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Hsieh CH, Ho PS, Wang WL, Shih FH, Hong CT, Wang PW, Shieh DB, Chang WL, Wang YC. Decreased plasma gelsolin fosters a fibrotic tumor microenvironment and promotes chemoradiotherapy resistance in esophageal squamous cell carcinoma. J Biomed Sci 2024; 31:90. [PMID: 39261905 PMCID: PMC11389350 DOI: 10.1186/s12929-024-01078-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 08/21/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Stromal fibrosis is highly associated with therapeutic resistance and poor survival in esophageal squamous cell carcinoma (ESCC) patients. Low expression of plasma gelsolin (pGSN), a serum abundant protein, has been found to correlate with inflammation and fibrosis. Here, we evaluated pGSN expression in patients with different stages of cancer and therapeutic responses, and delineated the molecular mechanisms involved to gain insight into therapeutic strategies for ESCC. METHODS Circulating pGSN level in ESCC patients was determined by enzyme-linked immunosorbent assay analysis, and the tissue microarray of tumors was analyzed by immunohistochemistry staining. Cell-based studies were performed to investigate cancer behaviors and molecular mechanisms, and mouse models were used to examine the pGSN-induced tumor suppressive effects in vivo. RESULTS Circulating pGSN expression is distinctively decreased during ESCC progression, and low pGSN expression correlates with poor therapeutic responses and poor survival. Methylation-specific PCR analysis confirmed that decreased pGSN expression is partly attributed to the hypermethylation of the GSN promoter, the gene encoding pGSN. Importantly, cell-based immunoprecipitation and protein stability assays demonstrated that pGSN competes with oncogenic tenascin-C (TNC) for the binding and degradation of integrin αvβ3, revealing that decreased pGSN expression leads to the promotion of oncogenic signaling transduction in cancer cells and fibroblasts. Furthermore, overexpression of pGSN caused the attenuation of TNC expression and inactivation of cancer-associated fibroblast (CAF), thereby leading to tumor growth inhibition in mice. CONCLUSIONS Our results demonstrated that GSN methylation causes decreased secretion of pGSN, leading to integrin dysregulation, oncogenic TNC activation, and CAF formation. These findings highlight the role of pGSN in therapeutic resistance and the fibrotic tumor microenvironment of ESCC.
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Affiliation(s)
- Chih-Hsiung Hsieh
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Shiuan Ho
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wen-Lun Wang
- Department of Internal Medicine, E-Da Hospital, College of Medicine, I-Shou University, Kaohsiung, Taiwan
| | - Fu-Hsuan Shih
- Institute of Basic Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chen-Tai Hong
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Pei-Wen Wang
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Dar-Bin Shieh
- Institute of Oral Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Applied Nanomedicine, National Cheng Kung University, Tainan, Taiwan
- Center for Micro/Nano Science and Technology, Advanced Optoelectronic Technology Center, Innovation Center for Advanced Medical Device Technology, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
- Institute of Basic Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Jones AC, Patki A, Srinivasasainagendra V, Hidalgo BA, Tiwari HK, Limdi NA, Armstrong ND, Chaudhary NS, Minniefield B, Absher D, Arnett DK, Lange LA, Lange EM, Young BA, Diamantidis CJ, Rich SS, Mychaleckyj JC, Rotter JI, Taylor KD, Kramer HJ, Tracy RP, Durda P, Kasela S, Lappalinen T, Liu Y, Johnson WC, Van Den Berg DJ, Franceschini N, Liu S, Mouton CP, Bhatti P, Horvath S, Whitsel EA, Irvin MR. A methylation risk score for chronic kidney disease: a HyperGEN study. Sci Rep 2024; 14:17757. [PMID: 39085340 PMCID: PMC11291488 DOI: 10.1038/s41598-024-68470-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2024] [Accepted: 07/24/2024] [Indexed: 08/02/2024] Open
Abstract
Chronic kidney disease (CKD) impacts about 1 in 7 adults in the United States, but African Americans (AAs) carry a disproportionately higher burden of disease. Epigenetic modifications, such as DNA methylation at cytosine-phosphate-guanine (CpG) sites, have been linked to kidney function and may have clinical utility in predicting the risk of CKD. Given the dynamic relationship between the epigenome, environment, and disease, AAs may be especially sensitive to environment-driven methylation alterations. Moreover, risk models incorporating CpG methylation have been shown to predict disease across multiple racial groups. In this study, we developed a methylation risk score (MRS) for CKD in cohorts of AAs. We selected nine CpG sites that were previously reported to be associated with estimated glomerular filtration rate (eGFR) in epigenome-wide association studies to construct a MRS in the Hypertension Genetic Epidemiology Network (HyperGEN). In logistic mixed models, the MRS was significantly associated with prevalent CKD and was robust to multiple sensitivity analyses, including CKD risk factors. There was modest replication in validation cohorts. In summary, we demonstrated that an eGFR-based CpG score is an independent predictor of prevalent CKD, suggesting that MRS should be further investigated for clinical utility in evaluating CKD risk and progression.
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Affiliation(s)
- Alana C Jones
- Medical Scientist Training Program, University of Alabama at Birmingham, 912 18th St S, Birmingham, AL, 35233, USA.
- Department of Epidemiology, University of Alabama at Birmingham, 912 18th St S, Birmingham, AL, 35233, USA.
| | - Amit Patki
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | | | - Bertha A Hidalgo
- Department of Epidemiology, University of Alabama at Birmingham, 912 18th St S, Birmingham, AL, 35233, USA
| | - Hemant K Tiwari
- Department of Biostatistics, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Nicole D Armstrong
- Department of Epidemiology, University of Alabama at Birmingham, 912 18th St S, Birmingham, AL, 35233, USA
| | | | - Bré Minniefield
- Department of Biology, Florida State University-Panama City, Panama City, FL, USA
| | - Devin Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Donna K Arnett
- Office of the Provost, University of South Carolina, Columbia, SC, USA
| | - Leslie A Lange
- Department of Biomedical Informatics, University of Colorado-Anschutz, Aurora, CO, USA
| | - Ethan M Lange
- Department of Biomedical Informatics, University of Colorado-Anschutz, Aurora, CO, USA
| | - Bessie A Young
- Division of Nephrology, University of Washington, Seattle, WA, USA
| | | | - Stephen S Rich
- Department of Genome Sciences, University of Virginia, Charlottesville, VA, USA
| | - Josyf C Mychaleckyj
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Holly J Kramer
- Departments of Public Health Sciences and Medicine, Loyola University Medical Center, Taywood, IL, USA
| | - Russell P Tracy
- Department of Pathology and Laboratory Medicine, University of Vermont, Colchester, VT, USA
| | - Peter Durda
- Department of Pathology and Laboratory Medicine, University of Vermont, Colchester, VT, USA
| | - Silva Kasela
- Department of Systems Biology, New York Genome Center, Columbia University, New York, NY, USA
| | - Tuuli Lappalinen
- Department of Systems Biology, New York Genome Center, Columbia University, New York, NY, USA
| | - Yongmei Liu
- Department of Medicine, Cardiology and Neurology, Duke University Medical Center, Durham, NC, USA
| | - W Craig Johnson
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - David J Van Den Berg
- Department of Population and Public Health Sciences, Keck School of Medicine of USC, University of Southern California, Los Angeles, CA, USA
| | - Nora Franceschini
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Simin Liu
- Department of Epidemiology, School of Public Health, Brown University, Providence, RI, USA
| | - Charles P Mouton
- Department of Family Medicine, University of Texas Medical Branch Health, Galveston, TX, USA
| | - Parveen Bhatti
- Department of Medicine, School of Population and Public Health, University of British Columbia, Vancouver, BC, CAN, USA
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, Gonda Research Center, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Marguerite R Irvin
- Department of Epidemiology, University of Alabama at Birmingham, 912 18th St S, Birmingham, AL, 35233, USA
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Zhao YX, Zhao HP, Zhao MY, Yu Y, Qi X, Wang JH, Lv J. Latest insights into the global epidemiological features, screening, early diagnosis and prognosis prediction of esophageal squamous cell carcinoma. World J Gastroenterol 2024; 30:2638-2656. [PMID: 38855150 PMCID: PMC11154680 DOI: 10.3748/wjg.v30.i20.2638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 04/26/2024] [Accepted: 05/13/2024] [Indexed: 05/27/2024] Open
Abstract
As a highly invasive carcinoma, esophageal cancer (EC) was the eighth most prevalent malignancy and the sixth leading cause of cancer-related death worldwide in 2020. Esophageal squamous cell carcinoma (ESCC) is the major histological subtype of EC, and its incidence and mortality rates are decreasing globally. Due to the lack of specific early symptoms, ESCC patients are usually diagnosed with advanced-stage disease with a poor prognosis, and the incidence and mortality rates are still high in many countries, especially in China. Therefore, enormous challenges still exist in the management of ESCC, and novel strategies are urgently needed to further decrease the incidence and mortality rates of ESCC. Although the key molecular mechanisms underlying ESCC pathogenesis have not been fully elucidated, certain promising biomarkers are being investigated to facilitate clinical decision-making. With the advent and advancement of high-throughput technologies, such as genomics, proteomics and metabolomics, valuable biomarkers with high sensitivity, specificity and stability could be identified for ESCC. Herein, we aimed to determine the epidemiological features of ESCC in different regions of the world, especially in China, and focused on novel molecular biomarkers associated with ESCC screening, early diagnosis and prognosis prediction.
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Affiliation(s)
- Yi-Xin Zhao
- Department of Clinical Laboratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi Province, China
| | - He-Ping Zhao
- Department of Clinical Laboratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi Province, China
| | - Meng-Yao Zhao
- Department of Clinical Laboratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi Province, China
| | - Yan Yu
- Department of Clinical Laboratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi Province, China
| | - Xi Qi
- Department of Clinical Laboratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi Province, China
| | - Ji-Han Wang
- Institute of Medical Research, Northwestern Polytechnical University, Xi’an 710072, Shaanxi Province, China
| | - Jing Lv
- Department of Clinical Laboratory, Honghui Hospital, Xi’an Jiaotong University, Xi’an 710054, Shaanxi Province, China
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Yang Z, Guan F, Bronk L, Zhao L. Multi-omics approaches for biomarker discovery in predicting the response of esophageal cancer to neoadjuvant therapy: A multidimensional perspective. Pharmacol Ther 2024; 254:108591. [PMID: 38286161 DOI: 10.1016/j.pharmthera.2024.108591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 12/02/2023] [Accepted: 01/04/2024] [Indexed: 01/31/2024]
Abstract
Neoadjuvant chemoradiotherapy (NCRT) followed by surgery has been established as the standard treatment strategy for operable locally advanced esophageal cancer (EC). However, achieving pathologic complete response (pCR) or near pCR to NCRT is significantly associated with a considerable improvement in survival outcomes, while pCR patients may help organ preservation for patients by active surveillance to avoid planned surgery. Thus, there is an urgent need for improved biomarkers to predict EC chemoradiation response in research and clinical settings. Advances in multiple high-throughput technologies such as next-generation sequencing have facilitated the discovery of novel predictive biomarkers, specifically based on multi-omics data, including genomic/transcriptomic sequencings and proteomic/metabolomic mass spectra. The application of multi-omics data has shown the benefits in improving the understanding of underlying mechanisms of NCRT sensitivity/resistance in EC. Particularly, the prominent development of artificial intelligence (AI) has introduced a new direction in cancer research. The integration of multi-omics data has significantly advanced our knowledge of the disease and enabled the identification of valuable biomarkers for predicting treatment response from diverse dimension levels, especially with rapid advances in biotechnological and AI methodologies. Herein, we summarize the current status of research on the use of multi-omics technologies in predicting NCRT response for EC patients. Current limitations, challenges, and future perspectives of these multi-omics platforms will be addressed to assist in experimental designs and clinical use for further integrated analysis.
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Affiliation(s)
- Zhi Yang
- Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, 15 West Changle Road, Xi'an, China
| | - Fada Guan
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, CT 06510, United States of America
| | - Lawrence Bronk
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, United States of America
| | - Lina Zhao
- Department of Radiation Oncology, Xijing Hospital, Fourth Military Medical University, 15 West Changle Road, Xi'an, China.
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5
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Chang WL, Hsieh CH, Kuo IY, Lin CH, Huang YL, Wang YC. Nutlin-3 acts as a DNA methyltransferase inhibitor to sensitize esophageal cancer to chemoradiation. Mol Carcinog 2023; 62:277-287. [PMID: 36342355 DOI: 10.1002/mc.23485] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 10/17/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is highly resistant to chemoradiation therapy. We aimed to examine whether Nutlin-3, a molecule that suppresses murine double min 2 (MDM2)-mediated p53 and Retinoblastoma (RB) protein degradation leading to downregulation of DNA methyltransferases (DNMTs), can be a novel therapeutic agent for ESCC. We used wild-type and chemoradiation-resistant ESCC cell lines in this study. The expression of DNMTs, p53 and RB, and methylation level of tumor suppressor genes (TSG) were analyzed upon Nutlin-3 treatment. The antitumor efficacy of Nutlin-3 was investigated in ESCC cell lines and xenograft tumor model. TSG protein expression was checked in the excised tumor tissue. Nutlin-3 induced upregulation of p53 and RB and downregulation of DNMTs proteins in the chemoradiation-resistant and aggressive ESCC cells. The methylation level of TSGs was decreased by Nutlin-3. Nutlin-3 inhibits clonogenic growth of ESCC cells and exerts a synergistic cytotoxic-effect when combined with chemotherapeutic agent cisplatin. Moreover, xenograft tumor growth in SCID mice was suppressed by Nutlin-3. The protein expression level of DNMTs was downregulated, and that of TSGs was upregulated by Nutlin-3 treatment in the excised tumor tissue. In conclusion, Nutlin-3 is a potential therapeutic agent that can potentiate the treatment efficacy of chemoradiation-resistant ESCC.
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Affiliation(s)
- Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chih-Hsiung Hsieh
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - I-Ying Kuo
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hsun Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Lin Huang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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Yun Y, Zhang Y, Xu Q, Ou Y, Zhou X, Lu Z. SOX17-mediated MALAT1-miR-199a-HIF1α axis confers sensitivity in esophageal squamous cell carcinoma cells to radiotherapy. Cell Death Dis 2022; 8:270. [PMID: 35614065 PMCID: PMC9132944 DOI: 10.1038/s41420-022-01012-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/17/2022] [Accepted: 03/30/2022] [Indexed: 11/21/2022]
Abstract
Radiotherapy is a main modality of esophageal squamous cell carcinoma (ESCC) treatment, while radioresistance largely limits the effect of this therapy. Evidence exists reporting that SOX17 may sensitize ESCC cells to irradiation, but the downstream mechanism remains poorly understood. Therefore, we attempt to explore the molecular basis of SOX17 effect on radioresistance in ESCC. The SOX17 expression was measured in ESCC tissues and cells, followed by evaluation of its relationship with patient survival. The fractionated irradiation-induced irradiation-resistant cell line KYSE150R was subjected to gain- and loss-of function studies to explore the effect of SOX17 and downstream effectors MALAT1, miR-199a, and HIF1α on the malignant phenotypes of ESCC. The interaction among these factors was explained using ChIP, dual luciferase reporter, RNA pull-down and RIP assays. Further, the in vivo effect of SOX17 on ESCC irradiation tolerance was assessed in nude mice. SOX17 was underexpressed in ESCC tissues and cells, which was negatively correlated with the prognosis of patients with ESCC. Besides, SOX17 inhibited irradiation tolerance of ESCC cells by suppressing MALAT1 transcription. Notably, MALAT1 acted as miR-199a sponge and thereby enhanced HIF1α expression. Moreover, SOX17 reduced the irradiation tolerance of ESCC cells by reducing HIF1α expression via the MALAT1-miR-199a axis, and attenuated tumor formation in nude mice. Our results indicate that SOX17 can impede the radioresistance of ESCC cells through the MALAT1-miR-199a-HIF1α axis, in support of further research for ESCC radiotherapy.
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Affiliation(s)
- Yifei Yun
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, 213000, China
| | - Yutong Zhang
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, 213000, China
| | - Qiqi Xu
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, 213000, China
| | - Yao Ou
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, 213000, China
| | - Xifa Zhou
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, 213000, China.
| | - Zhonghua Lu
- Department of Radiotherapy, Changzhou Tumor Hospital, Soochow University, Changzhou, 213000, China.
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Paired box 5 increases the chemosensitivity of esophageal squamous cell cancer cells by promoting p53 signaling activity. Chin Med J (Engl) 2022; 135:606-618. [PMID: 35191417 PMCID: PMC8920431 DOI: 10.1097/cm9.0000000000002018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
BACKGROUND Gene promoter methylation is a major epigenetic change in cancers, which plays critical roles in carcinogenesis. As a crucial regulator in the early stages of B-cell differentiation and embryonic neurodevelopment, the paired box 5 (PAX5) gene is downregulated by methylation in several kinds of tumors and the role of this downregulation in esophageal squamous cell carcinoma (ESCC) pathogenesis remains unclear. METHODS To elucidate the role of PAX5 in ESCC, eight ESCC cell lines, 51 primary ESCC tissue samples, and eight normal esophageal mucosa samples were studied and The Cancer Genome Atlas (TCGA) was queried. PAX5 expression was examined by reverse transcription-polymerase chain reaction and western blotting. Cell apoptosis, proliferation, and chemosensitivity were detected by flow cytometry, colony formation assays, and 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide assays in ESCC cell lines with PAX5 overexpression or silencing. Tumor xenograft models were established for in vivo verification. RESULTS PAX5 methylation was found in 37.3% (19/51) of primary ESCC samples, which was significantly associated with age (P = 0.007) and tumor-node-metastasis stage (P = 0.014). TCGA data analysis indicated that PAX5 expression was inversely correlated with promoter region methylation (r = -0.189, P = 0.011 for cg00464519 and r = -0.228, P = 0.002 for cg02538199). Restoration of PAX5 expression suppressed cell proliferation, promoted apoptosis, and inhibited tumor growth of ESCC cell lines, which was verified in xenografted mice. Ectopic PAX5 expression significantly increased p53 reporter luciferase activity and increased p53 messenger RNA and protein levels. A direct interaction of PAX5 with the p53 promoter region was confirmed by chromatin immunoprecipitation assays. Re-expression of PAX5 sensitized ESCC cell lines KYSE150 and KYSE30 to fluorouracil and docetaxel. Silencing of PAX5 induced resistance of KYSE450 cells to these drugs. CONCLUSIONS As a tumor suppressor gene regulated by promoter region methylation in human ESCC, PAX5 inhibits proliferation, promotes apoptosis, and induces activation of p53 signaling. PAX5 may serve as a chemosensitive marker of ESCC.
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Ma M, Chen Y, Chong X, Jiang F, Gao J, Shen L, Zhang C. Integrative analysis of genomic, epigenomic and transcriptomic data identified molecular subtypes of esophageal carcinoma. Aging (Albany NY) 2021; 13:6999-7019. [PMID: 33638948 PMCID: PMC7993659 DOI: 10.18632/aging.202556] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 12/29/2020] [Indexed: 12/16/2022]
Abstract
Esophageal cancer (EC) involves many genomic, epigenetic and transcriptomic disorders, which play key roles in the heterogeneous progression of cancer. However, the study of EC with multi-omics has not been conducted. This study identified a high consistency between DNA copy number variations and abnormal methylations in EC by analyzing genomics, epigenetics and transcriptomics data and investigating mutual correlations of DNA copy number variation, methylation and gene expressions, and stratified copy number variation genes (CNV-Gs) and methylation genes (MET-Gs). The methylation, CNVs and expression profiles of CNV-Gs and MET-Gs were analyzed by consistent clustering using iCluster integration, here, we determined three subtypes (iC1, iC2, iC3) with different molecular traits, prognostic characteristics and tumor immune microenvironment features. We also identified 4 prognostic genes (CLDN3, FAM221A, GDF15 and YBX2) differentially expressed in the three subtypes, and could therefore be used as representative biomarkers for the three subtypes of EC. In conclusion, by performing comprehensive analysis on genomic, epigenetic and transcriptomic regulations, the current study provided new insights into the multilayer molecular and pathological traits of EC, and contributed to the precision medication for EC patients.
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Affiliation(s)
- Mingyang Ma
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Yang Chen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaoyi Chong
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Fangli Jiang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Jing Gao
- National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital and Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, China
| | - Lin Shen
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Cheng Zhang
- Department of Gastrointestinal Oncology, Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education/Beijing), Peking University Cancer Hospital and Institute, Beijing 100142, China
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Song Y, Yang K, Sun T, Tang R. Development and validation of prognostic markers in sarcomas base on a multi-omics analysis. BMC Med Genomics 2021; 14:31. [PMID: 33509178 PMCID: PMC7841904 DOI: 10.1186/s12920-021-00876-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/13/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND In sarcomas, the DNA copy number and DNA methylation exhibit genomic aberrations. Transcriptome imbalances play a driving role in the heterogeneous progression of sarcomas. However, it is still unclear whether abnormalities of DNA copy numbers are systematically related to epigenetic DNA methylation, thus, a comprehensive analysis of sarcoma occurrence and development from the perspective of epigenetic and genomics is required. METHODS RNASeq, copy number variation (CNV), methylation data, clinical follow-up information were obtained from The Cancer Genome Atlas (TCGA) and GEO database. The association between methylation and CNV was analyzed to further identify methylation-related genes (MET-Gs) and CNV abnormality-related genes (CNV-Gs). Subsequently DNA copy number, methylation, and gene expression data associated with the MET-Gs and CNV-Gs were integrated to determine molecular subtypes and clinical and molecular characteristics of molecular subtypes. Finally, key biomarkers were determined and validated in independent validation sets. RESULTS A total of 5354 CNV-Gs and 4042 MET-Gs were screened and showed a high degree of consistency. Four molecular subtypes (iC1, iC2, iC3, and iC4) with different prognostic significances were identified by multiomics cluster analysis, specifically, iC2 had the worst prognosis and iC4 indicated an immune-enhancing state. Three potential prognostic markers (ENO1, ACVRL1 and APBB1IP) were determined after comparing the molecular characteristics of the four molecular subtypes. The expression of ENO1 gene was significantly correlated with CNV, and was noticeably higher in iC2 subtype with the worst prognosis than any other subtypes. The expressions of ACVRL1 and APBB1IP were negatively correlated with methylation, and were high-expressed in the iC4 subtype with the most favorable prognosis. In addition, the number of silent/nonsilent mutations and neoantigens in iC2 subtype were significantly more than those in iC1/iC3/iC4 subtype, and the same trend was also observed in CNV Gain/Loss. CONCLUSION The current comprehensive analysis of genomic and epigenomic regulation provides new insights into multilayered pathobiology of sarcomas. Four molecular subtypes and three prognostic markers developed in this study improve the current understanding of the molecular mechanisms underlying sarcoma.
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Affiliation(s)
- Yongchun Song
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Kui Yang
- Department of General Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, Shaanxi, China
| | - Tuanhe Sun
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China
| | - Ruixiang Tang
- Department of Oncology Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, 277 West Yanta Road, Xi'an, 710061, Shaanxi, China.
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Lavery A, Turkington RC. Transcriptomic biomarkers for predicting response to neoadjuvant treatment in oesophageal cancer. Gastroenterol Rep (Oxf) 2020; 8:411-424. [PMID: 33442473 PMCID: PMC7793050 DOI: 10.1093/gastro/goaa065] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 04/21/2020] [Accepted: 07/15/2020] [Indexed: 02/07/2023] Open
Abstract
Oesophageal cancer is a devastating disease with poor outcomes and is the sixth leading cause of cancer death worldwide. In the setting of resectable disease, there is clear evidence that neoadjuvant chemotherapy and chemoradiotherapy result in improved survival. Disappointingly, only 15%-30% of patients obtain a histopathological response to neoadjuvant therapy, often at the expense of significant toxicity. There are no predictive biomarkers in routine clinical use in this setting and the ability to stratify patients for treatment could dramatically improve outcomes. In this review, we aim to outline current progress in evaluating predictive transcriptomic biomarkers for neoadjuvant therapy in oesophageal cancer and discuss the challenges facing biomarker development in this setting. We place these issues in the wider context of recommendations for biomarker development and reporting. The majority of studies focus on messenger RNA (mRNA) and microRNA (miRNA) biomarkers. These studies report a range of different genes involved in a wide variety of pathways and biological processes, and this is explained to a large extent by the different platforms and analysis methods used. Many studies are also vastly underpowered so are not suitable for identifying a candidate biomarker. Multiple molecular subtypes of oesophageal cancer have been proposed, although little is known about how these relate to clinical outcomes. We anticipate that the accumulating wealth of genomic and transcriptomic data and clinical trial collaborations in the coming years will provide unique opportunities to stratify patients in this poor-prognosis disease and recommend that future biomarker development incorporates well-designed retrospective and prospective analyses.
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Affiliation(s)
- Anita Lavery
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
| | - Richard C Turkington
- Patrick G Johnston Centre for Cancer Research, Queen’s University Belfast, Belfast, UK
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11
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Chen H, Qin Q, Xu Z, Chen T, Yao X, Xu B, Sun X. DNA methylation data-based prognosis-subtype distinctions in patients with esophageal carcinoma by bioinformatic studies. J Cell Physiol 2020; 236:2126-2138. [PMID: 32830322 DOI: 10.1002/jcp.29999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Accepted: 07/24/2020] [Indexed: 02/06/2023]
Abstract
Esophageal carcinoma (ESCA) is caused by the accumulation of genetic and epigenetic alterations in esophageal mucosa. Of note, the earliest and the most frequent molecular behavior in the complicated pathogenesis of ESCA is DNA methylation. In the present study, we downloaded data of 178 samples from The Cancer Genome Atlas (TCGA) database to explore specific DNA methylation sites that affect prognosis in ESCA patients. Consequently, we identified 1,098 CpGs that were significantly associated with patient prognosis. Hence, these CpGs were used for consensus clustering of the 178 samples into seven clusters. Specifically, the samples in each group were different in terms of age, gender, tumor stage, histological type, metastatic status, and patient prognosis. We further analyzed 1,224 genes in the corresponding promoter regions of the 1,098 methylation sites, and enriched these genes in biological pathways with close correlation to cellular metabolism, enzymatic synthesis, and mitochondrial autophagy. In addition, nine representative specific methylation sites were screened using the weighted gene coexpression network analysis. Finally, a prognostic prediction model for ESCA patients was built in both training and validation cohorts. In summary, our study revealed that classification based on specific DNA methylation sites could reflect ESCA heterogeneity and contribute to the improvement of individualized treatment and precise prognostic prediction.
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Affiliation(s)
- Hui Chen
- Department of Radiation Oncology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Qin Qin
- Department of Radiation Oncology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Zhipeng Xu
- Department of Urology, Affiliated Zhongda Hospital of Southeast University, Nanjing, Jiangsu, China
| | - Tingting Chen
- Department of Oncology, Yangzhou University Affiliated Northern Jiangsu People's Hospital, Yangzhou, Jiangsu, China
| | - Xijuan Yao
- Department of Radiation Oncology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Bing Xu
- Department of Radiation Oncology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing, Jiangsu, China
| | - Xinchen Sun
- Department of Radiation Oncology, Nanjing Medical University First Affiliated Hospital, Jiangsu Province Hospital, Nanjing, Jiangsu, China
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Lin FC, Chang WL, Chiang NJ, Lin MY, Chung TJ, Pao TH, Lai WW, Tseng Y, Yen Y, Sheu BS. Radiation dose escalation can improve local disease control and survival among esophageal cancer patients with large primary tumor volume receiving definitive chemoradiotherapy. PLoS One 2020; 15:e0237114. [PMID: 32760099 PMCID: PMC7410311 DOI: 10.1371/journal.pone.0237114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/20/2020] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND This study aimed to investigate the correlation between primary tumor volume and cancer failure patterns in esophageal squamous cell carcinoma (ESCC) treated with definitive concurrent chemoradiotherapy (CCRT) and examine whether increasing radiation dose can improve the outcome. METHODS We retrospectively reviewed 124 patients with stage III ESCC treated by definitive CCRT. The primary tumor volume calculated from the radiotherapy planning computed tomography scans was correlated to treatment response, time to disease progression, and overall survival. We further analyzed whether a higher radiation dose correlated with better disease control and patient survival. RESULTS Patients with poor CCRT response had a larger primary tumor volume than those with good response (97.9 vs 64.3 cm3, P = 0.032). The optimal cutoff value to predict CCRT response was 55.3 cm3. Large primary tumor volume (≥ 55.3 cm3) correlated with shorter time to tumor progression in the esophagus (13.6 vs 48.6 months, P = 0.033) compared with small tumor volume (< 55.3 cm3). For the large esophageal tumors (≥ 55.3 cm3), radiation dose > 60 gray significantly prolonged the time to tumor progression in esophagus (20.3 vs 10.1 months, P = 0.036) and overall survival (12.2 vs 8.0 months, P = 0.030), compared with dose ≤ 60 gray. In contrast, higher radiation dose did not benefit local disease control or overall survival in the small esophageal tumors (< 55.3 cm3). CONCLUSION Large primary tumor volume correlates with poor local control and overall survival in ESCC treated with definitive CCRT. Radiation dose > 60 gray can improve the outcomes in patients with large primary tumor. Further prospective dose escalation trials are warranted.
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Affiliation(s)
- Forn-Chia Lin
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Nai-Jung Chiang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | - Meng-Ying Lin
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Ta-Jung Chung
- Department of Diagnostic Radiology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Tzu-Hui Pao
- Department of Radiation Oncology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wu-Wei Lai
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yau‐Lin Tseng
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yi‐Ting Yen
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Bor-Shyang Sheu
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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13
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d'Errico M, Alwers E, Zhang Y, Edelmann D, Brenner H, Hoffmeister M. Identification of prognostic DNA methylation biomarkers in patients with gastrointestinal adenocarcinomas: A systematic review of epigenome-wide studies. Cancer Treat Rev 2020; 82:101933. [DOI: 10.1016/j.ctrv.2019.101933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Revised: 11/14/2019] [Accepted: 11/15/2019] [Indexed: 02/07/2023]
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14
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Tang L, Liou YL, Wan ZR, Tang J, Zhou Y, Zhuang W, Wang G. Aberrant DNA methylation of PAX1, SOX1 and ZNF582 genes as potential biomarkers for esophageal squamous cell carcinoma. Biomed Pharmacother 2019; 120:109488. [DOI: 10.1016/j.biopha.2019.109488] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 09/08/2019] [Accepted: 09/22/2019] [Indexed: 12/23/2022] Open
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15
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Zhang C, Ge S, Wang J, Jing X, Li H, Mei S, Zhang J, Liang K, Xu H, Zhang X, Zhang C. Epigenomic profiling of DNA methylation for hepatocellular carcinoma diagnosis and prognosis prediction. J Gastroenterol Hepatol 2019; 34:1869-1877. [PMID: 31038805 DOI: 10.1111/jgh.14694] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 03/31/2019] [Accepted: 04/23/2019] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND AIM DNA hypermethylation has emerged as a novel molecular biomarker for the diagnosis and prognosis prediction of many cancers. We aimed to identify clinically useful biomarkers regulated by DNA methylation in hepatocellular carcinoma (HCC). METHODS Genome-wide methylation analysis in HCCs and paired noncancerous tissues was performed using an Illumina Infinium HumanMethylation 450K BeadChip array. Methylation-specific polymerase chain reaction and pyrosequencing were used to validate the methylation status of selected genes in 100 paired HCCs and noncancerous samples. RESULTS A total of 97 027 (20.0%) out of 485 577 CpG sites significantly were differed between HCC and noncancerous tissues. Among all the significant CpG sites, 48.8% are hypermethylated and 51.2% are hypomethylated in HCCs. Multiple signaling pathways (AMP-activated protein kinase, estrogen, and adipocytokine) involved in gene methylation were identified in HCC. FES was selected for further analysis based on its high level of methylation confirmed by polymerase chain reaction and pyrosequencing. The result showed that FES hypermethylation was correlated with tumor size (0.001), serum alpha fetoprotein (0.023), and tumor differentiation (0.006). FES protein was significantly downregulated in 51/100 (51%) HCCs, and 94.12% (48/51) of them were due to promoter hypermethylation. Both FES hypermethylation and protein downregulation were associated with the progression-free survival and overall survival of HCC patients. Overexpressed and knockdown of FES confirmed its inhibitory effect on the proliferation and migration of HCC cells. CONCLUSIONS We identified many new differentially methylated CpGs in HCCs and demonstrate that FES functions as a tumor suppressor gene in HCC and its methylation status could be used as an indicator for prognosis of HCC.
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Affiliation(s)
- Cheng Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Shuang Ge
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Jun Wang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaotong Jing
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | | | - Shuyu Mei
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Juan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Ke Liang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Hui Xu
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Xiaoying Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
| | - Cuijuan Zhang
- Institute of Pathology and Pathophysiology, Shandong University School of Medicine, Jinan, China
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Shen N, Wang T, Li D, Zhu Y, Xie H, Lu Y. Hypermethylation of the SEPT9 Gene Suggests Significantly Poor Prognosis in Cancer Patients: A Systematic Review and Meta-Analysis. Front Genet 2019; 10:887. [PMID: 31608117 PMCID: PMC6761278 DOI: 10.3389/fgene.2019.00887] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 08/22/2019] [Indexed: 12/27/2022] Open
Abstract
Background: Aberrant hypermethylation of the Septin 9 (SEPT9) is an early event in several human cancers, and increasing studies have reported good performance of methylated SEPT9 (mSEPT9) in cancer diagnosis. Recent studies further focused on its value in cancer prognosis, but results are not clearly elucidated. Methods: A comprehensive search to identify relevant studies about the association between mSEPT9 and cancer prognosis was conducted through the EMBASE, PubMed, and Web of Science databases (up to January 2019). The main outcomes were overall survival (OS) and disease-free survival (DFS). The hazard ratio (HR) and 95% confidence interval (CI) for OS and DFS were extracted from each included study and pooled using a random-effects model. Results: Ten eligible studies comprising 1,266 cancer patients were included. Results demonstrated that mSEPT9 was associated with poor OS (HR = 2.07, 95% CI = 1.40–3.06). Specially, mSEPT9 detected in preoperative plasma predicted worse OS in cancer patients (HR = 3.25, 95% CI = 1.93–5.48). In addition, we also identified a significant association of mSEPT9 with decreased DFS of cancer (HR = 3.24, 95% CI = 1.81–5.79). Conclusion: Our meta-analysis supports that mSEPT9 is associated with reduced OS and DFS in cancer patients. Moreover, detection of mSEPT9 using plasma appears to be a convenient and promising way to predict long-term survival of cancer patients.
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Affiliation(s)
- Na Shen
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Ting Wang
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Delei Li
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yaowu Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Huaping Xie
- Department of Gastroenterology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yanjun Lu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Higashijima Y, Kanki Y. Molecular mechanistic insights: The emerging role of SOXF transcription factors in tumorigenesis and development. Semin Cancer Biol 2019; 67:39-48. [PMID: 31536760 DOI: 10.1016/j.semcancer.2019.09.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 07/31/2019] [Accepted: 09/15/2019] [Indexed: 01/22/2023]
Abstract
Over the last decade, the development and progress of next-generation sequencers incorporated with classical biochemical analyses have drastically produced novel insights into transcription factors, including Sry-like high-mobility group box (SOX) factors. In addition to their primary functions in binding to and activating specific downstream genes, transcription factors also participate in the dedifferentiation or direct reprogramming of somatic cells to undifferentiated cells or specific lineage cells. Since the discovery of SOX factors, members of the SOXF (SOX7, SOX17, and SOX18) family have been identified to play broad roles, especially with regard to cardiovascular development. More recently, SOXF factors have been recognized as crucial players in determining the cell fate and in the regulation of cancer cells. Here, we provide an overview of research on the mechanism by which SOXF factors regulate development and cancer, and discuss their potential as new targets for cancer drugs while offering insight into novel mechanistic transcriptional regulation during cell lineage commitment.
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Affiliation(s)
- Yoshiki Higashijima
- Department of Bioinformational Pharmacology, Tokyo Medical and Dental University, Tokyo 113-8510, Japan; Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan
| | - Yasuharu Kanki
- Isotope Science Center, The University of Tokyo, Tokyo 113-0032, Japan.
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18
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Köhler CU, Bonberg N, Ahrens M, Behrens T, Hovanec J, Eisenacher M, Noldus J, Deix T, Braun K, Gohlke H, Walter M, Tannapfel A, Tam Y, Sommerer F, Marcus K, Jöckel KH, Erbel R, Cantor CR, Käfferlein HU, Brüning T. Noninvasive diagnosis of urothelial cancer in urine using DNA hypermethylation signatures-Gender matters. Int J Cancer 2019; 145:2861-2872. [PMID: 31008534 DOI: 10.1002/ijc.32356] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 04/01/2019] [Indexed: 01/28/2023]
Abstract
Urothelial cancer (UCa) is the most predominant cancer of the urinary tract and noninvasive diagnosis using hypermethylation signatures in urinary cells is promising. Here, we assess gender differences in a newly identified set of methylation biomarkers. UCa-associated hypermethylated sites were identified in urine of a male screening cohort (n = 24) applying Infinium-450K-methylation arrays and verified in two separate mixed-gender study groups (n = 617 in total) using mass spectrometry as an independent technique. Additionally, tissue samples (n = 56) of mixed-gender UCa and urological controls (UCt) were analyzed. The hypermethylation signature of UCa in urine was specific and sensitive across all stages and grades of UCa and independent on hematuria. Individual CpG sensitivities reached up to 81.3% at 95% specificity. Albeit similar methylation differences in tissue of both genders, differences were less pronounced in urine from women, most likely due to the frequent presence of squamous epithelial cells and leukocytes. Increased repression of methylation levels was observed at leukocyte counts ≥500/μl urine which was apparent in 30% of female and 7% of male UCa cases, further confirming the significance of the relative amounts of cancerous and noncancerous cells in urine. Our study shows that gender difference is a most relevant issue when evaluating the performance of urinary biomarkers in cancer diagnostics. In case of UCa, the clinical benefits of methylation signatures to male patients may outweigh those in females due to the general composition of women's urine. Accordingly, these markers offer a diagnostic option specifically in males to decrease the number of invasive cystoscopies.
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Affiliation(s)
- Christina U Köhler
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Nadine Bonberg
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Maike Ahrens
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Thomas Behrens
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Jan Hovanec
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | | | - Joachim Noldus
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Thomas Deix
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | - Katharina Braun
- Department of Urology, Marien Hospital Herne, Ruhr-University Bochum, Herne, Germany
| | | | - Michael Walter
- c.ATG Core Facility for NGS and Microarrays, University of Tübingen, Tübingen, Germany
| | - Andrea Tannapfel
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Yu Tam
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Florian Sommerer
- Institute of Pathology, Georgius Agricola Foundation, Ruhr-University Bochum, Bochum, Germany
| | - Katrin Marcus
- Medical Proteome Center, Ruhr University Bochum, Bochum, Germany
| | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Raimund Erbel
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Charles R Cantor
- Department of Biomedical Engineering, School of Medicine, Boston University, Boston, MA
| | - Heiko U Käfferlein
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
| | - Thomas Brüning
- Institute for Prevention and Occupational Medicine of the German Social Accident Insurance, Institute of the Ruhr-University Bochum (IPA), Bochum, Germany
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Kuo IY, Huang YL, Lin CY, Lin CH, Chang WL, Lai WW, Wang YC. SOX17 overexpression sensitizes chemoradiation response in esophageal cancer by transcriptional down-regulation of DNA repair and damage response genes. J Biomed Sci 2019; 26:20. [PMID: 30777052 PMCID: PMC6378712 DOI: 10.1186/s12929-019-0510-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2018] [Accepted: 02/04/2019] [Indexed: 12/16/2022] Open
Abstract
Background Prognosis of esophageal squamous cell carcinoma (ESCC) patients is poor and the concurrent chemoradiation therapy (CCRT) provided to ESCC patients often failed due to resistance. Therefore, development of biomarkers for predicting CCRT response is immensely important. In this study, we evaluated the predicting value of SRY (sex determining region Y)-box 17 (SOX17) protein during CCRT and its dysregulation of transcriptional targets in CCRT resistance in ESCC. Methods Pyrosequencing methylation, RT-qPCR and immunohistochemistry assays were performed to examine the DNA methylation, mRNA expression and protein expression levels of SOX17 in endoscopic biopsy from a total of 70 ESCC patients received CCRT. Cell proliferation, clonogenic survival and xenograft growth were used to confirm the sensitization of ESCC cell line KYSE510 in response to cisplatin, radiation or CCRT treatment by SOX17 overexpression in vitro and in vivo. Luciferase activity, RT-qPCR and ChIP-qPCR assays were conducted to examine transcription regulation of SOX17 in KYSE510 parental, KYSE510 radio-resistant cells and their derived xenografts. Results High DNA methylation coincided with low mRNA and protein expression levels of SOX17 in pre-treatment endoscopic biopsy from ESCC patients with poor CCRT response. SOX17 protein expression exhibited a good prediction performance in discriminating poor CCRT responders from good responder. Overexpression of SOX17 sensitized KYSE510 radio-resistant cells to cisplatin, radiation or CCRT treatment in cell and xenograft models. Importantly, SOX17 transcriptionally down-regulated DNA repair and damage response-related genes including BRCA1, BRCA2, RAD51, KU80 DNAPK, p21, SIRT1, NFAT5 and REV3L in KYSE510 radio-resistant cells to achieve the sensitization effect to anti-cancer treatment. Low expression of BRCA1, DNAPK, p21, RAD51 and SIRT1 was confirmed in SOX17 sensitized xenograft tissues derived from radio-resistant ESCC cells. Conclusions Our study reveals a novel mechanism by which SOX17 transcriptionally inactivates DNA repair and damage response-related genes to sensitize ESCC cell or xenograft to CCRT treatment. In addition, we establish a proof-of-concept CCRT prediction biomarker using SOX17 immunohistochemical staining in pre-treatment endoscopic biopsies to identify ESCC patients who are at high risk of CCRT failure and need intensive care. Electronic supplementary material The online version of this article (10.1186/s12929-019-0510-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- I-Ying Kuo
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan.,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Yu-Lin Huang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Chien-Yu Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Chien-Hsun Lin
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan
| | - Wei-Lun Chang
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan, 704, Taiwan
| | - Wu-Wei Lai
- Department of Surgery, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, No.138, Sheng Li Road, Tainan, 704, Taiwan.
| | - Yi-Ching Wang
- Department of Pharmacology, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan. .,Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, No.1, University Road, Tainan, 70101, Taiwan.
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