004, India
- Correspondence: (R.P.); (V.K.S.); Tel.: +1-205-996-8685 (R.P.); +91-9412137516 (V.K.S.); Fax: +1-205-996-8653 (R.P.)
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8
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MultiScale-CNN-4mCPred: a multi-scale CNN and adaptive embedding-based method for mouse genome DNA N4-methylcytosine prediction. BMC Bioinformatics 2023; 24:21. [PMID: 36653789 PMCID: PMC9847203 DOI: 10.1186/s12859-023-05135-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/04/2023] [Indexed: 01/19/2023] Open
Abstract
N4-methylcytosine (4mC) is an important epigenetic mechanism, which regulates many cellular processes such as cell differentiation and gene expression. The knowledge about the 4mC sites is a key foundation to exploring its roles. Due to the limitation of techniques, precise detection of 4mC is still a challenging task. In this paper, we presented a multi-scale convolution neural network (CNN) and adaptive embedding-based computational method for predicting 4mC sites in mouse genome, which was referred to as MultiScale-CNN-4mCPred. The MultiScale-CNN-4mCPred used adaptive embedding to encode nucleotides, and then utilized multi-scale CNNs as well as long short-term memory to extract more in-depth local properties and contextual semantics in the sequences. The MultiScale-CNN-4mCPred is an end-to-end learning method, which requires no sophisticated feature design. The MultiScale-CNN-4mCPred reached an accuracy of 81.66% in the 10-fold cross-validation, and an accuracy of 84.69% in the independent test, outperforming state-of-the-art methods. We implemented the proposed method into a user-friendly web application which is freely available at: http://www.biolscience.cn/MultiScale-CNN-4mCPred/ .
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Li J, He Y, Liang T, Wang J, Jiang X, Zhang G. Identification of potential differentially methylated gene-related biomarkers in endometriosis. Epigenomics 2022; 14:1157-1179. [DOI: 10.2217/epi-2022-0249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To identify epigenetic alterations of differentially expressed genes and screen out targeted therapeutic drugs in endometriosis. Methods: Based on the Gene Expression Omnibus database and a series of biological information analysis tools, supplemented by validation of clinical samples, aberrant DNA methylation-driven genes and their functions were explored, as well as possible targeted drugs. Results: This study screened out a range of DNA methylation-driven genes that were associated with powerful properties and corresponding pathways. Among them, BDNF and CCL2 were key genes in the development of endometriosis. Four chemical agents have been flagged as potential treatments for endometriosis. Conclusion: These candidate genes and small-molecule agents may be further explored as potential targets and drugs for endometriosis diagnosis and therapy, respectively.
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Affiliation(s)
- Jixin Li
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Yanan He
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Tian Liang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Jing Wang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Xinyan Jiang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
| | - Guangmei Zhang
- Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, 15000, China
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Bazard P, Pineros J, Acosta AA, Thivierge M, Paganella LR, Zucker S, Mannering FL, Modukuri S, Zhu X, Frisina RD, Ding B. Post-Translational Modifications and Age-related Hearing Loss. Hear Res 2022; 426:108625. [DOI: 10.1016/j.heares.2022.108625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 08/21/2022] [Accepted: 09/23/2022] [Indexed: 11/04/2022]
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Botezatu A, Vladoiu S, Fudulu A, Albulescu A, Plesa A, Muresan A, Stancu C, Iancu IV, Diaconu CC, Velicu A, Popa OM, Badiu C, Dinu-Draganescu D. Advanced molecular approaches in male infertility diagnosis. Biol Reprod 2022; 107:684-704. [PMID: 35594455 DOI: 10.1093/biolre/ioac105] [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: 12/30/2021] [Revised: 04/29/2022] [Accepted: 05/11/2022] [Indexed: 11/13/2022] Open
Abstract
In the recent years a special attention has been given to a major health concern namely to male infertility, defined as the inability to conceive after 12 months of regular unprotected sexual intercourse, taken into account the statistics that highlight that sperm counts have dropped by 50-60% in recent decades. According to the WHO, infertility affects approximately 9% of couples globally, and the male factor is believed to be present in roughly 50% of cases, with exclusive responsibility in 30%. The aim of this manuscript is to present an evidence-based approach for diagnosing male infertility that includes finding new solutions for diagnosis and critical outcomes, retrieving up-to-date studies and existing guidelines. The diverse factors that induce male infertility generated in a vast amount of data that needed to be analysed by a clinician before a decision could be made for each individual. Modern medicine faces numerous obstacles as a result of the massive amount of data generated by the molecular biology discipline. To address complex clinical problems, vast data must be collected, analysed, and used, which can be very challenging. The use of artificial intelligence (AI) methods to create a decision support system can help predict the diagnosis and guide treatment for infertile men, based on analysis of different data as environmental and lifestyle, clinical (sperm count, morphology, hormone testing, karyotype, etc.) and "omics" bigdata. Ultimately, the development of AI algorithms will assist clinicians in formulating diagnosis, making treatment decisions, and predicting outcomes for assisted reproduction techniques.
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Affiliation(s)
- A Botezatu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - S Vladoiu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - A Fudulu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - A Albulescu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania.,National Institute for Chemical pharmaceutical Research & Development
| | - A Plesa
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - A Muresan
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - C Stancu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - I V Iancu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - C C Diaconu
- "Stefan S. Nicolau" Institute of Virology, Bucharest, Romania
| | - A Velicu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - O M Popa
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania
| | - C Badiu
- "CI Parhon" National Institute of Endocrinology, Bucharest, Romania.,"Carol Davila" University of Medicine and Pharmacy, Bucharest, Romania
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Dahodwala H, Amenyah SD, Nicoletti S, Henry M, Lees-Murdock DJ, Sharfstein ST. Evaluation of site-specific methylation of the CMV promoter and its role in CHO cell productivity of a recombinant monoclonal antibody. Antib Ther 2022; 5:121-129. [PMID: 35719211 PMCID: PMC9199181 DOI: 10.1093/abt/tbac010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 04/13/2022] [Accepted: 03/02/2022] [Indexed: 11/17/2022] Open
Abstract
We previously demonstrated that increased monoclonal antibody productivity in dihydrofolate reductase (DHFR)-amplified CHO cells correlates with phosphorylated transcription factor-cytomegalovirus (CMV) promoter interactions. In this article, we extend the characterization to include CMV promoter methylation and its influence on NFκB and CREB1 transcription factor binding to the CMV promoter in two families of DHFR-amplified CHO cell lines. CMV promoter methylation was determined using bisulfite sequencing. To overcome Sanger-sequencing limitations due to high CG bias and multiple transgenes copies, pyrosequencing was used to determine the frequency of methylated cytosines in regions proximal to and containing the NFκB and CREB1 transcription-factor consensus binding sites. Chromatin immunoprecipitation was performed to interrogate transcription factor–DNA interactions. Antibodies to CREB1 and NFκB were used to immunoprecipitate formaldehyde-crosslinked protein-DNA fractions, followed by reverse transcription quantitative real-time polymerase chain reaction to quantitate the number of copies of CMV-promoter DNA bound to the various transcription factors. The relative unmethylated fraction at the CREB1 and NFκB consensus binding sites determined by pyrosequencing was correlated with transcription factor binding as determined by chromatin immunoprecipitation. Azacytidine treatment reduced methylation in all treated samples, though not at all methylation sites, while increasing transcription. Distinct promoter methylation patterns arise upon clonal selection in different families of cell lines. In both cell line families, increased methylation was observed upon amplification. In one family, the NFκB binding-site methylation was accompanied by increased CREB1 interaction with the promoter. In the other cell line family, lower methylation frequency at the NFκB consensus binding site was accompanied by more NFκB recruitment to the promoter region.
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Affiliation(s)
- Hussain Dahodwala
- National Institute for Innovation in Manufacturing Biopharmaceuticals, Newark, Delaware, USA
| | - Sophia D Amenyah
- School of Biomedical Sciences, Ulster University, Coleraine, Londonderry, Northern Ireland, UK
| | - Sarah Nicoletti
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York USA
| | - Matthew Henry
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St. Lucia, QLD, Australia
| | - Diane J Lees-Murdock
- School of Biomedical Sciences, Ulster University, Coleraine, Londonderry, Northern Ireland, UK
| | - Susan T Sharfstein
- College of Nanoscale Science and Engineering, SUNY Polytechnic Institute, Albany, New York USA
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Obesity-Associated Differentially Methylated Regions in Colon Cancer. J Pers Med 2022; 12:jpm12050660. [PMID: 35629083 PMCID: PMC9142939 DOI: 10.3390/jpm12050660] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 04/11/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Obesity with adiposity is a common disorder in modern days, influenced by environmental factors such as eating and lifestyle habits and affecting the epigenetics of adipose-based gene regulations and metabolic pathways in colorectal cancer (CRC). We compared epigenetic changes of differentially methylated regions (DMR) of genes in colon tissues of 225 colon cancer cases (154 non-obese and 71 obese) and 15 healthy non-obese controls by accessing The Cancer Genome Atlas (TCGA) data. We applied machine-learning-based analytics including generalized regression (GR) as a confirmatory validation model to identify the factors that could contribute to DMRs impacting colon cancer to enhance prediction accuracy. We found that age was a significant predictor in obese cancer patients, both alone (p = 0.003) and interacting with hypomethylated DMRs of ZBTB46, a tumor suppressor gene (p = 0.008). DMRs of three additional genes: HIST1H3I (p = 0.001), an oncogene with a hypomethylated DMR in the promoter region; SRGAP2C (p = 0.006), a tumor suppressor gene with a hypermethylated DMR in the promoter region; and NFATC4 (p = 0.006), an adipocyte differentiating oncogene with a hypermethylated DMR in an intron region, are also significant predictors of cancer in obese patients, independent of age. The genes affected by these DMR could be potential novel biomarkers of colon cancer in obese patients for cancer prevention and progression.
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14
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Koelsche C, von Deimling A. Methylation classifiers: brain tumors, sarcomas and what's next. Genes Chromosomes Cancer 2022; 61:346-355. [PMID: 35388566 DOI: 10.1002/gcc.23041] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 03/16/2022] [Accepted: 03/18/2022] [Indexed: 11/09/2022] Open
Abstract
Tumor classification has evolved over the last decades with technical progress contributing much to our current concepts. Among diagnostic hallmark novelties were immunostaining, Fluorescence in situ hybridization, Sanger sequencing followed by massive parallel DNA sequencing and recently, epigenetic analyses have entered the stage. Although each of these techniques was revolutionary and, in some way, also disruptive in certain diagnostic fields, it took years to decades for broad implementation into standard pathological-diagnostic algorithms. In contrast, DNA methylation profiling has been accepted in short time as a game changer with lasting impact on brain tumor classification and with potential for classification of other tumor types. This review provides a brief introduction in DNA methylation-based tumor classification. We present why DNA methylation signatures are attractive diagnostic biomarkers, discuss present achievements and future aims and explain the integration of methylation-based classifiers in diagnostic procedure. Finally, we provide an outlook on the challenges and opportunities associated with DNA methylation-based tumor profiling. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Christian Koelsche
- Department of General Pathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Andreas von Deimling
- Department of Neuropathology, Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Clinical Cooperation Unit Neuropathology, German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
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15
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Goenka SD, Gorzynski JE, Shafin K, Fisk DG, Pesout T, Jensen TD, Monlong J, Chang PC, Baid G, Bernstein JA, Christle JW, Dalton KP, Garalde DR, Grove ME, Guillory J, Kolesnikov A, Nattestad M, Ruzhnikov MRZ, Samadi M, Sethia A, Spiteri E, Wright CJ, Xiong K, Zhu T, Jain M, Sedlazeck FJ, Carroll A, Paten B, Ashley EA. Accelerated identification of disease-causing variants with ultra-rapid nanopore genome sequencing. Nat Biotechnol 2022; 40:1035-1041. [PMID: 35347328 PMCID: PMC9287171 DOI: 10.1038/s41587-022-01221-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/13/2022] [Indexed: 12/23/2022]
Abstract
Whole-genome sequencing (WGS) can identify variants that cause genetic disease, but the time required for sequencing and analysis has been a barrier to its use in acutely ill patients. In the present study, we develop an approach for ultra-rapid nanopore WGS that combines an optimized sample preparation protocol, distributing sequencing over 48 flow cells, near real-time base calling and alignment, accelerated variant calling and fast variant filtration for efficient manual review. Application to two example clinical cases identified a candidate variant in <8 h from sample preparation to variant identification. We show that this framework provides accurate variant calls and efficient prioritization, and accelerates diagnostic clinical genome sequencing twofold compared with previous approaches. A streamlined sequencing process enables identification of disease-causing variants in the clinic within 8 hours.
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Affiliation(s)
| | | | | | | | - Trevor Pesout
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | - Jean Monlong
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Tong Zhu
- NVIDIA Corporation, Santa Clara, CA, USA
| | - Miten Jain
- UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
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16
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Yang K, Feng X, Yu G, Han W, Liu F, Xie Y, Zhang H, Yu Y, Zou G. Single polymeric microfiber waveguide platform for sensitive detection and discrimination of DNA methylation. Analyst 2022; 147:1892-1898. [DOI: 10.1039/d1an02243a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel sensitive detection platform for p16 and p16 methylation based on a single polymeric fluorescent microfiber waveguide with sandwich-structured hybridization designs.
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Affiliation(s)
- Kexin Yang
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Xiaohui Feng
- Division of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gaoyuan Yu
- Undergraduate major in clinical medicine, grade 2017, class 1, Medical College of Hubei University of Science and Technology, Xianning, Hubei 437100, P. R. China
| | - Wenjie Han
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Funing Liu
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Yifan Xie
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Hongli Zhang
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
| | - Yue Yu
- Division of Gastroenterology, The First Affiliated Hospital of USTC, Division of Life Science and Medicine, University of Science and Technology of China, Hefei, Anhui 230026, P. R. China
| | - Gang Zou
- Department of Polymer Science and Engineering, University of Science and Technology of China, 96 Jinzhai Road, Hefei 230026, China
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17
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Yan X, Zhao X, Yan Q, Wang Y, Zhang C. Analysis of the role of METTL5 as a hub gene in lung adenocarcinoma based on a weighted gene co-expression network. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021; 18:6608-6619. [PMID: 34517547 DOI: 10.3934/mbe.2021327] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Lung adenocarcinoma (LUAD) is a frequently diagnosed malignant tumor that is highly invasive and lethal. The prognosis of patients with LUAD still needs to be improved, as conventional treatment is remarkably well tolerated. In this study, the expression profile of LUAD in the TCGA database was used for differential expression analysis, and differential expression genes were determined to construct a weighted gene co-expression network analysis (WGCNA) for dividing and finding the gene modules with the highest correlation with tumor stage. Here, METTL5, DDX23, GPSM2, CEP95, WDCP, and METL17 were identified as hub genes. According to the relation degree, METTL5 was determined as the candidate gene in this study. Difference analysis and receiver operating characteristic (ROC) curve were applied to identify the predictive performance of METTL5 in LUAD, and Kaplan-Meier (KM) analysis showed that the prognosis of LUAD patients with high METTL5 expression was poor. Further GSEA analysis showed that high-expressed METTL5 was related to epithelial-mesenchymal transition and other pathways. Therefore, METTL5 may be involved in the occurrence and malignant progression of LUAD. The current findings provide an effective molecular target for early diagnosis of LUAD, helping monitor the malignant progression of LUAD and improve the prognosis of LUAD patients.
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Affiliation(s)
- Xinwang Yan
- Medical College of Qingdao University, Jining NO.1 People's Hospital, Qingdao, Shandong Province 266042, China
| | - Xiaowen Zhao
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, Shandong Province 266042, China
| | - Qing Yan
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, Shandong Province 266042, China
| | - Ye Wang
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, Shandong Province 266042, China
| | - Chunling Zhang
- Clinical Laboratory, Qingdao Central Hospital, The Second Affiliated Hospital of Medical College of Qingdao University, Qingdao, Shandong Province 266042, China
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18
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Liu R, Long Q, Zou X, Wang Y, Pei Y. DNA methylation occurring in Cre-expressing cells inhibits loxP recombination and silences loxP-sandwiched genes. THE NEW PHYTOLOGIST 2021; 231:210-224. [PMID: 33742463 DOI: 10.1111/nph.17353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 03/12/2021] [Indexed: 06/12/2023]
Abstract
The low DNA recombination efficiency of site-specific recombinase systems in plants limits their application; however, the underlying mechanism is unknown. We evaluate the gene deletion performance of four recombinase systems (Cre/loxP, Flp/FRT, KD/KDRT and B3/B3RT) in tobacco where the recombinases are under the control of germline-specific promoters. We find that the expression of these recombinases results mostly in gene silencing rather than gene deletion. Using the Cre/loxP system as a model, we reveal that the region flanked by loxP sites (floxed) is hypermethylated, which prevents floxed genes from deletion while silencing the expression of the genes. We further show CG methylation alone in the recombinase binding element of the loxP site is unable to impede gene deletion; instead, CHH methylation in the crossover region is required to inhibit loxP recombination. Our study illustrates the important role of recombinase-induced DNA methylation in the inhibition of site-specific DNA recombination and uncovers the mechanism underlying recombinase-associated gene silence in plants.
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Affiliation(s)
- Ruochen Liu
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Qin Long
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Xiuping Zou
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - You Wang
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
| | - Yan Pei
- Chongqing Key Laboratory of Application and Safety Control of Genetically Modified Crops; Biotechnology Research Center, Southwest University, No. 2 Tiansheng Road, Beibei, Chongqing, 400715, China
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19
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Chen S, Xiao L, Peng H, Wang Z, Xie J. Methylation gene KCNC1 is associated with overall survival in patients with seminoma. Oncol Rep 2021; 45:73. [PMID: 34105734 PMCID: PMC8020201 DOI: 10.3892/or.2021.8024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 03/01/2021] [Indexed: 11/24/2022] Open
Abstract
The aim of the present study was to explore and verify the potential mechanism of seminoma progression. Data on 132 RNA-seq and 156 methylation sites from stage II/III and I seminoma specimens were downloaded from The Cancer Genome Atlas database. An initial filter of |fold-change| >2 and false discovery rate <0.05 were used to identify differentially expressed genes (DEGs) which were associated with differential methylation site genes; these genes were considered potential candidates for further investigation by survival analysis. Potassium voltage-gated channel subfamily C member 1 (KCNC1) expression was verified in seminoma human tissues and three seminoma cell lines. The invasive, proliferative and apoptotic abilities of the human testicular tumor Ntera-2 and normal human testis Hs1.Tes cell lines were assessed following aberrant KCNC1 expression. KCNC1 was identified as a DEG, in which hypermethylation inhibited its expression and it was associated with poor overall survival in patients with seminoma. The present results demonstrated that KCNC1 is negatively correlated with methylation. Due to the abnormal expression of KCNC1 in seminoma cells, it was suggested that KCNC1 could be used as a diagnostic indicator and therapeutic target for the progression of seminoma.
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Affiliation(s)
- Saipeng Chen
- Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China.,Department of Reproductive Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Longfei Xiao
- Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China.,Department of Reproductive Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
| | - Huahong Peng
- Tianjin Institute of Urology, The Second Hospital of Tianjin Medical University, Tianjin 300211, P.R. China
| | - Zhen Wang
- Taixing People's Hospital, Taixing, Jiangsu 225400, P.R. China
| | - Jianbing Xie
- Affiliated Hospital of Putian University, Putian, Fujian 351100, P.R. China.,Department of Reproductive Medicine, Xiangyang No. 1 People's Hospital, Hubei University of Medicine, Xiangyang, Hubei 441000, P.R. China
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20
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Salinas I, Sinha N, Sen A. Androgen-induced epigenetic modulations in the ovary. J Endocrinol 2021; 249:R53-R64. [PMID: 33764313 PMCID: PMC8080881 DOI: 10.1530/joe-20-0578] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 03/24/2021] [Indexed: 12/16/2022]
Abstract
In recent years, androgens have emerged as critical regulators of female reproduction and women's health in general. While high levels of androgens in women are associated with polycystic ovary syndrome (PCOS), recent evidence suggests that a certain amount of direct androgen action through androgen receptor is also essential for normal ovarian function. Moreover, prenatal androgen exposure has been reported to cause developmental reprogramming of the fetus that manifests into adult pathologies, supporting the Developmental Origins of Health and Disease (DOHaD) hypothesis. Therefore, it has become imperative to understand the underlying mechanism of androgen actions and its downstream effects under normal and pathophysiological conditions. Over the years, there has been a lot of studies on androgen receptor function as a transcriptional regulator in the nucleus as well as androgen-induced rapid extra-nuclear signaling. Conversely, new evidence suggests that androgen actions may also be mediated through epigenetic modulation involving both the nuclear and extra-nuclear androgen signaling. This review focuses on androgen-induced epigenetic modifications in female reproduction, specifically in the ovary, and discusses emerging concepts, latest perceptions, and highlight the areas that need further investigation.
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Affiliation(s)
- Irving Salinas
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
- Department of Physiology, Michigan State University, East Lansing, MI 48824, USA
| | - Niharika Sinha
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
- Department of Animal Sciences, Michigan State University, East Lansing, MI 48824, USA
| | - Aritro Sen
- Reproductive and Developmental Sciences Program, Michigan State University, East Lansing, MI 48824, USA
- Department of Animal Sciences, Michigan State University, East Lansing, MI 48824, USA
- Corresponding author and person to whom reprint request should be addressed: Aritro Sen Ph.D., Reproductive and Developmental Sciences Program, 3013 Interdisciplinary Science & Technology Building, 766 Service Road, Michigan State University, East Lansing, MI 48824, Ph:517-432-4585;
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21
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Lu Q, Chen X, Yang Z, Bashir NH, Liu J, Cui Y, Shao S, Chen MS, Chen H. Molecular and Histologic Adaptation of Horned Gall Induced by the Aphid Schlechtendalia chinensis (Pemphigidae). Int J Mol Sci 2021; 22:ijms22105166. [PMID: 34068250 PMCID: PMC8153119 DOI: 10.3390/ijms22105166] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/02/2022] Open
Abstract
Chinese galls are the result of hyperplasia in host plants induced by aphids. The metabolism and gene expression of these galls are modified to accommodate the aphids. Here, we highlight the molecular and histologic features of horned galls according to transcriptome and anatomical structures. In primary pathways, genes were found to be unevenly shifted and selectively expressed in the galls and leaves near the galls (LNG). Pathways for amino acid synthesis and degradation were also unevenly shifted, favoring enhanced accumulation of essential amino acids in galls for aphids. Although galls enhanced the biosynthesis of glucose, which is directly available to aphids, glucose content in the gall tissues was lower due to the feeding of aphids. Pathways of gall growth were up-regulated to provide enough space for aphids. In addition, the horned gall has specialized branched schizogenous ducts and expanded xylem in the stalk, which provide a broader feeding surface for aphids and improve the efficiency of transportation and nutrient exchange. Notably, the gene expression in the LNG showed a similar pattern to that of the galls, but on a smaller scale. We suppose the aphids manipulate galls to their advantage, and galls lessen competition by functioning as a medium between the aphids and their host plants.
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Affiliation(s)
- Qin Lu
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
| | - Xiaoming Chen
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
- The Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming 650224, China
| | - Zixiang Yang
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
| | - Nawaz Haider Bashir
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
| | - Juan Liu
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
| | - Yongzhong Cui
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
| | - Shuxiao Shao
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
| | - Ming-Shun Chen
- Department of Entomology, Kansas State University, 123 Waters Hall, Manhattan, KS 66506, USA;
| | - Hang Chen
- Research Institute of Resource Insects, Chinese Academy of Forestry, Kunming 650224, China; (Q.L.); (X.C.); (Z.Y.); (N.H.B.); (J.L.); (Y.C.); (S.S.)
- The Key Laboratory of Cultivating and Utilization of Resources Insects of State Forestry Administration, Kunming 650224, China
- Correspondence:
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22
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A proof-of-concept study for the pathogenetic role of enhancer hypomethylation of MYBPHL in multiple myeloma. Sci Rep 2021; 11:7009. [PMID: 33772052 PMCID: PMC7997988 DOI: 10.1038/s41598-021-86473-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 03/01/2021] [Indexed: 12/25/2022] Open
Abstract
Enhancer DNA methylation and expression of MYBPHL was studied in multiple myeloma (MM). By bisulfite genomic sequencing, among the three CpGs inside the MYBPHL enhancer, CpG1 was significantly hypomethylated in MM cell lines (6.7–50.0%) than normal plasma cells (37.5–75.0%) (P = 0.007), which was negatively correlated with qPCR-measured MYBPHL expression. In RPMI-8226 and WL-2 cells, bearing the highest CpG1 methylation, 5-azadC caused enhancer demethylation and expression of MYBPHL. In primary samples, higher CpG1 methylation was associated with lower MYBPHL expression. By luciferase assay, luciferase activity was enhanced by MYBPHL enhancer compared with empty vector control, but reduced by site-directed mutagenesis of each CpG. RNA-seq data of newly diagnosed MM patients showed that MYBPHL expression was associated with t(11;14). MOLP-8 cells carrying t(11;14) express the highest levels of MYBPHL, and its knockdown reduced cellular proliferation and increased cell death. Herein, as a proof-of-concept, our data demonstrated that the MYBPHL enhancer, particularly CpG1, was hypomethylated and associated with increased MYBPHL expression in MM, which was implicated in myelomagenesis.
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23
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Ansari I, Chaturvedi A, Chitkara D, Singh S. CRISPR/Cas mediated epigenome editing for cancer therapy. Semin Cancer Biol 2021; 83:570-583. [PMID: 33421620 DOI: 10.1016/j.semcancer.2020.12.018] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 12/26/2020] [Accepted: 12/28/2020] [Indexed: 02/07/2023]
Abstract
The understanding of the relationship between epigenetic alterations, their effects on gene expression and the knowledge that these epigenetic alterations are reversible, have opened up new therapeutic pathways for treating various diseases, including cancer. This has led the research for a better understanding of the mechanism and pathways of carcinogenesis and provided the opportunity to develop the therapeutic approaches by targeting such pathways. Epi-drugs, DNA methyl transferase (DNMT) inhibitors and histone deacetylase (HDAC) inhibitors are the best examples of epigenetic therapies with clinical applicability. Moreover, precise genome editing technologies such as CRISPR/Cas has proven their efficacy in epigenome editing, including the alteration of epigenetic markers, such as DNA methylation or histone modification. The main disadvantage with DNA gene editing technologies is off-target DNA sequence alteration, which is not an issue with epigenetic editing. It is known that cancer is linked with epigenetic alteration, and thus CRISPR/Cas system shows potential for cancer therapy via epigenome editing. This review outlines the epigenetic therapeutic approach for cancer therapy using CRISPR/Cas, from the basic understanding of cancer epigenetics to potential applications of CRISPR/Cas in treating cancer.
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Affiliation(s)
- Imran Ansari
- Department of Pharmacy, Birla Institute of Technology and Science (BITS)-Pilani, Pilani Campus, Vidya Vihar, Pilani, 333 031, Rajasthan, India
| | | | - Deepak Chitkara
- Department of Pharmacy, Birla Institute of Technology and Science (BITS)-Pilani, Pilani Campus, Vidya Vihar, Pilani, 333 031, Rajasthan, India.
| | - Saurabh Singh
- Novartis Healthcare Pvt Ltd., Hyderabad 500032, Telangana, India.
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24
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Promoter CpG island hypermethylation and down regulation of XRCC1 gene can augment in the gastric carcinogenesis events. Mol Biol Rep 2021; 48:405-412. [PMID: 33394233 DOI: 10.1007/s11033-020-06064-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Accepted: 12/03/2020] [Indexed: 02/07/2023]
Abstract
Gastric cancer (GC) is a multistep process characterized by a gradual accumulation of genetic and epigenetic alterations in genes at various stages of progression. Epigenetic alterations like DNA methylation play an important role in cancer and may serve as a biomarker for cancer. The present study was aimed to investigate the promoter hypermethylation, expression profile, and Arg399Gln gene polymorphism of DNA repair gene XRCC1 (X-ray repair cross complimentary group I) in GC patients. A total of 60 histopathologically confirmed GC subjects were recruited in the study. Information on various dietary, lifestyle and environmental factors was obtained in face-to-face interviews using a structured questionnaire from each subject. Tissue samples were taken along with adjacent non-cancerous tissues for analysis. Promoter methylation status and expression of XRCC1 gene was evaluated using MS-PCR and western blotting respectively; while as Arg399Gln polymorphism was analyzed by PCR-RFLP. We found that the XRCC1 gene promoter of 38.3% cancerous tissues were methylated compared to 13.3% of adjacent normal tissues. The promoter hypermethylation status of the gene was found to be significantly associated with the loss of protein expression (P < 0.0001, OR = 14.63; 95% CI 4.01-53.43). However, we did not find any significant association of polymorphism of XRCC1 Arg399Gln with promoter methylation or protein expression. Further, comparison of methylation status and protein expression with clinical parameters like age, smoking status, etc. was also not significant (P > 0.05). The present study indicates that XRCC1 undergoes aberrant promoter hypermethylation with subsequent loss of protein expression in gastric cancer.
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25
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Manipulating the Epigenome in Nuclear Transfer Cloning: Where, When and How. Int J Mol Sci 2020; 22:ijms22010236. [PMID: 33379395 PMCID: PMC7794987 DOI: 10.3390/ijms22010236] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Revised: 12/24/2020] [Accepted: 12/25/2020] [Indexed: 12/20/2022] Open
Abstract
The nucleus of a differentiated cell can be reprogrammed to a totipotent state by exposure to the cytoplasm of an enucleated oocyte, and the reconstructed nuclear transfer embryo can give rise to an entire organism. Somatic cell nuclear transfer (SCNT) has important implications in animal biotechnology and provides a unique model for studying epigenetic barriers to successful nuclear reprogramming and for testing novel concepts to overcome them. While initial strategies aimed at modulating the global DNA methylation level and states of various histone protein modifications, recent studies use evidence-based approaches to influence specific epigenetic mechanisms in a targeted manner. In this review, we describe-based on the growing number of reports published during recent decades-in detail where, when, and how manipulations of the epigenome of donor cells and reconstructed SCNT embryos can be performed to optimize the process of molecular reprogramming and the outcome of nuclear transfer cloning.
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Mohammadzadeh N, Mosaffa F, Khadivi E, Jahangiri R, Jamialahmadi K. Increased Expression of DNA Methyltransferase 1 and 3B Correlates with Tumor Grade in Laryngeal Squamous Cell Carcinoma. PHARMACEUTICAL SCIENCES 2020. [DOI: 10.34172/ps.2020.86] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Background: DNA methyltransferase (DNMT) enzymes, encoded by DNMT1, DNMT3A andDNMT3B genes, play a major role in the development of cancers through aberrant promotermethylation. Due to little information about the biological and clinical significance of expressionchanges of these genes in Laryngeal Squamous Cell carcinoma (LSCC), the current study wasdesigned to evaluate the contribution of DNMTs expression as potential diagnostic biomarkersin progression of LSCC. Methods: DNMT1, DNMT3A and DNMT3B expressions in tumoral and normal tissues fromthirty-three LSCC patients were evaluated by relative comparative real-time PCR, prior toany therapeutic intervention. Relationship between genes expression and clinicopathologicalfeatures were also analyzed. Results: The mRNA expression levels of all three DNMTs (DNMT1, DNMT3A and DNMT3B)were significantly elevated in LSCC tumor specimens compared to that of non-tumor tissues(P<0.0001, P=0.011 and P<0.0001, respectively). The expression of DNMT1 and DNMT3Bwas strongly associated with histopathological tumor grade. Moreover, the mRNA expressionlevels of DNMT3A were significantly correlated with laryngopharyngeal reflux. No significantrelationships existed with other clinicopathological parameters. Conclusion: Data showed that the expression levels of DNMT1, DNMT3A and DNMT3Bmarkedly increased in LSCC tissues. DNMT1 and DNMT3B were mainly overexpressed in highgrade LSCC tumors, therefore, they may have a role in LSCC progression. It seems that thesegenes may serve as diagnostic biomarkers in development of LSCC.
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Affiliation(s)
- Nooshin Mohammadzadeh
- School of Pharmacy, Mashhad University of Medical Sciences, Mashhad, Iran
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Fatemeh Mosaffa
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Ehsan Khadivi
- Sinus and Surgical Endoscopic Research Center, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Rosa Jahangiri
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | - Khadijeh Jamialahmadi
- Biotechnology Research Center, Pharmaceutical Technology Institute, Mashhad University of Medical Sciences, Mashhad, Iran
- Department of Medical Biotechnology and Nanotechnology, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
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Amenyah SD, Ward M, McMahon A, Deane J, McNulty H, Hughes C, Strain JJ, Horigan G, Purvis J, Walsh CP, Lees-Murdock DJ. DNA methylation of hypertension-related genes and effect of riboflavin supplementation in adults stratified by genotype for the MTHFR C677T polymorphism. Int J Cardiol 2020; 322:233-239. [PMID: 32920065 DOI: 10.1016/j.ijcard.2020.09.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/05/2020] [Accepted: 09/04/2020] [Indexed: 12/11/2022]
Abstract
BACKGROUND The interaction between genetic, epigenetic and environmental factors plays an important role in the aetiology of hypertension. GWAS and observational studies link the C677T polymorphism in methylenetetrahydrofolate reductase (MTHFR) with hypertension, while riboflavin, the MTHFR cofactor, has been shown to reduce blood pressure and global DNA methylation in homozygous (TT genotype) individuals. It is currently unclear whether riboflavin modulates DNA methylation of other hypertension-related genes. OBJECTIVES To compare DNA methylation of hypertension-related genes in adults stratified by MTHFR genotype and effect of riboflavin intervention in adults with the variant MTHFR 677TT genotype. METHOD Pyrosequencing was carried out for hypertension-related genes (ACE, AGTR1, GCK, GNA12, IGF2, MMP9 and NOS3) in blood samples from participants in previous trials (CC, n = 40; TT, n = 40). The effect of intervention with riboflavin (1.6 mg/d for16 weeks) or placebo on DNA methylation was investigated in adults with the variant MTHFR 677TT genotype (n = 80). RESULTS Individuals with the MTHFR 677TT v CC genotype had significantly higher average DNA methylation at NOS3 (+1.66%, P = 0.044). In response to riboflavin supplementation in TT individuals, there was an increase in average DNA methylation at IGF2 (+1.09%, P = 0.019) and a decrease at ACE (-0.44%, P = 0.021) in females only. Specific CpG sites were hypomethylated in GNA12 and hypermethylated in AGTR1. CONCLUSION This study provides the first RCT evidence that riboflavin alters DNA methylation of hypertension-related genes in adults with the MTHFR 677TT genotype, providing some insight into mechanisms linking hypertension with the genotype-specific response of BP to riboflavin.
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Affiliation(s)
- Sophia D Amenyah
- Genomic Medicine Research Group, Ulster University, Coleraine BT52 1SA, N. Ireland, UK; Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Amy McMahon
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Jennifer Deane
- Genomic Medicine Research Group, Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Catherine Hughes
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - J J Strain
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Geraldine Horigan
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - John Purvis
- Department of Cardiology, Altnagelvin Area Hospital, BT47 6SB, N. Ireland, UK
| | - Colum P Walsh
- Genomic Medicine Research Group, Ulster University, Coleraine BT52 1SA, N. Ireland, UK
| | - Diane J Lees-Murdock
- Genomic Medicine Research Group, Ulster University, Coleraine BT52 1SA, N. Ireland, UK.
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An N, Yu Z, He XJ, Zhao YY, Yu L, Zhang YC, Lu HJ, Yang X. Promoter Methylation of DNA Repair Genes Predicts Disease-free Survival of Gastric Adenocarcinoma after Adjuvant Radiotherapy. Mol Ther Oncolytics 2020; 18:109-117. [PMID: 32671186 PMCID: PMC7334297 DOI: 10.1016/j.omto.2020.06.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 06/03/2020] [Indexed: 12/27/2022] Open
Abstract
The relentless debate on postoperative adjuvant radiotherapy in gastric adenocarcinoma (GA) has been lasting for decades. In this study, a new biomarker, named promoter methylation burden of DNA repair genes (RPMB), was established to identify the subgroup of patients who might benefit from adjuvant radiotherapy. Methylation profiles of 397 GA tumor samples were downloaded from The Cancer Genome Atlas (TCGA). RPMB for a patient was defined as the ratio of methylated DNA repair genes to the number of all DNA repair genes. Subgroup analyses in term of overall survival (OS) and disease-free survival (DFS) indicated that most of the subgroups favored the high-RMPB group. Kaplan-Meier analysis showed that overall the patients with high RPMB after R0 resection had a significantly better clinical outcome regarding DFS (hazard ratio [HR] = 0.013, p = 0.042). Additionally, high-RPMB patients, who underwent adjuvant radiotherapy with both ≥T2 tumor and positive lymph nodes, showed superior DFS in comparison with the low-RPMB group (HR = 5.35 × 10−10, n = 26, p = 0.010). RPMB might be considered as a promising biomarker for decision-making with regard to postoperative adjuvant radiotherapy for GA patients.
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Affiliation(s)
- Ning An
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Zhuang Yu
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Xin-Jia He
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Yuan-Yuan Zhao
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Li Yu
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
| | - Yong-Chun Zhang
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
- Corresponding author: Yongchun Zhang, Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
| | - Hai-Jun Lu
- Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
- Corresponding author: Haijun Lu, Department of Radiation Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
| | - Xue Yang
- Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China
- Corresponding author: Xue Yang, Department of Medical Oncology, The Affiliated Hospital of Qingdao University, Qingdao, Shandong 266003, China.
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Franco-Enzástiga Ú, García G, Murbartián J, González-Barrios R, Salinas-Abarca AB, Sánchez-Hernández B, Tavares-Ferreira D, Herrera LA, Barragán-Iglesias P, Delgado-Lezama R, Price TJ, Granados-Soto V. Sex-dependent pronociceptive role of spinal α 5 -GABA A receptor and its epigenetic regulation in neuropathic rodents. J Neurochem 2020; 156:897-916. [PMID: 32750173 DOI: 10.1111/jnc.15140] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 06/26/2020] [Accepted: 07/22/2020] [Indexed: 12/23/2022]
Abstract
Extrasynaptic α5 -subunit containing GABAA (α5 -GABAA ) receptors participate in chronic pain. Previously, we reported a sex difference in the action of α5 -GABAA receptors in dysfunctional pain. However, the underlying mechanisms remain unknown. The aim of this study was to examine this sexual dimorphism in neuropathic rodents and the mechanisms involved. Female and male Wistar rats or ICR mice were subjected to nerve injury followed by α5 -GABAA receptor inverse agonist intrathecal administration, L-655,708. The drug produced an antiallodynic effect in nerve-injured female rats and mice, and a lower effect in males. We hypothesized that changes in α5 -GABAA receptor, probably influenced by hormonal and epigenetic status, might underlie this sex difference. Thus, we performed qPCR and western blot. Nerve injury increased α5 -GABAA mRNA and protein in female dorsal root ganglia (DRG) and decreased them in DRG and spinal cord of males. To investigate the hormonal influence over α5 -GABAA receptor actions, we performed nerve injury to ovariectomized rats and reconstituted them with 17β-estradiol (E2). Ovariectomy abrogated L-655,708 antiallodynic effect and E2 restored it. Ovariectomy decreased α5 -GABAA receptor and estrogen receptor α protein in DRG of neuropathic female rats, while E2 enhanced them. Since DNA methylation might contribute to α5 -GABAA receptor down-regulation in males, we examined CpG island DNA methylation of α5 -GABAA receptor coding gene through pyrosequencing. Nerve injury increased methylation in male, but not female rats. Pharmacological inhibition of DNA methyltransferases increased α5 -GABAA receptor and enabled L-655,708 antinociceptive effect in male rats. These results suggest that α5 -GABAA receptor is a suitable target to treat chronic pain in females.
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Affiliation(s)
- Úrzula Franco-Enzástiga
- Neurobiology of Pain Laboratory, Departamento de Farmacobiología, Cinvestav, South Campus, Mexico City, Mexico
| | - Guadalupe García
- Departamento de Farmacobiología, Cinvestav, South Campus, Mexico City, Mexico
| | - Janet Murbartián
- Departamento de Farmacobiología, Cinvestav, South Campus, Mexico City, Mexico
| | | | - Ana B Salinas-Abarca
- Neurobiology of Pain Laboratory, Departamento de Farmacobiología, Cinvestav, South Campus, Mexico City, Mexico
| | - Beatriz Sánchez-Hernández
- Departamento de Genética, Instituto Nacional de Ciencias Médicas y Nutrición Salvador Zubirán, Mexico City, Mexico
| | - Diana Tavares-Ferreira
- School of Behavioral and Brain Sciences, Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, USA
| | - Luis A Herrera
- Cancer Biomedical Research Unit, Instituto Nacional de Cancerología, Mexico City, Mexico
| | - Paulino Barragán-Iglesias
- School of Behavioral and Brain Sciences, Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, USA.,Department of Physiology and Pharmacology, Center for Basic Sciences, Autonomous University of Aguascalientes, Aguascalientes, Mexico
| | - Rodolfo Delgado-Lezama
- Departamento de Fisiología, Biofísica y Neurociencias, Cinvestav, Zacatenco, Mexico City, Mexico
| | - Theodore J Price
- School of Behavioral and Brain Sciences, Center for Advanced Pain Studies, University of Texas at Dallas, Richardson, TX, USA
| | - Vinicio Granados-Soto
- Neurobiology of Pain Laboratory, Departamento de Farmacobiología, Cinvestav, South Campus, Mexico City, Mexico
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Zhao J, Wang L, Li Y, Zhao W, Kang S. Hypomethylation of the GSTM1 promoter is associated with ovarian endometriosis. Hum Reprod 2020; 34:804-812. [PMID: 30989213 DOI: 10.1093/humrep/dez039] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 02/16/2019] [Accepted: 02/27/2019] [Indexed: 01/10/2023] Open
Abstract
STUDY QUESTION Is the methylation status of the glutathione S-transferase M1 (GSTM1) promoter region altered in patients with ovarian endometriosis, and does this affect the expression of GSTM1 in their endometrial tissues? SUMMARY ANSWER The promoter region of GSTM1 was significantly hypomethylated in the ectopic and eutopic endometrium of patients with ovarian endometriosis and this was associated with higher expression of GSTM1 mRNA. WHAT IS KNOWN ALREADY GSTM1, a member of the glutathione S-transferase family, is primarily known as a detoxification enzyme, but it has also been shown to negatively regulate apoptosis-related signalling cascades through protein-protein interactions with apoptosis signal-regulating kinase-1. STUDY DESIGN, SIZE, DURATION This is a case-control study between September 2013 and December 2016, involving 65 patients with ovarian endometriosis and 53 women without endometriosis. We analysed the methylation status and expression levels of GSTM1 in the ectopic and eutopic endometrium of patients with ovarian endometriosis and the endometrium of women without endometriosis. In addition, we collected endometrial samples from 12 women without endometriosis for endometrial epithelial cell cultures. PARTICIPANTS/MATERIALS, SETTING, METHODS Methylation levels of the GSTM1 promoter region in the ectopic and eutopic endometrial tissues of patients with ovarian endometriosis and the endometrial tissues of women without endometriosis were analysed by pyrosequencing. The expression of GSTM1 mRNA and protein in endometrial tissues was investigated by RT-qPCR and immunohistochemistry, respectively. Primary cell culture, gene transfection, Cell Counting Kit-8 assay and flow cytometry were used to analyse the effect of GSTM1 on viability and apoptosis in endometrial epithelial cells. MAIN RESULTS AND THE ROLE OF CHANCE Compared with that in the endometrium of women without endometriosis, the GSTM1 promoter region was significantly hypomethylated in the ectopic and eutopic endometrium of patients with ovarian endometriosis. Additionally, GSTM1 mRNA and protein levels were significantly higher in the ectopic and eutopic endometrium than in the control endometrium. Moreover, the methylation levels of the GSTM1 promoter region were significantly negatively correlated with the mRNA expression of GSTM1. Furthermore, in vitro results suggested that the over-expression of GSTM1 could significantly increase viability and inhibit apoptosis in endometrial epithelial cells following hormone treatment and withdrawal. LIMITATIONS, REASONS FOR CAUTION Due to restrictions in the isolation and culture of pure populations of endometrial epithelial cells, as well as limitations in the number of passages possible in primary cells, we could not explore the underlying molecular mechanism by which GSTM1 modulates apoptosis in endometrial cells. WIDER IMPLICATIONS OF THE FINDINGS This study provides new evidence to support the notion that endometriosis may be an epigenetic disease. STUDY FUNDING/COMPETING INTEREST(S) This work was supported by grants from the Natural Science Foundation of Hebei Province (Grant number: H2018206200) and the Department of Education of Hebei Province (Grant number: CXZZBS2017114). The authors have no conflicts of interest to declare.
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Affiliation(s)
- Jian Zhao
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Lixian Wang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Yan Li
- Department of Molecular Biology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Wei Zhao
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, PR China
| | - Shan Kang
- Department of Gynecology, Fourth Hospital, Hebei Medical University, Shijiazhuang, Hebei, PR China
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Wang Y, Franks JM, Whitfield ML, Cheng C. BioMethyl: an R package for biological interpretation of DNA methylation data. Bioinformatics 2020; 35:3635-3641. [PMID: 30799505 PMCID: PMC6761945 DOI: 10.1093/bioinformatics/btz137] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 01/25/2019] [Accepted: 02/22/2019] [Indexed: 12/16/2022] Open
Abstract
Motivation The accumulation of publicly available DNA methylation datasets has resulted in the need for tools to interpret the specific cellular phenotypes in bulk tissue data. Current approaches use either single differentially methylated CpG sites or differentially methylated regions that map to genes. However, these approaches may introduce biases in downstream analyses of biological interpretation, because of the variability in gene length. There is a lack of approaches to interpret DNA methylation effectively. Therefore, we have developed computational models to provide biological interpretation of relevant gene sets using DNA methylation data in the context of The Cancer Genome Atlas. Results We illustrate that Biological interpretation of DNA Methylation (BioMethyl) utilizes the complete DNA methylation data for a given cancer type to reflect corresponding gene expression profiles and performs pathway enrichment analyses, providing unique biological insight. Using breast cancer as an example, BioMethyl shows high consistency in the identification of enriched biological pathways from DNA methylation data compared to the results calculated from RNA sequencing data. We find that 12 out of 14 pathways identified by BioMethyl are shared with those by using RNA-seq data, with a Jaccard score 0.8 for estrogen receptor (ER) positive samples. For ER negative samples, three pathways are shared in the two enrichments with a slight lower similarity (Jaccard score = 0.6). Using BioMethyl, we can successfully identify those hidden biological pathways in DNA methylation data when gene expression profile is lacking. Availability and implementation BioMethyl R package is freely available in the GitHub repository (https://github.com/yuewangpanda/BioMethyl). Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yue Wang
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA
| | - Jennifer M Franks
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Michael L Whitfield
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA
| | - Chao Cheng
- Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.,Department of Biomedical Data Science, Geisel School of Medicine at Dartmouth, Lebanon, NH, USA.,Norris Cotton Cancer Center, Lebanon, NH, USA.,Department of Medicine, Baylor College of Medicine, Houston, TX, USA
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Omony J, Nussbaumer T, Gutzat R. DNA methylation analysis in plants: review of computational tools and future perspectives. Brief Bioinform 2020; 21:906-918. [PMID: 31220217 DOI: 10.1093/bib/bbz039] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 02/28/2019] [Accepted: 03/12/2019] [Indexed: 12/12/2022] Open
Abstract
Genome-wide DNA methylation studies have quickly expanded due to advances in next-generation sequencing techniques along with a wealth of computational tools to analyze the data. Most of our knowledge about DNA methylation profiles, epigenetic heritability and the function of DNA methylation in plants derives from the model species Arabidopsis thaliana. There are increasingly many studies on DNA methylation in plants-uncovering methylation profiles and explaining variations in different plant tissues. Additionally, DNA methylation comparisons of different plant tissue types and dynamics during development processes are only slowly emerging but are crucial for understanding developmental and regulatory decisions. Translating this knowledge from plant model species to commercial crops could allow the establishment of new varieties with increased stress resilience and improved yield. In this review, we provide an overview of the most commonly applied bioinformatics tools for the analysis of DNA methylation data (particularly bisulfite sequencing data). The performances of a selection of the tools are analyzed for computational time and agreement in predicted methylated sites for A. thaliana, which has a smaller genome compared to the hexaploid bread wheat. The performance of the tools was benchmarked on five plant genomes. We give examples of applications of DNA methylation data analysis in crops (with a focus on cereals) and an outlook for future developments for DNA methylation status manipulations and data integration.
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Affiliation(s)
- Jimmy Omony
- Plant Genome and Systems Biology, Helmholtz Center Munich-German Research Center for Environmental Health, Neuherberg, Germany
| | - Thomas Nussbaumer
- Institute of Network Biology, Department of Environmental Science, Helmholtz Center Munich, Neuherberg, Germany.,Institute of Environmental Medicine, UNIKA-T, Technical University of Munich and Helmholtz Center Munich, Research Center for Environmental Health, Augsburg, Germany; CK CARE Christine Kühne Center for Allergy Research and Education, Davos, Switzerland
| | - Ruben Gutzat
- Gregor Mendel Institute of Molecular Plant Biology, Austrian Academy of Sciences, Vienna BioCenter (VBC), Vienna, Austria
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Complex Network Characterization Using Graph Theory and Fractal Geometry: The Case Study of Lung Cancer DNA Sequences. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10093037] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
This paper discusses an approach developed for exploiting the local elementary movements of evolution to study complex networks in terms of shared common embedding and, consequently, shared fractal properties. This approach can be useful for the analysis of lung cancer DNA sequences and their properties by using the concepts of graph theory and fractal geometry. The proposed method advances a renewed consideration of network complexity both on local and global scales. Several researchers have illustrated the advantages of fractal mathematics, as well as its applicability to lung cancer research. Nevertheless, many researchers and clinicians continue to be unaware of its potential. Therefore, this paper aims to examine the underlying assumptions of fractals and analyze the fractal dimension and related measurements for possible application to complex networks and, especially, to the lung cancer network. The strict relationship between the lung cancer network properties and the fractal dimension is proved. Results show that the fractal dimension decreases in the lung cancer network while the topological properties of the network increase in the lung cancer network. Finally, statistical and topological significance between the complexity of the network and lung cancer network is shown.
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Amenyah SD, McMahon A, Ward M, Deane J, McNulty H, Hughes CF, Strain JJ, Horigan G, Purvis J, Walsh CP, Lees-Murdock DJ. Riboflavin supplementation alters global and gene-specific DNA methylation in adults with the MTHFR 677 TT genotype. Biochimie 2020; 173:17-26. [PMID: 32334045 DOI: 10.1016/j.biochi.2020.04.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Revised: 04/03/2020] [Accepted: 04/10/2020] [Indexed: 12/12/2022]
Abstract
DNA methylation is important in regulating gene expression and genomic stability while aberrant DNA methylation is associated with disease. Riboflavin (FAD) is a cofactor for methylenetetrahydrofolate reductase (MTHFR), a critical enzyme in folate recycling, which generates methyl groups for homocysteine remethylation to methionine, the pre-cursor to the universal methyl donor S-adenosylmethionine (SAM). A polymorphism (C677T) in MTHFR results in decreased MTHFR activity and increased homocysteine concentration. Previous studies demonstrated that riboflavin modulates this phenotype in homozygous adults (MTHFR 677 TT genotype), however, DNA methylation was not considered. This study examined DNA methylation, globally and at key MTHFR regulatory sites, in adults stratified by MTHFR genotype and the effect of riboflavin supplementation on DNA methylation in individuals with the 677 TT genotype. Samples were accessed from participants, screened for the MTHFR C677T polymorphism, who participated in observational (n = 80) and targeted riboflavin (1.6 mg/day) RCTs (n = 80). DNA methylation at LINE-1 and key regulatory regions of the MTHFR locus were analysed by pyrosequencing in peripheral blood leukocytes. LINE-1 (+1.6%; p = 0.011) and MTHFR south shelf (+4.7%, p < 0.001) were significantly hypermethylated in individuals with the MTHFR 677 TT compared to CC genotype. Riboflavin supplementation resulted in decreased global methylation, albeit only significant at one CpG. A significant reduction in DNA methylation at the MTHFR north shore (-1.2%, p < 0.001) was also observed in TT adults following intervention with riboflavin. This provides the first RCT evidence that DNA methylation may be modulated by riboflavin in adults with the MTHFR 677 TT genotype.
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Affiliation(s)
- Sophia D Amenyah
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, United Kingdom; Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Amy McMahon
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Mary Ward
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Jennifer Deane
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Helene McNulty
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Catherine F Hughes
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - J J Strain
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Geraldine Horigan
- Nutrition Innovation Centre for Food and Health (NICHE), Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - John Purvis
- Department of Cardiology, Altnagelvin Area Hospital, Londonderry, Northern Ireland, United Kingdom
| | - Colum P Walsh
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, United Kingdom
| | - Diane J Lees-Murdock
- Genomic Medicine Research Group, Ulster University, Coleraine, Northern Ireland, United Kingdom.
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35
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Singh A, Gupta S, Badarukhiya JA, Sachan M. Detection of aberrant methylation of HOXA9 and HIC1 through multiplex MethyLight assay in serum DNA for the early detection of epithelial ovarian cancer. Int J Cancer 2020; 147:1740-1752. [PMID: 32191343 DOI: 10.1002/ijc.32984] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Revised: 02/22/2020] [Accepted: 03/05/2020] [Indexed: 02/06/2023]
Abstract
Accumulated evidence revealed that aberrant CpG island hypermethylation plays an important role in carcinogenesis which can serve as a promising target for molecular detection in body fluids. Despite a myriad of attempts to diagnose ovarian cancer (OC) at an early stage, this clinical aim remains a major challenge. To date, no single biomarker is able to accurately detect early OC in either tissue or body fluid. Aberrant DNA methylation patterns in circulating DNA provide highly specific cancer signals. In our study, we establish a novel panel of methylation-specific genes for the development of a TaqMan based qPCR assay to quantify methylation levels. We analyzed promoter methylation of homeobox A9 (HOXA9) and hypermethylated in cancer 1 (HIC1) quantitatively in 120 tissue samples and in 70 matched serum cell-free DNA (CFDNA) of cancerous and noncancerous samples by MethyLight assay. HOXA9 and HIC1 methylation occurred in 82.3 and 80.0% of OC tissue samples in singleplex assay, thereby confirming that methylation was highly cancer-specific. When either or both gene promoter showed methylation, the sensitivity was 88.2% with a specificity of 88.6% in tissue samples. The combined sensitivity for this novel marker panel in serum CFDNA was 88.9% (area under the curve [AUC] = 0.95). In contrast, no hypermethylation was observed in serum from matched cancer-free control women. Our results confirm the elevated performance of novel epigenetic marker panel (HOXA9 and HIC1) when analyzed in tissue and matched serum samples. Our findings reveal the potential of this biomarker panel as a suitable diagnostic serum biomarker for early screening of OC.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | | | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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Hossan T, Kundu S, Alam SS, Nagarajan S. Epigenetic Modifications Associated with the Pathogenesis of Type 2 Diabetes Mellitus. Endocr Metab Immune Disord Drug Targets 2020; 19:775-786. [PMID: 30827271 DOI: 10.2174/1871530319666190301145545] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 12/10/2018] [Accepted: 12/28/2018] [Indexed: 12/26/2022]
Abstract
BACKGROUND AND OBJECTIVE Type 2 diabetes mellitus (T2DM) is a multifactorial metabolic disorder. Pancreatic β-cell dysfunction and insulin resistance are the most common and crucial events of T2DM. Increasing evidence suggests the association of epigenetic modifications with the pathogenesis of T2DM through the changes in important biological processes including pancreatic β- cell differentiation, development and maintenance of normal β-cell function. Insulin sensitivity by the peripheral glucose uptake tissues is also changed by the altered epigenetic mechanisms. In this review, we discussed the major epigenetic alterations and their effects on β-cell function, insulin secretion and insulin resistance in context of T2DM. METHODS We investigated the presently available epigenetic modifications including DNA methylation, posttranslational histone modifications, ATP-dependent chromatin remodeling and non-coding RNAs related to the pathogenesis of T2DM. Published literatures on this topic were searched both on Google Scholar and Pubmed with related keywords and investigated for relevant information. RESULTS The epigenetic modifications introduce changes in gene expression which are essential for appropriate β-cell development and functions, insulin secretion and sensitivity resulting in the pathogenesis of T2DM. Interestingly, T2DM could also be a prominent reason for the mentioned epigenetic alterations. CONCLUSION This review article emphasized on the epigenetic modifications associated with T2DM and discussed the consequences in deterioration of the disease condition.
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Affiliation(s)
- Tareq Hossan
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Shoumik Kundu
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sayeda Sadia Alam
- Department of Biochemistry and Molecular Biology, Jahangirnagar University, Savar, Dhaka-1342, Bangladesh
| | - Sankari Nagarajan
- Cancer Research UK Cambridge Institute (CRUK-CI), University of Cambridge, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, United Kingdom
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Faulk C, Mueller KR, Cheishvili D, Colwell M, Pepin AS, Syzf M, Hering BJ, Burlak C. Epigenetic biomarkers indicate islet cell death in xenotransplantation. Xenotransplantation 2020; 27:e12570. [PMID: 31984530 DOI: 10.1111/xen.12570] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 11/04/2019] [Accepted: 11/06/2019] [Indexed: 12/26/2022]
Abstract
BACKGROUND Xenotransplantation of porcine islets has emerged in recent decades as a potential treatment for type 1 diabetes (T1D). Current methods of detection, indicative of successful engraftment, occur downstream of actual islet death. Epigenetic biomarkers can be detected in circulating cell-free DNA (cfDNA) to provide an earlier indication of graft dysfunction. AIMS The present study identified a biomarker of islet death using differential methylation of the insulin gene, INS, originating from β-cells in porcine islets. MATERIALS & METHODS Pyrosequencing primers specific for porcine INS were designed to quantify hypomethylation along 12 cysteine-guanine dinucleotide (CpG) sites, including three sites in the cyclic adenosine monophosphate (cAMP) response element (CRE) binding protein 2 (CRE2) binding region of the 5' untranslated region (UTR) and nine sites within intron 2. RESULTS PCR amplification of bisulfite-converted DNA combined with pyrosequencing data support the conclusion that hypomethylated porcine INS is specific to islet origin. CONCLUSION Moreover, the results of this study indicate a highly specific epigenetic biomarker, capable of detecting a single islet, supporting the measurement of cfDNA as a biomarker for transplanted islet death. Defining the epigenetic characteristics of porcine-derived islets within cfDNA will be crucial to develop a better understanding of graft survival immunology for transplantation.
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Affiliation(s)
- Christopher Faulk
- Department of Animal Sciences, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Kate R Mueller
- Department of Surgery, Schulze Diabetes Institute, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - David Cheishvili
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Mathia Colwell
- Department of Animal Sciences, College of Food, Agricultural and Natural Resource Sciences, University of Minnesota, Saint Paul, MN, USA
| | - Anne-Sophie Pepin
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Moshe Syzf
- Department of Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada
| | - Bernhard J Hering
- Department of Surgery, Schulze Diabetes Institute, School of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Christopher Burlak
- Department of Surgery, Schulze Diabetes Institute, School of Medicine, University of Minnesota, Minneapolis, MN, USA
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Wang Y, Wang T, Xu M, Yu H, Ding C, Wang Z, Pan X, Li Y, Niu Y, Yan R, Song J, Yan H, Dai Y, Sun Z, Su W, Duan H. Independent effect of main components in particulate matter on DNA methylation and DNA methyltransferase: A molecular epidemiology study. ENVIRONMENT INTERNATIONAL 2020; 134:105296. [PMID: 31759273 DOI: 10.1016/j.envint.2019.105296] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 10/09/2019] [Accepted: 10/28/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND There is a paucity of mechanistic information on the DNA methylation and particulate matter (PM) exposure. This study aimed to investigate the association of PM and its component with DNA methylation, and the roles of DNA methyltransferase (DNMTs). METHODS There were 240 high-exposed, 318 low-exposed and 210 non-exposed participants in this study. Individual concentrations of PM, polycyclic aromatic hydrocarbons (PAHs) and metals were identified by the monitoring data in their workplaces. Urinary 1-OHP and metals were determined as exposure markers. The global DNA methylation (% 5mC) and the mRNA expression of DNMT1, DNMT3A and DNMT3B were measured. We used mediation analysis to evaluate the role of DNMTs expression on DNA methylation alteration induced by PAHs and metals components. RESULTS The decreasing trend of % 5mC was associated with increment of PM exposure in all subjects. We found that one IQR increase in total PAHs (3.82 μg/m3) and urinary 1-OHP (1.06 μmol/mol creatinine) were associated with a separate 6.08% and 7.26% decrease in % 5mC (P = 0.009, P < 0.001), and one IQR increase in urinary Ni (27.75 μmol/mol creatinine) was associated with a 3.29% decrease in % 5mC (P = 0.03). The interaction of urinary 1-OHP with Ni on global DNA methylation (%5mC) was not found (P interaction = 0.89). PM exposure was significantly associated with decreased mRNA level of DNMT3B, but the mediated effect of the PAHs and Ni levels on % 5mC through the DNMT3B pathway was not observed. CONCLUSIONS We found the decrement of global DNA methylation and DNMT3B expression with elevated PM levels in population. The independent mode of action on DNA hypomethylation was found from PAHs and metal components. Global DNA hypomethylation might be a potential biomarker for evaluation of adverse health effects in response to PM exposure.
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Affiliation(s)
- Yanhua Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ting Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Mengmeng Xu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China; School of Public Health, Shandong University, Jinan, China
| | - Haitao Yu
- Laigang Hospital Affiliated to Taishan Medical University, Laiwu, China
| | - Chunguang Ding
- National Center for Occupational Safety and Health, National Health Commission of the People's Republic of China, Beijing, China
| | - Zhenjie Wang
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xingfu Pan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yanbo Li
- School of Public Health, Capital Medical University, Beijing, China
| | - Yong Niu
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ruixue Yan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiayang Song
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Huifang Yan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yufei Dai
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhiwei Sun
- School of Public Health, Capital Medical University, Beijing, China
| | - Wenge Su
- Laigang Hospital Affiliated to Taishan Medical University, Laiwu, China
| | - Huawei Duan
- Key Laboratory of Chemical Safety and Health, National Institute for Occupational Health and Poison Control, Chinese Center for Disease Control and Prevention, Beijing, China.
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Leija-Martínez JJ, Huang F, Del-Río-Navarro BE, Sanchéz-Muñoz F, Romero-Nava R, Muñoz-Hernandez O, Rodríguez-Cortés O, Hall-Mondragon MS. Decreased methylation profiles in the TNFA gene promoters in type 1 macrophages and in the IL17A and RORC gene promoters in Th17 lymphocytes have a causal association with non-atopic asthma caused by obesity: A hypothesis. Med Hypotheses 2019; 134:109527. [PMID: 31877441 DOI: 10.1016/j.mehy.2019.109527] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 12/09/2019] [Indexed: 12/18/2022]
Abstract
Obesity is a serious public health problem worldwide and has been associated in epidemiological studies with a unique type of non-atopic asthma, although the causal association of asthma and obesity has certain criteria, such as the strength of association, consistency, specificity, temporality, biological gradient, coherence, analogy and experimentation; nevertheless, the biological plausibility of this association remains uncertain. Various mechanisms have been postulated, such as immunological, hormonal, mechanical, environmental, genetic and epigenetic mechanisms. Our hypothesis favours immunological mechanisms because some cytokines, such as tumour necrosis factor alpha (TNF-α) and interleukin (IL)-17A, are responsible for orchestrating low-grade systemic inflammation associated with obesity; however, these cytokines are regulated by epigenetic mechanisms, such as gene promoter methylation.
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Affiliation(s)
- José J Leija-Martínez
- Universidad Nacional Autónoma de México, Mexico City, Mexico; Hospital Infantil de Mexico Federico Gómez, Research Laboratory of Pharmacology, Mexico City, Mexico
| | - Fengyang Huang
- Universidad Nacional Autónoma de México, Mexico City, Mexico; Hospital Infantil de Mexico Federico Gómez, Research Laboratory of Pharmacology, Mexico City, Mexico.
| | - Blanca E Del-Río-Navarro
- Universidad Nacional Autónoma de México, Mexico City, Mexico; Hospital Infantil de México Federico Gómez, Department of Pediatric Allergy Clinical Immunology, Mexico City, Mexico
| | - Fausto Sanchéz-Muñoz
- Universidad Nacional Autónoma de México, Mexico City, Mexico; Departamento de Inmunología, Instituto Nacional de Cardiología "Ignacio Chávez", Mexico City, Mexico
| | - Rodrigo Romero-Nava
- Hospital Infantil de Mexico Federico Gómez, Research Laboratory of Pharmacology, Mexico City, Mexico; Laboratory of Pharmacology, Department of Health Sciences, Division of Health and Biological Sciences, Metropolitan Autonomous University of Iztapalapa, Mexico City, Mexico
| | | | - Octavio Rodríguez-Cortés
- Laboratorio 103, SEPI, Escuela Superior de Medicina, Instituto Politécnico Nacional, Calle Plan de San Luis y Díaz Mirón S/N, Casco de Santo Tomas, Miguel Hidalgo, 11340 Ciudad de México, Mexico
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Ben Maamar M, King SE, Nilsson E, Beck D, Skinner MK. Epigenetic transgenerational inheritance of parent-of-origin allelic transmission of outcross pathology and sperm epimutations. Dev Biol 2019; 458:106-119. [PMID: 31682807 PMCID: PMC6987017 DOI: 10.1016/j.ydbio.2019.10.030] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Revised: 09/25/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Epigenetic transgenerational inheritance potentially impacts disease etiology, phenotypic variation, and evolution. An increasing number of environmental factors from nutrition to toxicants have been shown to promote the epigenetic transgenerational inheritance of disease. Previous observations have demonstrated that the agricultural fungicide vinclozolin and pesticide DDT (dichlorodiphenyltrichloroethane) induce transgenerational sperm epimutations involving DNA methylation, ncRNA, and histone modifications or retention. These two environmental toxicants were used to investigate the impacts of parent-of-origin outcross on the epigenetic transgenerational inheritance of disease. Male and female rats were collected from a paternal outcross (POC) or a maternal outcross (MOC) F4 generation control and exposure lineages for pathology and epigenetic analysis. This model allows the parental allelic transmission of disease and epimutations to be investigated. There was increased pathology incidence in the MOC F4 generation male prostate, kidney, obesity, and multiple diseases through a maternal allelic transmission. The POC F4 generation female offspring had increased pathology incidence for kidney, obesity and multiple types of diseases through the paternal allelic transmission. Some disease such as testis or ovarian pathology appear to be transmitted through the combined actions of both male and female alleles. Analysis of the F4 generation sperm epigenomes identified differential DNA methylated regions (DMRs) in a genome-wide analysis. Observations demonstrate that DDT and vinclozolin have the potential to promote the epigenetic transgenerational inheritance of disease and sperm epimutations to the outcross F4 generation in a sex specific and exposure specific manner. The parent-of-origin allelic transmission observed appears similar to the process involved with imprinted-like genes.
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Affiliation(s)
- Millissia Ben Maamar
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Stephanie E King
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Eric Nilsson
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Daniel Beck
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA
| | - Michael K Skinner
- Center for Reproductive Biology, School of Biological Sciences, Washington State University, Pullman, WA, 99164-4236, USA.
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Rekawiecki R, Kisielewska K, Kowalik MK, Kotwica J. Methylation of progesterone receptor isoform A and B promoters in the reproductive system of cows. Reprod Fertil Dev 2019; 30:1634-1642. [PMID: 29898817 DOI: 10.1071/rd17518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 05/05/2018] [Indexed: 01/22/2023] Open
Abstract
The aim of this study was to investigate whether the promoters of progesterone receptor isoform A (PGRA) and B (PGRB) are methylated and to determine the percentage of methylation occurring for each isoform. Genomic DNA was isolated from the corpora lutea (CL) and endometrial slices from cows on Days 2-5, 6-10, 11-16 and 17-20 of the oestrous cycle. DNA was bisulphite-converted and amplified using methyl-specific polymerase chain reaction (PCR) with primers that detect both methylated and unmethylated sequences. The determination of the percentage of the methylation was performed using HpaII and MspI restriction enzymes. Methyl-specific PCR showed partial methylation of PGRA and PGRB promoters in the CL and endometrium during the oestrous cycle. Methylation for PGRA was between 15 and 17% and for PGRB was in the range of 6 to 7.7% during the oestrous cycle in the CL. In the endometrium, the methylation for PGRA was between 6 and 7.3% and for PGRB was between 3 and 4.8% during the oestrous cycle. The data obtained indicate that the higher promoter methylation of the PGRA isoform could be a mechanism for regulation of PGRA inhibitory activity against PGRB and, in this way, methylation may influence the regulation of progesterone action in the CL and endometrium.
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Affiliation(s)
- Robert Rekawiecki
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Katarzyna Kisielewska
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Magdalena K Kowalik
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
| | - Jan Kotwica
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, 10-748 Olsztyn, Poland
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Singh A, Gupta S, Sachan M. Epigenetic Biomarkers in the Management of Ovarian Cancer: Current Prospectives. Front Cell Dev Biol 2019; 7:182. [PMID: 31608277 PMCID: PMC6761254 DOI: 10.3389/fcell.2019.00182] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 08/19/2019] [Indexed: 12/15/2022] Open
Abstract
Ovarian cancer (OC) causes significant morbidity and mortality as neither detection nor screening of OC is currently feasible at an early stage. Difficulty to promptly diagnose OC in its early stage remains challenging due to non-specific symptoms in the early-stage of the disease, their presentation at an advanced stage and poor survival. Therefore, improved detection methods are urgently needed. In this article, we summarize the potential clinical utility of epigenetic signatures like DNA methylation, histone modifications, and microRNA dysregulation, which play important role in ovarian carcinogenesis and discuss its application in development of diagnostic, prognostic, and predictive biomarkers. Molecular characterization of epigenetic modification (methylation) in circulating cell free tumor DNA in body fluids offers novel, non-invasive approach for identification of potential promising cancer biomarkers, which can be performed at multiple time points and probably better reflects the prevailing molecular profile of cancer. Current status of epigenetic research in diagnosis of early OC and its management are discussed here with main focus on potential diagnostic biomarkers in tissue and body fluids. Rapid and point of care diagnostic applications of DNA methylation in liquid biopsy has been precluded as a result of cumbersome sample preparation with complicated conventional methods of isolation. New technologies which allow rapid identification of methylation signatures directly from blood will facilitate sample-to answer solutions thereby enabling next-generation point of care molecular diagnostics. To date, not a single epigenetic biomarker which could accurately detect ovarian cancer at an early stage in either tissue or body fluid has been reported. Taken together, the methodological drawbacks, heterogeneity associated with ovarian cancer and non-validation of the clinical utility of reported potential biomarkers in larger ovarian cancer populations has impeded the transition of epigenetic biomarkers from lab to clinical settings. Until addressed, clinical implementation as a diagnostic measure is a far way to go.
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Affiliation(s)
- Alka Singh
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
| | - Sameer Gupta
- Department of Surgical Oncology, King George Medical University, Lucknow, India
| | - Manisha Sachan
- Department of Biotechnology, Motilal Nehru National Institute of Technology, Allahabad, India
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Elmallah MIY, Micheau O. Epigenetic Regulation of TRAIL Signaling: Implication for Cancer Therapy. Cancers (Basel) 2019; 11:cancers11060850. [PMID: 31248188 PMCID: PMC6627638 DOI: 10.3390/cancers11060850] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/11/2019] [Accepted: 06/18/2019] [Indexed: 12/20/2022] Open
Abstract
One of the main characteristics of carcinogenesis relies on genetic alterations in DNA and epigenetic changes in histone and non-histone proteins. At the chromatin level, gene expression is tightly controlled by DNA methyl transferases, histone acetyltransferases (HATs), histone deacetylases (HDACs), and acetyl-binding proteins. In particular, the expression level and function of several tumor suppressor genes, or oncogenes such as c-Myc, p53 or TRAIL, have been found to be regulated by acetylation. For example, HATs are a group of enzymes, which are responsible for the acetylation of histone proteins, resulting in chromatin relaxation and transcriptional activation, whereas HDACs by deacetylating histones lead to chromatin compaction and the subsequent transcriptional repression of tumor suppressor genes. Direct acetylation of suppressor genes or oncogenes can affect their stability or function. Histone deacetylase inhibitors (HDACi) have thus been developed as a promising therapeutic target in oncology. While these inhibitors display anticancer properties in preclinical models, and despite the fact that some of them have been approved by the FDA, HDACi still have limited therapeutic efficacy in clinical terms. Nonetheless, combined with a wide range of structurally and functionally diverse chemical compounds or immune therapies, HDACi have been reported to work in synergy to induce tumor regression. In this review, the role of HDACs in cancer etiology and recent advances in the development of HDACi will be presented and put into perspective as potential drugs synergizing with TRAIL's pro-apoptotic potential.
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Affiliation(s)
- Mohammed I Y Elmallah
- INSERM, Université Bourgogne Franche-Comté, LNC UMR1231, F-21079 Dijon, France.
- Chemistry Department, Faculty of Science, Helwan University, Ain Helwan 11795 Cairo, Egypt.
| | - Olivier Micheau
- INSERM, Université Bourgogne Franche-Comté, LNC UMR1231, F-21079 Dijon, France.
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Patnaik S, Anupriya. Drugs Targeting Epigenetic Modifications and Plausible Therapeutic Strategies Against Colorectal Cancer. Front Pharmacol 2019; 10:588. [PMID: 31244652 PMCID: PMC6563763 DOI: 10.3389/fphar.2019.00588] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 05/08/2019] [Indexed: 12/14/2022] Open
Abstract
Genetic variations along with epigenetic modifications of DNA are involved in colorectal cancer (CRC) development and progression. CRC is the fourth leading cause of cancer-related deaths worldwide. Initiation and progression of CRC is the cumulation of a variety of genetic and epigenetic changes in colonic epithelial cells. Colorectal carcinogenesis is associated with epigenetic aberrations including DNA methylation, histone modifications, chromatin remodeling, and non-coding RNAs. Recently, epigenetic modifications have been identified like association of hypermethylated gene Claudin11 (CLDN11) with metastasis and prognosis of poor survival of CRC. DNA methylation of genes CMTM3, SSTR2, MDF1, NDRG4 and TGFB2 are potential epigenetic biomarkers for the early detection of CRC. Tumor suppressor candidate 3 (TUSC3) mRNA expression is silenced by promoter methylation, which promotes epidermal growth factor receptor (EGFR) signaling and rescues the CRC cells from apoptosis and hence leading to poor survival rate. Previous scientific evidences strongly suggest epigenetic modifications that contribute to anticancer drug resistance. Recent research studies emphasize development of drugs targeting histone deacetylases (HDACs) and DNA methyltransferase inhibitors as an emerging anticancer strategy. This review covers potential epigenetic modification targeting chemotherapeutic drugs and probable implementation for the treatment of CRC, which offers a strong rationale to explore therapeutic strategies and provides a basis to develop potent antitumor drugs.
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Affiliation(s)
| | - Anupriya
- School of Biotechnology, KIIT University, Bhubaneswar, India
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Zeng H, He B, Yi C. Compilation of Modern Technologies To Map Genome-Wide Cytosine Modifications in DNA. Chembiochem 2019; 20:1898-1905. [PMID: 30809902 DOI: 10.1002/cbic.201900035] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Indexed: 12/19/2022]
Abstract
Over the past few decades, various DNA modification detection methods have been developed; many of the high-resolution methods are based on bisulfite treatment, which leads to DNA degradation, to a degree. Thus, novel bisulfite-free approaches have been developed in recent years and shown to be useful for epigenome analysis in otherwise difficult-to-handle, but important, DNA samples, such as hmC-seal and hmC-CATCH. Herein, an overview of advances in the development of epigenome sequencing methods for these important DNA modifications is provided.
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Affiliation(s)
- Hu Zeng
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Bo He
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
| | - Chengqi Yi
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Department of Chemical Biology and, Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering and, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, 100871, P. R. China
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Wang L, Sun HZ, Guan LL, Liu JX. Short communication: Relationship of blood DNA methylation rate and milk performance in dairy cows. J Dairy Sci 2019; 102:5208-5211. [PMID: 30981478 DOI: 10.3168/jds.2018-15869] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 02/15/2019] [Indexed: 12/18/2022]
Abstract
The objective of this study was to investigate the global methylation rate in blood DNA and its relationship with lactation performance. A total of 196 mid-lactation dairy cows were fed the same diet under the same management. Milk yield was recorded and blood samples were collected from the jugular vein before morning feeding. The blood global DNA methylation rates were quantified using a methylation quantification kit. Overall, the average blood global DNA methylation rate of all cows was 12.4%. When DNA methylation rates were compared between cows with high (n = 40; 37.0 to 42.0 kg/d) and low (n = 33; 24.0 to 30.0 kg/d) milk yield, DNA methylation rates in the lower-yield cows (14.1 ± 0.7%) were significantly higher than those in the higher-yield animals (11.6 ± 0.7%). Our results indicated an association of milk and protein yields with global DNA methylation rates in lactating dairy cows. However, further research is needed to determine whether this association reflects the true influence of epigenetic mechanisms on yield or whether other factors, such as different proportions of blood cell types in high- and low-yielding cows, affect apparent global DNA methylation levels.
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Affiliation(s)
- L Wang
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, P. R. China
| | - H Z Sun
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, T6G 2P5, Canada
| | - L L Guan
- Department of Agricultural, Food & Nutritional Science, University of Alberta, Edmonton, T6G 2P5, Canada.
| | - J X Liu
- Institute of Dairy Science, MoE Key Laboratory of Molecular Animal Nutrition, College of Animal Sciences, Zhejiang University, Hangzhou 310058, P. R. China.
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Collin LJ, McCullough LE, Conway K, White AJ, Xu X, Cho YH, Shantakumar S, Teitelbaum SL, Neugut AI, Santella RM, Chen J, Gammon MD. Reproductive characteristics modify the association between global DNA methylation and breast cancer risk in a population-based sample of women. PLoS One 2019; 14:e0210884. [PMID: 30763347 PMCID: PMC6375664 DOI: 10.1371/journal.pone.0210884] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 01/03/2019] [Indexed: 12/29/2022] Open
Abstract
DNA methylation has been implicated in breast cancer aetiology, but little is known about whether reproductive history and DNA methylation interact to influence carcinogenesis. This study examined modification of the association between global DNA methylation and breast cancer risk by reproductive characteristics. A population-based case-control study assessed reproductive history in an interviewer-administered questionnaire. Global DNA methylation was measured from white blood cell DNA using luminometric methylation assay (LUMA) and pyrosequencing assay (long interspersed elements-1 (LINE-1). We estimated adjusted odds ratios (ORs) and 95% confidence intervals (CIs) among 1 070 breast cancer cases and 1 110 population-based controls. Effect modification was assessed on additive and multiplicative scales. LUMA methylation was associated with elevated breast cancer risk across all strata (comparing the highest to the lowest quartile), but estimates were higher among women with age at menarche ≤12 years (OR = 2.87, 95%CI = 1.96–4.21) compared to >12 years (OR = 1.66, 95%CI = 1.20–2.29). We observed a 2-fold increase in the LUMA methylation-breast cancer association among women with age at first birth >23 years (OR = 2.62, 95%CI = 1.90–3.62) versus ≤23 years (OR = 1.32, 95% CI = 0.84–2.05). No modification was evident for parity or lactation. Age at menarche and age at first birth may be modifiers of the association between global DNA methylation and breast cancer risk.
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Affiliation(s)
- Lindsay J. Collin
- Department of Epidemiology, Emory University, Atlanta, GA, United States of America
- * E-mail:
| | - Lauren E. McCullough
- Department of Epidemiology, Emory University, Atlanta, GA, United States of America
| | - Kathleen Conway
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
| | - Alexandra J. White
- Epidemiology Branch, National Institute of Environmental Health Science, Research Triangle Park, NC, United States of America
| | - Xinran Xu
- Roche Product Development in Asia-Pacific, Shanghai, China
| | - Yoon Hee Cho
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, MT, United States of America
| | | | - Susan L. Teitelbaum
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Alfred I. Neugut
- Department of Epidemiology, Columbia University, New York, NY,United States of America
- Department of Medicine, Columbia University, New York, NY, United States of America
| | - Regina M. Santella
- Department of Environmental Health, Columbia University, New York, NY, United States of America
| | - Jia Chen
- Department of Preventive Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Pediatrics, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
- Department of Oncological Science, Icahn School of Medicine at Mount Sinai, New York, NY, United States of America
| | - Marilie D. Gammon
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, United States of America
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Bhattacharjee R, Moriam S, Umer M, Nguyen NT, Shiddiky MJA. DNA methylation detection: recent developments in bisulfite free electrochemical and optical approaches. Analyst 2018; 143:4802-4818. [PMID: 30226502 DOI: 10.1039/c8an01348a] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
DNA methylation is one of the significant epigenetic modifications involved in mammalian development as well as in the initiation and progression of various diseases like cancer. Over the past few decades, an enormous amount of research has been carried out for the quantification of DNA methylation in the mammalian genome. Earlier, most of these methodologies used bisulfite treatment. However, the low conversion, false reading, longer assay time and complex chemical reaction are the common limitations of this method that hinder their application in routine clinical screening. Thus, as an alternative to bisulfite conversion-based DNA methylation detection, numerous bisulfite-free methods have been proposed. In this regard, electrochemical biosensors have gained much attention in recent years for being highly sensitive yet cost-effective, portable, and simple to operate. On the other hand, biosensors with optical readouts enable direct real time detection of biological molecules and are easily adaptable to multiplexing. Incorporation of electrochemical and optical readouts into bisulfite free DNA methylation analysis is paving the way for the translation of this important biomarker into standard patient care. In this review, we provide a critical overview of recent advances in the development of electrochemical and optical readout based bisulfite free DNA methylation assays.
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Affiliation(s)
- Ripon Bhattacharjee
- School of Environment and Science, Griffith University, Nathan Campus, Nathan, QLD 4111, Australia.
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Mitsiogianni M, Amery T, Franco R, Zoumpourlis V, Pappa A, Panayiotidis MI. From chemo-prevention to epigenetic regulation: The role of isothiocyanates in skin cancer prevention. Pharmacol Ther 2018; 190:187-201. [DOI: 10.1016/j.pharmthera.2018.06.001] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Investigating the Promoter of FAT10 Gene in HCC Patients. Genes (Basel) 2018; 9:genes9070319. [PMID: 29949944 PMCID: PMC6070910 DOI: 10.3390/genes9070319] [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: 04/04/2018] [Revised: 05/25/2018] [Accepted: 05/25/2018] [Indexed: 12/31/2022] Open
Abstract
FAT10, which is also known as diubiquitin, has been implicated to play important roles in immune regulation and tumorigenesis. Its expression is up-regulated in the tumors of Hepatocellular Carcinoma (HCC) and other cancer patients. High levels of FAT10 in cells have been shown to result in increased mitotic non-disjunction and chromosome instability, leading to tumorigenesis. To evaluate whether the aberrant up-regulation of the FAT10 gene in the tumors of HCC patients is due to mutations or the aberrant methylation of CG dinucleotides at the FAT10 promoter, sequencing and methylation-specific sequencing of the promoter of FAT10 was performed. No mutations were found that could explain the differential expression of FAT10 between the tumor and non-tumorous tissues of HCC patients. However, six single nucleotide polymorphisms (SNPs), including one that has not been previously reported, were identified at the promoter of the FAT10 gene. Different haplotypes of these SNPs were found to significantly mediate different FAT10 promoter activities. Consistent with the experimental observation, differential FAT10 expression in the tumors of HCC patients carrying haplotype 1 was generally higher than those carrying haplotype II. Notably, the methylation status of this promoter was found to correlate with FAT10 expression levels. Hence, the aberrant overexpression of the FAT10 gene in the tumors of HCC patients is likely due to aberrant methylation, rather than mutations at the FAT10 promoter.
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