1
|
Cai J, Zhu Q. New advances in signal amplification strategies for DNA methylation detection in vitro. Talanta 2024; 273:125895. [PMID: 38508130 DOI: 10.1016/j.talanta.2024.125895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
5-methylcytosine (5 mC) DNA methylation is a prominent epigenetic modification ubiquitous in the genome. It plays a critical role in the regulation of gene expression, maintenance of genome stability, and disease control. The potential of 5 mC DNA methylation for disease detection, prognostic information, and prediction of response to therapy is enormous. However, the quantification of DNA methylation from clinical samples remains a considerable challenge due to its low abundance (only 1% of total bases). To overcome this challenge, scientists have recently developed various signal amplification strategies to enhance the sensitivity of DNA methylation biosensors. These strategies include isothermal nucleic acid amplification and enzyme-assisted target cycling amplification, among others. This review summarizes the applications, advantages, and limitations of these signal amplification strategies over the past six years (2018-2023). Our goal is to provide new insights into the selection and establishment of DNA methylation analysis. We hope that this review will offer valuable insights to researchers in the field and facilitate further advancements in this area.
Collapse
Affiliation(s)
- Jiajing Cai
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China.
| | - Qubo Zhu
- Xiangya School of Pharmaceutical Sciences in Central South University, Changsha, Hunan, 410013, China
| |
Collapse
|
2
|
Distinct immunological and molecular signatures underpinning influenza vaccine responsiveness in the elderly. Nat Commun 2022; 13:6894. [PMID: 36371426 PMCID: PMC9653450 DOI: 10.1038/s41467-022-34487-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Seasonal influenza outbreaks, especially in high-risk groups such as the elderly, represent an important public health problem. Prevailing inadequate efficacy of seasonal vaccines is a crucial bottleneck. Understanding the immunological and molecular mechanisms underpinning differential influenza vaccine responsiveness is essential to improve vaccination strategies. Here we show comprehensive characterization of the immune response of randomly selected elderly participants (≥ 65 years), immunized with the adjuvanted influenza vaccine Fluad. In-depth analyses by serology, multi-parametric flow cytometry, multiplex and transcriptome analysis, coupled to bioinformatics and mathematical modelling, reveal distinguishing immunological and molecular features between responders and non-responders defined by vaccine-induced seroconversion. Non-responders are specifically characterized by multiple suppressive immune mechanisms. The generated comprehensive high dimensional dataset enables the identification of putative mechanisms and nodes responsible for vaccine non-responsiveness independently of confounding age-related effects, with the potential to facilitate development of tailored vaccination strategies for the elderly.
Collapse
|
3
|
Protocol to evaluate cell lineage stability of mouse natural and induced regulatory T cells using bisulfite sequencing. STAR Protoc 2022; 3:101694. [PMID: 36121747 PMCID: PMC9489535 DOI: 10.1016/j.xpro.2022.101694] [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: 07/06/2022] [Revised: 07/25/2022] [Accepted: 08/16/2022] [Indexed: 01/25/2023] Open
Abstract
The establishment of regulatory T cells (Treg)-specific demethylation regions (TSDRs) is essential for the Treg-lineage stability. Here, we present a protocol using bisulfite sequencing to assess Treg-lineage stability. The protocol describes the isolation of lymphocytes and DNA extraction, followed by bisulfite conversion in unmethylated CpG DNA, bisulfite PCR and cloning, and sequencing to define the TSDR methylation. This protocol uses lymph nodes and spleen tissues and can be adapted to assess the methylation status of Tregs in other tissue types.
Collapse
|
4
|
Liu Y, Chen S, Pang D, Zhou J, Xu X, Yang S, Huang Z, Yu B. Effects of paternal exposure to cigarette smoke on sperm DNA methylation and long-term metabolic syndrome in offspring. Epigenetics Chromatin 2022; 15:3. [PMID: 35063005 PMCID: PMC8780762 DOI: 10.1186/s13072-022-00437-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 01/06/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Although paternal exposure to cigarette smoke may contribute to obesity and metabolic syndrome in offspring, the underlying mechanisms remain uncertain. METHODS In the present study, we analyzed the sperm DNA-methylation profiles in tobacco-smoking normozoospermic (SN) men, non-tobacco-smoking normozoospermic (N) men, and non-smoking oligoasthenozoospermic (OA) men. Using a mouse model, we also analyzed global methylation and differentially methylated regions (DMRs) of the DLK1 gene in paternal spermatozoa and the livers of progeny. In addition, we quantified DLK1 expression, executed an intra-peritoneal glucose tolerance test (IPGTT), measured serum metabolites, and analyzed liver lipid accumulation in the F1 offspring. RESULTS Global sperm DNA-methylation levels were significantly elevated (p < 0.05) in the SN group, and the methylation patterns were different among N, SN, and OA groups. Importantly, the methylation level of the DLK1 locus (cg11193865) was significantly elevated in the SN group compared to both N and OA groups (p < 0.001). In the mouse model, the group exposed to cigarette smoke extract (CSE) exhibited a significantly higher global methylation DNA level in spermatozoa (p < 0.001) and on the DMR sites of Dlk1 in 10-week-old male offspring (p < 0.05), with a significant increase in Dlk1 expression in their livers (p < 0.001). In addition, IPGTT and LDL levels were significantly altered (p < 0.001), with elevated liver fat accumulation (p < 0.05) in F1 offspring. CONCLUSION Paternal exposure to cigarette smoke led to increased global methylation of sperm DNA and alterations to the DMR of the DLK1 gene in the F1 generation, which may be inherited parentally and may perturb long-term metabolic function.
Collapse
Affiliation(s)
- Yunyun Liu
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Shengzhu Chen
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Dejian Pang
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Jiayi Zhou
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Xiuting Xu
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Si Yang
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China
| | - Zhaofeng Huang
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Bolan Yu
- Department of Obstetrics and Gynecology, BioResource Research Center, Key Laboratory for Major Obstetric Diseases of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, No. 63 Duobao Road, Liwan District, Guangzhou, 510150, Guangdong, China.
| |
Collapse
|
5
|
Wang X, Zhou S, Chu C, Yang M, Huo D, Hou C. Dual Methylation-Sensitive Restriction Endonucleases Coupling with an RPA-Assisted CRISPR/Cas13a System (DESCS) for Highly Sensitive Analysis of DNA Methylation and Its Application for Point-of-Care Detection. ACS Sens 2021; 6:2419-2428. [PMID: 34019391 DOI: 10.1021/acssensors.1c00674] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
High-performance detection of DNA methylation possesses great significance for the diagnosis and therapy of cancer. Herein, for the first time, we present a digestion strategy based on dual methylation-sensitive restriction endonucleases coupling with a recombinase polymerase amplification (RPA)-assisted CRISPR/Cas13a system (DESCS) for accurate and sensitive determination of site-specific DNA methylation. This dual methylation-sensitive restriction endonuclease system selectively digests the unmethylated target but exhibits no response to methylated DNA. Therefore, the intact methylated DNA target triggers the RPA reaction for rapid signal amplification. In contrast, the digested unmethylated target initiates no RPA reaction. RPA products with a T7 promoter can execute the T7 transcription in the presence of T7 RNA polymerase to generate a large number of single-stranded RNA (ssRNA). This ssRNA can be recognized by CRISPR/Cas13a to induce the ssRNase activity of Cas13a, showing the indiscriminate cleavage of the collateral FQ reporter to release the fluorescence signal. With such a design, by combining the unique features of dual methylation-sensitive restriction endonucleases with RPA-assisted CRISPR/Cas13a, the DESCS system not only presents the rapid and powerful signal amplification for the determination of methylated DNA with ultrahigh sensitivity but also effectively eliminates the false positive influences from incomplete digestion of the unmethylated target. More importantly, 0.01% methylation level can be effectively distinguished with the existence of excess unmethylated DNA. In addition, the DESCS assay is integrated into the lateral flow biosensor (LFB) for the point-of-care determination of DNA methylation. In view of the superiorities in high sensitivity, outstanding selectivity, and ease of operation, the DESCS system will provide a reliable assay for site-specific analysis of methylation.
Collapse
Affiliation(s)
- Xianfeng Wang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Shiying Zhou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Chengxiang Chu
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Mei Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, State and Local Joint Engineering Laboratory for Vascular Implants, Bioengineering College of Chongqing University, Chongqing 400044, P. R. China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, P. R. China
| |
Collapse
|
6
|
Li S, Tollefsbol TO. DNA methylation methods: Global DNA methylation and methylomic analyses. Methods 2020; 187:28-43. [PMID: 33039572 DOI: 10.1016/j.ymeth.2020.10.002] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Revised: 10/02/2020] [Accepted: 10/05/2020] [Indexed: 12/13/2022] Open
Abstract
DNA methylation provides a pivotal layer of epigenetic regulation in eukaryotes that has significant involvement for numerous biological processes in health and disease. The function of methylation of cytosine bases in DNA was originally proposed as a "silencing" epigenetic marker and focused on promoter regions of genes for decades. Improved technologies and accumulating studies have been extending our understanding of the roles of DNA methylation to various genomic contexts including gene bodies, repeat sequences and transcriptional start sites. The demand for comprehensively describing DNA methylation patterns spawns a diversity of DNA methylation profiling technologies that target its genomic distribution. These approaches have enabled the measurement of cytosine methylation from specific loci at restricted regions to single-base-pair resolution on a genome-scale level. In this review, we discuss the different DNA methylation analysis technologies primarily based on the initial treatments of DNA samples: bisulfite conversion, endonuclease digestion and affinity enrichment, involving methodology evolution, principles, applications, and their relative merits. This review may offer referable information for the selection of various platforms for genome-wide analysis of DNA methylation.
Collapse
Affiliation(s)
- Shizhao Li
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States.
| | - Trygve O Tollefsbol
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, United States; Nutrition Obesity Research Center, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Center for Healthy Aging, University of Alabama at Birmingham, Birmingham, AL, United States; Comprehensive Diabetes Center, University of Alabama at Birmingham, Birmingham, AL, United States.
| |
Collapse
|
7
|
Bao-Caamano A, Rodriguez-Casanova A, Diaz-Lagares A. Epigenetics of Circulating Tumor Cells in Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1220:117-134. [PMID: 32304083 DOI: 10.1007/978-3-030-35805-1_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid biopsy based on the analysis of circulating tumor cells (CTCs) has emerged as an important field of research. Molecular characterization of CTCs can provide insights into cancer biology and biomarkers for the clinic, representing a non-invasive powerful tool for monitoring breast cancer metastasis and predict the therapeutic response. Epigenetic mechanisms play a key role in the control of gene expression and their alteration contributes to cancer development and progression. These epigenetic modifications in CTCs have been described mainly related to modifications of the DNA methylation pattern and changes in the expression profile of noncoding RNAs. Here we summarize the recent findings on the epigenetic characterization of CTCs in breast cancer and their clinical value as tumor biomarkers, and discuss challenges and opportunities in this field.
Collapse
Affiliation(s)
- Aida Bao-Caamano
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain
| | - Aitor Rodriguez-Casanova
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain.,Roche-Chus Joint Unit, Translational Medical Oncology Group (Oncomet), Health Research Institute of Santiago de Compostela, Santiago de Compostela, Spain
| | - Angel Diaz-Lagares
- Cancer Epigenomics, Translational Medical Oncology (Oncomet), Health Research Institute of Santiago (IDIS), University Clinical Hospital of Santiago (CHUS/SERGAS), Santiago de Compostela, Spain. .,Centro de Investigación Biomédica en Red Cáncer (CIBERONC), Madrid, Spain.
| |
Collapse
|
8
|
Zhang M, Liu L, Cao X, Liu Y, Di J, Huang X, Sun F, Huang W, Xu F. Efficiently accumulating germ-like stem cells from mouse postnatal ovary by in situ tissue culture. Dev Growth Differ 2020; 62:223-231. [PMID: 32189336 DOI: 10.1111/dgd.12656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 01/15/2020] [Accepted: 01/20/2020] [Indexed: 11/27/2022]
Abstract
Although recent studies have revealed that germline stem cells (GSCs) exist in the mouse postnatal ovary, how to efficiently obtain GSCs for regenerating neo-oogenesis is still a technical challenge. Here, we report that using in situ tissue culture we can efficiently accumulate large amounts of proliferating germ-like cells from mouse postnatal ovaries. Usually, more than 10,000 germ-like cells can be derived from one ovary by this method, and over 20% of these cells can grow into germ-like cells with self-renewal, which thus can serve as a good cell pool to isolate GSCs by other cell assorting methods such as FACS. This method is simple and time-saving, which should be useful for in future studies on mouse GSCs.
Collapse
Affiliation(s)
- Meizi Zhang
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Li Liu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Xiaomin Cao
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Ye Liu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Jianyong Di
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| | - Xiuying Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fangzhen Sun
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Weihong Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Fengqin Xu
- Reproductive Medicine Center, Tianjin First Central Hospital, Tianjin, China
| |
Collapse
|
9
|
Burska AN, Thu A, Parmar R, Bzoma I, Samans B, Raschke E, Olek S, Conaghan PG, Emery P, Ponchel F. Quantifying circulating Th17 cells by qPCR: potential as diagnostic biomarker for rheumatoid arthritis. Rheumatology (Oxford) 2019; 58:2015-2024. [PMID: 31081041 DOI: 10.1093/rheumatology/kez162] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/28/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE The diagnosis of RA patients remains a challenge, especially in ACPA-negative disease. Novel T-cell subsets, particularly Th17 may be useful, although data on Th17 frequency using flow cytometry in RA are conflicting. We investigated whether a novel epigenetic qPCR assay for the quantification of Th17 could differentiate patients with RA from those with symptoms evolving towards an alternative diagnosis. METHODS We used a qPCR assay measuring the extent of the methylation at a key position in the IL-17 and CD4 genes. Assays were performed on whole blood from 49 healthy controls (HC) and 165 early arthritis clinic patients. Flow cytometry was further used to detect the expression of CXCR4 on Th17 cells. RESULTS In 75 inflammatory arthritis patients who progressed to RA, the qPCR assays showed significantly fewer Th17 cells compared with 90 patients who did not (P<0.0001). Regression models demonstrated a high predictive value for RA development (75.8% correct prediction), and particularly for the ACPA-negative group (n = 125) where Th17 and swollen joint count (SJC) were the only predictors (73% correct prediction). The chemokine receptor CXCR4 had significantly higher expression on Th17 from early RA patients (n = 11) compared with HC (n = 15). CONCLUSION The results of the epigenetic qPCR assay showed that low levels of Th17 cells were predictive of developing RA, particularly in the ACPA-negative patients. This could have value for insights into pathogenesis and management. The results suggest the recruitment of Th17 to the inflammatory disease site, consistent with high CXCR4 expression.
Collapse
Affiliation(s)
- Agata N Burska
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Aye Thu
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Rekha Parmar
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Izabella Bzoma
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Bjoern Samans
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Eva Raschke
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Sven Olek
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Philip G Conaghan
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Paul Emery
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Frederique Ponchel
- Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, and NIHR Leeds Biomedical Research Centre, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| |
Collapse
|
10
|
Quantitative Methylation-Specific PCR: A Simple Method for Studying Epigenetic Modifications of Cell-Free DNA. Methods Mol Biol 2019; 1909:137-162. [PMID: 30580429 DOI: 10.1007/978-1-4939-8973-7_11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Aberrant DNA methylation of cell-free circulating DNA (cfDNA) has recently gained attention for its use as biomarker in cancer diagnosis, prognosis, and prediction of therapeutic response. Quantification of cfDNA methylation levels requires methods with high sensitivity and specificity due to low amounts of cfDNA available in plasma, high degradation of cfDNA, and/or contamination with genomic DNA. To date, several approaches for measuring cfDNA methylation have been established, including quantitative methylation-specific PCR (qMSP), which represents a simple, fast, and cost-effective technique that can be easily implemented into clinical practice. In this chapter, we provide a detailed protocol for SYBR Green qMSP analysis which is currently used in our laboratory for cfDNA methylation detection. Useful information regarding successful qMSP primers design are also provided.
Collapse
|
11
|
Dong D, Zhang L, Bai C, Ma N, Ji W, Jia L, Zhang A, Zhang P, Ren L, Zhou Y. UNC5D, suppressed by promoter hypermethylation, inhibits cell metastasis by activating death-associated protein kinase 1 in prostate cancer. Cancer Sci 2019; 110:1244-1255. [PMID: 30632669 PMCID: PMC6447834 DOI: 10.1111/cas.13935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2018] [Revised: 12/22/2018] [Accepted: 12/27/2018] [Indexed: 01/19/2023] Open
Abstract
Prostate cancer (PCa) death primarily occurs due to metastasis of the cells, but little is known about the underlying molecular mechanisms. This study aimed to evaluate the expression of UNC5D, a newly identified tumor suppressor gene, analyze its epigenetic alterations, and elucidate its functional relevance to PCa metastasis. Meta‐analysis of publicly available microarray datasets revealed that UNC5D expression was frequently downregulated in PCa tissues and inversely associated with PCa metastasis. These results were verified in clinical specimens by real‐time PCR and immunohistochemistry assays. Through methylation analysis, the downregulated expression of UNC5D in PCa tissues and cell lines was found to be attributable to the hypermethylation of the promoter. A negative correlation was observed between methylation and UNC5D mRNA expression in PCa samples. The ectopic expression of UNC5D in PCa cells effectively reduced their ability to migrate and invade both in vitro and in vivo, and siRNA‐mediated knockdown of UNC5D yielded consistent results. UNC5D can recruit and activate death‐associated protein kinase 1, which remained to be essential for its metastatic suppressor function. In conclusion, these results suggested that UNC5D as a novel putative metastatic suppressor gene that is commonly down‐regulated by hypermethylation in PCa.
Collapse
Affiliation(s)
- Dong Dong
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Lufang Zhang
- Department of Laboratory, Aviation General Hospital, Beijing, China
| | - Changsen Bai
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Na Ma
- Cancer Biobank, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Wei Ji
- Public Laboratory, Key Laboratory of Breast Cancer Prevention and Therapy, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer and Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Li Jia
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Aimin Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Pengyu Zhang
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Li Ren
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| | - Yunli Zhou
- Department of Laboratory, Tianjin Medical University Cancer Institute and Hospital, Tianjin's Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, National Clinical Research Center for Cancer, Tianjin, China
| |
Collapse
|
12
|
|
13
|
Kojima N, Suda T, Kurinomaru T, Kurita R. Immobilization of DNA with nitrogen mustard-biotin conjugate for global epigenetic analysis. Anal Chim Acta 2018; 1043:107-114. [PMID: 30392657 DOI: 10.1016/j.aca.2018.09.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2018] [Revised: 09/03/2018] [Accepted: 09/05/2018] [Indexed: 12/01/2022]
Abstract
We report the quantitative analysis of 5-methylcytosine, a representative epigenetic modification in genomic DNA, with an enzyme-linked immunosorbent assay (ELISA). We synthesized a novel hetero-bifunctional linker molecule consisting of nitrogen mustard and biotin to capture DNA on the surface of biosensing devices. The molecule can successfully immobilize genomic DNA on a streptavidin coated 96-well microplate, which was then employed for immunochemical epigenetic assessment. We achieved the sensitive and quantitative detection of 5-mC in genomic DNA samples. The CpG methylation ratios obtained from our system for mouse brain and mouse small intestine genomes were 79% and 82%, respectively. These numbers are in good agreement with the previously reported methylation ratio of 75-85%, which was identified by whole genome bisulfite sequencing. Accordingly, the present technology using our novel bifunctional linker molecule provides a fast, easy, and inexpensive method for epigenetic assessment, without the need for any conventional bisulfite treatment, polymerase chain reaction (PCR), or sequencing.
Collapse
Affiliation(s)
- Naoshi Kojima
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, DAICENTER, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Tomomi Suda
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, DAICENTER, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan
| | - Takaaki Kurinomaru
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-8-31 Midorigaoka, Ikeda, Osaka, 563-8577, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology (AIST) and DAILAB, DAICENTER, Central 6, 1-1-1 Higashi, Tsukuba, Ibaraki, 305-8566, Japan.
| |
Collapse
|
14
|
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.
Collapse
|
15
|
Sun Y, Sun Y, Tian W, Liu C, Gao K, Li Z. A novel restriction endonuclease GlaI for rapid and highly sensitive detection of DNA methylation coupled with isothermal exponential amplification reaction. Chem Sci 2017; 9:1344-1351. [PMID: 29675182 PMCID: PMC5887237 DOI: 10.1039/c7sc04975g] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Accepted: 12/09/2017] [Indexed: 12/22/2022] Open
Abstract
Sensitive and accurate detection of site-specific DNA methylation is of critical significance for early diagnosis of human diseases, especially cancers. Herein, for the first time we employ a novel methylation-dependent restriction endonuclease GlaI to detect site-specific DNA methylation in a highly specific and sensitive way by coupling with isothermal exponential amplification reaction (EXPAR). GlaI can only cut the methylated target site with excellent selectivity but leave the unmethylated DNA intact. Then the newly exposed end fragments of methylated DNA can trigger EXPAR for highly efficient signal amplification while the intact unmethylated DNA will not initiate EXPAR at all. As such, only the methylated DNA is quantitatively and faithfully reflected by the real-time fluorescence signal of the GlaI-EXPAR system, and the potential false positive interference from unmethylated DNA can be effectively eliminated. Therefore, by integrating the unique features of GlaI for highly specific methylation discrimination and EXPAR for rapid and powerful signal amplification, the elegant GlaI-EXPAR assay allows the direct quantification of methylated DNA with ultrahigh sensitivity and accuracy. The detection limit of methylated DNA target has been pushed down to the aM level and the whole detection process of GlaI-EXPAR can be accomplished within a short time of 2 h. More importantly, ultrahigh specificity is achieved and as low as 0.01% methylated DNA can be clearly identified in the presence of a large excess of unmethylated DNA. This GlaI-EXPAR is also demonstrated to be capable of determining site-specific DNA methylations in real genomic DNA samples. Sharing the distinct advantages of ultrahigh sensitivity, outstanding specificity and facile operation, this new GlaI-EXPAR strategy may provide a robust and reliable platform for the detection of site-specific DNA methylations with low abundances.
Collapse
Affiliation(s)
- Yueying Sun
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Yuanyuan Sun
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Weimin Tian
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Chenghui Liu
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Kejian Gao
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| | - Zhengping Li
- Key Laboratory of Applied Surface and Colloid Chemistry , Ministry of Education , Key Laboratory of Analytical Chemistry for Life Science of Shaanxi Province , School of Chemistry and Chemical Engineering , Shaanxi Normal University , Xi'an 710062 , Shaanxi Province , P. R. China . ;
| |
Collapse
|
16
|
Zhou X, Xiao X, Huang T, Du C, Wang S, Mo Y, Ma N, Murata M, Li B, Wen W, Huang G, Zeng X, Zhang Z. Epigenetic inactivation of follistatin-like 1 mediates tumor immune evasion in nasopharyngeal carcinoma. Oncotarget 2017; 7:16433-44. [PMID: 26918942 PMCID: PMC4941326 DOI: 10.18632/oncotarget.7654] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 02/06/2016] [Indexed: 01/25/2023] Open
Abstract
Follistatin like-1 (FSTL1) is a secreted glycoprotein involved in a series of physiological and pathological processes. However, its contribution to the development of cancer, especially the pathogenesis of nasopharyngeal carcinoma (NPC), remains to be elucidated. We aimed to investigate the dysregulation of FSTL1 and its possible function in NPC. FSTL1 was frequently downregulated in NPC cell lines and primary tumor biopsies by promoter hypermethylation. Ectopic expression of FSTL1 significantly suppressed the colony formation, proliferation, migration and invasion ability of NPC cells and induced cell apoptosis. Overexpression of FSTL1 decreased the tumorigenicity of NPC cells in vivo. In addition, the proliferation of NPC cells in vitro was inhibited by treatment with soluble recombinant FSTL1 protein. The protein level of FSTL1 was decreased in primary NPC tumors and was associated with downregulated interleukin 1β (IL-1β) and tumor necrosis factor α (TNF-α). Furthermore, recombinant human FSTL1 protein induced secretion of IL-1β and TNF-α in macrophage cultures, therefore FSTL1 might activate macrophages and attenuate the immune evasion of NPC cells. In conclusion, the epigenetic downregulation of FSTL1 may suppress the proliferation and migration of NPC cells, leading to dysfunctional innate responses in surrounding macrophages.
Collapse
Affiliation(s)
- Xiaoying Zhou
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Medical Research Center, Guangxi Medical University, Nanning, China
| | - Xue Xiao
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Tingting Huang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Chunping Du
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shumin Wang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Yingxi Mo
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China.,Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie, Japan
| | - Ning Ma
- Faculty of Nursing Science, Suzuka University of Medical Science, Suzuka, Japan
| | - Mariko Murata
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Mie, Japan
| | - Bo Li
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Wensheng Wen
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Guangwu Huang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianjie Zeng
- Department of Head and Neck Surgery, Affiliated Cancer Hospital of Guangxi Medical University, Nanning, China
| | - Zhe Zhang
- Department of Otolaryngology-Head & Neck Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, China
| |
Collapse
|
17
|
Sprangers B, DeWolf S, Savage TM, Morokata T, Obradovic A, LoCascio SA, Shonts B, Zuber J, Lau SP, Shah R, Morris H, Steshenko V, Zorn E, Preffer FI, Olek S, Dombkowski DM, Turka LA, Colvin R, Winchester R, Kawai T, Sykes M. Origin of Enriched Regulatory T Cells in Patients Receiving Combined Kidney-Bone Marrow Transplantation to Induce Transplantation Tolerance. Am J Transplant 2017; 17:2020-2032. [PMID: 28251801 PMCID: PMC5519438 DOI: 10.1111/ajt.14251] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/14/2017] [Accepted: 02/22/2017] [Indexed: 01/25/2023]
Abstract
We examined tolerance mechanisms in patients receiving HLA-mismatched combined kidney-bone marrow transplantation (CKBMT) that led to transient chimerism under a previously published nonmyeloablative conditioning regimen (Immune Tolerance Network study 036). Polychromatic flow cytometry and high-throughput sequencing of T cell receptor-β hypervariable regions of DNA from peripheral blood regulatory T cells (Tregs) and CD4 non-Tregs revealed marked early enrichment of Tregs (CD3+ CD4+ CD25high CD127low Foxp3+ ) in blood that resulted from peripheral proliferation (Ki67+ ), possibly new thymic emigration (CD31+ ), and, in one tolerant subject, conversion from non-Tregs. Among recovering conventional T cells, central memory CD4+ and CD8+ cells predominated. A large proportion of the T cell clones detected in posttransplantation biopsy specimens by T cell receptor sequencing were detected in the peripheral blood and were not donor-reactive. Our results suggest that enrichment of Tregs by new thymic emigration and lymphopenia-driven peripheral proliferation in the early posttransplantation period may contribute to tolerance after CKBMT. Further, most conventional T cell clones detected in immunologically quiescent posttransplantation biopsy specimens appear to be circulating cells in the microvasculature rather than infiltrating T cells.
Collapse
Affiliation(s)
- Ben Sprangers
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA,Department of Microbiology and Immunology, Laboratory of Experimental Transplantation, KU Leuven - University of Leuven, and Department of Nephrology, University Hospitals Leuven, Leuven, Belgium
| | - Susan DeWolf
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Thomas M. Savage
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Tatsuaki Morokata
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital (MGH)/Harvard Medical School (HMS), Boston, MA, USA
| | - Aleksandar Obradovic
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Samuel A. LoCascio
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Brittany Shonts
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Julien Zuber
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Sai ping Lau
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Ravi Shah
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Heather Morris
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Valeria Steshenko
- Division of Rheumatology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Emmanuel Zorn
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | | | - Sven Olek
- Epiontis Gmbh, Rudower Chaussee 29, 12489 Berlin, Germany
| | | | - Laurence A. Turka
- Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital (MGH)/Harvard Medical School (HMS), Boston, MA, USA,Immune Tolerance Network, Seattle, WA, USA
| | | | - Robert Winchester
- Division of Rheumatology, Department of Medicine, Columbia University Medical Center, New York, NY, USA
| | - Tatsuo Kawai
- Transplantation Unit, Department of Surgery, MGH/HMS, Boston, MA, USA
| | - Megan Sykes
- Columbia Center for Translational Immunology, Department of Medicine, Columbia University Medical Center, New York, NY, USA,Center for Transplantation Sciences, Department of Surgery, Massachusetts General Hospital (MGH)/Harvard Medical School (HMS), Boston, MA, USA,Department of Microbiology and Immunology, Columbia University Medical Center, Columbia University, New York, NY, USA
| |
Collapse
|
18
|
Ni H, Jiang B, Zhou Z, Yuan X, Cao X, Huang G, Li Y. Inactivation of MSH3 by promoter methylation correlates with primary tumor stage in nasopharyngeal carcinoma. Int J Mol Med 2017; 40:673-678. [PMID: 28656302 PMCID: PMC5547962 DOI: 10.3892/ijmm.2017.3044] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 06/22/2017] [Indexed: 11/06/2022] Open
Abstract
The aim of this study was to investigate the inactivation of the MutS homolog human 3 (MSH3) gene by promoter methylation in nasopharyngeal carcinoma (NPC). Methylation-specific PCR, semi-quantitative reverse transcription PCR and immunohistochemical analysis were used to detect methylation and the mRNA and protein expression levels of MSH3 in 54 cases of NPC tissues and 16 cases of normal nasopharyngeal epithelial (NNE) tissues. The association between promoter methylation and mRNA expression, and the mRNA and protein expression of the gene and clinical factors was analyzed. The promoter methylation of MSH3 was detected in 50% (27/54) of the primary tumors, but not in the 16 NNE tissues. The mRNA and protein expression levels were significantly decreased in the 54 cases of human NPC as compared to the 16 NNE tissues (P<0.05). The MSH3-methylated cases exhibited significantly lower mRNA and protein expression levels than the unmethylated cases (P<0.05). The MSH3 mRNA and protein expression levels were significantly associated with the variable T stage (P<0.05); however, they did not correlate with the age and sex of the patients, or with the N stage, TNM classification or histopathological subtype (P>0.05). On the whole, MSH3 was frequently inactivated by promoter methylation and its mRNA and protein expression correlated with the primary tumor stage in NPC.
Collapse
Affiliation(s)
- Haifeng Ni
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Bo Jiang
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Zhen Zhou
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaoyang Yuan
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Xiaolin Cao
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Guangwu Huang
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yong Li
- Department of Otolaryngology, Affiliated Hangzhou First People's Hospital of Nanjing Medical University, Hangzhou, Zhejiang 310006, P.R. China
| |
Collapse
|
19
|
Beers DR, Zhao W, Wang J, Zhang X, Wen S, Neal D, Thonhoff JR, Alsuliman AS, Shpall EJ, Rezvani K, Appel SH. ALS patients' regulatory T lymphocytes are dysfunctional, and correlate with disease progression rate and severity. JCI Insight 2017; 2:e89530. [PMID: 28289705 DOI: 10.1172/jci.insight.89530] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Neuroinflammation is a pathological hallmark of ALS in both transgenic rodent models and patients, and is characterized by proinflammatory T lymphocytes and activated macrophages/microglia. In ALS mouse models, decreased regulatory T lymphocytes (Tregs) exacerbate the neuroinflammatory process, leading to accelerated motoneuron death and shortened survival; passive transfer of Tregs suppresses the neuroinflammation and prolongs survival. Treg numbers and FOXP3 expression are also decreased in rapidly progressing ALS patients. A key question is whether the marked neuroinflammation in ALS can be attributed to the impaired suppressive function of ALS Tregs in addition to their decreased numbers. To address this question, T lymphocyte proliferation assays were performed. Compared with control Tregs, ALS Tregs were less effective in suppressing responder T lymphocyte proliferation. Although both slowly and rapidly progressing ALS patients had dysfunctional Tregs, the greater the clinically assessed disease burden or the more rapidly progressing the patient, the greater the Treg dysfunction. Epigenetically, the percentage methylation of the Treg-specific demethylated region was greater in ALS Tregs. After in vitro expansion, ALS Tregs regained suppressive abilities to the levels of control Tregs, suggesting that autologous passive transfer of expanded Tregs might offer a novel cellular therapy to slow disease progression.
Collapse
Affiliation(s)
- David R Beers
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Weihua Zhao
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Jinghong Wang
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Xiujun Zhang
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Shixiang Wen
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Dan Neal
- Department of Surgery, University of Florida, Gainesville, Florida, USA
| | - Jason R Thonhoff
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| | - Abdullah S Alsuliman
- Department of Stem Cell Transplant and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Elizabeth J Shpall
- Department of Stem Cell Transplant and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Katy Rezvani
- Department of Stem Cell Transplant and Cellular Therapy, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Stanley H Appel
- Peggy and Gary Edwards ALS Laboratory, Department of Neurology, Houston Methodist Neurological Institute, Houston Methodist Research Institute, Houston Methodist Hospital, Houston, Texas, USA
| |
Collapse
|
20
|
Analysis of DNA methylation in single circulating tumor cells. Oncogene 2017; 36:3223-3231. [PMID: 28068321 DOI: 10.1038/onc.2016.480] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 10/28/2016] [Accepted: 11/15/2016] [Indexed: 01/01/2023]
Abstract
Direct analysis of circulating tumor cells (CTCs) can inform on molecular mechanisms underlying systemic spread. Here we investigated promoter methylation of three genes regulating epithelial-to-mesenchymal transition (EMT), a key mechanism enabling epithelial tumor cells to disseminate and metastasize. For this, we developed a single-cell protocol based on agarose-embedded bisulfite treatment, which allows investigating DNA methylation of multiple loci via a multiplex PCR (multiplexed-scAEBS). We established our assay for the simultaneous analysis of three EMT-associated genes miR-200c/141, miR-200b/a/429 and CDH1 in single cells. The assay was validated in solitary cells of GM14667, MDA-MB-231 and MCF-7 cell lines, achieving a DNA amplification efficiency of 70% with methylation patterns identical to the respective bulk DNA. Then we applied multiplexed-scAEBS to 159 single CTCs from 11 patients with metastatic breast and six with metastatic castration-resistant prostate cancer, isolated via CellSearch (EpCAMpos/CKpos/CD45neg/DAPIpos) and subsequent FACS sorting. In contrast to CD45pos white blood cells isolated and processed by the identical approach, we observed in the isolated CTCs methylation patterns resembling more those of epithelial-like cells. Methylation at the promoter of microRNA-200 family was significantly higher in prostate CTCs. Data from our single-cell analysis revealed an epigenetic heterogeneity among CTCs and indicates tumor-specific active epigenetic regulation of EMT-associated genes during blood-borne dissemination.
Collapse
|
21
|
Ling KY, Cheow LF, Quake SR, Burkholder WF, Messerschmidt DM. Single Cell Restriction Enzyme-Based Analysis of Methylation at Genomic Imprinted Regions in Preimplantation Mouse Embryos. Methods Mol Biol 2017; 1605:171-189. [PMID: 28456965 DOI: 10.1007/978-1-4939-6988-3_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The methylation of cytosines in DNA is a fundamental epigenetic regulatory mechanism. During preimplantation development, mammalian embryos undergo extensive epigenetic reprogramming, including the global erasure of germ cell-specific DNA methylation marks, to allow for the establishment of the pluripotent state of the epiblast. However, DNA methylation marks at specific regions, such as imprinted gene regions, escape this reprogramming process, as their inheritance from germline to soma is paramount for proper development. To study the dynamics of DNA methylation marks in single blastomeres of mouse preimplantation embryos, we devised a new approach-single cell restriction enzyme analysis of methylation (SCRAM). SCRAM allows for reliable, fast, and high-throughput analysis of DNA methylation states of multiple regions of interest from single cells. In the method described below, SCRAM is specifically used to address loss of DNA methylation at genomic imprints or other highly methylated regions of interest.
Collapse
Affiliation(s)
- Ka Yi Ling
- Developmental Epigenetics and Disease Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Lih Feng Cheow
- Microfluidics Systems Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Stephen R Quake
- Department of Bioengineering and Applied Physics, Stanford University, Stanford, CA, USA
- Howard Hughes Medical Institute, Stanford, CA, USA
| | - William F Burkholder
- Microfluidics Systems Biology Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Daniel M Messerschmidt
- Developmental Epigenetics and Disease Laboratory, Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
| |
Collapse
|
22
|
Pradjatmo H. Methylation Status and Expression of BRCA2 in Epithelial Ovarian Cancers in Indonesia. Asian Pac J Cancer Prev 2016; 16:8599-604. [DOI: 10.7314/apjcp.2015.16.18.8599] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
|
23
|
Tao YF, Fang F, Hu SY, Lu J, Cao L, Zhao WL, Xiao PF, Li ZH, Wang NN, Xu LX, Du XJ, Sun LC, Li YH, Li YP, Xu YY, Ni J, Wang J, Feng X, Pan J. Hypermethylation of the GATA binding protein 4 (GATA4) promoter in Chinese pediatric acute myeloid leukemia. BMC Cancer 2015; 15:756. [PMID: 26490736 PMCID: PMC4618362 DOI: 10.1186/s12885-015-1760-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 10/09/2015] [Indexed: 12/12/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is the second-most common form of leukemia in children. Aberrant DNA methylation patterns are a characteristic feature of AML. GATA4 has been suggested to be a tumor suppressor gene regulated by promoter hypermethylation in various types of human cancers although the expression and promoter methylation of GATA4 in pediatric AML is still unclear. Methods Transcriptional expression levels of GATA4 were evaluated by semi-quantitative and real-time PCR. Methylation status was investigated by methylation-specific PCR (MSP) and bisulfate genomic sequencing (BGS). The prognostic significance of GATA4 expression and promoter methylation was assessed in 105 cases of Chinese pediatric acute myeloid leukemia patients with clinical follow-up records. Results MSP and BGS analysis showed that the GATA4 gene promoter is hypermethylated in AML cells, such as the HL-60 and MV4-11 human myeloid leukemia cell lines. 5-Aza treatment significantly upregulated GATA4 expression in HL-60 and MV4-11 cells. Aberrant methylation of GATA4 was observed in 15.0 % (3/20) of the normal bone marrow control samples compared to 56.2 % (59/105) of the pediatric AML samples. GATA4 transcript levels were significantly decreased in AML patients (33.06 ± 70.94; P = 0.011) compared to normal bone marrow/idiopathic thrombocytopenic purpura controls (116.76 ± 105.39). GATA4 promoter methylation was correlated with patient leukocyte counts (WBC, white blood cells) (P = 0.035) and minimal residual disease MRD (P = 0.031). Kaplan-Meier survival analysis revealed significantly shorter overall survival time in patients with GATA4 promoter methylation (P = 0.014). Conclusions Epigenetic inactivation of GATA4 by promoter hypermethylation was observed in both AML cell lines and pediatric AML samples; our study implicates GATA4 as a putative tumor suppressor gene in pediatric AML. In addition, our findings imply that GATA4 promoter methylation is correlated with WBC and MRD. Kaplan-Meier survival analysis revealed significantly shorter overall survival in pediatric AML with GATA4 promoter methylation but multivariate analysis shows that it is not an independent factor. However, further research focusing on the mechanism of GATA4 in pediatric leukemia is required. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1760-5) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Fang Fang
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Jun Lu
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Lan Cao
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Na-Na Wang
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Xiao-Juan Du
- Department of Gastroenterology, the 5th Hospital of Chinese PLA, Yin chuan, China.
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Yan-Hong Li
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Yi-Ping Li
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Yun-Yun Xu
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China.
| | - Jian Wang
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Xing Feng
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| | - Jian Pan
- Department of Hematology and Oncology, Childrens Hospital of Soochow University, Suzhou, China.
| |
Collapse
|
24
|
Epigenetics—Potential for Programming Fish for Aquaculture? JOURNAL OF MARINE SCIENCE AND ENGINEERING 2015. [DOI: 10.3390/jmse3020175] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
25
|
Tao YF, Li ZH, Wang NN, Fang F, Xu LX, Pan J. tp53-dependent G2 arrest mediator candidate gene, Reprimo, is down-regulated by promoter hypermethylation in pediatric acute myeloid leukemia. Leuk Lymphoma 2015; 56:2931-44. [PMID: 25629980 DOI: 10.3109/10428194.2015.1011157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Reprimo (RPRM) is a novel tumor suppressor. However, the expression and molecular function of RPRM in pediatric acute myeloid leukemia (AML) is still unknown. We observed hypermethylation of the RPRM promoter in 8/11 leukemia cell lines and in 44.8% (47/105) of pediatric AML samples compared with 6.7% (2/30) of control samples. Bisulfite genomic sequencing analysis showed that the RPRM promoter was methylated in the majority of AML samples (66.2-83.1%), whereas RPRM was almost unmethylated in normal bone marrow samples (20.0-27.7%). Kaplan-Meier survival analysis revealed poor survival outcomes in samples with RPRM promoter methylation (p < 0.001). Proliferation of AML cells was inhibited in a dose-dependent manner (p < 0.05) after RPRM overexpression with lentivirus transfection. Apoptosis was up-regulated in RPRM-overexpressing AML cells. Real-time polymerase chain reaction array analysis revealed 50 dysregulated genes that might be implicated in apoptosis of RPRM-induced AML cells. RPRM may be a putative tumor suppressor in pediatric AML.
Collapse
Affiliation(s)
- Yan-Fang Tao
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Zhi-Heng Li
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Na-Na Wang
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Fang Fang
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Li-Xiao Xu
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| | - Jian Pan
- a Department of Hematology and Oncology , Children's Hospital of Soochow University , Suzhou , China
| |
Collapse
|
26
|
Tao YF, Xu LX, Lu J, Hu SY, Fang F, Cao L, Xiao PF, Du XJ, Sun LC, Li ZH, Wang NN, Su GH, Li YH, Li G, Zhao H, Li YP, Xu YY, Zhou HT, Wu Y, Jin MF, Liu L, Zhu XM, Ni J, Wang J, Xing F, Zhao WL, Pan J. Early B-cell factor 3 (EBF3) is a novel tumor suppressor gene with promoter hypermethylation in pediatric acute myeloid leukemia. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2015; 34:4. [PMID: 25609158 PMCID: PMC4311429 DOI: 10.1186/s13046-014-0118-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 11/27/2014] [Indexed: 12/21/2022]
Abstract
Background Pediatric acute myeloid leukemia (AML) comprises up to 20% of all childhood leukemia. Recent research shows that aberrant DNA methylation patterning may play a role in leukemogenesis. The epigenetic silencing of the EBF3 locus is very frequent in glioblastoma. However, the expression profiles and molecular function of EBF3 in pediatric AML is still unclear. Methods Twelve human acute leukemia cell lines, 105 pediatric AML samples and 30 normal bone marrow/idiopathic thrombocytopenic purpura (NBM/ITP) control samples were analyzed. Transcriptional level of EBF3 was evaluated by semi-quantitative and real-time PCR. EBF3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BGS). The molecular mechanism of EBF3 was investigated by apoptosis assays and PCR array analysis. Results EBF3 promoter was hypermethylated in 10/12 leukemia cell lines. Aberrant EBF3 methylation was observed in 42.9% (45/105) of the pediatric AML samples using MSP analysis, and the BGS results confirmed promoter methylation. EBF3 expression was decreased in the AML samples compared with control. Methylated samples revealed similar survival outcomes by Kaplan-Meier survival analysis. EBF3 overexpression significantly inhibited cell proliferation and increased apoptosis. Real-time PCR array analysis revealed 93 dysregulated genes possibly implicated in the apoptosis of EBF3-induced AML cells. Conclusion In this study, we firstly identified epigenetic inactivation of EBF3 in both AML cell lines and pediatric AML samples for the first time. Our findings also showed for the first time that transcriptional overexpression of EBF3 could inhibit proliferation and induce apoptosis in AML cells. We identified 93 dysregulated apoptosis-related genes in EBF3-overexpressing, including DCC, AIFM2 and DAPK1. Most of these genes have never been related with EBF3 over expression. These results may provide new insights into the molecular mechanism of EBF3-induced apoptosis; however, further research will be required to determine the underlying details. Our findings suggest that EBF3 may act as a putative tumor suppressor gene in pediatric AML.
Collapse
Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Fang Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Lan Cao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Xiao-Juan Du
- Department of Gastroenterology, the 5th Hospital of Chinese PLA, Yin chuan, China.
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China.
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Na-Na Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Guang-Hao Su
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yan-Hong Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Gang Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - He Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yi-Ping Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yun-Yun Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Hui-Ting Zhou
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Yi Wu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Mei-Fang Jin
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Lin Liu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Xue-Ming Zhu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, China.
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Feng Xing
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China.
| |
Collapse
|
27
|
Tao YF, Hu SY, Lu J, Cao L, Zhao WL, Xiao PF, Xu LX, Li ZH, Wang NN, Du XJ, Sun LC, Zhao H, Fang F, Su GH, Li YH, Li YP, Xu YY, Ni J, Wang J, Feng X, Pan J. Zinc finger protein 382 is downregulated by promoter hypermethylation in pediatric acute myeloid leukemia patients. Int J Mol Med 2014; 34:1505-15. [PMID: 25319049 PMCID: PMC4214337 DOI: 10.3892/ijmm.2014.1966] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2014] [Accepted: 10/03/2014] [Indexed: 11/06/2022] Open
Abstract
Acute myeloid leukemia (AML) is the second-most common form of leukemia in children. Aberrant DNA methylation patterns are characteristic of AML. Zinc finger protein 382 (ZNF382) has been suggested to be a tumor suppressor gene possibly regulated by promoter hypermethylation in various types of human cancer. However, ZNF382 expression and methylation status in pediatric AML is unknown. In the present study, ZNF382 transcription levels were evaluated by quantitative reverse-transcription PCR. Methylation status was investigated by methylation-specific (MSP) PCR and bisulfate genomic sequencing (BGS). The prognostic significance of ZNF382 expression and promoter methylation was assessed in 105 cases of pediatric AML. The array data suggested that the ZNF382 promoter was hypermethylated in the AML cases examined. MSP PCR and BGS analysis revealed that ZNF382 was hypermethylated in leukemia cell lines. Furthermore, treatment with 5-aza-2'-deoxycytidine (5-Aza) upregulated ZNF382 expression in the selected leukemia cell lines. The aberrant methylation of ZNF382 was observed in 10% (2/20) of the control samples compared with 26.7% (28/105) of the AML samples. ZNF382 expression was significantly decreased in the 105 AML patients compared with the controls. Patients with ZNF382 methylation showed lower ZNF382 transcript levels compared with patients exhibiting no methylation. There were no significant differences in clinical characteristics or cytogenetic analysis between the patients with or without ZNF382 methylation. ZNF382 methylation correlated with minimal residual disease (MRD). Kaplan-Meier survival analysis revealed similar survival times in the samples with ZNF382 methylation, and multivariate analysis revealed that ZNF382 methylation was not an independent prognostic factor in pediatric AML. The epigenetic inactivation of ZNF382 by promoter hypermethylation can be observed in AML cell lines and pediatric AML samples. Therefore, our study suggests that ZNF382 may be considered a putative tumor suppressor gene in pediatric AML. However, further studies focusing on the mechanisms responsible for ZNF382 downregulation in pediatric leukemia are required.
Collapse
Affiliation(s)
- Yan-Fang Tao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Shao-Yan Hu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jun Lu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Lan Cao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Wen-Li Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Pei-Fang Xiao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Li-Xiao Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Zhi-Heng Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Na-Na Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Xiao-Juan Du
- Department of Gastroenterology, The 5th Hospital of Chinese PLA, Yinchuan, Ningxia, P.R. China
| | - Li-Chao Sun
- Department of Cell and Molecular Biology, Cancer Institute (Hospital), Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, P.R. China
| | - He Zhao
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Fang Fang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Guang-Hao Su
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yan-Hong Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yi-Ping Li
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Yun-Yun Xu
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jian Ni
- Translational Research Center, Second Hospital, The Second Clinical School, Nanjing Medical University, Nanjing, Jiangsu, P.R. China
| | - Jian Wang
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Xing Feng
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, Jiangsu, P.R. China
| |
Collapse
|
28
|
Processive DNA demethylation via DNA deaminase-induced lesion resolution. PLoS One 2014; 9:e97754. [PMID: 25025377 PMCID: PMC4098905 DOI: 10.1371/journal.pone.0097754] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2014] [Accepted: 04/23/2014] [Indexed: 12/13/2022] Open
Abstract
Base modifications of cytosine are an important aspect of chromatin biology, as they can directly regulate gene expression, while DNA repair ensures that those modifications retain genome integrity. Here we characterize how cytosine DNA deaminase AID can initiate DNA demethylation. In vitro, AID initiated targeted DNA demethylation of methyl CpGs when in combination with DNA repair competent extracts. Mechanistically, this is achieved by inducing base alterations at or near methyl-cytosine, with the lesion being resolved either via single base substitution or a more efficient processive polymerase dependent repair. The biochemical findings are recapitulated in an in vivo transgenic targeting assay, and provide the genetic support of the molecular insight into DNA demethylation. This targeting approach supports the hypothesis that mCpG DNA demethylation can proceed via various pathways and mCpGs do not have to be targeted to be demethylated.
Collapse
|
29
|
Metallothionein III (MT3) is a putative tumor suppressor gene that is frequently inactivated in pediatric acute myeloid leukemia by promoter hypermethylation. J Transl Med 2014; 12:182. [PMID: 24962166 PMCID: PMC4082423 DOI: 10.1186/1479-5876-12-182] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2014] [Accepted: 06/20/2014] [Indexed: 11/14/2022] Open
Abstract
Background Acute myeloid leukemia (AML) is the second most common form of leukemia in children. Aberrant DNA methylation patterns are a characteristic feature in various tumors, including AML. Metallothionein III (MT3) is a tumor suppresser reported to show promoter hypermethylated in various cancers. However, the expression and molecular function of MT3 in pediatric AML is unclear. Methods Eleven human leukemia cell lines and 41 pediatric AML samples and 20 NBM/ITP (Norma bone marrow/Idiopathic thrombocytopenic purpura) control samples were analyzed. Transcription levels of MT3 were evaluated by semi-quantitative and real-time PCR. MT3 methylation status was determined by methylation specific PCR (MSP) and bisulfite genomic sequencing (BSG). The molecular mechanism of MT3 was investigated by apoptosis assays and PCR array analysis. Results The MT3 promoter was hypermethylated in leukemia cell lines. More CpG’s methylated of MT3 was observed 39.0% pediatric AML samples compared to 10.0% NBM controls. Transcription of MT3 was also significantly decreased in AML samples compared to NBM/ITP controls (P < 0.001); patients with methylated MT3 exhibited lower levels of MT3 expression compared to those with unmethylated MT3 (P = 0.049). After transfection with MT3 lentivirus, proliferation was significantly inhibited in AML cells in a dose-dependent manner (P < 0.05). Annexin V assay showed that apoptosis was significantly upregulated MT3-overexpressing AML cells compared to controls. Real-time PCR array analysis revealed 34 dysregulated genes that may be implicated in MT3 overexpression and apoptosis in AML, including FOXO1. Conclusion MT3 may be a putative tumor suppressor gene in pediatric AML. Epigenetic inactivation of MT3 via promoter hypermethylation was observed in both AML cell lines and pediatric AML samples. Overexpression of MT3 may inhibit proliferation and induce apoptosis in AML cells. FOXO1 was dysregulated in MT3-overexpressing cells, offering an insight into the mechanism of MT3-induced apoptosis. However, further research is required to determine the underlying molecular details.
Collapse
|
30
|
Singh A, Yamamoto M, Ruan J, Choi JY, Gauvreau GM, Olek S, Hoffmueller U, Carlsten C, FitzGerald JM, Boulet LP, O'Byrne PM, Tebbutt SJ. Th17/Treg ratio derived using DNA methylation analysis is associated with the late phase asthmatic response. Allergy Asthma Clin Immunol 2014; 10:32. [PMID: 24991220 PMCID: PMC4078401 DOI: 10.1186/1710-1492-10-32] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 06/02/2014] [Indexed: 11/17/2022] Open
Abstract
Background The imbalance between Th17 and Treg cells has been studied in various diseases including allergic asthma but their roles have not been fully understood in the development of the late phase asthmatic response. Objectives To determine changes in Th17 and Treg cell numbers between isolated early responders (ERs) and dual responders (DRs) undergoing allergen inhalation challenge. To identify gene expression profiles associated with Th17 and Treg cells. Methods 14 participants (8 ERs and 6 DRs) with mild allergic asthma underwent allergen inhalation challenge. Peripheral blood was collected prior to and 2 hours post allergen challenge. DNA methylation analysis was used to quantifiy the relative frequencies of Th17, Tregs, total B cells, and total T cells. Gene expression from whole blood was measured using microarrays. Technical replication of selected genes was performed using nanoString nCounter Elements. Results The Th17/Treg ratio significantly increased in DRs compared to ERs post allergen challenge compared to pre-challenge. Genes significantly correlated to Th17 and Treg cell counts were inversely correlated with each other. Genes significantly correlated with Th17/Treg ratio included the cluster of genes of the leukocyte receptor complex located on chromosome 19q 13.4. Conclusions Th17/Treg imbalance post-challenge may contribute to the development of the late phase inflammatory phenotype.
Collapse
Affiliation(s)
- Amrit Singh
- James Hogg Research Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Institute for HEART + LUNG Health, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Masatsugu Yamamoto
- James Hogg Research Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Institute for HEART + LUNG Health, Vancouver, BC, Canada.,Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, UBC, Vancouver, BC, Canada
| | - Jian Ruan
- James Hogg Research Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Institute for HEART + LUNG Health, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada
| | - Jung Young Choi
- James Hogg Research Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Institute for HEART + LUNG Health, Vancouver, BC, Canada
| | - Gail M Gauvreau
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | | | | | - Christopher Carlsten
- James Hogg Research Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Institute for HEART + LUNG Health, Vancouver, BC, Canada.,Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, UBC, Vancouver, BC, Canada
| | - J Mark FitzGerald
- Institute for HEART + LUNG Health, Vancouver, BC, Canada.,Vancouver Coastal Health Research Institute, Vancouver General Hospital, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, UBC, Vancouver, BC, Canada
| | | | - Paul M O'Byrne
- Department of Medicine, McMaster University, Hamilton, ON, Canada
| | - Scott J Tebbutt
- James Hogg Research Centre for Heart Lung Innovation, St. Paul's Hospital, University of British Columbia, Vancouver, BC, Canada.,Institute for HEART + LUNG Health, Vancouver, BC, Canada.,Prevention of Organ Failure (PROOF) Centre of Excellence, Vancouver, BC, Canada.,Department of Medicine, Division of Respiratory Medicine, UBC, Vancouver, BC, Canada
| |
Collapse
|
31
|
Nawaz I, Qiu X, Wu H, Li Y, Fan Y, Hu LF, Zhou Q, Ernberg I. Development of a multiplex methylation specific PCR suitable for (early) detection of non-small cell lung cancer. Epigenetics 2014; 9:1138-48. [PMID: 24937636 DOI: 10.4161/epi.29499] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Lung cancer is a worldwide health problem and a leading cause of cancer-related deaths. Silencing of potential tumor suppressor genes (TSGs) by aberrant promoter methylation is an early event in the initiation and development of cancer. Thus, methylated cancer type-specific TSGs in DNA can serve as useful biomarkers for early cancer detection. We have now developed a "Multiplex Methylation Specific PCR" (MMSP) assay for analysis of the methylation status of multiple potential TSGs by a single PCR reaction. This method will be useful for early diagnosis and treatment outcome studies of non-small cell lung cancer (NSCLC). Genome-wide CpG methylation and expression microarrays were performed on lung cancer tissues and matched distant non-cancerous tissues from three NSCLC patients from China. Thirty-eight potential TSGs were selected and analyzed by methylation PCR on bisulfite treated DNA. On the basis of sensitivity and specificity, six marker genes, HOXA9, TBX5, PITX2, CALCA, RASSF1A, and DLEC1, were selected to establish the MMSP assay. This assay was then used to analyze lung cancer tissues and matched distant non-cancerous tissues from 70 patients with NSCLC, as well as 24 patients with benign pulmonary lesion as controls. The sensitivity of the assay was 99% (69/70). HOXA9 and TBX5 were the 2 most sensitive marker genes: 87% (61/70) and 84% (59/70), respectively. RASSF1A and DLEC1 showed the highest specificity at 99% (69/70). Using the criterion of identifying at least any two methylated marker genes, 61/70 cancer samples were positive, corresponding to a sensitivity of 87% and a specificity of 94%. Early stage I or II NSCLC could even be detected with a 100% specificity and 86% sensitivity. In conclusion, MMSP has the potential to be developed into a population-based screening tool and can be useful for early diagnosis of NSCLC. It might also be suitable for monitoring treatment outcome and recurrence.
Collapse
Affiliation(s)
- Imran Nawaz
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institute; Stockholm, Sweden; Department of Microbiology; Faculty of Life Sciences; University of Balochistan; Quetta, Pakistan
| | - Xiaoming Qiu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Heng Wu
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Yang Li
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Yaguang Fan
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Li-Fu Hu
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institute; Stockholm, Sweden
| | - Qinghua Zhou
- Tianjin Key Laboratory of Lung Cancer Metastasis and Tumor Microenvironment; Tianjin Lung Cancer Institute; Tianjin Medical University General Hospital; Tianjin, PR China
| | - Ingemar Ernberg
- Department of Microbiology; Tumor and Cell Biology; Karolinska Institute; Stockholm, Sweden
| |
Collapse
|
32
|
He CG, Huang QY, Chen LS, Ling ZA, Wu HG, Deng HQ. p33 ING1b methylation in fecal DNA as a molecular screening tool for colorectal cancer and precancerous lesions. Oncol Lett 2014; 7:1639-1644. [PMID: 24765192 PMCID: PMC3997675 DOI: 10.3892/ol.2014.1923] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2013] [Accepted: 01/09/2014] [Indexed: 02/06/2023] Open
Abstract
The present study aimed to investigate the feasibility of detecting p33 inhibitor of growth 1b (p33ING1b) gene methylation in fecal DNA as a screening method for colorectal carcinoma (CRC) and precancerous lesions. The methylation of p33ING1b was analyzed in fecal samples from 61 patients with CRCs, 27 patients with precancerous lesions (advanced adenoma) and 20 normal individuals by nested methylation-specific polymerase chain reaction (nMSP) and fecal occult blood test. Methylated p33ING1b was detected in 73.77% of CRC patients and 62.96% of adenoma patients. By contrast, only 5% of normal individuals had methylated p33ING1b. These results indicated 73.77% sensitivity for detecting CRC, 62.96% sensitivity for detecting precancerous lesions and 95% specificity of the assay for detecting CRCs and precancerous lesions. The detection of p33ING1b methylation status by incubation of DNA contained in agarose beads for bisulfite modification, followed by nMSP, is a promising non-invasive screening method for CRCs and precancerous lesions.
Collapse
Affiliation(s)
- Chun-Gang He
- Department of General and Pediatric Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Qin-Yuan Huang
- Nursing College of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Li-Sheng Chen
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Zhi-An Ling
- Department of Colorectal and Anal Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong-Gen Wu
- Department of General and Pediatric Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| | - Hong-Qiang Deng
- Department of General and Pediatric Surgery, The People's Hospital of Guangxi Zhuang Autonomous Region, Nanning, Guangxi Zhuang Autonomous Region 530021, P.R. China
| |
Collapse
|
33
|
Henrique R, Oliveira AI, Costa VL, Baptista T, Martins AT, Morais A, Oliveira J, Jerónimo C. Epigenetic regulation of MDR1 gene through post-translational histone modifications in prostate cancer. BMC Genomics 2013; 14:898. [PMID: 24344919 PMCID: PMC3878566 DOI: 10.1186/1471-2164-14-898] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2013] [Accepted: 12/11/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Multidrug resistance 1 (MDR1) gene encodes for an ATP binding cassette transporter--P-glycoprotein (P-gp)-- involved in chemoresistance to taxanes. MDR1 promoter methylation is frequent in prostate carcinoma (PCa), suggesting an epigenetic regulation but no functional correlation has been established. We aimed to elucidate the epigenetic mechanisms involved in MDR1 deregulation in PCa. RESULTS MDR1 promoter methylation and P-gp expression were assessed in 121 PCa, 39 high-grade prostatic intraepithelial neoplasia (HGPIN), 28 benign prostatic hyperplasia (BPH) and 10 morphologically normal prostate tissue (NPT) samples, using quantitative methylation specific PCR and immunohistochemistry, respectively. PCa cell lines were exposed to a DNA methyltransferases inhibitor 5-aza-2'deoxycytidine (DAC) and histone deacetylases inhibitor trichostatin A (TSA). Methylation and histone posttranscriptional modifications status were characterized and correlated with mRNA and protein expression. MDR1 promoter methylation levels and frequency significantly increased from NPTs, to HGPIN and to PCa. Conversely, decreased or absent P-gp immunoexpression was observed in HGPIN and PCa, inversely correlating with methylation levels. Exposure to DAC alone did not alter significantly methylation levels, although increased expression was apparent. However, P-gp mRNA and protein re-expression were higher in cell lines exposed to TSA alone or combined with DAC. Accordingly, histone active marks H3Ac, H3K4me2, H3K4me3, H3K9Ac, and H4Ac were increased at the MDR1 promoter after exposure to TSA alone or combined with DAC. CONCLUSION Our data suggests that, in prostate carcinogenesis, MDR1 downregulation is mainly due to histone post-translational modifications. This occurs concomitantly with aberrant promoter methylation, substantiating the association with P-gp decreased expression.
Collapse
MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/genetics
- ATP Binding Cassette Transporter, Subfamily B, Member 1/metabolism
- Adult
- Aged
- Aged, 80 and over
- Azacitidine/pharmacology
- Cell Line, Tumor
- CpG Islands
- DNA Methylation
- Epigenesis, Genetic/drug effects
- Gene Expression Regulation, Neoplastic/drug effects
- Histones/metabolism
- Humans
- Male
- Middle Aged
- Neoplasm Grading
- Neoplasm Staging
- Promoter Regions, Genetic
- Prostate/metabolism
- Prostatic Hyperplasia/genetics
- Prostatic Hyperplasia/metabolism
- Prostatic Neoplasms/genetics
- Prostatic Neoplasms/metabolism
- Prostatic Neoplasms/pathology
- Protein Processing, Post-Translational
Collapse
Affiliation(s)
- Rui Henrique
- Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Largo Prof. Abel Salazar 2, 4099-003 Porto, Portugal
| | - Ana Isabel Oliveira
- Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Vera L Costa
- Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Tiago Baptista
- Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Ana Teresa Martins
- Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology, Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - António Morais
- Department of Urology, Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Jorge Oliveira
- Department of Urology, Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
| | - Carmen Jerónimo
- Cancer Epigenetics Group, Research Center of the Portuguese Oncology Institute, Porto, Rua Dr. António Bernardino de Almeida, 4200-072 Porto, Portugal
- Department of Pathology and Molecular Immunology, Institute of Biomedical Sciences Abel Salazar, University of Porto, Largo Prof. Abel Salazar 2, 4099-003 Porto, Portugal
| |
Collapse
|
34
|
Xiao X, Zhao W, Tian F, Zhou X, Zhang J, Huang T, Hou B, Du C, Wang S, Mo Y, Yu N, Zhou S, You J, Zhang Z, Huang G, Zeng X. Cytochrome b5 reductase 2 is a novel candidate tumor suppressor gene frequently inactivated by promoter hypermethylation in human nasopharyngeal carcinoma. Tumour Biol 2013; 35:3755-63. [PMID: 24338690 PMCID: PMC3980038 DOI: 10.1007/s13277-013-1497-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 11/28/2013] [Indexed: 01/30/2023] Open
Abstract
Cytochrome b5 reductase 2 (CYB5R2), a member of the flavoprotein pyridine nucleotide cytochrome reductase family, is associated with a number of physiological reactions. However, its role in cancer, especially nasopharyngeal carcinoma (NPC), has not been addressed. Here, we investigate the transcript levels and promoter methylation status of CYB5R2 in NPC derived cell lines and tumor biopsies and experimentally address its role as a tumor suppressor gene. We find that CYB5R2 transcript levels are decreased in NPC cell lines and tumor biopsies. Promoter hypermethylation of CYB5R2 was detected in all six tested NPC cell lines and in 84 % of primary NPC tumor biopsies but not in normal nasopharyngeal epithelium. Clinically, CYB5R2 methylation was associated with lymph node metastasis in NPC patients (P < 0.05). The endogenous expression of CYB5R2 could be restored in vitro by the methyltransferase inhibitor 5-aza-2′-deoxycytidine in NPC cell lines. Ectopic expression of CYB5R2 had an inhibitory effect on proliferation, clonogenicity and migration of NPC cells. Moreover, in vivo tests in nude mice indicated that ectopic expression of CYB5R2 reduces the tumorigenicity of CYB5R2-negative NPC cells. Collectively, these findings suggest that CYB5R2 may be a functional tumor suppressor gene, frequently inactivated by hypermethylation of its promoter in NPC. We report here the first instance of epigenetic downregulation in NPC tumor biopsies of a key enzyme, CYB5R2, which is responsible for the detoxification of environmental carcinogens. We propose the possibility of utilizing CYB5R2 promoter methylation as a diagnostic biomarker of NPC in the future.
Collapse
Affiliation(s)
- Xue Xiao
- Department of Otolaryngology-Head and Neck Surgery, First Affiliated Hospital of Guangxi Medical University, 6# Shuangyong Road, Nanning, 530021, China
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
35
|
Rieusset A, Schaller F, Unmehopa U, Matarazzo V, Watrin F, Linke M, Georges B, Bischof J, Dijkstra F, Bloemsma M, Corby S, Michel FJ, Wevrick R, Zechner U, Swaab D, Dudley K, Bezin L, Muscatelli F. Stochastic loss of silencing of the imprinted Ndn/NDN allele, in a mouse model and humans with prader-willi syndrome, has functional consequences. PLoS Genet 2013; 9:e1003752. [PMID: 24039599 PMCID: PMC3764186 DOI: 10.1371/journal.pgen.1003752] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 07/10/2013] [Indexed: 12/27/2022] Open
Abstract
Genomic imprinting is a process that causes genes to be expressed from one allele only according to parental origin, the other allele being silent. Diseases can arise when the normally active alleles are not expressed. In this context, low level of expression of the normally silent alleles has been considered as genetic noise although such expression has never been further studied. Prader-Willi Syndrome (PWS) is a neurodevelopmental disease involving imprinted genes, including NDN, which are only expressed from the paternally inherited allele, with the maternally inherited allele silent. We present the first in-depth study of the low expression of a normally silent imprinted allele, in pathological context. Using a variety of qualitative and quantitative approaches and comparing wild-type, heterozygous and homozygous mice deleted for Ndn, we show that, in absence of the paternal Ndn allele, the maternal Ndn allele is expressed at an extremely low level with a high degree of non-genetic heterogeneity. The level of this expression is sex-dependent and shows transgenerational epigenetic inheritance. In about 50% of mutant mice, this expression reduces birth lethality and severity of the breathing deficiency, correlated with a reduction in the loss of serotonergic neurons. In wild-type brains, the maternal Ndn allele is never expressed. However, using several mouse models, we reveal a competition between non-imprinted Ndn promoters which results in monoallelic (paternal or maternal) Ndn expression, suggesting that Ndn allelic exclusion occurs in the absence of imprinting regulation. Importantly, specific expression of the maternal NDN allele is also detected in post-mortem brain samples of PWS individuals. Our data reveal an unexpected epigenetic flexibility of PWS imprinted genes that could be exploited to reactivate the functional but dormant maternal alleles in PWS. Overall our results reveal high non-genetic heterogeneity between genetically identical individuals that might underlie the variability of the phenotype.
Collapse
Affiliation(s)
- Anne Rieusset
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - Fabienne Schaller
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - Unga Unmehopa
- Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Valery Matarazzo
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - Françoise Watrin
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - Matthias Linke
- Universitätsmedizin der Johannes Gutenberg-Universität Mainz Institut für Humangenetik, Mainz, Germany
| | - Beatrice Georges
- INSERM, U1028, CNRS, UMR5292, Université Claude Bernard Lyon 1, Lyon Neuroscience Center, Villeurbanne, France
| | - Jocelyn Bischof
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Femke Dijkstra
- Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Monique Bloemsma
- Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Severine Corby
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - François J. Michel
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - Rachel Wevrick
- Department of Medical Genetics, University of Alberta, Edmonton, Alberta, Canada
| | - Ulrich Zechner
- Universitätsmedizin der Johannes Gutenberg-Universität Mainz Institut für Humangenetik, Mainz, Germany
| | - Dick Swaab
- Netherlands Institute for Neuroscience, an Institute of the Royal Netherlands Academy of Arts and Sciences, Amsterdam, The Netherlands
| | - Keith Dudley
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
| | - Laurent Bezin
- INSERM, U1028, CNRS, UMR5292, Université Claude Bernard Lyon 1, Lyon Neuroscience Center, Villeurbanne, France
| | - Françoise Muscatelli
- INSERM, Institut de Neurobiologie de la Méditerranée (INMED) U901, Marseille, France
- Aix-Marseille Université, INMED UMR901, Marseille, France
- * E-mail:
| |
Collapse
|
36
|
Cruickshanks HA, Vafadar-Isfahani N, Dunican DS, Lee A, Sproul D, Lund JN, Meehan RR, Tufarelli C. Expression of a large LINE-1-driven antisense RNA is linked to epigenetic silencing of the metastasis suppressor gene TFPI-2 in cancer. Nucleic Acids Res 2013; 41:6857-69. [PMID: 23703216 PMCID: PMC3737543 DOI: 10.1093/nar/gkt438] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2013] [Revised: 04/29/2013] [Accepted: 04/29/2013] [Indexed: 12/18/2022] Open
Abstract
LINE-1 retrotransposons are abundant repetitive elements of viral origin, which in normal cells are kept quiescent through epigenetic mechanisms. Activation of LINE-1 occurs frequently in cancer and can enable LINE-1 mobilization but also has retrotransposition-independent consequences. We previously reported that in cancer, aberrantly active LINE-1 promoters can drive transcription of flanking unique sequences giving rise to LINE-1 chimeric transcripts (LCTs). Here, we show that one such LCT, LCT13, is a large transcript (>300 kb) running antisense to the metastasis-suppressor gene TFPI-2. We have modelled antisense RNA expression at TFPI-2 in transgenic mouse embryonic stem (ES) cells and demonstrate that antisense RNA induces silencing and deposition of repressive histone modifications implying a causal link. Consistent with this, LCT13 expression in breast and colon cancer cell lines is associated with silencing and repressive chromatin at TFPI-2. Furthermore, we detected LCT13 transcripts in 56% of colorectal tumours exhibiting reduced TFPI-2 expression. Our findings implicate activation of LINE-1 elements in subsequent epigenetic remodelling of surrounding genes, thus hinting a novel retrotransposition-independent role for LINE-1 elements in malignancy.
Collapse
Affiliation(s)
- Hazel A. Cruickshanks
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Natasha Vafadar-Isfahani
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Donncha S. Dunican
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Andy Lee
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Duncan Sproul
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Jonathan N. Lund
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Richard R. Meehan
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| | - Cristina Tufarelli
- Wolfson Centre for Stem Cells, Tissue Engineering and Modelling (STEM), School of Clinical Sciences, University of Nottingham, Centre for Biomedical Sciences, Nottingham NG7 2RD, UK, School of Graduate Entry Medicine, University of Nottingham, Royal Derby Hospital, Derby DE22 3DT, UK, MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK, Breakthrough Research Unit, University of Edinburgh, Edinburgh EH4 2XU, UK and Centre for Genetics and Genomics, University of Nottingham, Queens Medical Centre, Nottingham NG7 2RD, UK
| |
Collapse
|
37
|
Lu D, Dong D, Zhou Y, Lu M, Pang XW, Li Y, Tian XJ, Zhang Y, Zhang J. The tumor-suppressive function of UNC5D and its repressed expression in renal cell carcinoma. Clin Cancer Res 2013; 19:2883-92. [PMID: 23589179 DOI: 10.1158/1078-0432.ccr-12-2978] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE As a newly added member of the UNC5H receptors, the function of UNC5D/H4 in tumorigenesis remains poorly defined. The aim of this study was to examine the expression of UNC5D in primary renal cell carcinomas (RCC), analyze the mechanisms responsible for its downregulation in RCC, and assess its functional relevance to tumor growth and migration. EXPERIMENTAL DESIGN Forty-four paired primary RCCs and corresponding adjacent noncancerous tissues were collected. The mRNA and protein expression level of UNC5D was assessed by reverse transcriptase-PCR, real-time PCR, or immunohistochemistry. Epigenetic alterations in UNC5D promoter and LOH in the UNC5D locus were also analyzed. Ectopic expression of UNC5D in renal cancer cells with silenced expression of UNC5D was used for analysis of the biologic functions of UNC5D. RESULTS UNC5D expression was attenuated in multiple carcinoma cell lines including renal cancer cells. Similar reduction was also observed in primary RCC tissues as compared with paired adjacent noncancerous tissues. Methylation-specific PCR showed hypermethylation in UNC5D promoter in a significant proportion (18 of 44) of tumor tissue (40.9%). LOH of UNC5D was observed in 13 of 44 patients with RCCs (29.5%). Restoration of UNC5D expression in renal cancer cells significantly inhibited cell proliferation, anchorage-dependent and -independent growth, as well as migration and invasion, whereas knockdown of UNC5D promoted cell growth. Furthermore, ectopic expression of UNC5D induced G2-M cell-cycle arrest. CONCLUSIONS UNC5D is a functional tumor suppressor that is frequently downregulated in RCCs due to promoter hypermethylation and LOH.
Collapse
Affiliation(s)
- Dan Lu
- Department of Immunology, Key Laboratory of Medical Immunology (Ministry of Health), Peking University Health Science Center, Beijing, China
| | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Barres R, Kirchner H, Rasmussen M, Yan J, Kantor FR, Krook A, Näslund E, Zierath JR. Weight loss after gastric bypass surgery in human obesity remodels promoter methylation. Cell Rep 2013; 3:1020-7. [PMID: 23583180 DOI: 10.1016/j.celrep.2013.03.018] [Citation(s) in RCA: 193] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2011] [Revised: 01/23/2013] [Accepted: 03/14/2013] [Indexed: 01/06/2023] Open
Abstract
DNA methylation provides a mechanism by which environmental factors can control insulin sensitivity in obesity. Here, we assessed DNA methylation in skeletal muscle from obese people before and after Roux-en-Y gastric bypass (RYGB). Obesity was associated with altered expression of a subset of genes enriched in metabolic process and mitochondrial function. After weight loss, the expression of the majority of the identified genes was normalized to levels observed in normal-weight, healthy controls. Among the 14 metabolic genes analyzed, promoter methylation of 11 genes was normalized to levels observed in the normal-weight, healthy subjects. Using bisulfite sequencing, we show that promoter methylation of PGC-1α and PDK4 is altered with obesity and restored to nonobese levels after RYGB-induced weight loss. A genome-wide DNA methylation analysis of skeletal muscle revealed that obesity is associated with hypermethylation at CpG shores and exonic regions close to transcription start sites. Our results provide evidence that obesity and RYGB-induced weight loss have a dynamic effect on the epigenome.
Collapse
Affiliation(s)
- Romain Barres
- Department of Molecular Medicine and Surgery, Karolinska Institutet, SE-171 77 Stockholm, Sweden
| | | | | | | | | | | | | | | |
Collapse
|
39
|
Aberrant gene expression and sexually incompatible genomic imprinting in oocytes derived from XY mouse embryonic stem cells in vitro. PLoS One 2013; 8:e58555. [PMID: 23472205 PMCID: PMC3589367 DOI: 10.1371/journal.pone.0058555] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2012] [Accepted: 02/07/2013] [Indexed: 11/19/2022] Open
Abstract
Mouse embryonic stem cells (ESCs) have the potential to differentiate into germ cells (GCs) in vivo and in vitro. Interestingly, XY ESCs can give rise to both male and female GCs in culture, irrespective of the genetic sex. Recent studies showed that ESC-derived primordial GCs contributed to functional gametogenesis in vivo; however, in vitro differentiation techniques have never succeeded in generating mature oocytes from ESCs due to cryptogenic growth arrest during the preantral follicle stages of development. To address this issue, a mouse ESC line, capable of producing follicle-like structures (FLSs) efficiently, was established to investigate their properties using conventional molecular biological methods. The results revealed that the ESC-derived FLSs were morphologically similar to ovarian primary-to-secondary follicles but never formed an antrum; instead, the FLSs eventually underwent abnormal development or cell death in culture, or formed teratomas when transplanted under the kidney capsule in mice. Gene expression analyses demonstrated that the FLSs lacked transcripts for genes essential to late folliculogenesis, including gonadotropin receptors and steroidogenic enzymes, whereas some other genes were overexpressed in FLSs compared to the adult ovary. The E-Cadherin protein, which is involved in cell-to-cell interactions, was also expressed ectopically. Remarkably, it was seen that oocyte-like cells in the FLSs exhibited androgenetic genomic imprinting, which is ordinarily indicative of male GCs. Although the FLSs did not express male GC marker genes, the DNA methyltransferase, Dnmt3L, was expressed at an abnormally high level. Furthermore, the expression of sex determination factors was ambiguous in FLSs as both male and female determinants were expressed weakly. These data suggest that the developmental dysfunction of the ESC-derived FLSs may be attributable to aberrant gene expression and genomic imprinting, possibly associated with uncertain sex determination in culture.
Collapse
|
40
|
Pohla H, Buchner A, Stadlbauer B, Frankenberger B, Stevanovic S, Walter S, Frank R, Schwachula T, Olek S, Kopp J, Willimsky G, Stief CG, Hofstetter A, Pezzutto A, Blankenstein T, Oberneder R, Schendel DJ. High immune response rates and decreased frequencies of regulatory T cells in metastatic renal cell carcinoma patients after tumor cell vaccination. Mol Med 2013; 18:1499-508. [PMID: 23269976 DOI: 10.2119/molmed.2012.00221] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2012] [Accepted: 12/19/2012] [Indexed: 11/06/2022] Open
Abstract
Our previously reported phase I clinical trial with the allogeneic gene-modified tumor cell line RCC-26/CD80/IL-2 showed that vaccination was well tolerated and feasible in metastatic renal cell carcinoma (RCC) patients. Substantial disease stabilization was observed in most patients despite a high tumor burden at study entry. To investigate alterations in immune responses that might contribute to this effect, we performed an extended immune monitoring that included analysis of reactivity against multiple antigens, cytokine/chemokine changes in serum and determination of the frequencies of immune suppressor cell populations, including natural regulatory T cells (nTregs) and myeloid-derived suppressor cell subsets (MDSCs). An overall immune response capacity to virus-derived control peptides was present in 100% of patients before vaccination. Vaccine-induced immune responses to tumor-associated antigens occurred in 75% of patients, demonstrating the potent immune stimulatory capacity of this generic vaccine. Furthermore, some patients reacted to peptide epitopes of antigens not expressed by the vaccine, showing that epitope-spreading occurred in vivo. Frequencies of nTregs and MDSCs were comparable to healthy donors at the beginning of study. A significant decrease of nTregs was detected after vaccination (p = 0.012). High immune response rates, decreased frequencies of nTregs and a mixed T helper 1/T helper 2 (T(H)1/T(H)2)-like cytokine pattern support the applicability of this RCC generic vaccine for use in combination therapies.
Collapse
Affiliation(s)
- Heike Pohla
- Laboratory of Tumor Immunology, LIFE Center, Ludwig Maximilians University, Munich, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
41
|
Darehdori AS, Dastjerdi MN, Dahim H, Slahshoor M, Babazadeh Z, Taghavi MM, Taghipour Z, Gaafarineveh H. Lack of significance of the BRCA2 promoter methylation status in different genotypes of the MTHFR a1298c polymorphism in ovarian cancer cases in Iran. Asian Pac J Cancer Prev 2013; 13:1833-6. [PMID: 22901131 DOI: 10.7314/apjcp.2012.13.5.1833] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVE Promoter methylation, which can be regulated by MTHFR activity, is associated with silencing of genes. In this study we evaluated the methylation status (type) of the BRCA2 promoter in ovarian cancer patients carrying different genotypes of the MTHFR gene (A or C polymorphisms at position 1298). METHODS The methylation type of the BRCA2 promoter was evaluated using bisulfate-modified DNA in methylation- specific PCR and the MTHFRa1278c polymorphism was assessed by PCR-RFLP. RESULTS Analysis of the BRCA2 promoter methylation type of cases showed that 7 out of 60 cases (11.7%) were methylated while the remaining 53 (88.3%) were unmethylated. In methylated cases, one out of the 7 cases had a CC genotype and the remaining 6 methylated cases had an AC genotype. The AA genotype was absent. In unmethylated cases, 34, 18, and one out of these had AC, AA and CC genotype, respectively. CONCLUSION There was no significant relationship between the methylation types of the BRCA2 promoter in different genotypes of MTHFRa1298c polymorphism in ovarian cancer; p=0.255. There was no significant relation between the methylation types of the BRCA2 promoter in different genotypes of the MTHFRa1298c polymorphism in ovarian cancer.
Collapse
|
42
|
Irandoust M, Alvarez Zarate J, Hubeek I, van Beek EM, Schornagel K, Broekhuizen AJF, Akyuz M, van de Loosdrecht AA, Delwel R, Valk PJ, Sonneveld E, Kearns P, Creutzig U, Reinhardt D, de Bont ESJM, Coenen EA, van den Heuvel-Eibrink MM, Zwaan CM, Kaspers GJL, Cloos J, van den Berg TK. Engagement of SIRPα inhibits growth and induces programmed cell death in acute myeloid leukemia cells. PLoS One 2013; 8:e52143. [PMID: 23320069 PMCID: PMC3540026 DOI: 10.1371/journal.pone.0052143] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Accepted: 11/08/2012] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Recent studies show the importance of interactions between CD47 expressed on acute myeloid leukemia (AML) cells and the inhibitory immunoreceptor, signal regulatory protein-alpha (SIRPα) on macrophages. Although AML cells express SIRPα, its function has not been investigated in these cells. In this study we aimed to determine the role of the SIRPα in acute myeloid leukemia. DESIGN AND METHODS We analyzed the expression of SIRPα, both on mRNA and protein level in AML patients and we further investigated whether the expression of SIRPα on two low SIRPα expressing AML cell lines could be upregulated upon differentiation of the cells. We determined the effect of chimeric SIRPα expression on tumor cell growth and programmed cell death by its triggering with an agonistic antibody in these cells. Moreover, we examined the efficacy of agonistic antibody in combination with established antileukemic drugs. RESULTS By microarray analysis of an extensive cohort of primary AML samples, we demonstrated that SIRPα is differentially expressed in AML subgroups and its expression level is dependent on differentiation stage, with high levels in FAB M4/M5 AML and low levels in FAB M0-M3. Interestingly, AML patients with high SIRPα expression had a poor prognosis. Our results also showed that SIRPα is upregulated upon differentiation of NB4 and Kasumi cells. In addition, triggering of SIRPα with an agonistic antibody in the cells stably expressing chimeric SIRPα, led to inhibition of growth and induction of programmed cell death. Finally, the SIRPα-derived signaling synergized with the activity of established antileukemic drugs. CONCLUSIONS Our data indicate that triggering of SIRPα has antileukemic effect and may function as a potential therapeutic target in AML.
Collapse
MESH Headings
- Adult
- Antibodies, Monoclonal/administration & dosage
- Antigens, Differentiation/genetics
- Antigens, Differentiation/metabolism
- Antineoplastic Agents/administration & dosage
- Apoptosis/genetics
- Cell Differentiation/genetics
- Cell Line, Tumor
- Child
- Gene Expression Regulation, Neoplastic
- Growth Inhibitors/physiology
- Humans
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myeloid, Acute/therapy
- Leukemia, Promyelocytic, Acute/metabolism
- Leukemia, Promyelocytic, Acute/pathology
- Leukemia, Promyelocytic, Acute/therapy
- Molecular Targeted Therapy
- Prognosis
- Receptors, Immunologic/genetics
- Receptors, Immunologic/metabolism
- Signal Transduction/genetics
Collapse
Affiliation(s)
- Mahban Irandoust
- Department of Pediatric Hematology/Oncology, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Hematology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Julian Alvarez Zarate
- Sanquin Research & Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Isabelle Hubeek
- Department of Pediatric Hematology/Oncology, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Hematology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Ellen M. van Beek
- Sanquin Research & Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Karin Schornagel
- Sanquin Research & Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
| | - Aart J. F. Broekhuizen
- Department of Pediatric Hematology/Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Mercan Akyuz
- Department of Pediatric Hematology/Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | | | - Ruud Delwel
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Peter J. Valk
- Department of Hematology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Edwin Sonneveld
- Dutch Childhood Oncology Group (DCOG), The Hague, The Netherlands
| | - Pamela Kearns
- School of Cancer Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Ursula Creutzig
- Department of Pediatric Hematology/Oncology, Medical School Hannover, Hannover, Germany
| | - Dirk Reinhardt
- Department of Pediatric Hematology/Oncology, Medical School Hannover, Hannover, Germany
| | | | - Eva A. Coenen
- Department of Pediatric Hematology/Oncology, Erasmus MC/Sophia Children's Hospital, Rotterdam, The Netherlands
| | | | - C. Michel Zwaan
- Department of Pediatric Hematology/Oncology, Erasmus MC/Sophia Children's Hospital, Rotterdam, The Netherlands
| | - Gertjan J. L. Kaspers
- Department of Pediatric Hematology/Oncology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Jacqueline Cloos
- Department of Pediatric Hematology/Oncology, VU University Medical Centre, Amsterdam, The Netherlands
- Department of Hematology, VU University Medical Centre, Amsterdam, The Netherlands
| | - Timo K. van den Berg
- Sanquin Research & Landsteiner Laboratory, Academic Medical Centre, University of Amsterdam, Amsterdam, The Netherlands
- * E-mail:
| |
Collapse
|
43
|
Development of a non-invasive method, multiplex methylation specific PCR (MMSP), for early diagnosis of nasopharyngeal carcinoma. PLoS One 2012; 7:e45908. [PMID: 23144779 PMCID: PMC3489875 DOI: 10.1371/journal.pone.0045908] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2012] [Accepted: 08/23/2012] [Indexed: 12/15/2022] Open
Abstract
Increasing evidence demonstrated that inactivation of tumor suppressor genes (TSGs) by aberrant promoter methylation is an early event during carcinogenesis. Aiming at developing early diagnostic or prognostic tools for various tumors, we took an EBV-associated tumor, nasopharyngeal carcinoma (NPC), as a model and developed a powerful assay based on "multiplex methylation specific-PCR (MMSP)". The MMSP assay was designed to detect tumor-specific methylation status of several NPC-related genes and was capable of acquiring multiplex information simultaneously through a single PCR reaction with the tiny tumor DNA derived from the direct body fluid close to the primary tumor. In this study, we collected paired nasopharyngeal (NP) swabs and NPC biopsies from 49 NPC patients and twenty noncancerous controls. A panel of markers including two EBV, and two cellular TSG markers were applied in this NPC-specific-MMSP assay. We optimized the working condition of MMSP so that it provides information equal to that from the corresponding separate PCRs. The results showed that MMSP patterns of NPC swab were largely consistent with those of corresponding biopsies and significantly distinguished themselves from those of 20 noncancerous volunteers. Among the 69 samples (49 NPCs and 20 normal controls), the sensitivity of detecting NPC from NP swabs is 98%. The specificity is as high as 100%. In conclusion, being characterized by its noninvasiveness, high reproducibility and informativeness, MMSP assay is a reliable and potential diagnostic tool for NPC. It paves the way for the development of population screening and early diagnosis approaches for various tumor types.
Collapse
|
44
|
Chen Q, Zhang L, Zhao J, Ma Y. DNA methylation analysis of exon-1 of the ovine HOXC-8 gene in Mongolian sheep using bisulphite sequencing. JOURNAL OF APPLIED ANIMAL RESEARCH 2012. [DOI: 10.1080/09712119.2012.658059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
45
|
Rosenbaum E, Begum S, Brait M, Zahurak M, Maldonado L, Mangold LA, Eisenberger MA, Epstein JI, Partin AW, Sidransky D, Hoque MO. AIM1 promoter hypermethylation as a predictor of decreased risk of recurrence following radical prostatectomy. Prostate 2012; 72:1133-9. [PMID: 22127895 PMCID: PMC3360823 DOI: 10.1002/pros.22461] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Accepted: 10/27/2011] [Indexed: 11/09/2022]
Abstract
PURPOSE To evaluate the prognostic significance of six epigenetic biomarkers (AIM1, CDH1, KIF1A, MT1G, PAK3, and RBM6 promoter hypermethlation) in a homogeneous group of prostate cancer patients, following radical prostatectomy (RP). PATIENTS AND METHODS Biomarker analyses were performed retrospectively on tumors from 95 prostate cancer patients all with a Gleason score of 3 + 4 = 7 and a minimum follow-up period of 8 years. Using Quantitative Methylation Specific PCR (QMSP), we analyzed the promoter region of six genes in primary prostate tumor tissues. Time to any progression was the primary endpoint and development of metastatic disease and/or death from prostate cancer was a secondary endpoint. The association of clinicopathological and biomolecular risk factors to recurrence was performed using the Log-rank test and Cox proportional hazards model for multivariate analysis. To identify independent prognostic factors, a stepwise selection method was used. RESULTS At a median follow-up time of 10 years, 48 patients (50.5%) had evidence of recurrence: Biochemical/PSA relapse, metastases, or death from prostate cancer. In the final multivariate analysis for time to progression, the significant factors were: Older age, HR = 0.95 (95% CI: 0.91, 1.0) (P = 0.03), positive lymph nodes HR = 2.11 (95% CI: 1.05, 4.26) (P = 0.04), and decreased hypermethylation of AIM1 HR = 0.45 (95% CI: 0.2, 1.0) (P = 0.05). CONCLUSIONS Methylation status of AIM1 in the prostate cancer specimen may predict for time to recurrence in Gleason 3 + 4 = 7 patients undergoing prostatectomy. These results should be validated in a larger and unselected cohort.
Collapse
Affiliation(s)
- Eli Rosenbaum
- Department of Otolaryngology and Head & Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Abstract
Epigenetics encompasses all heritable and reversible modifications to chromatin that alter gene accessibility, and thus are the primary mechanisms for regulating gene transcription. DNA methylation is an epigenetic modification that acts predominantly as a repressive mark. Through the covalent addition of a methyl group onto cytosines in CpG dinucleotides, it can recruit additional repressive proteins and histone modifications to initiate processes involved in condensing chromatin and silencing genes. DNA methylation is essential for normal development as it plays a critical role in developmental programming, cell differentiation, repression of retroviral elements, X-chromosome inactivation and genomic imprinting. One of the most powerful methods for DNA methylation analysis is bisulfite mutagenesis. Sodium bisulfite is a DNA mutagen that deaminates cytosines into uracils. Following PCR amplification and sequencing, these conversion events are detected as thymines. Methylated cytosines are protected from deamination and thus remain as cytosines, enabling identification of DNA methylation at the individual nucleotide level. Development of the bisulfite mutagenesis assay has advanced from those originally reported towards ones that are more sensitive and reproducible. One key advancement was embedding smaller amounts of DNA in an agarose bead, thereby protecting DNA from the harsh bisulfite treatment. This enabled methylation analysis to be performed on pools of oocytes and blastocyst-stage embryos. The most sophisticated bisulfite mutagenesis protocol to date is for individual blastocyst-stage embryos. However, since blastocysts have on average 64 cells (containing 120-720 pg of genomic DNA), this method is not efficacious for methylation studies on individual oocytes or cleavage-stage embryos. Taking clues from agarose embedding of minute DNA amounts including oocytes, here we present a method whereby oocytes are directly embedded in an agarose and lysis solution bead immediately following retrieval and removal of the zona pellucida from the oocyte. This enables us to bypass the two main challenges of single oocyte bisulfite mutagenesis: protecting a minute amount of DNA from degradation, and subsequent loss during the numerous protocol steps. Importantly, as data are obtained from single oocytes, the issue of PCR bias within pools is eliminated. Furthermore, inadvertent cumulus cell contamination is detectable by this method since any sample with more than one methylation pattern may be excluded from analysis. This protocol provides an improved method for successful and reproducible analyses of DNA methylation at the single-cell level and is ideally suited for individual oocytes as well as cleavage-stage embryos.
Collapse
Affiliation(s)
- Michelle M Denomme
- Department of Obstretrics & Gynaecology, Schulich School of Medicine and Dentistry, University of Western Ontario, Ontario, Canada
| | | | | |
Collapse
|
47
|
Lisanti S, von Zglinicki T, Mathers JC. Standardization and quality controls for the methylated DNA immunoprecipitation technique. Epigenetics 2012; 7:615-25. [PMID: 22507898 DOI: 10.4161/epi.20028] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
MeDIP (Methylated DNA Immunoprecipitation) is a relatively recent technique aimed to enrich the methylated fraction of DNA with an antibody directed against 5-methyl-cytosine. MeDIP processed samples are suitable for investigation of the methylation status of specific genomic loci and for performing genome-wide screening when hybridized to DNA methylation microarrays or analyzed by deep sequencing. Here, we describe a standardization protocol and quality controls to assess the specificity, reproducibility and efficiency of the MeDIP procedure. These may have utility when comparing results between samples and experiments within laboratories and between laboratories.
Collapse
Affiliation(s)
- Sofia Lisanti
- Centre for Integrated Systems Biology of Aging and Nutrition; Institute for Aging and Health; Newcastle University; Newcastle upon Tyne, UK.
| | | | | |
Collapse
|
48
|
Nikbakht M, Shabanizadeh A, Salehi M, Talebi A, Arababadi MK, Dahim H, Kennedy D. BRCA1Promoter Methylation Status in Ovarian Cancer. Lab Med 2012. [DOI: 10.1309/lm36temluwnzj0tz] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
|
49
|
Mo Y, Midorikawa K, Zhang Z, Zhou X, Ma N, Huang G, Hiraku Y, Oikawa S, Murata M. Promoter hypermethylation of Ras-related GTPase gene RRAD inactivates a tumor suppressor function in nasopharyngeal carcinoma. Cancer Lett 2012; 323:147-54. [PMID: 22487779 DOI: 10.1016/j.canlet.2012.03.042] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2011] [Revised: 03/30/2012] [Accepted: 03/31/2012] [Indexed: 10/28/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is endemic in southern China. In a genome-wide screen for genes inactivated by promoter hypermethylation, we identified Ras-related associated with diabetes (RRAD). Expression of RRAD was down-regulated in 83.3% (30/36) of the biopsies from NPC patients. RRAD was aberrantly methylated in 74.3% (26/35) of primary tumors, but not in normal nasopharyngeal epithelium. Ectopic RRAD expression in NPC cell lines inhibited the cell growth, colony formation, and cell migration. These results indicate that RRAD might act as a functional tumor suppressor and its epigenetic inactivation may play an important role in NPC development.
Collapse
Affiliation(s)
- Yingxi Mo
- Department of Environmental and Molecular Medicine, Mie University Graduate School of Medicine, Japan
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Pedersen IS, Krarup HB, Thorlacius-Ussing O, Madsen PH. High recovery of cell-free methylated DNA based on a rapid bisulfite-treatment protocol. BMC Mol Biol 2012; 13:12. [PMID: 22448717 PMCID: PMC3324385 DOI: 10.1186/1471-2199-13-12] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 03/26/2012] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Detection of cell-free methylated DNA in plasma is a promising tool for tumour diagnosis and monitoring. Due to the very low amounts of cell-free DNA in plasma, analytical sensitivity is of utmost importance. The vast majority of currently available methods for analysing DNA methylation are based on bisulfite-mediated deamination of cytosine. Cytosine is rapidly converted to uracil during bisulfite treatment, whereas 5-methylcytosine is only slowly converted. Hence, bisulfite treatment converts an epigenetic modification into a difference in sequence, amenable to analysis either by sequencing or PCR based methods. However, the recovery of bisulfite-converted DNA is very poor. RESULTS Here we introduce an alternative method for the crucial steps of bisulfite treatment with high recovery. The method is based on an accelerated deamination step and alkaline desulfonation in combination with magnetic silica purification of DNA, allowing preparation of deaminated DNA from patient samples in less than 2 hours. CONCLUSIONS The method presented here allows low levels of DNA to be easily and reliably analysed, a prerequisite for the clinical usefulness of cell-free methylated DNA detection in plasma.
Collapse
Affiliation(s)
- Inge Søkilde Pedersen
- Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Denmark, DK
| | - Henrik Bygum Krarup
- Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Denmark, DK
| | | | - Poul Henning Madsen
- Section of Molecular Diagnostics, Department of Clinical Biochemistry, Aalborg University Hospital, Denmark, DK
| |
Collapse
|