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McGuire MH, Dasari SK, Yao H, Wen Y, Mangala LS, Bayraktar E, Ma W, Ivan C, Shoshan E, Wu SY, Jonasch E, Bar-Eli M, Wang J, Baggerly KA, Sood AK. Gene Body Methylation of the Lymphocyte-Specific Gene CARD11 Results in Its Overexpression and Regulates Cancer mTOR Signaling. Mol Cancer Res 2021; 19:1917-1928. [PMID: 34348992 PMCID: PMC8568653 DOI: 10.1158/1541-7786.mcr-20-0753] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 06/16/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022]
Abstract
Investigations into the function of nonpromoter DNA methylation have yielded new insights into epigenetic regulation of gene expression. Previous studies have highlighted the importance of distinguishing between DNA methylation in discrete functional regions; however, integrated nonpromoter DNA methylation and gene expression analyses across a wide number of tumor types and corresponding normal tissues have not been performed. Through integrated analysis of gene expression and DNA methylation profiles, we examined 32 tumor types and identified 57 tumor suppressors and oncogenes out of 260 genes exhibiting a correlation of > 0.5 between gene body methylation and gene expression in at least one tumor type. The lymphocyte-specific gene CARD11 exhibits robust association between gene body methylation and expression across 19 of 32 tumor types examined. It is significantly overexpressed in kidney renal cell carcinoma (KIRC) and lung adenocarcinoma (LUAD) tumor tissues in comparison with respective control samples; and is significantly associated with lower overall survival in KIRC. Contrary to its canonical function in lymphocyte NFκB activation, CARD11 activates the mTOR pathway in KIRC and LUAD, resulting in suppressed autophagy. Furthermore, demethylation of a CpG island within the gene body of CARD11 decreases gene expression. Collectively, our study highlights how DNA methylation outside the promoter region can impact tumor progression. IMPLICATIONS: Our study describes a novel regulatory role of gene body DNA methylation-dependent CARD11 expression on mTOR signaling and its impact on tumor progression.
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Affiliation(s)
- Michael H McGuire
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Santosh K Dasari
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hui Yao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yunfei Wen
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lingegowda S Mangala
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Emine Bayraktar
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wencai Ma
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Cristina Ivan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Einav Shoshan
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Sherry Y Wu
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Eric Jonasch
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Menashe Bar-Eli
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Keith A Baggerly
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Anil K Sood
- Department of Gynecologic Oncology and Reproductive Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas.
- Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, Houston, Texas
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2
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Kim JY, Choi BG, Jelinek J, Kim DH, Lee SH, Cho K, Rha SH, Lee YH, Jin HS, Choi DK, Kim GE, Kwon SU, Hwang J, Cha JK, Lee S, Issa JPJ, Kim J. Promoter methylation changes in ALOX12 and AIRE1: novel epigenetic markers for atherosclerosis. Clin Epigenetics 2020; 12:66. [PMID: 32398127 PMCID: PMC7218560 DOI: 10.1186/s13148-020-00846-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2019] [Accepted: 04/08/2020] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Atherosclerosis is the main cause of cardiovascular diseases such as ischemic stroke and coronary heart disease. Gene-specific promoter methylation changes have been suggested as one of the causes underlying the development of atherosclerosis. We aimed to identify and validate specific genes that are differentially expressed through promoter methylation in atherosclerotic plaques. We performed the present study in four steps: (1) profiling and identification of gene-specific promoter methylation changes in atherosclerotic tissues; (2) validation of the promoter methylation changes of genes in plaques by comparison with non-plaque intima; (3) evaluation of promoter methylation status of the genes in vascular cellular components composing atherosclerotic plaques; and (4) evaluation of promoter methylation differences in genes among monocytes, T cells, and B cells isolated from the blood of ischemic stroke patients. RESULTS Upon profiling, AIRE1, ALOX12, FANK1, NETO1, and SERHL2 were found to have displayed changes in promoter methylation. Of these, AIRE1 and ALOX12 displayed higher methylation levels in plaques than in non-plaque intima, but lower than those in the buffy coat of blood. Between inflammatory cells, the three genes were significantly less methylated in monocytes than in T and B cells. In the vascular cells, AIRE1 methylation was lower in endothelial and smooth muscle cells. ALOX12 methylation was higher in endothelial, but lower in smooth muscle cells. Immunofluorescence staining showed that co-localization of ALOX12 and AIRE1 was more frequent in CD14(+)-monocytes than in CD4(+)-T cell in plaque than in non-plaque intima. CONCLUSIONS Promoter methylation changes in AIRE1 and ALOX12 occur in atherosclerosis and can be considered as novel epigenetic markers.
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Affiliation(s)
- Jee Yeon Kim
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea
| | - Bong-Geun Choi
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea
- Biomedical Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | | | - Dae Hyun Kim
- Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Seo Hyun Lee
- Division of Medical Mathematics Researches, National Institute for Mathematical Sciences, Daejeon, South Korea
| | - Kwangjo Cho
- Department of Thoracic and Cardiovascular Surgery, Dong-A University Hospital, Busan, South Korea
| | - Seo Hee Rha
- Department of Pathology, Dong-A University Hospital, Busan, South Korea
| | - Young Ho Lee
- Department of Anatomy, School of Medicine, Chungnam National University, Daejeon, South Korea
| | - Hyo Sun Jin
- Biomedical Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | - Dae-Kyoung Choi
- Biomedical Research Center, Chungnam National University Hospital, Daejeon, South Korea
| | - Geun-Eun Kim
- Department of Vascular Surgery, Asan Medical Center, Seoul, South Korea
| | - Sun U Kwon
- Department of Neurology, Asan Medical Center, Seoul, South Korea
| | - Junha Hwang
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea
| | - Jae Kwan Cha
- Department of Neurology, Dong-A University Hospital, Busan, South Korea
| | - Sukhoon Lee
- Division of Medical Mathematics Researches, National Institute for Mathematical Sciences, Daejeon, South Korea
| | | | - Jei Kim
- Department of Neurology and Neuroepigenetics Laboratory, School of Medicine and Hospital, Chungnam National University, Daejeon, South Korea.
- Department of Neurology, Chungnam National University Hospital, 282 Moonhwaro, Joongku, Daejeon, 35015, South Korea.
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3
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Herrera-Merchan A, Cuadros M, Rodriguez MI, Rodriguez S, Torres R, Estecio M, Coira IF, Loidi C, Saiz M, Carmona-Saez P, Medina PP. The value of lncRNA FENDRR and FOXF1 as a prognostic factor for survival of lung adenocarcinoma. Oncotarget 2020; 11:1172-1185. [PMID: 32284793 PMCID: PMC7138163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 10/02/2017] [Indexed: 11/25/2022] Open
Abstract
It is increasingly evident that non-coding RNAs play a significant role in tumour development. However, we still have a limited knowledge of the clinical significance of long non-coding RNAs (lncRNAs) in lung cancer. The FENDRR is a long coding RNA (also named FOXF1-AS1) located in the vicinity of the protein-coding gene FOXF1 at 16q24.1 chromosomal region. The present study aimed to define the clinic pathological significance of the long-non-coding RNA FENDRR in lung adenocarcinomas. FENDRR expression measured by quantitative PCR was found significantly downregulated (p<0.001) in lung adenocarcinoma samples in comparison with their normal adjacent tissues (n=70). RNA in situ hybridization (RNA-FISH) corroborated independently the down-regulation of FENDRR. Interestingly, the expression of FENDRR correlated positively (p<0.001) with the expression of its protein-coding neighbor gene FOXF1. Additionally, FOXF1 expression was also found downregulated in adenocarcinomas compared to normal samples (p<0.001) and its expression was significantly correlated with overall survival alone (p=0.003) or in combination with FENDRR expression (p=0.01). In conclusion, our data support that FENDRR and FOXF1 expression is decreased in lung adenocarcinoma and should be considered as new potential diagnostic/prognosis biomarkers.
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Affiliation(s)
- Antonio Herrera-Merchan
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Marta Cuadros
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Maria Isabel Rodriguez
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Sandra Rodriguez
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Raul Torres
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Marcos Estecio
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Isabel F. Coira
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Claudia Loidi
- Pathological Anatomy, University Hospital Cruces, University of Pais Vasco, Spain
| | - Monica Saiz
- Pathological Anatomy, University Hospital Cruces, University of Pais Vasco, Spain
| | - Pedro Carmona-Saez
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
| | - Pedro P. Medina
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
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4
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Sirasunthorn N, Jailwala A, Gerber A, Comstock LR. Evaluation of
N
‐Mustard Analogues of
S
‐Adenosyl‐L‐methionine with Eukaryotic DNA Methyltransferase 1. ChemistrySelect 2019. [DOI: 10.1002/slct.201902940] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Nichanun Sirasunthorn
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Anuj Jailwala
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Anna Gerber
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
| | - Lindsay R. Comstock
- Department of Chemistry Wake Forest University 455 Vine Street Winston-Salem NC 27101–4135 USA
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5
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Epigenetic loss of AOX1 expression via EZH2 leads to metabolic deregulations and promotes bladder cancer progression. Oncogene 2019; 39:6265-6285. [PMID: 31383940 DOI: 10.1038/s41388-019-0902-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/04/2019] [Accepted: 04/05/2019] [Indexed: 12/24/2022]
Abstract
Advanced Bladder Cancer (BLCA) remains a clinical challenge that lacks effective therapeutic measures. Here, we show that distinct, stage-wise metabolic alterations in BLCA are associated with the loss of function of aldehyde oxidase (AOX1). AOX1 associated metabolites have a high predictive value for advanced BLCA and our findings demonstrate that AOX1 is epigenetically silenced during BLCA progression by the methyltransferase activity of EZH2. Knockdown (KD) of AOX1 in normal bladder epithelial cells re-wires the tryptophan-kynurenine pathway resulting in elevated NADP levels which may increase metabolic flux through the pentose phosphate (PPP) pathway, enabling increased nucleotide synthesis, and promoting cell invasion. Inhibition of NADP synthesis rescues the metabolic effects of AOX1 KD. Ectopic AOX1 expression decreases NADP production, PPP flux and nucleotide synthesis, while decreasing invasion in cell line models and suppressing growth in tumor xenografts. Further gain and loss of AOX1 confirm the EZH2-dependent activation, metabolic deregulation, and tumor growth in BLCA. Our findings highlight the therapeutic potential of AOX1 and provide a basis for the development of prognostic markers for advanced BLCA.
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6
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Pan-cancer genomic analysis links 3'UTR DNA methylation with increased gene expression in T cells. EBioMedicine 2019; 43:127-137. [PMID: 31056473 PMCID: PMC6558231 DOI: 10.1016/j.ebiom.2019.04.045] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 04/09/2019] [Accepted: 04/23/2019] [Indexed: 01/12/2023] Open
Abstract
Background Investigations into the function of non-promoter DNA methylation have yielded new insights into the epigenetic regulation of gene expression. However, integrated genome-wide non-promoter DNA methylation and gene expression analyses across a wide number of tumour types and corresponding normal tissues have not been performed. Methods To investigate the impact of non-promoter DNA methylation on cancer pathogenesis, we performed a large-scale analysis of gene expression and DNA methylation profiles, finding enrichment in the 3’UTR DNA methylation positively correlated with gene expression. Filtering for genes in which 3’UTR DNA methylation strongly correlated with gene expression yielded a list of genes enriched for functions involving T cell activation. Findings The important immune checkpoint gene Havcr2 showed a substantial increase in 3’UTR DNA methylation upon T cell activation and subsequent upregulation of gene expression in mice. Furthermore, this increase in Havcr2 gene expression was abrogated by treatment with decitabine. Interpretation These findings indicate that the 3’UTR is a functionally relevant DNA methylation site. Additionally, we show a potential novel mechanism of HAVCR2 regulation in T cells, providing new insights for modulating immune checkpoint blockade.
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7
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Sutton MN, Huang GY, Zhou J, Mao W, Langley R, Lu Z, Bast RC. Amino Acid Deprivation-Induced Autophagy Requires Upregulation of DIRAS3 through Reduction of E2F1 and E2F4 Transcriptional Repression. Cancers (Basel) 2019; 11:cancers11050603. [PMID: 31052266 PMCID: PMC6562629 DOI: 10.3390/cancers11050603] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/19/2019] [Accepted: 04/26/2019] [Indexed: 01/07/2023] Open
Abstract
Failure to cure ovarian cancer relates to the persistence of dormant, drug-resistant cancer cells following surgery and chemotherapy. “Second look” surgery can detect small, poorly vascularized nodules of persistent ovarian cancer in ~50% of patients, where >80% are undergoing autophagy and express DIRAS3. Autophagy is one mechanism by which dormant cancer cells survive in nutrient poor environments. DIRAS3 is a tumor suppressor gene downregulated in >60% of primary ovarian cancers by genetic, epigenetic, transcriptional and post-transcriptional mechanisms, that upon re-expression can induce autophagy and dormancy in a xenograft model of ovarian cancer. We examined the expression of DIRAS3 and autophagy in ovarian cancer cells following nutrient deprivation and the mechanism by which they are upregulated. We have found that DIRAS3 mediates autophagy induced by amino acid starvation, where nutrient sensing by mTOR plays a central role. Withdrawal of amino acids downregulates mTOR, decreases binding of E2F1/4 to the DIRAS3 promoter, upregulates DIRAS3 and induces autophagy. By contrast, acute amino acid deprivation did not affect epigenetic regulation of DIRAS3 or expression of miRNAs that regulate DIRAS3. Under nutrient poor conditions DIRAS3 can be transcriptionally upregulated, inducing autophagy that could sustain dormant ovarian cancer cells.
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Affiliation(s)
- Margie N Sutton
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Gilbert Y Huang
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Jinhua Zhou
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Soochow University, Suzhou 215006, China.
| | - Weiqun Mao
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert Langley
- Office of Translational Research, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Zhen Lu
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
| | - Robert C Bast
- Department of Experimental Therapeutics, The University of Texas M.D. Anderson Cancer Center, Houston, TX 77030, USA.
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8
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Garafutdinov RR, Galimova AA, Sakhabutdinova AR. The influence of CpG (5'-d(CpG)-3' dinucleotides) methylation on ultrasonic DNA fragmentation. J Biomol Struct Dyn 2018; 37:3877-3886. [PMID: 30351231 DOI: 10.1080/07391102.2018.1533888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
DNA methylation is an important way of gene regulation. The variety of methods for DNA methylation analysis based on chemical modification or enzyme digestion has been proposed. However, DNA is able to undergo transformations under physical power. Here, we report that the cytosine methylation in CpG dinucleotides determines the difference in fragmentation rate of methylated and unmethylated DNA under sonication. We found that at the beginning of sonication, methylated DNAs are degraded faster than unmethylated one, and the difference in fragmentation degree can be evaluated with high reliability by quantitative polymerase chain reaction (qPCR). The optimal parameters that provide the greatest difference in amount of amplifiable DNA targets corresponding to fragmentation degree are the following: moderate amplicon size (about 150-250 bp), medium CpG sparseness (one CpG dinucleotide per ∼12-14 nucleotides of the chain), and short sonication time (less than 5 min). Along with CpG, the CpA and CpT contents of amplified regions should be taken into account for proper DNA fragmentation by ultrasound as well. The obtained data could be used for elaboration of a method for comparative methylation testing, when there is no need to detect methylation of certain CpG dinucleotides. This method will be simple (can be used by any technician familiar with PCR), low cost (no need to use an expensive reagents), and fast (only brief DNA sonication and conventional qPCR are carried out). Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ravil R Garafutdinov
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
| | - Aizilya A Galimova
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
| | - Assol R Sakhabutdinova
- a Institute of Biochemistry and Genetics, Ufa Federal Research Centre, Russian Academy of Sciences , Ufa , Bashkortostan , Russia
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9
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Abstract
Digital Restriction Enzyme Analysis of Methylation (DREAM) is a method for quantitative mapping of DNA methylation across genomes using next-generation sequencing (NGS) technology. The method is based on sequential cuts of genomic DNA with a pair of restriction enzymes (SmaI and XmaI) at CCCGGG target sites. Unmethylated sites are first digested with SmaI. This enzyme cuts the sites in the middle at CCC^GGG, leaving behind blunt ended fragments. CpG methylation completely blocks SmaI; therefore, only unmethylated sites are cleaved. The remaining methylated sites are digested with XmaI in the next step. This enzyme is not blocked by CpG methylation. It cuts the recognition site sideways at C^CCGGG forming 5'-CCGG overhangs. The sequential cuts thus create distinct methylation-specific signatures at the ends of restriction fragments: 5'-GGG for unmethylated CpG sites and 5'-CCGGG for methylated sites. The DNA fragments resulting from the digestions are ligated to NGS adapters. Sequencing libraries are prepared using hexanucleotide barcodes for sample identification. Individual libraries with distinct barcodes are pooled and sequenced using a paired ends protocol. The sequencing reads are aligned to the genome and mapped to unique CCCGGG target sites. Methylation at individual CpG sites is calculated as the ratio of sequencing reads with the methylated signature to the total number of reads mapping to the site. Sequencing of 25 million reads per sample typically yields 50,000 unique CpG sites covered with hundreds of reads enabling accurate determination of DNA methylation levels. DREAM does not require bisulfite conversion, has a very low background, and has high sensitivity to low levels of methylation. The method is simple, cost-effective, quantitative, highly reproducible, and can be applied to any species.
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10
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Herrera-Merchan A, Cuadros M, Rodriguez MI, Rodriguez S, Torres R, Estecio M, Coira IF, Loidi C, Saiz M, Carmona-Saez P, Medina PP. The value of lncRNAFENDRRandFOXF1as a prognostic factor for survival of lung adenocarcinoma. Oncotarget 2017. [DOI: 10.18632/oncotarget.22154] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Antonio Herrera-Merchan
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Marta Cuadros
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology III and Immunology, University of Granada, Granada, Spain
| | - Maria Isabel Rodriguez
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Sandra Rodriguez
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Raul Torres
- Molecular Cytogenetics Group, Human Cancer Genetics Program, Spanish National Cancer Research Centre-CNIO, Madrid, Spain
| | - Marcos Estecio
- Department of Epigenetics and Molecular Carcinogenesis, UT MD Anderson Cancer Center, Houston, TX, USA
| | - Isabel F. Coira
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Claudia Loidi
- Pathological Anatomy, University Hospital Cruces, University of Pais Vasco, Spain
| | - Monica Saiz
- Pathological Anatomy, University Hospital Cruces, University of Pais Vasco, Spain
| | - Pedro Carmona-Saez
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
| | - Pedro P. Medina
- Centre for Genomics and Oncological Research, PTS Granada, Centro Pfizer - Universidad de Granada - Junta de Andalucía de Genómica e Investigación Oncológica (GENYO), Granada, Spain
- Department of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
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11
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Soozangar N, Sadeghi MR, Jeddi F, Somi MH, Shirmohamadi M, Samadi N. Comparison of genome‐wide analysis techniques to DNA methylation analysis in human cancer. J Cell Physiol 2017; 233:3968-3981. [DOI: 10.1002/jcp.26176] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/24/2017] [Indexed: 12/11/2022]
Affiliation(s)
- Narges Soozangar
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Molecular Medicine Research CenterTabriz University of Medical SciencesTabrizIran
| | - Mohammad R. Sadeghi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Farhad Jeddi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Mohammad H. Somi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
| | - Masoud Shirmohamadi
- Liver and Gastrointestinal Diseases Research CenterTabriz University of Medical SciencesTabrizIran
| | - Nasser Samadi
- Department of Molecular Medicine, Faculty of Advanced Medical Sciences,Tabriz University of Medical SciencesTabrizIran
- Department of Biochemistry, Faculty of MedicineTabriz University of Medical SciencesTabrizIran
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12
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Sambuudash O, Kim HS, Cho MY. Lack of Aberrant Methylation in an Adjacent Area of Left-Sided Colorectal Cancer. Yonsei Med J 2017; 58:749-755. [PMID: 28540987 PMCID: PMC5447105 DOI: 10.3349/ymj.2017.58.4.749] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Revised: 03/14/2017] [Accepted: 03/14/2017] [Indexed: 12/20/2022] Open
Abstract
PURPOSE The molecular nature and the rate-limiting step of epigenetic field defects in the evolution of left-sided colorectal cancer (LCA) remain uncertain. MATERIALS AND METHODS The methylation status of 27 candidate field defect markers, six classic CpG island methylator phenotype (CIMP) markers, and LINE-1 were determined in LCA and adjacent normal mucosas (ADJs) from 33 LCA patients and in left normal colorectal mucosa (LNM) from 33 age- and sex-matched controls. Hotspot mutation analyses in KRAS codons 12 and 13 and BRAF V600E were performed by genomic PCR and pyrosequencing using DNA extracted from endoscopically biopsied tissues. RESULTS Among the 27 candidate genes tested, we confirmed 15 differentially methylated genes in cancer (15 DMGs; ER, SFRP1, MYOD1, MGMT, CD8a, SPOCK2, ABHD9, BNIP3, IGFBP3, WIF1, MAL, GDNF, ALX4, DOK5, and SLC16A12) in comparison to ADJ samples. We further compared the methylation status of 15 DMGs of ADJs to LNM and found only methylation levels of SLC16A12 in ADJs of LCA patients to be significantly higher than that in LNM (17.3% vs. 11.5%, p=0.002). Based on the CIMP, no significant differences in methylation levels of the 15 DMGs were found between ADJs in CIMP positive LCA cases and those without CIMP. In mutation analyses, no mutation was found in ADJs, while significant KRAS mutations (6/33, 18%) were noted in LCA samples. CONCLUSION Epigenetic field defect marked by aberrant methylation is uncommon in normal-appearing ADJs of LCA, indicating the critical rate-limiting change of methylation is likely to occur with morphological alterations in the evolution of LCA.
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Affiliation(s)
- Otgontuya Sambuudash
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea
| | - Hyun Soo Kim
- Department of Internal Medicine, Yonsei University Wonju College of Medicine, Wonju, Korea.
| | - Mee Yon Cho
- Department of Pathology, Yonsei University Wonju College of Medicine, Wonju, Korea
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13
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Kai M, Niinuma T, Kitajima H, Yamamoto E, Harada T, Aoki H, Maruyama R, Toyota M, Sasaki Y, Sugai T, Tokino T, Nakase H, Suzuki H. TET1 Depletion Induces Aberrant CpG Methylation in Colorectal Cancer Cells. PLoS One 2016; 11:e0168281. [PMID: 27977763 PMCID: PMC5158030 DOI: 10.1371/journal.pone.0168281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/29/2016] [Indexed: 01/02/2023] Open
Abstract
Aberrant DNA methylation is commonly observed in colorectal cancer (CRC), but the underlying mechanism is not fully understood. 5-hydroxymethylcytosine levels and TET1 expression are both reduced in CRC, while epigenetic silencing of TET1 is reportedly associated with the CpG island methylator phenotype. In the present study, we aimed to clarify the relationship between loss of TET1 and aberrant DNA methylation in CRC. Stable TET1 knockdown clones were established using Colo320DM cells, which express high levels of TET1, and HCT116 cells, which express TET1 at a level similar to that in normal colonic tissue. Infinium HumanMethylation450 BeadChip assays revealed increased levels of 5-methylcytosine at more than 10,000 CpG sites in TET1-depleted Colo320DM cells. Changes in DNA methylation were observed at various positions within the genome, including promoters, gene bodies and intergenic regions, and the altered methylation affected expression of a subset of genes. By contrast, TET1 knockdown did not significantly affect DNA methylation in HCT116 cells. However, TET1 depletion was associated with attenuated effects of 5-aza-2’-deoxycytidine on gene expression profiles in both cell lines. These results suggest that loss of TET1 may induce aberrant DNA methylation and may attenuate the effect of 5-aza-2’-deoxycytidine in CRC cells.
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Affiliation(s)
- Masahiro Kai
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Takeshi Niinuma
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Kitajima
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Taku Harada
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hironori Aoki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Mutsumi Toyota
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Yasushi Sasaki
- Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Tamotsu Sugai
- Department of Molecular Diagnostic Pathology, Iwate Medical University, Morioka, Japan
| | - Takashi Tokino
- Medical Genome Science, Research Institute for Frontier Medicine, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiroshi Nakase
- Department of Gastroenterology and Hepatology, Sapporo Medical University School of Medicine, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University School of Medicine, Sapporo, Japan
- * E-mail:
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14
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Han Y, He X. Integrating Epigenomics into the Understanding of Biomedical Insight. Bioinform Biol Insights 2016; 10:267-289. [PMID: 27980397 PMCID: PMC5138066 DOI: 10.4137/bbi.s38427] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 11/01/2016] [Accepted: 11/06/2016] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is one of the most rapidly expanding fields in biomedical research, and the popularity of the high-throughput next-generation sequencing (NGS) highlights the accelerating speed of epigenomics discovery over the past decade. Epigenetics studies the heritable phenotypes resulting from chromatin changes but without alteration on DNA sequence. Epigenetic factors and their interactive network regulate almost all of the fundamental biological procedures, and incorrect epigenetic information may lead to complex diseases. A comprehensive understanding of epigenetic mechanisms, their interactions, and alterations in health and diseases genome widely has become a priority in biological research. Bioinformatics is expected to make a remarkable contribution for this purpose, especially in processing and interpreting the large-scale NGS datasets. In this review, we introduce the epigenetics pioneering achievements in health status and complex diseases; next, we give a systematic review of the epigenomics data generation, summarize public resources and integrative analysis approaches, and finally outline the challenges and future directions in computational epigenomics.
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Affiliation(s)
- Yixing Han
- Mouse Cancer Genetics Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, USA.; Present address: Genetics and Biochemistry Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ximiao He
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA.; Present address: Department of Medical Genetics, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
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15
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Ansari J, Shackelford RE, El-Osta H. Epigenetics in non-small cell lung cancer: from basics to therapeutics. Transl Lung Cancer Res 2016; 5:155-71. [PMID: 27186511 DOI: 10.21037/tlcr.2016.02.02] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Lung cancer remains the number one cause of cancer-related deaths worldwide with 221,200 estimated new cases and 158,040 estimated deaths in 2015. Approximately 80% of cases are non-small cell lung cancer (NSCLC). The diagnosis is usually made at an advanced stage where the prognosis is poor and therapeutic options are limited. The evolution of lung cancer is a multistep process involving genetic, epigenetic, and environmental factor interactions that result in the dysregulation of key oncogenes and tumor suppressor genes, culminating in activation of cancer-related signaling pathways. The past decade has witnessed the discovery of multiple molecular aberrations that drive lung cancer growth, among which are epidermal growth factor receptor (EGFR) mutations and translocations involving the anaplastic lymphoma kinase (ALK) gene. This has translated into therapeutic agent developments that target these molecular alterations. The absence of targetable mutations in 50% of NSCLC cases and targeted therapy resistance development underscores the importance for developing alternative therapeutic strategies for treating lung cancer. Among these strategies, pharmacologic modulation of the epigenome has been used to treat lung cancer. Epigenetics approaches may circumvent the problem of tumor heterogeneity by affecting the expression of multiple tumor suppression genes (TSGs), halting tumor growth and survival. Moreover, it may be effective for tumors that are not driven by currently recognized druggable mutations. This review summarizes the molecular pathology of lung cancer epigenetic aberrations and discusses current efforts to target the epigenome with different pharmacological approaches. Our main focus will be on hypomethylating agents, histone deacetylase (HDAC) inhibitors, microRNA modulations, and the role of novel epigenetic biomarkers. Last, we will address the challenges that face this old-new strategy in treating lung cancer.
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Affiliation(s)
- Junaid Ansari
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Rodney E Shackelford
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
| | - Hazem El-Osta
- 1 Department of Medicine, Feist-Weiller Cancer Center, LSU Health, Shreveport, LA, USA ; 2 Department of Pathology, LSU Health Shreveport, Shreveport, LA, USA
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16
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Kleb B, Estécio MRH, Zhang J, Tzelepi V, Chung W, Jelinek J, Navone NM, Tahir S, Marquez VE, Issa JP, Maity S, Aparicio A. Differentially methylated genes and androgen receptor re-expression in small cell prostate carcinomas. Epigenetics 2016; 11:184-93. [PMID: 26890396 DOI: 10.1080/15592294.2016.1146851] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Small cell prostate carcinoma (SCPC) morphology is rare at initial diagnosis but often emerges during prostate cancer progression and portends a dismal prognosis. It does not express androgen receptor (AR) or respond to hormonal therapies. Clinically applicable markers for its early detection and treatment with effective chemotherapy are needed. Our studies in patient tumor-derived xenografts (PDX) revealed that AR-negative SCPC (AR(-)SCPC) expresses neural development genes instead of the prostate luminal epithelial genes characteristic of AR-positive castration-resistant adenocarcinomas (AR(+)ADENO). We hypothesized that the differences in cellular lineage programs are reflected in distinct epigenetic profiles. To address this hypothesis, we compared the DNA methylation profiles of AR(-) and AR(+) PDX using methylated CpG island amplification and microarray (MCAM) analysis and identified a set of differentially methylated promoters, validated in PDX and corresponding donor patient samples. We used the Illumina 450K platform to examine additional regions of the genome and the correlation between the DNA methylation profiles of the PDX and their corresponding patient tumors. Struck by the low frequency of AR promoter methylation in the AR(-)SCPC, we investigated this region's specific histone modification patterns by chromatin immunoprecipitation. We found that the AR promoter was enriched in silencing histone modifications (H3K27me3 and H3K9me2) and that EZH2 inhibition with 3-deazaneplanocin A (DZNep) resulted in AR expression and growth inhibition in AR(-)SCPC cell lines. We conclude that the epigenome of AR(-) is distinct from that of AR(+) castration-resistant prostate carcinomas, and that the AR(-) phenotype can be reversed with epigenetic drugs.
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Affiliation(s)
- Brittany Kleb
- a Department of Genitourinary Medical Oncology Unit 1374 , The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
| | - Marcos R H Estécio
- b Department of Epigenetics and Molecular Carcinogenesis , Unit 0081, The University of Texas, MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
| | - Jiexin Zhang
- c Department of Bioinformatics and Computational Biology , Unit 1410, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
| | - Vassiliki Tzelepi
- d Department of Pathology , University of Patras, Panepistimioupoli Patron , Greece
| | - Woonbok Chung
- e Fels Institute of Cancer Research and Molecular Biology, Temple University , 3307 N Broad Street, Philadelphia , PA
| | - Jaroslav Jelinek
- e Fels Institute of Cancer Research and Molecular Biology, Temple University , 3307 N Broad Street, Philadelphia , PA
| | - Nora M Navone
- f Department of Genitourinary Medical Oncology , Unit 1374, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
| | - Salahaldin Tahir
- f Department of Genitourinary Medical Oncology , Unit 1374, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
| | - Victor E Marquez
- g Center for Cancer Research, National Cancer Institute, Building 376 Frederick , MD
| | - Jean-Pierre Issa
- e Fels Institute of Cancer Research and Molecular Biology, Temple University , 3307 N Broad Street, Philadelphia , PA
| | - Sankar Maity
- f Department of Genitourinary Medical Oncology , Unit 1374, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
| | - Ana Aparicio
- f Department of Genitourinary Medical Oncology , Unit 1374, The University of Texas MD Anderson Cancer Center , 1515 Holcombe Blvd., Houston , Texas
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17
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Moarii M, Reyal F, Vert JP. Integrative DNA methylation and gene expression analysis to assess the universality of the CpG island methylator phenotype. Hum Genomics 2015; 9:26. [PMID: 26463173 PMCID: PMC4603341 DOI: 10.1186/s40246-015-0048-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/01/2015] [Indexed: 01/26/2023] Open
Abstract
Background The CpG island methylator phenotype (CIMP) was first characterized in colorectal cancer but since has been extensively studied in several other tumor types such as breast, bladder, lung, and gastric. CIMP is of clinical importance as it has been reported to be associated with prognosis or response to treatment. However, the identification of a universal molecular basis to define CIMP across tumors has remained elusive. Results We perform a genome-wide methylation analysis of over 2000 tumor samples from 5 cancer sites to assess the existence of a CIMP with common molecular basis across cancers. We then show that the CIMP phenotype is associated with specific gene expression variations. However, we do not find a common genetic signature in all tissues associated with CIMP. Conclusion Our results suggest the existence of a universal epigenetic and transcriptomic signature that defines the CIMP across several tumor types but does not indicate the existence of a common genetic signature of CIMP. Electronic supplementary material The online version of this article (doi:10.1186/s40246-015-0048-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matahi Moarii
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
| | - Fabien Reyal
- UMR932, Immunity and Cancer Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France. .,Department of Translational Research, Residual Tumor and Response to Treatment Team, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France. .,Department of Surgery, Institut Curie, 26 Rue d'Ulm, Paris, 75006, France.
| | - Jean-Philippe Vert
- CBIO-Centre for Computational Biology, Mines Paristech, PSL-Research University, 35 Rue Saint-Honore, Fontainebleau, F-77300, France. .,Department of Bioinformatics, Biostatistics and System Biology, Institut Curie, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France. .,U900, INSERM, 11-13 Rue Pierre et Marie Curie, Paris, F-75248, France.
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18
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Foy JP, Pickering CR, Papadimitrakopoulou VA, Jelinek J, Lin SH, William WN, Frederick MJ, Wang J, Lang W, Feng L, Zhang L, Kim ES, Fan YH, Hong WK, El-Naggar AK, Lee JJ, Myers JN, Issa JP, Lippman SM, Mao L, Saintigny P. New DNA methylation markers and global DNA hypomethylation are associated with oral cancer development. Cancer Prev Res (Phila) 2015; 8:1027-35. [PMID: 26342026 DOI: 10.1158/1940-6207.capr-14-0179] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2014] [Accepted: 08/20/2015] [Indexed: 01/07/2023]
Abstract
DNA promoter methylation of tumor suppressor genes and global DNA hypomethylation are common features of head and neck cancers. Our goal was to identify early DNA methylation changes in oral premalignant lesions (OPL) that may serve as predictive markers of developing oral squamous cell carcinoma (OSCC). Using high-throughput DNA methylation profiles of 24 OPLs, we found that the top 86 genes differentially methylated between patients who did or did not develop OSCC were simultaneously hypermethylated, suggesting that a CpG island methylation phenotype may occur early during OSCC development. The vast majority of the 86 genes were nonmethylated in normal tissues and hypermethylated in OSCC versus normal mucosa. We used pyrosequencing in a validation cohort of 44 patients to evaluate the degree of methylation of AGTR1, FOXI2, and PENK promoters CpG sites that were included in the top 86 genes and of LINE1 repetitive element methylation, a surrogate of global DNA methylation. A methylation index was developed by averaging the percent methylation of AGTR1, FOXI2, and PENK promoters; patients with a high methylation index had a worse oral cancer-free survival (P = 0.0030). On the other hand, patients with low levels of LINE1 methylation had a significantly worse oral cancer-free survival (P = 0.0153). In conclusion, AGTR1, FOXI2, and PENK promoter methylation and LINE1 hypomethylation may be associated with an increased risk of OSCC development in patients with OPLs.
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Affiliation(s)
- Jean-Philippe Foy
- Cancer Research Center of Lyon, UMR INSERM 1052-CNRS 5286, Lyon, France. Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France. Department of Oral and Maxillo-Facial Surgery, Hôpital Pitié Salpêtrière, Paris, France
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Steven H Lin
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - William N William
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Mitchell J Frederick
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Wenhua Lang
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Li Zhang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Edward S Kim
- Levine Cancer Institute, Carolinas Health Care System, Charlotte, North Carolina
| | - You H Fan
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Waun K Hong
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Adel K El-Naggar
- Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - J Jack Lee
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jean-Pierre Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | | | - Li Mao
- Oncology and Diagnostic Science, University of Maryland Dental School, Baltimore, Maryland.
| | - Pierre Saintigny
- Cancer Research Center of Lyon, UMR INSERM 1052-CNRS 5286, Lyon, France. Department of Translational Research and Innovation, Centre Léon Bérard, Lyon, France. Department of Medicine, Centre Léon Bérard, Lyon, France. Université de Lyon, Lyon, France.
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19
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Ichimura N, Shinjo K, An B, Shimizu Y, Yamao K, Ohka F, Katsushima K, Hatanaka A, Tojo M, Yamamoto E, Suzuki H, Ueda M, Kondo Y. Aberrant TET1 Methylation Closely Associated with CpG Island Methylator Phenotype in Colorectal Cancer. Cancer Prev Res (Phila) 2015; 8:702-11. [PMID: 26063725 DOI: 10.1158/1940-6207.capr-14-0306] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Accepted: 12/16/2014] [Indexed: 11/16/2022]
Abstract
Inactivation of methylcytosine dioxygenase, ten-eleven translocation (TET) is known to be associated with aberrant DNA methylation in cancers. Tumors with a CpG island methylator phenotype (CIMP), a distinct subgroup with extensive DNA methylation, show characteristic features in the case of colorectal cancer. The relationship between TET inactivation and CIMP in colorectal cancers is not well understood. The expression level of TET family genes was compared between CIMP-positive (CIMP-P) and CIMP-negative (CIMP-N) colorectal cancers. Furthermore, DNA methylation profiling, including assessment of the TET1 gene, was assessed in colorectal cancers, as well as colon polyps. The TET1 was silenced by DNA methylation in a subset of colorectal cancers as well as cell lines, expression of which was reactivated by demethylating agent. TET1 methylation was more frequent in CIMP-P (23/55, 42%) than CIMP-N (2/113, 2%, P < 0.0001) colorectal cancers. This trend was also observed in colon polyps (CIMP-P, 16/40, 40%; CIMP-N, 2/24, 8%; P = 0.002), suggesting that TET1 methylation is an early event in CIMP tumorigenesis. TET1 methylation was significantly associated with BRAF mutation but not with hMLH1 methylation in the CIMP-P colorectal cancers. Colorectal cancers with TET1 methylation have a significantly greater number of DNA methylated genes and less pathological metastasis compared to those without TET1 methylation (P = 0.007 and 0.045, respectively). Our data suggest that TET1 methylation may contribute to the establishment of a unique pathway in respect to CIMP-mediated tumorigenesis, which may be incidental to hMLH1 methylation. In addition, our findings provide evidence that TET1 methylation may be a good biomarker for the prediction of metastasis in colorectal cancer.
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Affiliation(s)
- Norihisa Ichimura
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan. Department of Oral and Maxillofacial Surgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Keiko Shinjo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Byonggu An
- Department of Surgery, Ako City Hospital, Ako, Japan
| | - Yasuhiro Shimizu
- Department of Gastrointestinal Surgery, Aichi Cancer Center, Nagoya, Japan
| | - Kenji Yamao
- Department of Gastroenterology, Aichi Cancer Center, Nagoya, Japan
| | - Fumiharu Ohka
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Keisuke Katsushima
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Akira Hatanaka
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Masayuki Tojo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan
| | - Eiichiro Yamamoto
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Minoru Ueda
- Department of Oral and Maxillofacial Surgery, Nagoya University School of Medicine, Nagoya, Japan
| | - Yutaka Kondo
- Department of Epigenomics, Nagoya City University Graduate School of Medical Sciences, Nagoya, Japan.
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Deoxyribonucleic acid methylation profiling of single human blastocysts by methylated CpG-island amplification coupled with CpG-island microarray. Fertil Steril 2015; 103:1566-71.e1-4. [PMID: 25914096 PMCID: PMC4449363 DOI: 10.1016/j.fertnstert.2015.03.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 03/19/2015] [Accepted: 03/20/2015] [Indexed: 11/23/2022]
Abstract
Objective To study whether methylated CpG-island (CGI) amplification coupled with microarray (MCAM) can be used to generate DNA (deoxyribonucleic acid) methylation profiles from single human blastocysts. Design A pilot microarray study with methylated CpG-island amplification applied to human blastocyst genomic DNA and hybridized on CpG-island microarrays. Setting University research laboratory. Patient(s) Five cryopreserved sibling 2-pronuclear zygotes that were surplus to requirements for clinical treatment by in vitro fertilization were donated with informed consent from a patient attending Bourn Hall Clinic, Cambridge, United Kingdom. Intervention(s) None. Main Outcome Measure(s) Successful generation of genome-wide DNA methylation profiles at CpG islands from individual human blastocysts, with common genomic regions of DNA methylation identified between embryos. Result(s) Between 472 and 734 CpG islands were methylated in each blastocyst, with 121 CpG islands being commonly methylated in all 5 blastocysts. A further 159 CGIs were commonly methylated in 4 of the 5 tested blastocysts. Methylation was observed at a number of CGIs within imprinted-gene, differentially methylated regions (DMRs), including placental and preimplantation-specific DMRs. Conclusion(s) The MCAM method is capable of providing comprehensive DNA methylation data in individual human blastocysts.
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21
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Affiliation(s)
- Steven A. Belinsky
- Lung Cancer Program, Lovelace Respiratory Research Institute, Albuquerque, New Mexico 87108;
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22
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Kim SJ, Tae CH, Hong SN, Min BH, Chang DK, Rhee PL, Kim JJ, Kim HC, Kim DH, Kim YH. EYA4 Acts as a New Tumor Suppressor Gene in Colorectal Cancer. Mol Carcinog 2015; 54:1748-57. [PMID: 25620232 DOI: 10.1002/mc.22247] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 10/05/2014] [Accepted: 10/10/2014] [Indexed: 12/19/2022]
Abstract
A previous genome-wide methylation array for colorectal cancer (CRC) identified aberrant promoter methylation of eyes absent 4 (EYA4). However, the correlations between EYA4 methylation and gene expression, the role played by EYA4 protein in colorectal carcinogenesis, and results of the gene-enrichment and functional annotation analysis have not yet been established. We analyzed the EYA4 methylation status and found EYA4 promoter methylation in CRC cell lines (100%), CRC tissues (93.5%) and advanced adenoma tissues (50.7%), compared with normal mucosa (32.6%). There was a significant inverse correlation between EYA4 methylation and expression. EYA4 transfection led to inhibition of cell proliferation in colony assays and xenograft studies. On performing the gene-enrichment and functional annotation analysis, we observed that the differentially expressed genes have been associated with the Wnt and MAPK signaling pathways. Our results demonstrate that EYA4 is under epigenetic regulation in CRC. It is a candidate tumor suppressor gene that acts by inducing up-regulation of DKK1 and inhibiting the Wnt signaling pathway. In addition, EYA4 methylation may be identified in stool samples and it serves as a potential stool biomarker for detection of advanced adenoma and CRC.
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Affiliation(s)
- Sung-Jin Kim
- Samsung Biomedical Research Institute, Samsung Medical Center, Seoul, Korea
| | - Chung Hyun Tae
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Sung Noh Hong
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Byung-Hoon Min
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Dong Kyung Chang
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Poong-Lyul Rhee
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Jae J Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Hee Cheol Kim
- Department of Surgery, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Duk-Hwan Kim
- Center for Genome Research, Samsung Biomedical Research Institute, Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Seoul, Korea
| | - Young-Ho Kim
- Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Korea
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Dueñas-Gonzalez A, Alatorre B, Gonzalez-Fierro A. The impact of DNA methylation technologies on drug toxicology. Expert Opin Drug Metab Toxicol 2014; 10:637-46. [DOI: 10.1517/17425255.2014.889682] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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DNA methylation: potential biomarker in Hepatocellular Carcinoma. Biomark Res 2014; 2:5. [PMID: 24635883 PMCID: PMC4022334 DOI: 10.1186/2050-7771-2-5] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2014] [Accepted: 03/07/2014] [Indexed: 12/12/2022] Open
Abstract
Hepatocellular Carcinoma (HCC) is one of the most common cancers in the world and it is often associated with poor prognosis. Liver transplantation and resection are two currently available curative therapies. However, most patients cannot be treated with such therapies due to late diagnosis. This underscores the urgent need to identify potential markers that ensure early diagnosis of HCC. As more evidences are suggesting that epigenetic changes contribute hepatocarcinogenesis, DNA methylation was poised as one promising biomarker. Indeed, genome wide profiling reveals that aberrant methylation is frequent event in HCC. Many studies showed that differentially methylated genes and CpG island methylator phenotype (CIMP) status in HCC were associated with clinicopathological data. Some commonly studied hypermethylated genes include p16, SOCS1, GSTP1 and CDH1. In addition, studies have also revealed that methylation markers could be detected in patient blood samples and associated with poor prognosis of the disease. Undeniably, increasing number of methylation markers are being discovered through high throughput genome wide data in recent years. Proper and systematic validation of these candidate markers in prospective cohort is required so that their actual prognostication and surveillance value could be accurately determined. It is hope that in near future, methylation marker could be translate into clinical use, where patients at risk could be diagnosed early and that the progression of disease could be more correctly assessed.
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Tahara T, Yamamoto E, Madireddi P, Suzuki H, Maruyama R, Chung W, Garriga J, Jelinek J, Yamano HO, Sugai T, Kondo Y, Toyota M, Issa JPJ, Estécio MRH. Colorectal carcinomas with CpG island methylator phenotype 1 frequently contain mutations in chromatin regulators. Gastroenterology 2014; 146:530-38.e5. [PMID: 24211491 PMCID: PMC3918446 DOI: 10.1053/j.gastro.2013.10.060] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/07/2013] [Revised: 10/03/2013] [Accepted: 10/30/2013] [Indexed: 01/04/2023]
Abstract
BACKGROUND & AIMS Subgroups of colorectal carcinomas (CRCs) characterized by DNA methylation anomalies are termed CpG island methylator phenotype (CIMP)1, CIMP2, or CIMP-negative. The pathogenesis of CIMP1 colorectal carcinomas, and their effects on patients' prognoses and responses to treatment, differ from those of other CRCs. We sought to identify genetic somatic alterations associated with CIMP1 CRCs. METHODS We examined genomic DNA samples from 100 primary CRCs, 10 adenomas, and adjacent normal-appearing mucosae from patients undergoing surgery or colonoscopy at 3 tertiary medical centers. We performed exome sequencing of 16 colorectal tumors and their adjacent normal tissues. Extensive comparison with known somatic alterations in CRCs allowed segregation of CIMP1-exclusive alterations. The prevalence of mutations in selected genes was determined from an independent cohort. RESULTS We found that genes that regulate chromatin were mutated in CIMP1 CRCs; the highest rates of mutation were observed in CHD7 and CHD8, which encode members of the chromodomain helicase/adenosine triphosphate-dependent chromatin remodeling family. Somatic mutations in these 2 genes were detected in 5 of 9 CIMP1 CRCs. A prevalence screen showed that nonsilencing mutations in CHD7 and CHD8 occurred significantly more frequently in CIMP1 tumors (18 of 42 [43%]) than in CIMP2 (3 of 34 [9%]; P < .01) or CIMP-negative tumors (2 of 34 [6%]; P < .001). CIMP1 markers had increased binding by CHD7, compared with all genes. Genes altered in patients with CHARGE syndrome (congenital malformations involving the central nervous system, eye, ear, nose, and mediastinal organs) who had CHD7 mutations were also altered in CRCs with mutations in CHD7. CONCLUSIONS Aberrations in chromatin remodeling could contribute to the development of CIMP1 CRCs. A better understanding of the biological determinants of CRCs can be achieved when these tumors are categorized according to their epigenetic status.
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Affiliation(s)
- Tomomitsu Tahara
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Eiichiro Yamamoto
- First Department of Internal Medicine, Sapporo Medical University, Sapporo, Japan; Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Priyanka Madireddi
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Hiromu Suzuki
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Reo Maruyama
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Woonbok Chung
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Judith Garriga
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Jaroslav Jelinek
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Hiro-O Yamano
- Department of Gastroenterology, Akita Red Cross Hospital, Akita, Japan
| | - Tamotsu Sugai
- Department of Pathology, Iwate Medical University, Morioka, Japan
| | - Yutaka Kondo
- Division of Molecular Oncology, Aichi Cancer Center Research Institute, Nagoya, Japan
| | - Minoru Toyota
- Department of Molecular Biology, Sapporo Medical University, Sapporo, Japan
| | - Jean-Pierre J Issa
- Fels Institute for Cancer Research and Molecular Biology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Marcos R H Estécio
- Department of Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Houston, Texas; Center for Cancer Epigenetics, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Abstract
The myelodysplastic syndrome (MDS) is a clonal hematologic disorder that frequently evolves to acute myeloid leukemia (AML). Its pathogenesis remains unclear, but mutations in epigenetic modifiers are common and the disease often responds to DNA methylation inhibitors. We analyzed DNA methylation in the bone marrow and spleen in two mouse models of MDS/AML, the NUP98-HOXD13 (NHD13) mouse and the RUNX1 mutant mouse model. Methylation array analysis showed an average of 512/3445 (14.9%) genes hypermethylated in NHD13 MDS, and 331 (9.6%) genes hypermethylated in RUNX1 MDS. Thirty-two percent of genes in common between the two models (2/3 NHD13 mice and 2/3 RUNX1 mice) were also hypermethylated in at least two of 19 human MDS samples. Detailed analysis of 41 genes in mice showed progressive drift in DNA methylation from young to old normal bone marrow and spleen; to MDS, where we detected accelerated age-related methylation; and finally to AML, which markedly extends DNA methylation abnormalities. Most of these genes showed similar patterns in human MDS and AML. Repeat element hypomethylation was rare in MDS but marked the transition to AML in some cases. Our data show consistency in patterns of aberrant DNA methylation in human and mouse MDS and suggest that epigenetically, MDS displays an accelerated aging phenotype.
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Jiménez-Chillarón JC, Díaz R, Ramón-Krauel M. Omics Tools for the Genome-Wide Analysis of Methylation and Histone Modifications. FUNDAMENTALS OF ADVANCED OMICS TECHNOLOGIES: FROM GENES TO METABOLITES 2014. [DOI: 10.1016/b978-0-444-62651-6.00004-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Abstract
Epigenetics has undergone an explosion in the past decade. DNA methylation, consisting of the addition of a methyl group at the fifth position of cytosine (5-methylcytosine, 5-mC) in a CpG dinucleotide, is a well-recognized epigenetic mark with important functions in cellular development and pathogenesis. Numerous studies have focused on the characterization of DNA methylation marks associated with disease development as they may serve as useful biomarkers for diagnosis, prognosis, and prediction of response to therapy. Recently, novel cytosine modifications with potential regulatory roles such as 5-hydroxymethylcytosine (5-hmC), 5-formylcytosine (5-foC), and 5-carboxylcytosine (5-caC) have been discovered. Study of the functions of 5-mC and its oxidation derivatives promotes the understanding of the mechanism underlying association of epigenetic modifications with disease biology. In this respect, much has been accomplished in the development of methods for the discovery, detection, and location analysis of 5-mC and its oxidation derivatives. In this review, we focus on the recent advances for the global detection and location study of 5-mC and its oxidation derivatives 5-hmC, 5-foC, and 5-caC.
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Iacobazzi V, Castegna A, Infantino V, Andria G. Mitochondrial DNA methylation as a next-generation biomarker and diagnostic tool. Mol Genet Metab 2013; 110:25-34. [PMID: 23920043 DOI: 10.1016/j.ymgme.2013.07.012] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/03/2013] [Revised: 07/12/2013] [Accepted: 07/12/2013] [Indexed: 10/26/2022]
Abstract
Recent expansion of our knowledge on epigenetic changes strongly suggests that not only nuclear DNA (nDNA), but also mitochondrial DNA (mtDNA) may be subjected to epigenetic modifications related to disease development, environmental exposure, drug treatment and aging. Thus, mtDNA methylation is attracting increasing attention as a potential biomarker for the detection and diagnosis of diseases and the understanding of cellular behavior in particular conditions. In this paper we review the current advances in mtDNA methylation studies with particular attention to the evidences of mtDNA methylation changes in diseases and physiological conditions so far investigated. Technological advances for the analysis of epigenetic variations are promising tools to provide insights into methylation of mtDNA with similar resolution levels as those reached for nDNA. However, many aspects related to mtDNA methylation are still unclear. More studies are needed to understand whether and how changes in mtDNA methylation patterns, global and gene specific, are associated to diseases or risk factors.
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Affiliation(s)
- Vito Iacobazzi
- Department of Biosciences, Biotechnology and Pharmacological Sciences, University of Bari, via Orabona 4, 70125 Bari, Italy.
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Besaratinia A, Cockburn M, Tommasi S. Alterations of DNA methylome in human bladder cancer. Epigenetics 2013; 8:1013-22. [PMID: 23975266 DOI: 10.4161/epi.25927] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Bladder cancer is the fourth most common cancer in men in the United States, and its recurrence rate is highest among all malignancies. The unmet need for improved strategies for early detection, treatment, and monitoring of the progression of this disease continues to translate into high mortality and morbidity. The quest for advanced diagnostic, therapeutic, and prognostic approaches for bladder cancer is a high priority, which can be achieved by understanding the molecular mechanisms of the initiation and progression of this malignancy. Aberrant DNA methylation in single or multiple cancer-related genes/loci has been found in human bladder tumors and cancer cell lines, and urine sediments, and correlated with many clinicopathological features of this disease, including tumor relapse, muscle-invasiveness, and survival. The present review summarizes the published research on aberrant DNA methylation in connection with human bladder cancer. Representative studies are highlighted to set forth the current state of knowledge, gaps in the knowledgebase, and future directions in this prime epigenetic field of research. Identifying the potentially reversible and 'drugable' aberrant DNA methylation events that initiate and promote bladder cancer development can highlight biological markers for early diagnosis, effective therapy and accurate prognosis of this malignancy.
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Affiliation(s)
- Ahmad Besaratinia
- Department of Preventive Medicine; Keck School of Medicine of USC; University of Southern California; Los Angeles, CA USA
| | - Myles Cockburn
- Department of Preventive Medicine; Keck School of Medicine of USC; University of Southern California; Los Angeles, CA USA
| | - Stella Tommasi
- Department of Preventive Medicine; Keck School of Medicine of USC; University of Southern California; Los Angeles, CA USA
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McGraw S, Shojaei Saadi HA, Robert C. Meeting the methodological challenges in molecular mapping of the embryonic epigenome. Mol Hum Reprod 2013; 19:809-27. [PMID: 23783346 DOI: 10.1093/molehr/gat046] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The past decade of life sciences research has been driven by progress in genomics. Many voices are already proclaiming the post-genomics era, in which phenomena other than sequence polymorphism influence gene expression and also explain complex phenotypes. One of these burgeoning fields is the study of the epigenome. Although the mechanisms by which chromatin structure and reorganization as well as cytosine methylation influence gene expression are not fully understood, they are being invoked to explain the now-accepted long-term impact of the environment on gene expression, which appears to be a factor in the development of numerous diseases. Such studies are particularly relevant in early embryonic development, during which waves of epigenetic reprogramming are known to have profound impacts. Since gametes and zygotes are in the process of resetting the genome in order to create embryonic stem cells that will each differentiate to create one of many specific tissue types, this phase of life is now viewed as a window of susceptibility to epigenetic reprogramming errors. Epigenetics could explain the influence of factors such as the nutritional/metabolic status of the mother or the artificial environment of assisted reproductive technologies. However, the peculiar nature of early embryos in addition to their scarcity poses numerous technological challenges that are slowly being overcome. The principal subject of this article is to review the suitability of various current and emerging technological platforms to study oocytes and early embryonic epigenome with more emphasis on studying DNA methylation. Furthermore, the constraint of samples size, inherent to the study of preimplantation embryo development, was put in perspective with the various molecular platforms described.
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Affiliation(s)
- Serge McGraw
- Department of Human Genetics, Montreal Children's Hospital Research Institute, McGill University, Montréal, QC H3Z 2Z3, Canada
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Natsume A, Ito M, Katsushima K, Ohka F, Hatanaka A, Shinjo K, Sato S, Takahashi S, Ishikawa Y, Takeuchi I, Shimogawa H, Uesugi M, Okano H, Kim SU, Wakabayashi T, Issa JPJ, Sekido Y, Kondo Y. Chromatin regulator PRC2 is a key regulator of epigenetic plasticity in glioblastoma. Cancer Res 2013; 73:4559-70. [PMID: 23720055 DOI: 10.1158/0008-5472.can-13-0109] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Tumor cell plasticity contributes to functional and morphologic heterogeneity. To uncover the underlying mechanisms of this plasticity, we examined glioma stem-like cells (GSC) where we found that the biologic interconversion between GSCs and differentiated non-GSCs is functionally plastic and accompanied by gain or loss of polycomb repressive complex 2 (PRC2), a complex that modifies chromatin structure. PRC2 mediates lysine 27 trimethylation on histone H3 and in GSC it affected pluripotency or development-associated genes (e.g., Nanog, Wnt1, and BMP5) together with alterations in the subcellular localization of EZH2, a catalytic component of PRC2. Intriguingly, exogenous expression of EZH2-dNLS, which lacks nuclear localization sequence, impaired the repression of Nanog expression under differentiation conditions. RNA interference (RNAi)-mediated attenuation or pharmacologic inhibition of EZH2 had little to no effect on apoptosis or bromodeoxyuridine incorporation in GSCs, but it disrupted morphologic interconversion and impaired GSC integration into the brain tissue, thereby improving survival of GSC-bearing mice. Pathologic analysis of human glioma specimens revealed that the number of tumor cells with nuclear EZH2 is larger around tumor vessels and the invasive front, suggesting that nuclear EZH2 may help reprogram tumor cells in close proximity to this microenvironment. Our results indicate that epigenetic regulation by PRC2 is a key mediator of tumor cell plasticity, which is required for the adaptation of glioblastoma cells to their microenvironment. Thus, PRC2-targeted therapy may reduce tumor cell plasticity and tumor heterogeneity, offering a new paradigm for glioma treatment.
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Affiliation(s)
- Atsushi Natsume
- Department of Neurosurgery, Nagoya University School of Medicine, Divisions of Epigenomics and Molecular Oncology, Aichi Cancer Center Research Institute
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Umer M, Herceg Z. Deciphering the epigenetic code: an overview of DNA methylation analysis methods. Antioxid Redox Signal 2013; 18:1972-86. [PMID: 23121567 PMCID: PMC3624772 DOI: 10.1089/ars.2012.4923] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
SIGNIFICANCE Methylation of cytosine in DNA is linked with gene regulation, and this has profound implications in development, normal biology, and disease conditions in many eukaryotic organisms. A wide range of methods and approaches exist for its identification, quantification, and mapping within the genome. While the earliest approaches were nonspecific and were at best useful for quantification of total methylated cytosines in the chunk of DNA, this field has seen considerable progress and development over the past decades. RECENT ADVANCES Methods for DNA methylation analysis differ in their coverage and sensitivity, and the method of choice depends on the intended application and desired level of information. Potential results include global methyl cytosine content, degree of methylation at specific loci, or genome-wide methylation maps. Introduction of more advanced approaches to DNA methylation analysis, such as microarray platforms and massively parallel sequencing, has brought us closer to unveiling the whole methylome. CRITICAL ISSUES Sensitive quantification of DNA methylation from degraded and minute quantities of DNA and high-throughput DNA methylation mapping of single cells still remain a challenge. FUTURE DIRECTIONS Developments in DNA sequencing technologies as well as the methods for identification and mapping of 5-hydroxymethylcytosine are expected to augment our current understanding of epigenomics. Here we present an overview of methodologies available for DNA methylation analysis with special focus on recent developments in genome-wide and high-throughput methods. While the application focus relates to cancer research, the methods are equally relevant to broader issues of epigenetics and redox science in this special forum.
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Affiliation(s)
- Muhammad Umer
- Epigenetics Group, International Agency for Research on Cancer IARC, Lyon 69008, France
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Chen W, Xiang J, Chen DF, Ni BB, Chen H, Fan XJ, Wang PN, Song SX, Fang LK, Xiao HY, Wang L, Wang JP. Screening for differentially methylated genes among human colorectal cancer tissues and normal mucosa by microarray chip. Mol Biol Rep 2013; 40:3457-64. [PMID: 23471507 DOI: 10.1007/s11033-012-2338-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2012] [Accepted: 10/01/2012] [Indexed: 01/04/2023]
Abstract
UNLABELLED High density DNA methylation microarrays were used to study the differences of gene methylation level in six pairs of colorectal cancer (CRC) and adjacent normal mucosa. We analyzed the profile of methylated genes by NimbleGen Microarray and the biologic functions by NIH-NAVID. In addition, preliminary validation studies were done in six pairs of samples by MSP (methylation-specific PCR). A total of 4,644 genes had a difference in methylation levels. Among them 2,296 were hypermethylated (log2ratio > 1), 2,348 genes were hypomethylated (log2ratio < -1), in which 293 hypermethylated and 313 hypomethylated genes were unmapped according to the NIH-NAVID. All these genes were randomly distributed on all the chromosomes. However, chromosome 1 contained the most of the hypermethylated genes (232 genes), followed by chromosome 19 (149 genes), chromosome 11 (144 genes), chromosome 2 (141 genes), chromosomes 3 (127 genes). Through the analysis of the statistics, There were 2 hypermethylated/3 hypomethylated genes involved in six pairs of samples simultaneously, followed by 10/14 in five samples, 34/37 in four samples, 101/113 in three samples, 341/377 in two samples, 1,808/1,804 in one sample. According to gene ontology analysis, some physiological processes play important roles in the cell division and the development of tumor, such as apoptosis, DNA repair, immune, cell cycle, cell cycle checkpoint, cell adhesion and invasion etc. Through Preliminary validation, there were two genes (St3gal6, Opcml) in thirty top-ranking genes shown hypermethylated in six pairs of CRC and adjacent normal mucosa. CONCLUSIONS High density DNA methylation microarrays is an effective method for screening aberrantly methylated genes in CRC. The methylated genes should be further studied for diagnostic or prognostic markers for CRC.
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Affiliation(s)
- Wei Chen
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, 26 Yuancunerheng Rd, Guangzhou, Guangdong 510655, People's Republic of China
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Developmentally programmed 3' CpG island methylation confers tissue- and cell-type-specific transcriptional activation. Mol Cell Biol 2013; 33:1845-58. [PMID: 23459939 DOI: 10.1128/mcb.01124-12] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
During development, a small but significant number of CpG islands (CGIs) become methylated. The timing of developmentally programmed CGI methylation and associated mechanisms of transcriptional regulation during cellular differentiation, however, remain poorly characterized. Here, we used genome-wide DNA methylation microarrays to identify epigenetic changes during human embryonic stem cell (hESC) differentiation. We discovered a group of CGIs associated with developmental genes that gain methylation after hESCs differentiate. Conversely, erasure of methylation was observed at the identified CGIs during subsequent reprogramming to induced pluripotent stem cells (iPSCs), further supporting a functional role for the CGI methylation. Both global gene expression profiling and quantitative reverse transcription-PCR (RT-PCR) validation indicated opposing effects of CGI methylation in transcriptional regulation during differentiation, with promoter CGI methylation repressing and 3' CGI methylation activating transcription. By studying diverse human tissues and mouse models, we further confirmed that developmentally programmed 3' CGI methylation confers tissue- and cell-type-specific gene activation in vivo. Importantly, luciferase reporter assays provided evidence that 3' CGI methylation regulates transcriptional activation via a CTCF-dependent enhancer-blocking mechanism. These findings expand the classic view of mammalian CGI methylation as a mechanism for transcriptional silencing and indicate a functional role for 3' CGI methylation in developmental gene regulation.
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Sipos F, Mũzes G, Patai AV, Fũri I, Péterfia B, Hollósi P, Molnár B, Tulassay Z. Genome-wide screening for understanding the role of DNA methylation in colorectal cancer. Epigenomics 2013; 5:569-81. [PMID: 24059802 DOI: 10.2217/epi.13.52] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
DNA methylation analysis methods have undergone an impressive revolution over the past 15 years. Regarding colorectal cancer (CRC), the localization and distribution of several differently methylated genes have been determined by genome-wide DNA methylation assays. These genes do not just influence the pathogenesis of CRC, but can be used further as diagnostic or prognostic markers. Moreover, the identified four DNA methylation-based subgroups of CRC have important clinical and therapeutic merit. Since genome-wide DNA methylation analyzes result in a large amount of data, there is a need for complex bioinformatic and pathway analysis. Future challenges in epigenetic alterations of CRC include the demand for comprehensive identification and experimental validation of gene abnormalities. By introduction of genome-wide DNA methylation profiling into clinical practice not only the patients' risk stratification but development of targeted therapies will also be possible.
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Affiliation(s)
- Ferenc Sipos
- 2nd Department of Internal Medicine, Semmelweis University, Budapest, Hungary
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37
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Abstract
The functional impact of aberrant DNA methylation and the widespread alterations in DNA methylation in cancer development have led to the development of a variety of methods to characterize the DNA methylation patterns. This chapter critiques and describes the major approaches to analyzing DNA methylation.
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Abstract
After completion of the human genome, genome-wide association studies were conducted to identify single nucleotide polymorphisms (SNPs) associated with cancer initiation and progression. Most of the studies identified SNPs that were located outside the coding region, and the odds ratios were too low to implement in clinical practice. Although the genome gives information about genome sequence and structure, the human epigenome provides functional aspects of the genome. Epigenome-wide association studies (EWAS) provide an opportunity to identify genome-wide epigenetic variants that are associated with cancer. However, there are problems and issues in implementing EWAS to establish an association between epigenetic profiles and cancer. Few challenges include selection and handling of samples, choice of population and sample size, accurate measurement of exposure, integrating data, and insufficient information about the role of repeat sequences. The current status of EWAS, challenges in the field, and their potential solutions are discussed in this article.
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Affiliation(s)
- Mukesh Verma
- Epidemiology and Genetics Research Program, Division of Cancer Control and Population Sciences, Division of Epidemiology and Genetics, National Cancer Institute, National Institutes of Health (NIH), 6130 Executive Boulevard, Suite 5100, Bethesda, MD 20892-7324, USA
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Abstract
Bisulfite conversion of genomic DNA combined with next-generation sequencing (NGS) has become a very effective approach for mapping the whole-genome and sub-genome wide DNA methylation landscapes. However, whole methylome shotgun bisulfite sequencing is still expensive and not suitable for analyzing large numbers of human cancer specimens. Recent advances in the development of targeted bisulfite sequencing approaches offer several attractive alternatives. The characteristics and applications of these methods are discussed in this review article. In addition, the bioinformatic tools that can be used for sequence capture probe design as well as downstream sequence analyses are also addressed.
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Tsujioka T, Yokoi A, Uesugi M, Kishimoto M, Tochigi A, Suemori S, Tohyama Y, Tohyama K. Effects of DNA methyltransferase inhibitors (DNMTIs) on MDS-derived cell lines. Exp Hematol 2012; 41:189-97. [PMID: 23085465 DOI: 10.1016/j.exphem.2012.10.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2012] [Revised: 10/03/2012] [Accepted: 10/12/2012] [Indexed: 10/27/2022]
Abstract
DNA methyltransferase inhibitors (DNMTIs), including decitabine (DAC) and azacitidine (AZA), have recently been highlighted for the treatment of high-risk myelodysplastic syndrome (MDS); however, their action mechanisms have not been clearly defined. Therefore, we investigated the effects of DNMTIs on MDS-derived cell lines in vitro. An MDS-derived cell line MDS92 and its blastic subline MDS-L and HL-60 were used. All three cell lines were sensitive to DNMTIs, but MDS-L was the most susceptible. DAC-induced cell death in MDS-L was preceded by DNA damage-induced G2 arrest via a p53-independent pathway. AZA did not influence the pattern of cell cycle, although it induced DNA damage response. The IC(50) of DAC or AZA on MDS-L cells was associated with the dose inducing the maximal hypomethylation in long interspersed nuclear elements-1 (LINE-1) methylation assay. AZA suppressed the level of methylation in a time-dependent manner (days 4, 7, and 10), whereas DAC maintained the level of methylation from day 4 to 11. The protein expression of DNMT1 and DNMT3a decreased with the suppression of growth and methylation. We conclude that this study provides in vitro models for understanding the effects of DNMTIs on cell growth and gene regulation, including differences in the possible action mechanism of DAC and AZA.
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Affiliation(s)
- Takayuki Tsujioka
- Department of Laboratory Medicine, Kawasaki Medical School, 577 Matsushima, Kurashiki, Okayama, Japan.
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Olkhov-Mitsel E, Bapat B. Strategies for discovery and validation of methylated and hydroxymethylated DNA biomarkers. Cancer Med 2012; 1:237-60. [PMID: 23342273 PMCID: PMC3544446 DOI: 10.1002/cam4.22] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2012] [Revised: 06/29/2012] [Accepted: 07/02/2012] [Indexed: 12/13/2022] Open
Abstract
DNA methylation, consisting of the addition of a methyl group at the fifth-position of cytosine in a CpG dinucleotide, is one of the most well-studied epigenetic mechanisms in mammals with important functions in normal and disease biology. Disease-specific aberrant DNA methylation is a well-recognized hallmark of many complex diseases. Accordingly, various studies have focused on characterizing unique DNA methylation marks associated with distinct stages of disease development as they may serve as useful biomarkers for diagnosis, prognosis, prediction of response to therapy, or disease monitoring. Recently, novel CpG dinucleotide modifications with potential regulatory roles such as 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine have been described. These potential epigenetic marks cannot be distinguished from 5-methylcytosine by many current strategies and may potentially compromise assessment and interpretation of methylation data. A large number of strategies have been described for the discovery and validation of DNA methylation-based biomarkers, each with its own advantages and limitations. These strategies can be classified into three main categories: restriction enzyme digestion, affinity-based analysis, and bisulfite modification. In general, candidate biomarkers are discovered using large-scale, genome-wide, methylation sequencing, and/or microarray-based profiling strategies. Following discovery, biomarker performance is validated in large independent cohorts using highly targeted locus-specific assays. There are still many challenges to the effective implementation of DNA methylation-based biomarkers. Emerging innovative methylation and hydroxymethylation detection strategies are focused on addressing these gaps in the field of epigenetics. The development of DNA methylation- and hydroxymethylation-based biomarkers is an exciting and rapidly evolving area of research that holds promise for potential applications in diverse clinical settings.
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Affiliation(s)
- Ekaterina Olkhov-Mitsel
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
| | - Bharati Bapat
- Samuel Lunenfeld Research Institute, Mount Sinai HospitalToronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of TorontoToronto, Ontario, Canada
- Department of Pathology, University Health Network, University of TorontoToronto, Ontario, Canada
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42
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Oki Y, Kondo Y, Yamamoto K, Ogura M, Kasai M, Kobayashi Y, Watanabe T, Uike N, Ohyashiki K, Okamoto SI, Ohnishi K, Tomita A, Miyazaki Y, Tohyama K, Mukai HY, Hotta T, Tomonaga M. Phase I/II study of decitabine in patients with myelodysplastic syndrome: a multi-center study in Japan. Cancer Sci 2012; 103:1839-47. [PMID: 22816487 DOI: 10.1111/j.1349-7006.2012.02386.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2012] [Revised: 07/10/2012] [Accepted: 07/10/2012] [Indexed: 12/23/2022] Open
Abstract
The management of myelodysplastic syndrome (MDS) remains challenging. We performed a phase I/II study to evaluate the safety and efficacy of decitabine in patients with MDS in Japan. Patients with MDS with red cell transfusion dependence or 5-30% blasts in marrow and with an International Prognostic Scoring System score of intermediate-1 or higher were eligible. Patients received intravenous decitabine at 15 or 20 mg/m(2) daily for 5 days every 4 weeks. A total of 37 patients were enrolled. Three patients received 15 mg/m(2) and experienced no dose limiting toxicity during the first cycle. Thirty-four patients received 20 mg/m(2) . Grade 3 or greater non-hematologic toxicities included cerebral infarction (n = 1), subdural hematoma (n = 1), elevated blood glucose (n = 1), and pulmonary hypertension (n = 1). At 20 mg/m(2) , complete response, partial response, and hematologic improvement were observed in 7 (20.6%), 2 (5.9%), and 7 (20.6%) patients, respectively. Complete cytogenetic response was observed in 30% of evaluable 20 patients. The median number of cycles to clinical response was 4 (range 4-8), and duration of remission was 474+ days (range 294-598+). The 2-year rate of acute myeloid leukemia-free survival was 52%. Correlative studies revealed hypomethylation in multiple genes in peripheral blood cells after treatment. Hypomethylation was generally more profound in CD15 + peripheral blood cells, which reflects myeloid cells, than in peripheral blood mononuclear cells. In summary, decitabine was safe and demonstrated efficacy in Japanese patients with high-risk MDS. This trial was registered at ClinicalTrials.gov (NCT00796003).
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Affiliation(s)
- Yasuhiro Oki
- Department of Hematology and Cell Therapy, Aichi Cancer Center Hospital, Nagoya, Japan.
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43
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del Rey M, O'Hagan K, Dellett M, Aibar S, Colyer HAA, Alonso ME, Díez-Campelo M, Armstrong RN, Sharpe DJ, Gutiérrez NC, García JL, De Las Rivas J, Mills KI, Hernández-Rivas JM. Genome-wide profiling of methylation identifies novel targets with aberrant hypermethylation and reduced expression in low-risk myelodysplastic syndromes. Leukemia 2012; 27:610-8. [PMID: 22936014 DOI: 10.1038/leu.2012.253] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Gene expression profiling signatures may be used to classify the subtypes of Myelodysplastic syndrome (MDS) patients. However, there are few reports on the global methylation status in MDS. The integration of genome-wide epigenetic regulatory marks with gene expression levels would provide additional information regarding the biological differences between MDS and healthy controls. Gene expression and methylation status were measured using high-density microarrays. A total of 552 differentially methylated CpG loci were identified as being present in low-risk MDS; hypermethylated genes were more frequent than hypomethylated genes. In addition, mRNA expression profiling identified 1005 genes that significantly differed between low-risk MDS and the control group. Integrative analysis of the epigenetic and expression profiles revealed that 66.7% of the hypermethylated genes were underexpressed in low-risk MDS cases. Gene network analysis revealed molecular mechanisms associated with the low-risk MDS group, including altered apoptosis pathways. The two key apoptotic genes BCL2 and ETS1 were identified as silenced genes. In addition, the immune response and micro RNA biogenesis were affected by the hypermethylation and underexpression of IL27RA and DICER1. Our integrative analysis revealed that aberrant epigenetic regulation is a hallmark of low-risk MDS patients and could have a central role in these diseases.
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Affiliation(s)
- M del Rey
- Centro de Investigación del Cáncer, Universidad de Salamanca-CSIC, Salamanca, Spain
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44
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Luo Y, Tsuchiya KD, Il Park D, Fausel R, Kanngurn S, Welcsh P, Dzieciatkowski S, Wang J, Grady WM. RET is a potential tumor suppressor gene in colorectal cancer. Oncogene 2012; 32:2037-47. [PMID: 22751117 PMCID: PMC3465636 DOI: 10.1038/onc.2012.225] [Citation(s) in RCA: 67] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Cancer arises as the consequence of mutations and epigenetic alterations that activate oncogenes and inactivate tumor suppressor genes. Through a genome-wide screen for methylated genes in colon neoplasms, we identified aberrantly methylated RET in colorectal cancer. RET, a transmembrane receptor tyrosine kinase and a receptor for the glial cell-derived neurotrophic factor family ligands, was one of the first oncogenes to be identified, and has been shown to be an oncogene in thyroid cancer and pheochromocytoma. However, unexpectedly, we found RET is methylated in 27% of colon adenomas and in 63% of colorectal cancers, and now provide evidence that RET has tumor suppressor activity in colon cancer. The aberrant methylation of RET correlates with decreased RET expression, whereas the restoration of RET in colorectal cancer cell lines results in apoptosis. Furthermore, in support of a tumor suppressor function of RET, mutant RET has also been found in primary colorectal cancer. We now show that these mutations inactivate RET, which is consistent with RET being a tumor suppressor gene in the colon. These findings suggest that the aberrant methylation of RET and the mutational inactivation of RET promote colorectal cancer formation, and that RET can serve as a tumor suppressor gene in the colon. Moreover, the increased frequency of methylated RET in colon cancers compared with adenomas suggests RET inactivation is involved in the progression of colon adenomas to cancer.
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Affiliation(s)
- Y Luo
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-Sen University, Guangzhou, China
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45
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Rahmatpanah FB, Carstens S, Hooshmand SI, Welsh EC, Sjahputera O, Taylor KH, Bennett LB, Shi H, Davis JW, Arthur GL, Shanafelt TD, Kay NE, Wooldridge JE, Caldwell CW. Large-scale analysis of DNA methylation in chronic lymphocytic leukemia. Epigenomics 2012; 1:39-61. [PMID: 20495622 DOI: 10.2217/epi.09.10] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
AIMS B-cell chronic lymphocytic leukemia (CLL) is a heterogeneous malignancy that clinically ranges from indolent to rapidly progressive. CLL, like other cancers, can be affected by epigenetic alterations. MATERIALS & METHODS A microarray discovery-based study was initiated to determine DNA methylation in CLL cases with a range of CD38 expression (1–92%). RESULTS Many loci were either methylated or unmethylated across all CD38 levels, but differential methylation was also observed for some genes. Genomic sequencing of DLEU7 confirmed extensive cytosine methylation preferentially in patient samples with low CD38 expression, whereas NRP2, SFRP2 and ADAM12 were more commonly methylated in those with high CD38 expression. CONCLUSION This study demonstrates that CLL is affected by CpG island methylation in some genes that segregate with CD38 expression levels, while most others show similar methylation patterns across all levels. The CpG island methylation in certain functional gene groups and pathway-associated genes that are known to be deregulated in CLL provides additional insights into the CLL methylome and epigenetic contribution to cellular dysfunction. It will now be useful to investigate the effectiveness of epigenetic therapeutic reversal of these alterations to develop effective treatments for the disease.
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Affiliation(s)
- Farahnaz B Rahmatpanah
- Department of Pathology and Anatomical Sciences, Ellis Fischel Cancer Center, University of Missouri School of Medicine, Columbia, Missouri 65212, USA
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46
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Van De Voorde L, Speeckaert R, Van Gestel D, Bracke M, De Neve W, Delanghe J, Speeckaert M. DNA methylation-based biomarkers in serum of patients with breast cancer. Mutat Res 2012; 751:304-325. [PMID: 22698615 DOI: 10.1016/j.mrrev.2012.06.001] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Revised: 06/03/2012] [Accepted: 06/05/2012] [Indexed: 12/18/2022]
Abstract
Alterations of genetic and epigenetic features can provide important insights into the natural history of breast cancer. Although DNA methylation analysis is a rapidly developing field, a reproducible epigenetic blood-based assay for diagnosis and follow-up of breast cancer has yet to be successfully developed into a routine clinical test. The aim of this study was to review multiple serum DNA methylation assays and to highlight the value of those novel biomarkers in diagnosis, prognosis and prediction of therapeutic outcome. Serum is readily accessible for molecular diagnosis in all individuals from a peripheral blood sample. The list of hypermethylated genes in breast cancer is heterogeneous and no single gene is methylated in all breast cancer types. There is increasing evidence that a panel of epigenetic markers is essential to achieve a higher sensitivity and specificity in breast cancer detection. However, the reported percentages of methylation are highly variable, which can be partly explained by the different sensitivities and the different intra-/inter-assay coefficients of variability of the analysis methods. Moreover, there is a striking lack of receiver operating characteristic (ROC) curves of the proposed biomarkers. Another point of criticism is the fact that 'normal' patterns of DNA methylation of some tumor suppressor and other cancer-related genes are influenced by several factors and are often poorly characterized. A relatively frequent methylation of those genes has been observed in high-risk asymptomatic women. Finally, there is a call for larger prospective cohort studies to determine methylation patterns during treatment and follow-up. Identification of patterns specific for a differential response to therapeutic interventions should be useful. Only in this way, it will be possible to evaluate the predictive and prognostic characteristics of those novel promising biomarkers.
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Affiliation(s)
- Lien Van De Voorde
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | | | - Dirk Van Gestel
- Department of Radiation Oncology, Antwerp University Hospital, Antwerp, Belgium
| | - Marc Bracke
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Wilfried De Neve
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Joris Delanghe
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium
| | - Marijn Speeckaert
- Department of Clinical Chemistry, Ghent University Hospital, Ghent, Belgium; Department of Internal Medicine, Ghent University Hospital, Ghent, Belgium.
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47
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Toyota M, Suzuki H, Yamamoto E, Yamano H, Imai K, Shinomura Y. Integrated analysis of genetic and epigenetic alterations in cancer. Epigenomics 2012; 1:291-9. [PMID: 22122704 DOI: 10.2217/epi.09.20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
A proposed genetic model describing the transition from normal colonic epithelium to malignant cancer involves mutation of a number of key oncogenes and tumor suppressor genes. However, only subsets of colorectal cancers contain such mutations. Moreover, the heterogeneous pattern of tumor mutations suggests there are multiple alternative pathways leading to colonic tumorigenesis. These alternative pathways involve epigenetic alterations such as the methylation of multiple CpG islands, termed the CpG island methylator phenotype, and cancers with CpG island methylator phenotype show distinct genetic and clinicopathological features. The causes of these epigenetic alterations are still not fully understood, but exogenous pathogens such as Helicobacter pylori and Epstein-Barr virus, and the chromosomal translocations seen in leukemia, have all been shown to induce epigenetic alterations of genes.
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Affiliation(s)
- Minoru Toyota
- Department of Biochemistry, Sapporo Medical University, South-1 West-17, Chuo-ku, Sapporo, Japan.
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48
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Arai E, Kanai Y. DNA methylation profiles in precancerous tissue and cancers: carcinogenetic risk estimation and prognostication based on DNA methylation status. Epigenomics 2012; 2:467-81. [PMID: 22121905 DOI: 10.2217/epi.10.16] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Alterations in DNA methylation, which are associated with DNA methyltransferase abnormalities and result in silencing of tumor-related genes and chromosomal instability, are involved even in precancerous changes in various organs. DNA methylation alterations also account for the histological heterogeneity and clinicopathological diversity of human cancers. Therefore, we have analyzed DNA methylation on a genome-wide scale in clinical tissue samples. Our approach using the bacterial artificial chromosome array-based methylated CpG island amplification method has revealed that DNA methylation alterations correlated with the future development of more malignant cancers are already accumulated at the precancerous stage in the kidney, liver and urinary tract. DNA methylation profiles at precancerous stages are basically inherited by the corresponding cancers developing in individual patients. Such DNA methylation alterations may confer vulnerability to further genetic and epigenetic alterations, generate more malignant cancers, and thus determine patient outcome. On the basis of bacterial artificial chromosome array-based methylated CpG island amplification data, indicators for carcinogenetic risk estimation have been established using liver tissue specimens from patients with hepatitis virus infection, chronic hepatitis and liver cirrhosis or histologically normal urothelia, and for prognostication using biopsy or surgically resected specimens from patients with renal cell carcinoma, hepatocellular carcinoma and urothelial carcinoma. Such genome-wide DNA methylation profiling has now firmly established the clinical relevance of translational epigenetics.
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Affiliation(s)
- Eri Arai
- Pathology Division, National Cancer Center Research Institute, 5-1-1 Tsukiji, Chuo-ku, Tokyo 104-0045, Japan
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49
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Olaru AV, Cheng Y, Agarwal R, Yang J, David S, Abraham JM, Yu W, Lazarev M, Brant SR, Marohn MR, Hutcheon DF, Harpaz N, Meltzer SJ, Mori Y, Mori Y. Unique patterns of CpG island methylation in inflammatory bowel disease-associated colorectal cancers. Inflamm Bowel Dis 2012; 18:641-8. [PMID: 21830278 PMCID: PMC3214229 DOI: 10.1002/ibd.21826] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 06/20/2011] [Indexed: 12/20/2022]
Abstract
BACKGROUND CpG island (CGI) hypermethylation at discrete loci is a prevalent cancer-promoting abnormality in sporadic colorectal carcinomas (S-CRCs). We investigated genome-wide CGI methylation in inflammatory bowel disease (IBD)-associated CRCs (IBD-CRCs). METHODS Methylation microarray analyses were conducted on seven IBD-CRCs, 17 S-CRCs, and eight normal control colonic tissues from patients without CRC or IBD. CGI methylator phenotype (CIMP), a surrogate marker for widespread cancer-specific CGI hypermethylation, was examined in 30 IBD-CRCs and 43 S-CRCs. RESULTS The genome-wide CGI methylation pattern of IBD-CRCs was CIMP status-dependent. Based on methylation array data profiling of all autosomal loci, CIMP(+) IBD-CRCs grouped together with S-CRCs, while CIMP(-) IBD-CRCs grouped together with control tissues. CIMP(-) IBD-CRCs demonstrated less methylation than did age-matched CIMP(-) S-CRCs at autosomal CGIs (z-score -0.17 vs. 0.09, P = 3 × 10(-3)) and CRC-associated hypermethylation target CGIs (z-score -0.43 vs. 0.68, P = 1 × 10(-4)). Age-associated hypermethylation target CGIs were significantly overrepresented in CGIs that were hypermethylated in S-CRCs (P = 1 × 10(-192)), but not in CGIs that were hypermethylated in IBD-CRCs (P = 0.11). In contrast, KRAS mutation prevalence was similar between IBD-CRCs and S-CRCs. Notably, CIMP(+) prevalence was significantly higher in older than in younger IBD-CRC cases (50.0 vs. 4.2, P = 0.02), but not in S-CRC cases (9.7 vs. 16.7, P = 0.92). CONCLUSIONS Cancer-specific CGI hypermethylation and age-associated CGI hypermethylation are diminished in IBD-CRCs relative to S-CRCs, while the KRAS mutation rate is comparable between these cancers. CGI hypermethylation appears to play only a minor role in IBD-associated carcinogenesis. We speculate that aging, rather than inflammation per se, promotes CIMP(+) CRCs in IBD patients.
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Affiliation(s)
- Alexandru V. Olaru
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Yulan Cheng
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Rachana Agarwal
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Jian Yang
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Stefan David
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - John M. Abraham
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Wayne Yu
- Sidney Kimmel Comprehensive Cancer Center, DNA Microarray Core Facility, Johns Hopkins University School of Medicine; 1503 E. Jefferson Street, Baltimore, Maryland 21287
| | - Mark Lazarev
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Steven R. Brant
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Michael R. Marohn
- Department of Surgery, Johns Hopkins University School of Medicine; 600 N. Wolfe Street, Baltimore MD 21207
| | - David F. Hutcheon
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
| | - Noam Harpaz
- Department of Pathology, Mount Sinai School of Medicine; One Gustave L. Levy Place, New York, New York 10029
| | - Stephen J. Meltzer
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205, Department of Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center; 1503 E. Jefferson Street, Baltimore, Maryland 21287
| | - Yuriko Mori
- Department of Medicine, Division of Gastroenterology, Johns Hopkins University School of Medicine; 720 Rutland Avenue, Baltimore, Maryland 21205
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50
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Levenson VV, Melnikov AA. DNA methylation as clinically useful biomarkers-light at the end of the tunnel. Pharmaceuticals (Basel) 2012; 5:94-113. [PMID: 24288045 PMCID: PMC3763627 DOI: 10.3390/ph5010094] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 01/10/2012] [Accepted: 01/11/2012] [Indexed: 12/20/2022] Open
Abstract
A recent expansion of our knowledge about epigenetic changes strongly suggests that epigenetic rather than genetic features better reflect disease development, and consequently, can become more conclusive biomarkers for the detection and diagnosis of different diseases. In this paper we will concentrate on the current advances in DNA methylation studies that demonstrate a direct link between abnormal DNA methylation and a disease. This link can be used to develop diagnostic biomarkers that will precisely identify a particular disease. It also appears that disease-specific DNA methylation patterns undergo unique changes in response to treatment with a particular drug, thus raising the possibility of DNA methylation-based biomarkers for the monitoring of treatment efficacy, for prediction of response to treatment, and for the prognosis of outcome. While biomarkers for oncology are the most obvious applications, other fields of medicine are likely to benefit as well. This potential is demonstrated by DNA methylation-based biomarkers for neurological and psychiatric diseases. A special requirement for a biomarker is the possibility of longitudinal testing. In this regard cell-free circulating DNA from blood is especially interesting because it carries methylation markers specific for a particular disease. Although only a few DNA methylation-based biomarkers have attained clinical relevance, the ongoing efforts to decipher disease-specific methylation patterns are likely to produce additional biomarkers for detection, diagnosis, and monitoring of different diseases in the near future.
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Affiliation(s)
- Victor V Levenson
- Department of Radiation Oncology, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
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