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Investigation of the Mechanism of Periploca forrestii against Rheumatoid Arthritis with Network Pharmacology-Based Analysis. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:2993374. [PMID: 35836835 PMCID: PMC9276489 DOI: 10.1155/2022/2993374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 05/16/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022]
Abstract
Periploca forrestii Schltr (P. forrestii) is an edible medicinal herb with various health benefits such as treating antirheumatoid arthritis (RA), reducing inflammation, and preventing tumor growth. The active ingredients in P. forrestii responsible for its protective effect against RA, however, remain unknown. In this study, the active ingredient of P. forrestii and its potential mechanism of action against RA were investigated by network pharmacology and enrichment analysis. The methods included predicting target genes of P. forrestii, constructing a protein interaction network, and performing gene-ontology (GO) and Kyoto-encyclopedia of genes and genomes (KEGG) enrichment analysis. We discovered targets of RA through retrieval of OMIM and GeneCards public databases. Cardiac glycosides (CGs) are considered the primarily active ingredients of P. forrestii, and the target genes of GCs were discovered to be overlapped with relevant targets of RA using the Venn diagram. After that, prediction of relevant targets of P. forrestii was accomplished with a network pharmacology-based approach. Through the Venn diagram, we discovered 99 genes shared in the target genes of P. forrestii and RA. Gene enrichment analysis showed that the mechanisms of CGs against RA are associated with 55 signaling pathways, including endocrine resistance, Epstein-Barr virus infection, bladder cancer, prostate cancer, and coronavirus disease (COVID-19) signaling pathways. Coexpression analysis indicated ADSL, ATIC, AR, CCND1, MDM2, and HSP90AA1 as the hub genes between putative targets of P. forrestii-derived CGs and known therapeutic targets of RA. In conclusion, we clarified the mechanism of action of P. forrestii against RA, which would provide a basis for further understanding the clinical application of P. forrestii.
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Multi-omic characterization of genome-wide abnormal DNA methylation reveals diagnostic and prognostic markers for esophageal squamous-cell carcinoma. Signal Transduct Target Ther 2022; 7:53. [PMID: 35210398 PMCID: PMC8873499 DOI: 10.1038/s41392-022-00873-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 11/23/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
This study investigates aberrant DNA methylations as potential diagnosis and prognosis markers for esophageal squamous-cell carcinoma (ESCC), which if diagnosed at advanced stages has <30% five-year survival rate. Comparing genome-wide methylation sites of 91 ESCC and matched adjacent normal tissues, we identified 35,577 differentially methylated CpG sites (DMCs) and characterized their distribution patterns. Integrating whole-genome DNA and RNA-sequencing data of the same samples, we found multiple dysregulated transcription factors and ESCC-specific genomic correlates of identified DMCs. Using featured DMCs, we developed a 12-marker diagnostic panel with high accuracy in our dataset and the TCGA ESCC dataset, and a 4-marker prognostic panel distinguishing high-risk patients. In-vitro experiments validated the functions of 4 marker host genes. Together these results provide additional evidence for the important roles of aberrant DNA methylations in ESCC development and progression. Our DMC-based diagnostic and prognostic panels have potential values for clinical care of ESCC, laying foundations for developing targeted methylation assays for future non-invasive cancer detection methods.
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Khairan P, Sobue T, Eshak ES, Zha L, Kitamura T, Sawada N, Iwasaki M, Inoue M, Yamaji T, Shimazu T, Iso H, Tsugane S. Association of dietary intakes of vitamin B12, vitamin B6, folate, and methionine with the risk of esophageal cancer: the Japan Public Health Center-based (JPHC) prospective study. BMC Cancer 2021; 21:982. [PMID: 34470601 PMCID: PMC8411535 DOI: 10.1186/s12885-021-08721-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/18/2021] [Indexed: 01/12/2023] Open
Abstract
Background B vitamins and methionine are essential substrates in the one-carbon metabolism pathway involved in DNA synthesis and methylation. They may have essential roles in cancer development. We aimed to evaluate the associations of dietary intakes of vitamin B12, vitamin B6, folate, and methionine with the risk of esophageal cancer (EC) using data from the Japan Public Health Center-based Prospective Study. Methods We included 87,053 Japanese individuals who completed a food frequency questionnaire and were followed up from 1995–1998 to 2013 and 2015. Hazard ratios (HRs) and 95% confidence intervals (CIs) were calculated by Cox proportional-hazard regression across quintiles of dietary intakes of B vitamins and methionine. Results After 1,456,678 person-years of follow-up, 427 EC cases were documented. The multivariable HR (95% CI) of incident EC in the highest versus lowest quintile of dietary intake of vitamin B12 was 1.75 (1.13–2.71; p-trend=0.01). Stratification analysis based on alcohol consumption showed that higher dietary intakes of vitamin B12 and methionine were associated with an increased risk of EC among never-drinkers; HRs (95% CIs) were 2.82 (1.18–6.74; p-trend=0.009; p-interaction=0.18) and 3.45 (1.32–9.06; p-trend=0.003; p-interaction 0.02) for vitamin B12 and methionine, respectively. Meanwhile, there was no association between vitamin B12 and methionine intake with the risk of EC among drinkers. There were no associations between dietary intake of folate or vitamin B6 and the risk of EC. Conclusion Dietary intake of vitamin B12 was positively associated with the risk of EC in the Japanese population. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08721-8.
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Affiliation(s)
- Paramita Khairan
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Department of Internal Medicine, Faculty of Medicine, University of Muhammadiyah, Jakarta, Indonesia
| | - Tomotaka Sobue
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Ehab Salah Eshak
- Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan.,Department of Public Health and Preventive Medicine, Faculty of Medicine, Minia University, Minya, Egypt
| | - Ling Zha
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tetsuhisa Kitamura
- Department of Social and Environmental Medicine, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Norie Sawada
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Chuo-ku Tokyo, 104-0045, Japan
| | - Motoki Iwasaki
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Chuo-ku Tokyo, 104-0045, Japan
| | - Manami Inoue
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Chuo-ku Tokyo, 104-0045, Japan
| | - Taiki Yamaji
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Chuo-ku Tokyo, 104-0045, Japan
| | - Taichi Shimazu
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Chuo-ku Tokyo, 104-0045, Japan
| | - Hiroyasu Iso
- Public Health, Department of Social Medicine, Osaka University Graduate School of Medicine, Suita, Osaka, 565-0871, Japan
| | - Shoichiro Tsugane
- Epidemiology and Prevention Group, Center for Public Health Sciences, National Cancer Center, Chuo-ku Tokyo, 104-0045, Japan
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4
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Talukdar FR, Soares Lima SC, Khoueiry R, Laskar RS, Cuenin C, Sorroche BP, Boisson AC, Abedi-Ardekani B, Carreira C, Menya D, Dzamalala CP, Assefa M, Aseffa A, Miranda-Gonçalves V, Jerónimo C, Henrique RM, Shakeri R, Malekzadeh R, Gasmelseed N, Ellaithi M, Gangane N, Middleton DRS, Le Calvez-Kelm F, Ghantous A, Roux ML, Schüz J, McCormack V, Parker MI, Pinto LFR, Herceg Z. Genome-Wide DNA Methylation Profiling of Esophageal Squamous Cell Carcinoma from Global High-Incidence Regions Identifies Crucial Genes and Potential Cancer Markers. Cancer Res 2021; 81:2612-2624. [PMID: 33741694 DOI: 10.1158/0008-5472.can-20-3445] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 01/04/2021] [Accepted: 03/18/2021] [Indexed: 12/24/2022]
Abstract
Epigenetic mechanisms such as aberrant DNA methylation (DNAme) are known to drive esophageal squamous cell carcinoma (ESCC), yet they remain poorly understood. Here, we studied tumor-specific DNAme in ESCC cases from nine high-incidence countries of Africa, Asia, and South America. Infinium MethylationEPIC array was performed on 108 tumors and 51 normal tissues adjacent to the tumors (NAT) in the discovery phase, and targeted pyrosequencing was performed on 132 tumors and 36 NAT in the replication phase. Top genes for replication were prioritized by weighting methylation results using RNA-sequencing data from The Cancer Genome Atlas and GTEx and validated by qPCR. Methylome analysis comparing tumor and NAT identified 6,796 differentially methylated positions (DMP) and 866 differential methylated regions (DMR), with a 30% methylation (Δβ) difference. The majority of identified DMPs and DMRs were hypermethylated in tumors, particularly in promoters and gene-body regions of genes involved in transcription activation. The top three prioritized genes for replication, PAX9, SIM2, and THSD4, had similar methylation differences in the discovery and replication sets. These genes were exclusively expressed in normal esophageal tissues in GTEx and downregulated in tumors. The specificity and sensitivity of these DNAme events in discriminating tumors from NAT were assessed. Our study identified novel, robust, and crucial tumor-specific DNAme events in ESCC tumors across several high-incidence populations of the world. Methylome changes identified in this study may serve as potential targets for biomarker discovery and warrant further functional characterization. SIGNIFICANCE: This largest genome-wide DNA methylation study on ESCC from high-incidence populations of the world identifies functionally relevant and robust DNAme events that could serve as potential tumor-specific markers. GRAPHICAL ABSTRACT: http://cancerres.aacrjournals.org/content/canres/81/10/2612/F1.large.jpg.
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Affiliation(s)
| | - Sheila C Soares Lima
- Department of Molecular Carcinogenesis, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Rita Khoueiry
- International Agency for Research on Cancer, Lyon, France
| | | | - Cyrille Cuenin
- International Agency for Research on Cancer, Lyon, France
| | - Bruna Pereira Sorroche
- International Agency for Research on Cancer, Lyon, France
- Molecular Oncology Research Center, Barretos Cancer Hospital, Barretos, Brazil
| | | | | | | | | | | | | | - Abraham Aseffa
- Armauer Hansen Research Institute, Addis Ababa, Ethiopia
| | - Vera Miranda-Gonçalves
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Carmen Jerónimo
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Rui M Henrique
- Department of Pathology and Cancer Biology and Epigenetics Group, Portuguese Oncology Institute of Porto and Biomedical Sciences Institute of University of Porto, Porto, Portugal
| | - Ramin Shakeri
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Nagla Gasmelseed
- Department of Molecular Biology, National Cancer Institute, University of Gezira, Gezira, Sudan
| | - Mona Ellaithi
- Department of Histopathology and Cytology, Al-Neelain University, Khartoum, Sudan
| | - Nitin Gangane
- Mahatma Gandhi Institute of Medical Sciences, Sevagram, India
| | | | | | - Akram Ghantous
- International Agency for Research on Cancer, Lyon, France
| | | | - Joachim Schüz
- International Agency for Research on Cancer, Lyon, France
| | | | - M Iqbal Parker
- Integrative Biomedical Sciences and IDM, University of Cape Town, Cape Town, South Africa
| | | | - Zdenko Herceg
- International Agency for Research on Cancer, Lyon, France.
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5
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Tang L, Chen Y, Peng X, Zhou Y, Jiang H, Wang G, Zhuang W. Identification and Validation of Potential Pathogenic Genes and Prognostic Markers in ESCC by Integrated Bioinformatics Analysis. Front Genet 2020; 11:521004. [PMID: 33362844 PMCID: PMC7758294 DOI: 10.3389/fgene.2020.521004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 10/26/2020] [Indexed: 11/13/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most fatal malignancies of the digestive tract, but its underlying molecular mechanisms are not known. We aim to identify the genes involved in ESCC carcinogenesis and discover potential prognostic markers using integrated bioinformatics analysis. Three pairs of ESCC tissues and paired normal tissues were sequenced by high-throughput RNA sequencing (RNA-seq). Integrated bioinformatics analysis was used to identify differentially expressed coding genes (DECGs) and differentially expressed long non-coding RNA (lncRNA) genes (DELGs). A protein-protein interaction (PPI) network of DECGs was established using the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING) website and visualized with Cytoscape. Survival analysis was conducted by log-rank tests to identify "hub" genes with potential prognostic value, and real-time reverse transcription-quantitative polymerase chain reaction (RT-qPCR) was conducted to assess expression of these genes in ESCC tissues. TranswellTM assays were employed to examine the migration ability of cells after knockdown of LINC01614 expression, followed by investigation of epithelial-mesenchymal transition (EMT) by western blotting (WB). A total of 106 upregulated genes and 42 downregulated genes were screened out from the ESCC data sets. Survival analysis showed two hub protein-coding genes with higher expression in module 1 of the PPI network (SPP1 and BGN) and another three upregulated lncRNAs (LINC01614, LINC01415, NKILA) that were associated with a poor prognosis. High expression of SPP1, BGN, LINC01614, and LINC01415 in tumor samples was validated further by RT-qPCR. In vitro experiments show that knockdown of LINC01614 expression could significantly inhibit the migration of ESCC cells by regulating EMT, which was confirmed by WB. These results indicate that BGN, SPP1, LINC01614, and LINC01415 might be critical genes in ESCC and potential prognostic biomarkers.
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Affiliation(s)
- Lu Tang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Yuqiao Chen
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Xiong Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, China
| | - Yuan Zhou
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
| | - Hong Jiang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, China
| | - Guo Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, China
| | - Wei Zhuang
- Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha, China
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Milutin Gašperov N, Sabol I, Božinović K, Dediol E, Mravak-Stipetić M, Licastro D, Dal Monego S, Grce M. DNA Methylome Distinguishes Head and Neck Cancer from Potentially Malignant Oral Lesions and Healthy Oral Mucosa. Int J Mol Sci 2020; 21:ijms21186853. [PMID: 32961999 PMCID: PMC7554960 DOI: 10.3390/ijms21186853] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
There is a strong need to find new, good biomarkers of head and neck squamous cell carcinoma (HNSCC) because of the bad prognoses and high mortality rates. The aim of this study was to identify the potential biomarkers in HNSCC that have differences in their DNA methylome and potentially premalignant oral lesions, in comparison to healthy oral mucosa. In this study, 32 oral samples were tested: nine healthy oral mucosae, 13 HNSCC, and 10 oral lesions for DNA methylation by the Infinium MethylationEPIC BeadChip. Our findings showed that a panel of genes significantly hypermethylated in their promoters or specific sites in HNSCC samples in comparison to healthy oral samples, which are mainly oncogenes, receptor, and transcription factor genes, or genes included in cell cycle, transformation, apoptosis, and autophagy. A group of hypomethylated genes in HNSCC, in comparison to healthy oral mucosa, are mainly involved in the host immune response and transcriptional regulation. The results also showed significant differences in gene methylation between HNSCC and potentially premalignant oral lesions, as well as differently methylated genes that discriminate between oral lesions and healthy mucosa. The given methylation panels point to novel potential biomarkers for early diagnostics of HNSCC, as well as potentially premalignant oral lesions.
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Affiliation(s)
- Nina Milutin Gašperov
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
- Correspondence: (N.M.G.); (M.G.)
| | - Ivan Sabol
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
| | - Ksenija Božinović
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
| | - Emil Dediol
- Department of Maxillofacial Surgery, School of Medicine, Clinical Hospital Dubrava, University of Zagreb, 10000 Zagreb, Croatia;
| | - Marinka Mravak-Stipetić
- Department of Oral Medicine, School of Dental Medicine, University of Zagreb, 10000 Zagreb, Croatia;
| | - Danilo Licastro
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy; (D.L.); (S.D.M.)
| | - Simeone Dal Monego
- ARGO Open Lab Platform for Genome sequencing, AREA Science Park, Padriciano, 99, 34149 Trieste, Italy; (D.L.); (S.D.M.)
| | - Magdalena Grce
- Division of Molecular Medicine, Ruđer Bošković Institute, 10000 Zagreb, Croatia; (I.S.); (K.B.)
- Correspondence: (N.M.G.); (M.G.)
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7
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Methylation silencing of TGF-β receptor type II is involved in malignant transformation of esophageal squamous cell carcinoma. Clin Epigenetics 2020; 12:25. [PMID: 32046777 PMCID: PMC7014638 DOI: 10.1186/s13148-020-0819-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Accepted: 01/28/2020] [Indexed: 12/24/2022] Open
Abstract
Background Although massive studies have been conducted to investigate the mechanisms of esophageal squamous cell carcinoma (ESCC) carcinogenesis, the understanding of molecular alterations during the malignant transformation of epithelial dysplasia is still lacking, especially regarding epigenetic changes. Results To better characterize the methylation changes during the malignant transformation of epithelial dysplasia, a whole-genome bisulfite sequencing analysis was performed on a series of tumor, dysplastic, and non-neoplastic epithelial tissue samples from esophageal squamous cell carcinoma (ESCC) patients. Promoter hypermethylation in TGF-β receptor type II (TGFBR2), an important mediator of TGF-β signaling, was identified. Further, we evaluated the methylation and expression of TGFBR2 in tumor samples through The Cancer Genome Atlas multiplatform data as well as immunohistochemistry. Moreover, treatment of ESCC cell lines with5-Aza-2′-deoxycytidine, a DNA methyltransferase inhibitor, reactivated the expression of TGFBR2. The lentiviral mediating the overexpression of TGFBR2 inhibited the proliferation of ESCC cell line by inducing cell cycle G2/M arrest. Furthermore, the overexpression of TGFBR2 inhibited the tumor growth obviously in vivo. Conclusions The characterization of methylation silencing of TGFBR2 in ESCC will enable us to further explore whether this epigenetic change could be considered as a predictor of malignant transformation in esophageal epithelial dysplasia and whether use of a TGFBR2 agonist may lead to a new therapeutic strategy in patients with ESCC.
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8
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Ma Y, He S, Gao A, Zhang Y, Zhu Q, Wang P, Yang B, Yin H, Li Y, Song J, Yue P, Li M, Zhang D, Liu Y, Wang X, Guo M, Jiao Y. Methylation silencing of TGF-β receptor type II is involved in malignant transformation of esophageal squamous cell carcinoma. Clin Epigenetics 2020. [PMID: 32046777 DOI: 10.1186/s13148-020-0819-6.pmid:32046777;pmcid:pmc7014638] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/09/2023] Open
Abstract
BACKGROUND Although massive studies have been conducted to investigate the mechanisms of esophageal squamous cell carcinoma (ESCC) carcinogenesis, the understanding of molecular alterations during the malignant transformation of epithelial dysplasia is still lacking, especially regarding epigenetic changes. RESULTS To better characterize the methylation changes during the malignant transformation of epithelial dysplasia, a whole-genome bisulfite sequencing analysis was performed on a series of tumor, dysplastic, and non-neoplastic epithelial tissue samples from esophageal squamous cell carcinoma (ESCC) patients. Promoter hypermethylation in TGF-β receptor type II (TGFBR2), an important mediator of TGF-β signaling, was identified. Further, we evaluated the methylation and expression of TGFBR2 in tumor samples through The Cancer Genome Atlas multiplatform data as well as immunohistochemistry. Moreover, treatment of ESCC cell lines with5-Aza-2'-deoxycytidine, a DNA methyltransferase inhibitor, reactivated the expression of TGFBR2. The lentiviral mediating the overexpression of TGFBR2 inhibited the proliferation of ESCC cell line by inducing cell cycle G2/M arrest. Furthermore, the overexpression of TGFBR2 inhibited the tumor growth obviously in vivo. CONCLUSIONS The characterization of methylation silencing of TGFBR2 in ESCC will enable us to further explore whether this epigenetic change could be considered as a predictor of malignant transformation in esophageal epithelial dysplasia and whether use of a TGFBR2 agonist may lead to a new therapeutic strategy in patients with ESCC.
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Affiliation(s)
- Yarui Ma
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Siyuan He
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Aiai Gao
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Research Building, No.28 Fuxing Road, Haidian District, Beijing, 100853, China
| | - Ying Zhang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Qing Zhu
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Pei Wang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Beibei Yang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Huihui Yin
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Yifei Li
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Jinge Song
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Pinli Yue
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Mo Li
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
| | - Dandan Zhang
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Yun Liu
- MOE Key Laboratory of Metabolism and Molecular Medicine, Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences and Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Xiaobing Wang
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
| | - Mingzhou Guo
- Department of Gastroenterology & Hepatology, Chinese PLA General Hospital, Research Building, No.28 Fuxing Road, Haidian District, Beijing, 100853, China.
| | - Yuchen Jiao
- State Key Lab of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Research Building, No.17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China.
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Cancer mutational burden is shaped by G4 DNA, replication stress and mitochondrial dysfunction. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:47-61. [PMID: 30880007 DOI: 10.1016/j.pbiomolbio.2019.03.004] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 02/01/2023]
Abstract
A hallmark of cancer is genomic instability, which can enable cancer cells to evade therapeutic strategies. Here we employed a computational approach to uncover mechanisms underlying cancer mutational burden by focusing upon relationships between 1) translocation breakpoints and the thousands of G4 DNA-forming sequences within retrotransposons impacting transcription and exemplifying probable non-B DNA structures and 2) transcriptome profiling and cancer mutations. We determined the location and number of G4 DNA-forming sequences in the Genome Reference Consortium Human Build 38 and found a total of 358,605 covering ∼13.4 million bases. By analyzing >97,000 unique translocation breakpoints from the Catalogue Of Somatic Mutations In Cancer (COSMIC), we found that breakpoints are overrepresented at G4 DNA-forming sequences within hominid-specific SVA retrotransposons, and generally occur in tumors with mutations in tumor suppressor genes, such as TP53. Furthermore, correlation analyses between mRNA levels and exome mutational loads from The Cancer Genome Atlas (TCGA) encompassing >450,000 gene-mutation regressions revealed strong positive and negative associations, which depended upon tissue of origin. The strongest positive correlations originated from genes not listed as cancer genes in COSMIC; yet, these show strong predictive power for survival in most tumor types by Kaplan-Meier estimation. Thus, correlation analyses of DNA structure and gene expression with mutation loads complement and extend more traditional approaches to elucidate processes shaping genomic instability in cancer. The combined results point to G4 DNA, activation of cell cycle/DNA repair pathways, and mitochondrial dysfunction as three major factors driving the accumulation of somatic mutations in cancer cells.
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Chen JL, Lin ZX, Qin YS, She YQ, Chen Y, Chen C, Qiu GD, Zheng JT, Chen ZL, Zhang SY. Overexpression of long noncoding RNA LINC01419 in esophageal squamous cell carcinoma and its relation to the sensitivity to 5-fluorouracil by mediating GSTP1 methylation. Ther Adv Med Oncol 2019; 11:1758835919838958. [PMID: 31019568 PMCID: PMC6463338 DOI: 10.1177/1758835919838958] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 01/23/2019] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Genome-wide sequencing investigations have identified numerous long noncoding RNAs (lncRNAs) among mammals, many of which exhibit aberrant expression in cancers, including esophageal squamous cell carcinoma (ESCC). Herein, this study elucidates the role and mechanism by which LINC01419 regulates the DNA methylation of glutathione S-transferase pi 1 (GSTP1) in relation to ESCC progression and the sensitivity of ESCC cells to 5-fluorouracil (5-FU). METHODS LINC01419 and GSTP1 levels were quantified among 38 paired ESCC and adjacent tissue samples collected from patients with ESCC. To ascertain the contributory role of LINC01419 in the progression of ESCC and identify the interaction between LINC01419 and GSTP1 promoter methylation, LINC01419 was overexpressed or silenced, and the DNA methyltransferase inhibitor 5-Aza-CdR was treated. RESULTS Data from the GEO database (GSE21362) and the Cancer Genome Atlas displayed elevated levels of LINC01419 and downregulated levels of GSTP1 in the ESCC tissues and cells. The silencing of LINC01419 led to decreased proliferation, increased apoptosis, and enhanced sensitivity to 5-FU in ESCC cells. Notably, LINC01419 could bind to the promoter region of the GSTP1 gene, resulting in elevated GSTP1 methylation and reduced GSTP1 levels via the recruitment of DNA methyltransferase among ESCC cells, whereby ESCC progression was stimulated accompanied by reduced ESCC cell sensitivity to 5-FU. GSTP1 demethylation by 5-Aza-CdR was observed to reverse the effects of LINC01419 overexpression in ESCC cells and the response to 5-FU. CONCLUSION Highly expressed LINC01419 in ESCC promotes GSTP1 methylation, which ultimately acts to promote the event of ESCC and diminish the sensitivity of ESCC cells to 5-FU, highlighting a novel potential strategy to improve 5-FU-based chemotherapy in ESCC.
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Affiliation(s)
- Jian-Liang Chen
- Clinical Laboratory, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zhi-Xiong Lin
- Radiotherapy Department, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Yun-Sheng Qin
- Chest Surgery, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Yu-Qi She
- Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Yun Chen
- Clinical Pharmacy Research Center, Shantou University Medical College, Shantou, China
| | - Chen Chen
- Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Guo-Dong Qiu
- Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Jie-Ting Zheng
- Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou, China
| | - Zhong-Lin Chen
- Department of Pharmacy, Cancer Hospital of Shantou University Medical College, Shantou, China
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11
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Talukdar FR, di Pietro M, Secrier M, Moehler M, Goepfert K, Lima SSC, Pinto LFR, Hendricks D, Parker MI, Herceg Z. Molecular landscape of esophageal cancer: implications for early detection and personalized therapy. Ann N Y Acad Sci 2018; 1434:342-359. [PMID: 29917250 DOI: 10.1111/nyas.13876] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/08/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022]
Abstract
Esophageal cancer (EC) is one of the most lethal cancers and a public health concern worldwide, owing to late diagnosis and lack of efficient treatment. Esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma (EAC) are main histopathological subtypes of EC that show striking differences in geographical distribution, possibly due to differences in exposure to risk factors and lifestyles. ESCC and EAC are distinct diseases in terms of cell of origin, epidemiology, and molecular architecture of tumor cells. Past efforts aimed at translating potential molecular candidates into clinical practice proved to be challenging, underscoring the need for identifying novel candidates for early diagnosis and therapy of EC. Several major international efforts have brought about important advances in identifying molecular landscapes of ESCC and EAC toward understanding molecular mechanisms and critical molecular events driving the progression and pathological features of the disease. In our review, we summarize recent advances in the areas of genomics and epigenomics of ESCC and EAC, their mutational signatures and immunotherapy. We also discuss implications of recent advances in characterizing the genome and epigenome of EC for the discovery of diagnostic/prognostic biomarkers and development of new targets for personalized treatment and prevention.
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Affiliation(s)
- Fazlur Rahman Talukdar
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer (WHO), Lyon, France
| | | | - Maria Secrier
- Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Markus Moehler
- First Department of Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | - Katrin Goepfert
- First Department of Internal Medicine, Johannes Gutenberg-University of Mainz, Mainz, Germany
| | | | | | - Denver Hendricks
- Division of Medical Biochemistry & Structural Biology, University of Cape Town, Cape Town, South Africa
| | - Mohamed Iqbal Parker
- Division of Medical Biochemistry & Structural Biology, University of Cape Town, Cape Town, South Africa
| | - Zdenko Herceg
- Section of Mechanisms of Carcinogenesis, International Agency for Research on Cancer (WHO), Lyon, France
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12
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Prognostic and diagnostic potential of isocitrate dehydrogenase 1 in esophageal squamous cell carcinoma. Oncotarget 2018; 7:86148-86160. [PMID: 27863386 PMCID: PMC5349903 DOI: 10.18632/oncotarget.13351] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 11/09/2016] [Indexed: 02/06/2023] Open
Abstract
We aimed to investigate the pattern of expression and clinical significance of isocitrate dehydrogenase 1(IDH1) in esophageal squamous cell carcinoma (ESCC). The IDH1 expression was determined by quantitative real-time polymerase chain reaction, immunohistochemistry, and Western blot analysis using 38 pairs of frozen tissues. Enzyme-linked immunosorbent assay was employed to measure 67 pairs of serum samples from patients and their controls to evaluate its diagnostic value. Immunohistochemistry analysis of 111 formalin-fixed paraffin embedded tissue samples was conducted for explaining its prognostic value. After shRNA transfection, CCK8 and clonal efficiency assays were carried on for verifying the function of IDH1 in vitro. Increased expression at mRNA (P < 0.001) and protein levels (immunohistochemistry: P < 0.001, Western blot analysis: P < 0.001) were observed. Similarly, the IDH1 expression in serum from patients with ESCC was significantly upregulated relative to that from healthy controls (P < 0.001). Kaplan–Meier curve indicated that IDH1 upregulation predicted worse overall survival (OS) and progression-free survival (PFS). Univariate and multivariate analyses identified IDH1 expression as an independent prognostic factor for OS and PFS. Furthermore, OD450 values and colony numbers were decreased in sh-IDH1 groups (all P < 0.05). In conclusion, IDH1 is upregulated in patients with ESCC and can be used as a good potential biomarker for diagnosis and prognosis.
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13
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Murphy G, McCormack V, Abedi-Ardekani B, Arnold M, Camargo MC, Dar NA, Dawsey SM, Etemadi A, Fitzgerald RC, Fleischer DE, Freedman ND, Goldstein AM, Gopal S, Hashemian M, Hu N, Hyland PL, Kaimila B, Kamangar F, Malekzadeh R, Mathew CG, Menya D, Mulima G, Mwachiro MM, Mwasamwaja A, Pritchett N, Qiao YL, Ribeiro-Pinto LF, Ricciardone M, Schüz J, Sitas F, Taylor PR, Van Loon K, Wang SM, Wei WQ, Wild CP, Wu C, Abnet CC, Chanock SJ, Brennan P. International cancer seminars: a focus on esophageal squamous cell carcinoma. Ann Oncol 2017; 28:2086-2093. [PMID: 28911061 PMCID: PMC5834011 DOI: 10.1093/annonc/mdx279] [Citation(s) in RCA: 133] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The International Agency for Research on Cancer (IARC) and the US National Cancer Institute (NCI) have initiated a series of cancer-focused seminars [Scelo G, Hofmann JN, Banks RE et al. International cancer seminars: a focus on kidney cancer. Ann Oncol 2016; 27(8): 1382-1385]. In this, the second seminar, IARC and NCI convened a workshop in order to examine the state of the current science on esophageal squamous cell carcinoma etiology, genetics, early detection, treatment, and palliation, was reviewed to identify the most critical open research questions. The results of these discussions were summarized by formulating a series of 'difficult questions', which should inform and prioritize future research efforts.
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Affiliation(s)
- G. Murphy
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | | | | | - M. Arnold
- Cancer Surveillance, International Agency for Research on Cancer, Lyon, France
| | - M. C. Camargo
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - N. A. Dar
- Department of Biochemistry, University of Kashmir, Hazratbal, Srinagar, Jammu and Kashmir, India
| | - S. M. Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - A. Etemadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - R. C. Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Cambridge, UK
| | - D. E. Fleischer
- Department of Internal Medicine, Mayo Clinic, Scottsdale, Arizona, USA
| | - N. D. Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - A. M. Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - S. Gopal
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - M. Hashemian
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - N. Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - P. L. Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - B. Kaimila
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | - F. Kamangar
- Department of Public Health Analysis, School of Community Health and Policy, Morgan State University, Baltimore, Maryland, USA
| | - R. Malekzadeh
- Digestive Oncology Research Center, Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - C. G. Mathew
- Department of Medical and Molecular Genetics, Kings College London
- Sydney Brenner Institute for Molecular Bioscience, University of Witwatersrand, Johannesburg, South Africa
| | - D. Menya
- School of Public Health, Moi University, Eldoret, Kenya
| | - G. Mulima
- University of North Carolina Project-Malawi, Lilongwe, Malawi
| | | | - A. Mwasamwaja
- Kilimanjaro Christian Medical Centre, Moshi, Tanzania
| | - N. Pritchett
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - Y.-L. Qiao
- Department of Etiology and Carcinogenesis & Department of Cancer Epidemiology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - L. F. Ribeiro-Pinto
- Molecular Carcinogenesis Program, Institute Nacional de Cancer, Sao Paulo, Brazil
| | - M. Ricciardone
- National Cancer Institute, Center for Global Health, National Institutes of Health, Bethesda, Maryland, USA
| | - J. Schüz
- Section of Environment and Radiation
| | - F. Sitas
- School of Public Health, University of Sydney, New South Wales, Australia
- School of Public Health & Community Medicine, University of New South Wales, Sydney, Australia
| | - P. R. Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - K. Van Loon
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, USA
| | - S.-M. Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
- Department of Etiology and Carcinogenesis & Department of Cancer Epidemiology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - W.-Q. Wei
- Department of Etiology and Carcinogenesis & Department of Cancer Epidemiology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - C. P. Wild
- Director's office, International Agency for Research on Cancer, Lyon, France
| | - C. Wu
- Department of Etiology and Carcinogenesis & Department of Cancer Epidemiology, Cancer Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - C. C. Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
| | - S. J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda Maryland, USA
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Peng M, Chen C, Hulbert A, Brock MV, Yu F. Non-blood circulating tumor DNA detection in cancer. Oncotarget 2017; 8:69162-69173. [PMID: 28978187 PMCID: PMC5620327 DOI: 10.18632/oncotarget.19942] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2017] [Accepted: 07/25/2017] [Indexed: 01/01/2023] Open
Abstract
Tumor DNA contains specific somatic alterations that are crucial for the diagnosis and treatment of cancer. Due to the spatial and temporal intra-tumor heterogeneity, multi-sampling is needed to adequately characterize the somatic alterations. Tissue biopsy, however, is limited by the restricted access to sample and the challenges to recapitulate the tumor clonal diversity. Non-blood circulating tumor DNA are tumor DNA fragments presents in non-blood body fluids, such as urine, saliva, sputum, stool, pleural fluid, and cerebrospinal fluid (CSF). Recent studies have demonstrated the presence of tumor DNA in these non-blood body fluids and their application to the diagnosis, screening, and monitoring of cancers. Non-blood circulating tumor DNA has an enormous potential for large-scale screening of local neoplasms because of its non-invasive nature, close proximity to the tumors, easiness and it is an economically viable option. It permits longitudinal assessments and allows sequential monitoring of response and progression. Enrichment of tumor DNA of local cancers in non-blood body fluids may help to archive a higher sensitivity than in plasma ctDNA. The direct contact of cancerous cells and body fluid may facilitate the detection of tumor DNA. Furthermore, normal DNA always dilutes the plasma ctDNA, which may be aggravated by inflammation and injury when very high amounts of normal DNA are released into the circulation. Altogether, our review indicate that non-blood circulating tumor DNA presents an option where the disease can be tracked in a simple and less-invasive manner, allowing for serial sampling informing of the tumor heterogeneity and response to treatment.
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Affiliation(s)
- Muyun Peng
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Chen Chen
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
| | - Alicia Hulbert
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Malcolm V Brock
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Fenglei Yu
- Department of Thoracic Surgery, The Second Xiangya Hospital, Central South University, Changsha, Hunan, P.R China
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Zhou S, Gao X, Sun J, Lin Z, Huang Y. DNA Methylation of thePDGFDGene Promoter Increases the Risk for Intracranial Aneurysms and Brain Arteriovenous Malformations. DNA Cell Biol 2017; 36:436-442. [PMID: 28346846 DOI: 10.1089/dna.2016.3499] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
- Shengjun Zhou
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Xiang Gao
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Jie Sun
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Zhiqing Lin
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
| | - Yi Huang
- Department of Neurosurgery, Ningbo First Hospital, Ningbo Hospital of Zhejiang University, Ningbo, China
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16
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The Genomic Impact of DNA CpG Methylation on Gene Expression; Relationships in Prostate Cancer. Biomolecules 2017; 7:biom7010015. [PMID: 28216563 PMCID: PMC5372727 DOI: 10.3390/biom7010015] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 01/23/2017] [Accepted: 02/06/2017] [Indexed: 12/15/2022] Open
Abstract
The process of DNA CpG methylation has been extensively investigated for over 50 years and revealed associations between changing methylation status of CpG islands and gene expression. As a result, DNA CpG methylation is implicated in the control of gene expression in developmental and homeostasis processes, as well as being a cancer-driver mechanism. The development of genome-wide technologies and sophisticated statistical analytical approaches has ushered in an era of widespread analyses, for example in the cancer arena, of the relationships between altered DNA CpG methylation, gene expression, and tumor status. The remarkable increase in the volume of such genomic data, for example, through investigators from the Cancer Genome Atlas (TCGA), has allowed dissection of the relationships between DNA CpG methylation density and distribution, gene expression, and tumor outcome. In this manner, it is now possible to test that the genome-wide correlations are measurable between changes in DNA CpG methylation and gene expression. Perhaps surprisingly is that these associations can only be detected for hundreds, but not thousands, of genes, and the direction of the correlations are both positive and negative. This, perhaps, suggests that CpG methylation events in cancer systems can act as disease drivers but the effects are possibly more restricted than suspected. Additionally, the positive and negative correlations suggest direct and indirect events and an incomplete understanding. Within the prostate cancer TCGA cohort, we examined the relationships between expression of genes that control DNA methylation, known targets of DNA methylation and tumor status. This revealed that genes that control the synthesis of S-adenosyl-l-methionine (SAM) associate with altered expression of DNA methylation targets in a subset of aggressive tumors.
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