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Rivera-Peña B, Folawiyo O, Turaga N, Rodríguez-Benítez RJ, Felici ME, Aponte-Ortiz JA, Pirini F, Rodríguez-Torres S, Vázquez R, López R, Sidransky D, Guerrero-Preston R, Báez A. Promoter DNA methylation patterns in oral, laryngeal and oropharyngeal anatomical regions are associated with tumor differentiation, nodal involvement and survival. Oncol Lett 2024; 27:89. [PMID: 38268779 PMCID: PMC10804364 DOI: 10.3892/ol.2024.14223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
Differentially methylated regions (DMRs) can be used as head and neck squamous cell carcinoma (HNSCC) diagnostic, prognostic and therapeutic targets in precision medicine workflows. DNA from 21 HNSCC and 10 healthy oral tissue samples was hybridized to a genome-wide tiling array to identify DMRs in a discovery cohort. Downstream analyses identified differences in promoter DNA methylation patterns in oral, laryngeal and oropharyngeal anatomical regions associated with tumor differentiation, nodal involvement and survival. Genome-wide DMR analysis showed 2,565 DMRs common to the three subsites. A total of 738 DMRs were unique to laryngeal cancer (n=7), 889 DMRs were unique to oral cavity cancer (n=10) and 363 DMRs were unique to pharyngeal cancer (n=6). Based on the genome-wide analysis and a Gene Ontology analysis, 10 candidate genes were selected to test for prognostic value and association with clinicopathological features. TIMP3 was associated with tumor differentiation in oral cavity cancer (P=0.039), DAPK1 was associated with nodal involvement in pharyngeal cancer (P=0.017) and PAX1 was associated with tumor differentiation in laryngeal cancer (P=0.040). A total of five candidate genes were selected, DAPK1, CDH1, PAX1, CALCA and TIMP3, for a prevalence study in a larger validation cohort: Oral cavity cancer samples (n=42), pharyngeal cancer tissues (n=25) and laryngeal cancer samples (n=52). PAX1 hypermethylation differed across HNSCC anatomic subsites (P=0.029), and was predominantly detected in laryngeal cancer. Kaplan-Meier survival analysis (P=0.043) and Cox regression analysis of overall survival (P=0.001) showed that DAPK1 methylation is associated with better prognosis in HNSCC. The findings of the present study showed that the HNSCC subsites oral cavity, pharynx and larynx display substantial differences in aberrant DNA methylation patterns, which may serve as prognostic biomarkers and therapeutic targets.
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Affiliation(s)
- Bianca Rivera-Peña
- Department of Biology, University of Puerto Rico, San Juan 00925, Puerto Rico
- Department of Pharmacology, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
- Department of Otolaryngology-Head and Neck Surgery, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
| | - Oluwasina Folawiyo
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Nitesh Turaga
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rosa J. Rodríguez-Benítez
- Department of General Social Sciences, Faculty of Social Sciences, University of Puerto Rico, San Juan 00925, Puerto Rico
| | - Marcos E. Felici
- Oral Health Division, Puerto Rico Department of Health, San Juan 00927, Puerto Rico
| | - Jaime A. Aponte-Ortiz
- Department of General Surgery, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
| | - Francesca Pirini
- Biosciences Laboratory, IRCCS Instituto Romagnolo per lo Studio dei Tumori ‘Dino Amadori’, Meldola I-47014, Italy
| | | | - Roger Vázquez
- Department of Biology, University of Puerto Rico, San Juan 00925, Puerto Rico
| | - Ricardo López
- Department of Biology, University of Puerto Rico, San Juan 00925, Puerto Rico
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Rafael Guerrero-Preston
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Research and Development, LifeGene-Biomarks, San Juan 00909, Puerto Rico
| | - Adriana Báez
- Department of Pharmacology, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
- Department of Otolaryngology-Head and Neck Surgery, University of Puerto Rico School of Medicine, San Juan 00936, Puerto Rico
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Wang MQ, Yin QY, Chen YR, Zhu SL. Diagnostic and prognostic value of HOXC family members in gastric cancer. Future Oncol 2021; 17:4907-4923. [PMID: 34751593 DOI: 10.2217/fon-2021-0291] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Aims: HOX clusters encode proteins that play pivotal roles in regulating transcription factors and many other proteins during embryogenesis. However, little is known about the diagnostic and prognostic values of HOXC family members in gastric cancer (GC). Materials and methods: The authors evaluated the data in patients with GC based on bioinformatics analysis. Results: HOXC6/8/9/10/11/13 were overexpressed in GC and associated with a poor prognosis. HOXC4/5 were downregulated in GC tissues. Receiver operating characteristic curve analysis demonstrated that they have high diagnostic value. In addition, HOXC4/5/6/9/10/11/13 were negatively correlated with DNA methylation level. The gene set enrichment analysis results implied that they play essential roles in multiple biological processes underlying tumorigenesis. Conclusion: HOXC family members are potential targets for diagnosis and may work as prognostic biomarkers of GC.
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Affiliation(s)
- Mei-Qian Wang
- Department of Gastroenterology & Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Qi-Yun Yin
- Department of Intensive Care Unit, The First Affiliated Hospital of Shandong First Medical University, Jinan, China
| | - Yi-Ru Chen
- Department of Gastroenterology & Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
| | - Sen-Lin Zhu
- Department of Gastroenterology & Hepatology, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, Guangdong, China
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Malyshev BS, Netesova NA, Smetannikova NA, Abdurashitov MA, Akishev AG, Dubinin EV, Azanov AZ, Vihlyanov IV, Nikitin MK, Karpov AB, Degtyarev SK. GLAD-PCR Assay of R(5mC)GY Sites in the Regulatory Region of Tumor-Suppressor Genes Associated with Gastric Cancer. Acta Naturae 2020; 12:124-133. [PMID: 33173602 PMCID: PMC7604892 DOI: 10.32607/actanaturae.11070] [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: 01/20/2020] [Accepted: 07/22/2020] [Indexed: 11/23/2022] Open
Abstract
At early stages of carcinogenesis, the regulatory regions of some tumor suppressor genes become aberrantly methylated at RCGY sites, which are substrates of DNA methyltransferase Dnmt3. Identification of aberrantly methylated sites in tumor DNA is considered to be the first step in the development of epigenetic PCR test systems for early diagnosis of cancer. Recently, we have developed a GLAD-PCR assay, a method for detecting the R(5mC)GY site in the genome position of interest even at significant excess of DNA molecules with a non-methylated RCGY site in this location. The aim of the present work is to use the GLAD-PCR assay to detect the aberrantly methylated R(5mC)GY sites in the regulatory regions of tumor suppressor genes (brinp1, bves, cacna2d3, cdh11, cpeb1, epha7, fgf2, galr1, gata4, hopx, hs3st2, irx1, lrrc3b, pcdh10, rprm, runx3, sfrp2, sox17, tcf21, tfpi2, wnt5a, zfp82, and znf331) in DNA samples obtained from gastric cancer (GC) tissues. The study of the DNA samples derived from 29 tumor and 25 normal gastric tissue samples demonstrated a high diagnostic potential of the selected RCGY sites in the regulatory regions of the irx1, cacna2d3, and epha7 genes; the total indices of sensitivity and specificity for GC detection being 96.6% and 100%, respectively.
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Affiliation(s)
- B. S. Malyshev
- State Research Center of Virology and Biotechnology «Vector», Novosibirsk region, Koltsovo, 630559 Russia
| | - N. A. Netesova
- State Research Center of Virology and Biotechnology «Vector», Novosibirsk region, Koltsovo, 630559 Russia
| | - N. A. Smetannikova
- State Research Center of Virology and Biotechnology «Vector», Novosibirsk region, Koltsovo, 630559 Russia
| | | | | | | | - A. Z. Azanov
- Regional Clinical Oncology Center, Kemerovo, 650036 Russia
| | - I. V. Vihlyanov
- Altai Regional Oncology, CenterAltai region, Barnaul, 656049 Russia
| | - M. K. Nikitin
- Altai Regional Oncology, CenterAltai region, Barnaul, 656049 Russia
| | - A. B. Karpov
- Seversk Biophysical Research Centre, Tomsk region, Seversk, 636039 Russia
| | - S. Kh. Degtyarev
- State Research Center of Virology and Biotechnology «Vector», Novosibirsk region, Koltsovo, 630559 Russia
- EpiGene LLC, Novosibirsk, 630090 Russia
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Smetannikova NA, Evdokimov AA, Netesova NA, Abdurashitov MA, Akishev AG, Dubinin EV, Pozdnyakov PI, Vihlyanov IV, Nikitin MK, Topolnitsky EB, Karpov AB, Kolomiets SA, Degtyarev SK. [Application of GLAD-PCR Assay for Study on DNA Methylation in Regulatory Regions of Some Tumor-Suppressor Genes in Lung Cancer]. ZHONGGUO FEI AI ZA ZHI = CHINESE JOURNAL OF LUNG CANCER 2019; 22:551-561. [PMID: 31526458 PMCID: PMC6754573 DOI: 10.3779/j.issn.1009-3419.2019.09.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Hypermethylation of the gene regulatory regions are common for many cancer diseases. In this work we applied GLAD-PCR assay for identificating of the aberrantly methylated RCGY sites in the regulatory regions of some downregulated genes in tissue samples of lung cancer (LC). This list includes EFEMP1, EPHA5, HOXA5, HOXA9, LHX1, MYF6, NID2, OTX1, PAX9, RARB, RASSF1A, RXRG, SIX6, SKOR1 and TERT genes. The results of DNA samples from 40 cancer and 25 normal lung tissues showed a good diagnostic potential of selected RCGY sites in regulatory regions of MYF6, SIX6, RXRG, LHX1, RASSF1A and TERT genes with relatively high sensitivity (80.0 %) and specificity (88.0 %) of LC detection in tumor DNA.
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Affiliation(s)
- N A Smetannikova
- State Research Center of Virology and Biotechnology, Koltsovo, Russia.,EpiGene LLC, Novosibirsk, Russia
| | - A A Evdokimov
- State Research Center of Virology and Biotechnology, Koltsovo, Russia.,EpiGene LLC, Novosibirsk, Russia
| | - N A Netesova
- State Research Center of Virology and Biotechnology, Koltsovo, Russia.,EpiGene LLC, Novosibirsk, Russia
| | | | | | | | - P I Pozdnyakov
- State Research Center of Virology and Biotechnology, Koltsovo, Russia
| | | | - M K Nikitin
- Altai Regional Oncology Center, Barnaul, Russia
| | | | - A B Karpov
- Seversk Biophysical Research Centre, Seversk, Russia
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IJzerman MJ, Berghuis AMS, de Bono JS, Terstappen LWMM. Health economic impact of liquid biopsies in cancer management. Expert Rev Pharmacoecon Outcomes Res 2018; 18:593-599. [PMID: 30052095 DOI: 10.1080/14737167.2018.1505505] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
INTRODUCTION Liquid biopsies (LBs) are referred to as the sampling and analysis of non-solid tissue, primarily blood, as a diagnostic and monitoring tool for cancer. Because LBs are largely non-invasive, they are a less-costly alternative for serial analysis of tumor progression and heterogeneity to facilitate clinical management. Although a variety of tumor markers are proposed (e.g., free-circulating DNA), the clinical evidence for Circulating Tumor Cells (CTCs) is currently the most developed. Areas covered: This paper presents a health economic perspective of LBs in cancer management. We first briefly introduce the requirements in biomarker development and validation, illustrated for CTCs. Second, we discuss the state-of-art on the clinical utility of LBs in breast cancer in more detail. We conclude with a future perspective on the clinical use and reimbursement of LBs Expert commentary: A significant increase in clinical research on LBs can be observed and the results suggest a rapid change of cancer management. In addition to studies evaluating clinical utility of LBs, a smooth translation into clinical practice requires systematic assessment of the health economic benefits. This paper argues that (early stage) health economic research is required to facilitate its clinical use and to prioritize further evidence development.
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Affiliation(s)
- Maarten J IJzerman
- a Department of Health Technology and Services Research , University of Twente , Enschede , the Netherlands.,b University of Melbourne, Faculty of Medicine, Dentistry and Health Sciences , Victorian Comprehensive Cancer Centre and Centre for Cancer Research , Melbourne , Australia.,c Luxembourg Institute of Health, Dept. Health Economics and Evidence Synthesis , Luxembourg
| | - A M Sofie Berghuis
- a Department of Health Technology and Services Research , University of Twente , Enschede , the Netherlands
| | - Johann S de Bono
- d Royal Marsden Hospital, Institute for Cancer Research , Clinical studies department , Surrey , UK
| | - Leon W M M Terstappen
- e Department of Medical Cell Biophysics , University of Twente , Enschede , the Netherlands
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Claycombe KJ, Brissette CA, Ghribi O. Epigenetics of inflammation, maternal infection, and nutrition. J Nutr 2015; 145:1109S-1115S. [PMID: 25833887 PMCID: PMC4410493 DOI: 10.3945/jn.114.194639] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Accepted: 08/21/2014] [Indexed: 12/12/2022] Open
Abstract
Studies have demonstrated that epigenetic changes such as DNA methylation, histone modification, and chromatin remodeling are linked to an increased inflammatory response as well as increased risk of chronic disease development. A few studies have begun to investigate whether dietary nutrients play a beneficial role by modifying or reversing epigenetically induced inflammation. Results of these studies show that nutrients modify epigenetic pathways. However, little is known about how nutrients modulate inflammation by regulating immune cell function and/or immune cell differentiation via epigenetic pathways. This overview will provide information about the current understanding of the role of nutrients in the epigenetic control mechanisms of immune function.
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Affiliation(s)
- Kate J Claycombe
- USDA-Agricultural Research Service, Grand Forks Human Nutrition Research Center, Grand Forks, ND; and
| | - Catherine A Brissette
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND
| | - Othman Ghribi
- Department of Basic Sciences, University of North Dakota School of Medicine and Health Sciences, Grand Forks, ND
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8
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Yu JL, Lv P, Han J, Zhu X, Hong LL, Zhu WY, Wang XB, Wu YC, Li P, Ling ZQ. Methylated TIMP-3 DNA in body fluids is an independent prognostic factor for gastric cancer. Arch Pathol Lab Med 2015; 138:1466-73. [PMID: 25357107 DOI: 10.5858/arpa.2013-0285-oa] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
CONTEXT Fluid methylated DNA may be a suitable biomarker for cancer patients. OBJECTIVE To investigate whether circulating methylated tissue inhibitor of metalloproteinase 3 (TIMP-3) DNA in body fluids is a useful prognostic biomarker in gastric cancer (GC). DESIGN TIMP-3 methylation was detected by real-time methylation-specific polymerase chain reaction in tumor tissues, paired preoperative peritoneal washes (PPWs), and paired serum samples from 92 GC patients. RESULTS The frequency of TIMP-3 methylation was significantly elevated in GC tissues (63.04%; 58 of 92) compared with that in paired adjacent normal tissue (4.3%; 4 of 92) (P < .001). TIMP-3 methylation correlated closely with peritoneal metastasis and TNM stage (all P < .001). The frequency of TIMP-3 methylation in preoperative peritoneal washes and serum samples was 53.3% (49 of 92) and 58.7% (54 of 92), respectively. The Aζ values of the receiver operator characteristic curve for methylated TIMP-3 were 0.966 and 0.922 for serum and preoperative peritoneal washes, respectively, compared with those in GC tissues. The patients with elevated methylated TIMP-3 levels in body fluids had poorer disease-free survival rates than those without (all P < .001). Cox regression analysis showed that detection of methylated TIMP-3 DNA in body fluids was an independent risk factor for GC patients, with a remarkable decrease in disease-free survival 30 months after surgical resection of the gastric tumor. CONCLUSION Presence of methylated TIMP-3 DNA in body fluids is a useful biomarker for predicting the progression and prognosis of GC patients.
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Affiliation(s)
- Jiang-Liu Yu
- From the Zhejiang Cancer Research Institute (Drs Yu, Han, X. Zhu, Wu, Hong, and Ling) and the Department of Surgical Oncology (Dr Wang), Zhejiang Province Cancer Hospital, Zhejiang Cancer Center, Hangzhou, China; the Department of Surgical Oncology (Dr Lv) and the Central Laboratory (Dr W-Y Zhu), Zhoushan Hospital, Zhoushan, China; and the Department of Pathophysiology, School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, China (Dr Li)
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Miceli M, Bontempo P, Nebbioso A, Altucci L. Natural compounds in epigenetics: a current view. Food Chem Toxicol 2014; 73:71-83. [PMID: 25139119 DOI: 10.1016/j.fct.2014.08.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 01/03/2023]
Abstract
The successful treatment of many human diseases, including cancer, has come to be considered a major challenge, as patient response to therapy is difficult to predict. Recently, considerable efforts are being focused on the development of new tools to meet the growing demand for personalized medicine. With few exceptions, synthetic compounds have been unable to meet initial expectations for their clinical use. The last twenty years have been characterized by the failure of several drugs in advanced clinical development, possibly due to the insufficient understanding of molecular pathways underlying their mechanism of action. Although the biodiversity of compounds found in nature has been poorly explored until now, the field of naturally occurring drugs is rapidly expanding. Here, we review the current knowledge on the use of natural compounds with particular emphasis on those that display a chromatin remodeling effect coupled with anticancer action.
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Affiliation(s)
- Marco Miceli
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati-Traverso, IGB, Via P. Castellino 111, 80131 Napoli, Italy
| | - Paola Bontempo
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Angela Nebbioso
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy
| | - Lucia Altucci
- Dipartimento di Biochimica, Biofisica e Patologia Generale, Seconda Universita' di Napoli, Via L. De Crecchio 7, 80138 Napoli, Italy; Istituto di Genetica e Biofisica, Adriano Buzzati-Traverso, IGB, Via P. Castellino 111, 80131 Napoli, Italy.
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Botana-Rial M, De Chiara L, Valverde D, Leiro-Fernández V, Represas-Represas C, Del Campo-Pérez V, Fernández-Villar A. Prognostic value of aberrant hypermethylation in pleural effusion of lung adenocarcinoma. Cancer Biol Ther 2012; 13:1436-42. [PMID: 22954699 DOI: 10.4161/cbt.22004] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Lung adenocarcinoma is one of the most frequent causes of malignant pleural effusions (MPE). The presence of MPE bears a poor prognosis. Although epigenetic changes are commonly related to human neoplasia, scarce date is available on patients with MPE. We aimed to estimate the prognostic value of DNA methylation of tumor suppressor genes from pleural fluid. Thirty patients with MPE due to lung adenocarcinoma were prospectively included. Methylation-specific (MS) PCR was used to study the methylation status of the promoter region of tumor suppressor genes p16/INK4a, MGMT, BRCA1 and RARβ in pleural fluid. Clinical data and survival were collected. Survival analysis was performed using Kaplan-Meier plots and Cox regression. Hypermethylation in at least one gene was detected in 25 patients (83.3%). On multivariate analysis factors significantly associated with shorter survival were the lack of hypermethylation in any of the studied genes (hazard ratio = 9.3; p = 0.001), Charlson index ≥ 3 (hazard ratio = 9.6, p = 0.002) and no oncological treatment (hazard ratio = 11.1; p < 0.001). Analysis of aberrant promoter hypermethylation of tumor suppressor genes may be useful in predicting prognosis, but further studies are needed to validate our findings.
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Affiliation(s)
- Maribel Botana-Rial
- Bronchopleural Unit, Respiratory and Infectious Disease Research Group, Pneumology Service of Complexo Hospitalario Universitario de Vigo, Bio-medical Research Institute of Vigo, Vigo, Spain.
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Wang L, Chen S, Xue M, Zhong J, Wang X, Gan L, Lam EKY, Liu X, Zhang J, Zhou T, Yu J, Jin H, Si J. Homeobox D10 gene, a candidate tumor suppressor, is downregulated through promoter hypermethylation and associated with gastric carcinogenesis. Mol Med 2012; 18:389-400. [PMID: 22160393 DOI: 10.2119/molmed.2011.00172] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2011] [Accepted: 12/06/2011] [Indexed: 12/12/2022] Open
Abstract
Homeobox D10 (HoxD10 ) gene plays a critical role in cell differentiation and morphogenesis during development. However, the function of HoxD10 in tumor progression remains largely unknown. We demonstrate that the expression of HoxD10 is commonly downregulated in gastric cancer tissues (n = 33) and cell lines (n = 8) relative to normal stomach tissues. Functionally, reexpression of HoxD10 results in significant inhibition of cell survival, induction of cell apoptosis, and impairment of cell migration and invasion. Moreover, ectopic expression of HoxD10 suppresses gastric tumor growth in a mouse xenograft model. To identify target candidates of HoxD10, we performed cDNA microarray and showed that HoxD10 regulates multiple downstream genes including IGFBP3. Reintroduction of HoxD10 transcriptionally upregulates IGFBP3, activates caspase 3 and caspase 8, and subsequently induces cell apoptosis. Methylation specific PCR revealed that HoxD10 promoter DNA was hypermethylated in gastric cancer cell lines. Additionally, 5-aza demethylation treatment could transiently reactivate the expression of HoxD10 in gastric cancer cells. HoxD10 promoter methylation frequently was detected in gastric cancer tissues obtained from endoscopic biopsies (85.7%, 24/28) and surgically resected samples (82.6%, 57/69). Intestinal metaplasia tissues showed a 60% methylation rate (18/30), but no detectable methylation in normal stomach tissues (0%, 0/10). Taken together, our results suggest that HoxD10 functions as a candidate tumor suppressor in gastric cancer, which is inactivated through promoter hypermethylation.
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Affiliation(s)
- Liangjing Wang
- Laboratory of Digestive Disease, Sir Run Run Shaw Clinical Medicine Institution of Zhejiang University, Hangzhou, China
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12
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Yu QM, Wang XB, Luo J, Wang S, Fang XH, Yu JL, Ling ZQ. CDH1 methylation in preoperative peritoneal washes is an independent prognostic factor for gastric cancer. J Surg Oncol 2012; 106:765-71. [PMID: 22514028 PMCID: PMC3495294 DOI: 10.1002/jso.23116] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2011] [Accepted: 03/15/2012] [Indexed: 02/06/2023]
Abstract
Background and Objectives To investigate the clinical value of CDH1 methylation in preoperative peritoneal washes (PPW) from gastric cancer patients. Methods CDH1 methylation was detected by real-time methylation specific-PCR in tumor tissues and corresponding PPW from 92 gastric cancer patients, gastric mucosa from 40 chronic gastritis patients and 48 normal persons. Results CDH1 methylation was found in 75 of 92 (81.5%) gastric cancer tissues, which significantly correlated with size, growth pattern, differentiation, lymphatic invasion, venous invasion, invasion depth, lymph node metastasis, distant metastasis, and TNM stage of tumor (all P < 0.05), but its relationship to age, gender, tumor site, and H. pylori infection was not found (all P > 0.05). The percentage of CDH1 methylation in PPW was 48.9%, of which the Aζ value of ROC curve was 0.8 compared to that in gastric cancer tissues. Kaplan–Meier analysis showed that there was a significant difference in disease-free survival (DFS) between the patients with or without methylated CDH1 in their PPW (χ2 = 109.64, P < 0.000). Cox regression analysis revealed CDH1 methylation in PPW was an independent risk factor for gastric cancer patients, with a remarkable decrease in DFS after postoperative 30 months. Conclusions Methylated CDH1 in PPW predicts poor prognosis for gastric cancer patients. J. Surg. Oncol. 2012; 106:765–771. © 2012 Wiley Periodicals, Inc.
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Affiliation(s)
- Qi-Ming Yu
- Zhejiang Cancer Research Institute, Zhejiang Province Cancer Hospital, Zhejiang Cancer Center, Banshanqiao District, Hangzhou, China
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Riordan AM, Thomas MK, Ronnekleiv-Kelly S, Warner T, Geiger PG, Kennedy GD. Utility of micro-ribonucleic acid profile for predicting recurrence of rectal cancer. J Surg Res 2012; 177:87-92. [PMID: 22480843 DOI: 10.1016/j.jss.2012.02.052] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2011] [Revised: 02/06/2012] [Accepted: 02/22/2012] [Indexed: 02/06/2023]
Abstract
BACKGROUND In early-stage rectal cancer, the surgeon must decide between the high morbidity of radical surgery and the high recurrence rates of local excision. A prognostic marker could improve patient selection and lower recurrence rates. Micro-ribonucleic acids (miRNAs), small RNAs that often inhibit tumor suppressors, have shown prognostic potential in colorectal cancer. We hypothesized that high miRNA levels in malignant tissue from early-stage rectal cancer patients could predict recurrence after local excision. MATERIALS AND METHODS We identified 17 early-stage rectal cancer patients treated with local excision between 1990 and 2005, four of whom had recurrences. Total RNA was extracted from benign and malignant tissue and used in quantitative real-time reverse transcriptase polymerase chain reaction to probe for miR-20a, miR-21, miR-106a, miR-181b, and miR-203. MiRNA data were evaluated for association with recurrence using univariate analysis with Wilcoxon rank sum test. RESULTS Malignant tissue in both patients who had recurrences and patients who did not have recurrences had equivalently high levels of miRNA. However, the benign tissue of patients who recurred contained significantly higher levels of all five miRNAs when compared with the benign tissue of nonrecurrent patients despite having no histological differences. CONCLUSIONS This is the first study to show that high miRNA levels of histologically benign tissue obtained from the surgical margin of locally excised rectal cancers can predict recurrence. The malignant miRNA levels did not have predictive value. Further investigation of miRNAs is needed to explore their potential for a more accurate prognosis of rectal cancer.
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Affiliation(s)
- Alexander M Riordan
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin, USA
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Translational application of epigenetic alterations: ovarian cancer as a model. FEBS Lett 2011; 585:2112-20. [PMID: 21402071 DOI: 10.1016/j.febslet.2011.03.016] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2011] [Revised: 03/04/2011] [Accepted: 03/07/2011] [Indexed: 12/12/2022]
Abstract
Cancer is a disease initiated and driven by the accumulation and interplay of genetic and epigenetic mutations of genes involved in the regulation of cell growth and signaling. Dysregulation of these genes and pathways in a cell leads to a growth advantage and clonal expansion. The epigenetic alterations involved in the initiation and progression of cancer are DNA methylation and histone modifications which interact to remodel chromatin, as well as RNA interference. These alterations can be used as candidate targets in molecular tests for risk, early detection, prognosis, prediction of response to therapy, and monitoring, as well as new therapeutic targets in cancer. In this review, we discuss the rationale, studies to date, and issues in the translational application of epigenetics using epithelial ovarian cancer as a specific example of all types of cancer.
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Abstract
It has become increasingly evident that the study of DNA is inadequate to explain many, if not most, aspects of the development and progression of neoplastic lesions from pre-invasive lesions to metastasis. Thus, the term "genetic" can no longer refer to just the study of the genome. Much of the action in genetic research now shifts to the methods by which the pre-mRNA from one gene is processed to yield multiple different proteins, different quantities of the same protein as well as other forms of regulating RNA. Thus, the age of post-transcriptional processing and epigenetic control of the transfer of information from the genome has arrived. The mechanisms of post-transcriptional processing and epigenetic control that must be characterized in greater detail including alternate splicing, regulation of mRNA degradation, RNA regulatory factors including those factors which extensively edit mRNAs, control of translation, and control of protein stability and degradation. This chapter reviews many of the processes that control information from the genome to proteins and how these factors lead from less than 40,000 genes to more than an order of magnitude increase more proteins which actually control the phenotypes of cells - normal or neoplastic. It is usually the products of genes (e.g., mRNA, microRNA and proteins) that are the molecular markers that will control translational research and ultimately, individualized (personal) medical approaches to disease. This chapter emphasizes how the process of neoplasia "hijacks" the normal processes of cellular operations, especially those processes that are important in the normal development of the organisms - including proliferation, cellular death, angiogenesis, cellular mobility and invasion, and immunoregulation to ensure neoplastic development, survival and progression. This chapter reviews the wide range of processes controlling the information that flows from the genome to proteins and emphasizes how molecular steps in pure processes can be used as biomarkers to study prevention, treatment and/or management of diseases.
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Affiliation(s)
- Sudhir Srivastava
- National Cancer Institute, National Institutes of Health, Bethesda MD, USA.
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Tainsky MA. Genomic and proteomic biomarkers for cancer: a multitude of opportunities. BIOCHIMICA ET BIOPHYSICA ACTA 2009; 1796:176-93. [PMID: 19406210 PMCID: PMC2752479 DOI: 10.1016/j.bbcan.2009.04.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2009] [Revised: 04/14/2009] [Accepted: 04/21/2009] [Indexed: 02/06/2023]
Abstract
Biomarkers are molecular indicators of a biological status, and as biochemical species can be assayed to evaluate the presence of cancer and therapeutic interventions. Through a variety of mechanisms cancer cells provide the biomarker material for their own detection. Biomarkers may be detectable in the blood, other body fluids, or tissues. The expectation is that the level of an informative biomarker is related to the specific type of disease present in the body. Biomarkers have potential both as diagnostic indicators and monitors of the effectiveness of clinical interventions. Biomarkers are also able to stratify cancer patients to the most appropriate treatment. Effective biomarkers for the early detection of cancer should provide a patient with a better outcome which in turn will translate into more efficient delivery of healthcare. Technologies for the early detection of cancer have resulted in reductions in disease-associated mortalities from cancers that are otherwise deadly if allowed to progress. Such screening technologies have proven that early detection will decrease the morbidity and mortality from cancer. An emerging theme in biomarker research is the expectation that panels of biomarker analytes rather than single markers will be needed to have sufficient sensitivity and specificity for the presymptomatic detection of cancer. Biomarkers may provide prognostic information of disease enabling interventions using targeted therapeutic agents as well as course-corrections in cancer treatment. Novel genomic, proteomic and metabolomic technologies are being used to discover and validate tumor biomarkers individually and in panels.
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Affiliation(s)
- Michael A Tainsky
- Program in Molecular Biology and Genetics, Barbara Ann Karmanos Cancer Institute, Department of Pathology, Wayne State University School of Medicine, USA.
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