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Hu Y, Zhao Y, Zhang Y, Chen W, Zhang H, Jin X. Cell-free DNA: a promising biomarker in infectious diseases. Trends Microbiol 2024:S0966-842X(24)00168-9. [PMID: 38997867 DOI: 10.1016/j.tim.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 06/08/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024]
Abstract
Infectious diseases pose serious threats to public health worldwide. Conventional diagnostic methods for infectious diseases often exhibit low sensitivity, invasiveness, and long turnaround times. User-friendly point-of-care tests are urgently needed for early diagnosis, treatment monitoring, and prognostic prediction of infectious diseases. Cell-free DNA (cfDNA), a promising non-invasive biomarker widely used in oncology and pregnancy, has shown great potential in clinical applications for diagnosing infectious diseases. Here, we discuss the most recent cfDNA research on infectious diseases from both the pathogen and host perspectives. We also discuss the technical challenges in this field and propose solutions to overcome them. Additionally, we provide an outlook on the potential of cfDNA as a diagnostic, treatment, and prognostic marker for infectious diseases.
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Affiliation(s)
- Yuxuan Hu
- BGI Research, Shenzhen 518083, China; School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | | | - Yan Zhang
- BGI Research, Shenzhen 518083, China
| | - Weijun Chen
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; PathoGenesis, BGI Genomics, Shenzhen 518083, China
| | | | - Xin Jin
- BGI Research, Shenzhen 518083, China; The Innovation Centre of Ministry of Education for Development and Diseases, School of Medicine, South China University of Technology, Guangzhou 510006, China; Shanxi Medical University-BGI Collaborative Center for Future Medicine, Shanxi Medical University, Taiyuan 030001, China; Shenzhen Key Laboratory of Transomics Biotechnologies, BGI Research, Shenzhen, China.
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Miller JA, Liu Z, Pinsky BA, Le QT, Li T, Yu KJ, Hildesheim A, Cao SM. Optimization and Local Cost-Effectiveness of Nasopharyngeal Carcinoma Screening Strategies in Southern China: Secondary Analysis of the Guangdong Randomized Trial. Cancer Epidemiol Biomarkers Prev 2024; 33:884-895. [PMID: 38695706 DOI: 10.1158/1055-9965.epi-23-1486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 01/23/2024] [Accepted: 04/29/2024] [Indexed: 07/02/2024] Open
Abstract
BACKGROUND Screening with anti-Epstein-Barr virus (EBV) serology and endoscopy decreased nasopharyngeal carcinoma (NPC) mortality in Guangdong in a randomized trial. We conducted a secondary analysis of this trial using local incidence and cost data to optimize screening programs, hypothesizing that screening could be cost-effective in southern China. METHODS Screening costs and life-years after NPC diagnosis were obtained from the Guangdong trial's intent-to-screen population (men and women aged 30-69). Seropositive subjects were rescreened annually for 5 years. Thereafter, we evaluated 12 screening strategies in Guangdong and Guangxi using a validated model. Strategies used combinations of serology, nasopharyngeal swab PCR (NP PCR), endoscopy, and MRI from trial subcohorts. Incidence data and costs were obtained from local cancer registries and the provincial healthcare system. RESULTS In the intent-to-screen population, screening with serology and endoscopy was cost-effective (¥42,366/life-year, 0.52 GDP per capita). Screening for 5 to 15 years between ages 35 and 59 years met a willingness-to-pay threshold of 1.5 GDP/quality-adjusted life-years in all modeled populations. Despite doubling costs, adding MRI could be cost-effective via improved sensitivity. NP PCR triage reduced endoscopy/MRI referrals by 37%. One-lifetime screen could reduce NPC mortality by approximately 20%. CONCLUSIONS EBV-based serologic screening for NPC is likely to be cost-effective in southern China. Among seropositive subjects, the preferred strategies use endoscopy alone or selective endoscopy triaged by MRI with or without NP PCR. These data may aid the design of screening programs in this region. IMPACT These findings support population-based screening in southern China by defining the target population, cost-effectiveness, and optimized screening approach.
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Affiliation(s)
- Jacob A Miller
- Department of Radiation Oncology, Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio
- Center for Immunotherapy and Precision Immuno-Oncology, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio
| | - Zhiwei Liu
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University, Palo Alto, California
- Department of Medicine, Division of Infectious Diseases and Geographic Medicine, Stanford University, Palo Alto, California
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University, Palo Alto, California
| | - Tong Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Kelly J Yu
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, Maryland
| | - Allan Hildesheim
- Agencia Costarricense de Investigaciones Biomédicas, Fundación INCIENSA, San José, Costa Rica
| | - Su-Mei Cao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou, China
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, China
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Huang Z, Fu Y, Yang H, Zhou Y, Shi M, Li Q, Liu W, Liang J, Zhu L, Qin S, Hong H, Liu Y. Liquid biopsy in T-cell lymphoma: biomarker detection techniques and clinical application. Mol Cancer 2024; 23:36. [PMID: 38365716 PMCID: PMC10874034 DOI: 10.1186/s12943-024-01947-7] [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: 11/03/2023] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
T-cell lymphoma is a highly invasive tumor with significant heterogeneity. Invasive tissue biopsy is the gold standard for acquiring molecular data and categorizing lymphoma patients into genetic subtypes. However, surgical intervention is unfeasible for patients who are critically ill, have unresectable tumors, or demonstrate low compliance, making tissue biopsies inaccessible to these patients. A critical need for a minimally invasive approach in T-cell lymphoma is evident, particularly in the areas of early diagnosis, prognostic monitoring, treatment response, and drug resistance. Therefore, the clinical application of liquid biopsy techniques has gained significant attention in T-cell lymphoma. Moreover, liquid biopsy requires fewer samples, exhibits good reproducibility, and enables real-time monitoring at molecular levels, thereby facilitating personalized health care. In this review, we provide a comprehensive overview of the current liquid biopsy biomarkers used for T-cell lymphoma, focusing on circulating cell-free DNA (cfDNA), circulating tumor DNA (ctDNA), circulating tumor cells (CTCs), Epstein-Barr virus (EBV) DNA, antibodies, and cytokines. Additionally, we discuss their clinical application, detection methodologies, ongoing clinical trials, and the challenges faced in the field of liquid biopsy.
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Affiliation(s)
- Zongyao Huang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yao Fu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Hong Yang
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Yehan Zhou
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Min Shi
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China
| | - Qingyun Li
- Genecast Biotechnology Co., Ltd, Wuxi, 214104, China
| | - Weiping Liu
- Department of Pathology, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Junheng Liang
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Liuqing Zhu
- Nanjing Geneseeq Technology Inc., Nanjing, 210032, Jiangsu, China
| | - Sheng Qin
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Huangming Hong
- Department of Medical Oncology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
| | - Yang Liu
- Department of Pathology, Sichuan Clinical Research Center for Cancer, Sichuan Cancer Hospital & Institute, Sichuan Cancer Center, Affiliated Cancer Hospital of University of Electronic Science and Technology of China, Chengdu, China.
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Zheng XH, Hildesheim A, Jia WH. Advances of biomarkers in nasopharyngeal carcinoma's early detection. Sci Bull (Beijing) 2024; 69:141-145. [PMID: 38087738 DOI: 10.1016/j.scib.2023.11.059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2024]
Affiliation(s)
- Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
| | - Allan Hildesheim
- Costa Rican Agency for Biomedical Investigation, INCIENSA Foundation, San Jose 10108, Costa Rica
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, Guangzhou 510060, China.
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Wu ZC, Lin KN, Li XQ, Ye X, Chen H, Tao J, Zhou HN, Chen WJ, Lin DF, Xie SH, Cao SM. Development and analytical validation of a novel nasopharynx swab-based Epstein-Barr virus C promoter methylation quantitative assay for nasopharyngeal carcinoma detection. Clin Chem Lab Med 2024; 62:187-198. [PMID: 37531579 DOI: 10.1515/cclm-2023-0510] [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: 01/16/2023] [Accepted: 07/11/2023] [Indexed: 08/04/2023]
Abstract
OBJECTIVES Epstein-Barr virus (EBV) C promoter (Cp) hypermethylation, a crucial factor for EBV latent infection of nasopharyngeal epithelial cells, has been recognized as a promising biomarker for nasopharyngeal carcinoma (NPC) detection. In this study, we develop a novel EBV Cp methylation quantification (E-CpMQ) assay and evaluate its diagnostic performance for NPC detection. METHODS A novel qPCR assay for simultaneous quantification of methylated- and unmethylated EBV Cp was developed by the combinational modification of MethyLight and QASM, with an innovative calibrator to improve the detection accuracy and consistency. The NP swab samples and synthetic standards were used for the analytical validation of the E-CpMQ. The diagnostic efficacy of the developed E-CpMQ assay was validated in 137 NPC patients and 137 non-NPC controls. RESULTS The E-CpMQ assay can detect the EBV Cp methylation ratio in one reaction system under 10 copies with 100 % recognition specificity, which is highly correlated to pyrosequencing with a correlation coefficient over 0.99. The calibrated E-CpMQ assay reduces the coefficient of variation by an average of 55.5 % with a total variance of less than 0.06 units standard deviation (SD). Linear methylation ratio detection range from 4.76 to 99.01 %. The sensitivity and specificity of the E-CpMQ respectively are 96.4 % (95 % CI: 91.7-98.8 %), 89.8 % (95 % CI: 83.5-94.3 %). CONCLUSIONS The developed E-CpMQ assay with a calibrator enables accurate and reproducible EBV Cp methylation ratio quantification and offers a sensitive, specific, cost-effective method for NPC early detection.
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Affiliation(s)
- Zhi-Cong Wu
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Ke-Na Lin
- School of Public Health, Guangdong Medical University, Dongguan, Guangdong, P.R. China
| | - Xue-Qi Li
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
| | - Xin Ye
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- School of Public Health, Sun Yat-sen University, Guangzhou, P.R. China
| | - Hua Chen
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Jun Tao
- School of Public Health, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, P.R. China
| | - Hang-Ning Zhou
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Wen-Jie Chen
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Dong-Feng Lin
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Shang-Hang Xie
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
| | - Su-Mei Cao
- Department of Cancer Prevention, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, P.R. China
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Samayoa-Reyes G, Weigel C, Koech E, Waomba K, Jackson C, Onditi IA, Sabourin KR, Kenney S, Baiocchi RA, Oakes CC, Ogolla S, Rochford R. Effect of Malaria Infection on Epstein-Barr Virus Persistence in Kenyan Children. J Infect Dis 2024; 229:73-82. [PMID: 37433031 PMCID: PMC10786253 DOI: 10.1093/infdis/jiad264] [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: 02/14/2023] [Revised: 06/29/2023] [Accepted: 07/10/2023] [Indexed: 07/13/2023] Open
Abstract
BACKGROUND The 2 cofactors in the etiology of Burkitt lymphoma (BL) are Epstein-Barr virus (EBV) and repeated Plasmodium falciparum malaria infections. This study evaluated EBV loads in mucosal and systemic compartments of children with malaria and controls. Age was analyzed as a covariate because immunity to malaria in endemic regions is age dependent. METHODS Children (2-10 years) with clinical malaria from Western Kenya and community controls without malaria were enrolled. Saliva and blood samples were collected, EBV viral load was assessed by quantitative polymerase chain reaction, and EpiTYPER MassARRAY was used to assess methylation of 3 different EBV genes. RESULTS Regardless of the compartment, we detected EBV more frequently in malaria cases compared to controls, although the difference was not significant. When EBV was detected, there were no differences in viral load between cases and controls. However, EBV methylation was significantly lower in the malaria group compared to controls in both plasma and saliva (P < .05), indicating increased EBV lytic replication. In younger children before development of immunity to malaria, there was a significant effect of malaria on EBV load in peripheral blood mononuclear cells (P = .04). CONCLUSIONS These data suggest that malaria can directly modulate EBV persistence in children, increasing their risk for BL.
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Affiliation(s)
- Gabriela Samayoa-Reyes
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Christoph Weigel
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, Ohio, USA
| | - Emmily Koech
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Kevin Waomba
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Conner Jackson
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado-Denver Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ian A Onditi
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Katherine R Sabourin
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Shannon Kenney
- Department of Oncology, McArdle Laboratory, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin, USA
| | - Robert A Baiocchi
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, Ohio, USA
| | - Christopher C Oakes
- Department of Internal Medicine, Division of Hematology, The Ohio State University, Columbus, Ohio, USA
| | - Sidney Ogolla
- Centre for Global Health Research, Kenya Medical Research Institute, Kisumu, Kenya
| | - Rosemary Rochford
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
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Tang CL, Li XZ, Zhou T, Deng CM, Jiang CT, Zhang YM, Liao Y, Wang TM, He YQ, Xue WQ, Jia WH, Zheng XH. EBV DNA methylation profiles and its application in distinguishing nasopharyngeal carcinoma and nasal NK/T-cell lymphoma. Clin Epigenetics 2024; 16:11. [PMID: 38212818 PMCID: PMC10785554 DOI: 10.1186/s13148-024-01624-y] [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: 05/30/2023] [Accepted: 01/03/2024] [Indexed: 01/13/2024] Open
Abstract
BACKGROUND As an oncovirus, EBV is associated with multiple cancers, including solid tumors and hematological malignancies. EBV methylation plays an important role in regulating tumor occurrence. However, the EBV methylation profiles in EBV-associated tumor tissues are poorly understood. RESULTS In this study, EBV methylation capture sequencing was conducted in several different tumor tissue samples, including NPC, EBVaGC, lung LELC and parotid LELC. Besides, EBV capture sequencing and following qMSP were performed on nasopharyngeal brushing samples from NPC and nasal NKTCL patients. Our results showed that the EBV genome among different types of tumors displayed specific methylation patterns. Among the four types of tumors from epithelial origin (NPC, EBVaGC, lung LELC and parotid LELC), the most significant differences were found between EBVaGC and the others. For example, in EBVaGC, all CpG sites within 1,44,189-1,45,136 bp of the EBV genome sequence on gene RPMS1 were hyper-methylated compared to the others. Differently, significant differences of EBV CpG sites, particularly those located on gene BILF2, were observed between NPC and nasal NKTCL patients in nasopharyngeal brushing samples. Further, the methylated level of BILF2 was further detected using qMSP, and a diagnostic model distinguishing NPC and nasal NKTCL was established. The AUC of the model was 0.9801 (95% CI 0.9524-1.0000), with the sensitivity and specificity of 98.81% (95% CI 93.63-99.94%) and 76.92% (95% CI 49.74-91.82%), respectively. CONCLUSIONS Our study reveals more clues for further understanding the pathogenesis of EBV, and provides a possibility for distinguishing EBV-related tumor by detecting specific EBV CpG sites.
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Affiliation(s)
- Cao-Li Tang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Cheng-Tao Jiang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Yu-Meng Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Wen-Qiong Xue
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China.
- School of Public Health, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangdong Provincial Clinical Research Center for Cancer, Sun Yat-sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, Guangdong, 510060, People's Republic of China.
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Zhang T, Pei L, Qiu WL, Wei YX, Liao BY, Yang FL. Uncovering the ceRNA network and DNA methylation associated with gene expression in nasopharyngeal carcinoma. BMC Med Genomics 2023; 16:218. [PMID: 37710236 PMCID: PMC10500855 DOI: 10.1186/s12920-023-01653-1] [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: 07/26/2022] [Accepted: 08/31/2023] [Indexed: 09/16/2023] Open
Abstract
OBJECTIVE This study aimed to uncover abnormally expressed genes regulated by competitive endogenous RNA (ceRNA) and DNA methylation nasopharyngeal carcinoma and to validate the role of lncRNAs in the ceRNA network on nasopharyngeal carcinoma progression. METHODS Based on the GSE64634 (mRNA), GSE32960 (miRNA), GSE95166 (lncRNA), and GSE126683 (lncRNA) datasets, we screened differentially expressed mRNAs, miRNAs and lncRNAs in nasopharyngeal carcinoma. A ceRNA network was subsequently constructed. Differentially methylated genes were screened using the GSE62336 dataset. The abnormally expressed genes regulated by both the ceRNA network and DNA methylation were identified. In the ceRNA network, the expression of RP11-545G3.1 lncRNA was validated in nasopharyngeal carcinoma tissues and cells by RT-qPCR. After a knockdown of RP11-545G3.1, the viability, migration, and invasion of CNE-2 and NP69 cells was assessed by CCK-8, wound healing and Transwell assays. RESULTS This study identified abnormally expressed mRNAs, miRNAs and lncRNAs in nasopharyngeal carcinoma tissues. A ceRNA network was constructed, which contained three lncRNAs, 15 miRNAs and 129 mRNAs. Among the nodes in the PPI network based on the mRNAs in the ceRNA network, HMGA1 was assessed in relation to the overall and disease-free survival of nasopharyngeal carcinoma. We screened two up-regulated genes regulated by the ceRNA network and hypomethylation and 26 down-regulated genes regulated by the ceRNA network and hypermethylation. RP11-545G3.1 was highly expressed in the nasopharyngeal carcinoma tissues and cells. Moreover, the knockdown of RP11-545G3.1 reduced the viability, migration, and invasion of CNE-2 and NP69 cells. CONCLUSION Our findings uncovered the epigenetic regulation in nasopharyngeal carcinoma and identified the implications of RP11-545G3.1 on the progression of nasopharyngeal carcinoma.
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Affiliation(s)
- Ting Zhang
- Center of Reproductive medicine, Affiliated hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Lu Pei
- Youjiang medical university for nationalities, Baise, 533000, Guangxi, China
| | - Wen-Li Qiu
- Youjiang medical university for nationalities, Baise, 533000, Guangxi, China
| | - Yu-Xia Wei
- Center of Reproductive medicine, Affiliated hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Bi-Yun Liao
- Center of Reproductive medicine, Affiliated hospital of Youjiang Medical University for Nationalities, Baise, 533000, Guangxi, China
| | - Feng-Lian Yang
- Youjiang medical university for nationalities, Baise, 533000, Guangxi, China.
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9
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Xian RR, Ambinder RF. Cell-Free Circulating Tumor DNA and Epstein-Barr Virus DNA for Early Diagnosis of Epstein-Barr Virus-Associated Cancers. J Clin Oncol 2023; 41:4290-4292. [PMID: 37478392 DOI: 10.1200/jco.23.00687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 04/11/2023] [Indexed: 07/23/2023] Open
Affiliation(s)
- Rena R Xian
- Department of Pathology, Johns Hopkins University, School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
| | - Richard F Ambinder
- Department of Oncology, Johns Hopkins University, School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD
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Li T, Li F, Guo X, Hong C, Yu X, Wu B, Lian S, Song L, Tang J, Wen S, Gao K, Hao M, Cheng W, Su Y, Zhang S, Huang S, Fang M, Wang Y, Ng MH, Chen H, Luo W, Ge S, Zhang J, Xia N, Ji M. Anti-Epstein-Barr Virus BNLF2b for Mass Screening for Nasopharyngeal Cancer. N Engl J Med 2023; 389:808-819. [PMID: 37646678 DOI: 10.1056/nejmoa2301496] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
BACKGROUND Population screening of asymptomatic persons with Epstein-Barr virus (EBV) DNA or antibodies has improved the diagnosis of nasopharyngeal carcinoma and survival among affected persons. However, the positive predictive value of current screening strategies is unsatisfactory even in areas where nasopharyngeal carcinoma is endemic. METHODS We designed a peptide library representing highly ranked B-cell epitopes of EBV coding sequences to identify novel serologic biomarkers for nasopharyngeal carcinoma. After a retrospective case-control study, the performance of the novel biomarker anti-BNLF2b total antibody (P85-Ab) was validated through a large-scale prospective screening program and compared with that of the standard two-antibody-based screening method (EBV nuclear antigen 1 [EBNA1]-IgA and EBV-specific viral capsid antigen [VCA]-IgA). RESULTS P85-Ab was the most promising biomarker for nasopharyngeal carcinoma screening, with high sensitivity (94.4%; 95% confidence interval [CI], 86.4 to 97.8) and specificity (99.6%; 95% CI, 97.8 to 99.9) in the retrospective case-control study. Among the 24,852 eligible participants in the prospective cohort, 47 cases of nasopharyngeal carcinoma (38 at an early stage) were identified. P85-Ab showed higher sensitivity than the two-antibody method (97.9% vs. 72.3%; ratio, 1.4 [95% CI, 1.1 to 1.6]), higher specificity (98.3% vs. 97.0%; ratio, 1.01 [95% CI, 1.01 to 1.02]), and a higher positive predictive value (10.0% vs. 4.3%; ratio, 2.3 [95% CI, 1.8 to 2.8]). The combination of P85-Ab and the two-antibody method markedly increased the positive predictive value to 44.6% (95% CI, 33.8 to 55.9), with sensitivity of 70.2% (95% CI, 56.0 to 81.4). CONCLUSIONS Our results suggest that P85-Ab is a promising novel biomarker for nasopharyngeal carcinoma screening, with higher sensitivity, specificity, and positive predictive value than the standard two-antibody method. (Funded by the National Key Research and Development Program of China and others; ClinicalTrials.gov number, NCT04085900.).
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Affiliation(s)
- Tingdong Li
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Fugui Li
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Xiaoyi Guo
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Congming Hong
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Xia Yu
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Biaohua Wu
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shifeng Lian
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Liuwei Song
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Jiabao Tang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shunhua Wen
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Kaimin Gao
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mengling Hao
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Weimin Cheng
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Yingying Su
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shiyin Zhang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shoujie Huang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mujin Fang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Yingbin Wang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mun-Hon Ng
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Honglin Chen
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Wenxin Luo
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Shengxiang Ge
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Jun Zhang
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Ningshao Xia
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
| | - Mingfang Ji
- From the State Key Laboratory of Vaccines for Infectious Diseases, National Institute of Diagnostics and Vaccine Development in Infectious Diseases, Strait Collaborative Innovation Center of Biomedicine and Pharmaceutics, Department of Laboratory Medicine, School of Public Health, Xiamen University (T.L., X.G., C.H., J.T., M.H., Y.S., S.Z., S.H., M.F., Y.W., M.-H.N., W.L., S.G., J.Z., N.X.), and Xiamen Innodx Biotechnology (L.S., S.W., K.G.), Xiamen, the Cancer Research Institute of Zhongshan City, Zhongshan City People's Hospital, Zhongshan (F.L., X.Y., B.W., W.C., M.J.), and the State Key Laboratory for Emerging Infectious Diseases, Department of Microbiology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong (H.C.) - all in China; and the Unit of Integrative Epidemiology, Institute of Environmental Medicine, Karolinska Institute, Stockholm (S.L.)
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Zheng XH, Deng CM, Zhou T, Li XZ, Tang CL, Jiang CT, Liao Y, Wang TM, He YQ, Jia WH. Saliva biopsy: Detecting the difference of EBV DNA methylation in the diagnosis of nasopharyngeal carcinoma. Int J Cancer 2023; 153:882-892. [PMID: 37170851 DOI: 10.1002/ijc.34561] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 04/04/2023] [Accepted: 04/14/2023] [Indexed: 05/13/2023]
Abstract
Saliva sampling is a non-invasive method, and could be performed by donors themselves. However, there are few studies reporting biomarkers in saliva in the diagnosis of NPC. A total of 987 salivary samples were used in this study. First, EBV DNA methylation was profiled by capture sequencing in the discovery cohort (n = 36). Second, a q-PCR based method was developed and five representative EBV DNA CpG sites (11 029 bp, 45 849 bp, 57 945 bp, 66 226 bp and 128 102 bp) were selected and quantified to obtain the methylated density in the validation cohort1 (n = 801). Third, a validation cohort2 (n = 108) was used to further verify the differences of EBV methylation in saliva. A significant increase of EBV methylation was found in NPC patients compared with controls. The methylated score of EBV genome obtained by capture sequencing could distinguish NPC from controls (sensitivity 90%, specificity 100%). Further, the methylated density of EBV DNA CpG sites revealed by q-PCR showed a good diagnostic performance. The sensitivity and specificity of detecting a single CpG site (11 029 bp) could reach 75.4% and 99.7% in the validation cohort1, and 78.2% and 100% in the validation cohort2. Besides, the methylated density of the CpG site was found to decrease below the COV in NPC patients after therapy, and increase above the COV after recurrence. Our study provides an appealing alternative for the non-invasive detection of NPC without clinical setting. It paves the way for conducting a home-based large-scale screening in the future.
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Affiliation(s)
- Xiao-Hui Zheng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Chang-Mi Deng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ting Zhou
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Xi-Zhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Cao-Li Tang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Cheng-Tao Jiang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Ying Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Tong-Min Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Yong-Qiao He
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
| | - Wei-Hua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-Sen University Cancer Center, Guangzhou, Guangdong, China
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12
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MacLennan SA, Marra MA. Oncogenic Viruses and the Epigenome: How Viruses Hijack Epigenetic Mechanisms to Drive Cancer. Int J Mol Sci 2023; 24:ijms24119543. [PMID: 37298494 DOI: 10.3390/ijms24119543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/26/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Globally, viral infections substantially contribute to cancer development. Oncogenic viruses are taxonomically heterogeneous and drive cancers using diverse strategies, including epigenomic dysregulation. Here, we discuss how oncogenic viruses disrupt epigenetic homeostasis to drive cancer and focus on how virally mediated dysregulation of host and viral epigenomes impacts the hallmarks of cancer. To illustrate the relationship between epigenetics and viral life cycles, we describe how epigenetic changes facilitate the human papillomavirus (HPV) life cycle and how changes to this process can spur malignancy. We also highlight the clinical impact of virally mediated epigenetic changes on cancer diagnosis, prognosis, and treatment.
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Affiliation(s)
- Signe A MacLennan
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
| | - Marco A Marra
- Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC V5Z 4S6, Canada
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13
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Scholte LL, Bethony JM, Xian RR. Diagnosis and monitoring of virus-associated cancer using cell-free DNA. Curr Opin Virol 2023; 60:101331. [PMID: 37187125 DOI: 10.1016/j.coviro.2023.101331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 02/14/2023] [Accepted: 04/05/2023] [Indexed: 05/17/2023]
Abstract
Viral-associated cancers are a distinct group of malignancies with a unique pathogenesis and epidemiology. Liquid biopsy is a minimally invasive way to identify tumor-associated abnormalities in blood derivatives, such as plasma, to guide the diagnosis, prognosis, and treatment of patients with cancer. Liquid biopsy encompasses a multitude of circulating analytes with the most extensively studied being cell-free DNA (cfDNA). In recent decades, substantial advances have been made toward the study of circulating tumor DNA in nonviral-associated cancers. Many of these observations have been translated to the clinic to improve the outcomes of patients with cancer. The study of cfDNA in viral-associated cancers is rapidly evolving and reveals tremendous potential for clinical applications. This review provides an overview of the pathogenesis of viral-associated malignancies, the current state of cfDNA analysis in oncology, the current state of cfDNA analysis in viral-associated cancers, and perspectives for the future of liquid biopsies in viral-associated cancers.
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Affiliation(s)
- Larissa Ls Scholte
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, United States
| | - Jeffrey M Bethony
- Department of Microbiology, Immunology and Tropical Medicine, The George Washington University, Washington DC, United States
| | - Rena R Xian
- Department of Pathology and Department of Oncology, Johns Hopkins School of Medicine, Baltimore, MD, United States; Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, United States.
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14
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Lupo J, Truffot A, Andreani J, Habib M, Epaulard O, Morand P, Germi R. Virological Markers in Epstein–Barr Virus-Associated Diseases. Viruses 2023; 15:v15030656. [PMID: 36992365 PMCID: PMC10051789 DOI: 10.3390/v15030656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/21/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023] Open
Abstract
Epstein–Barr virus (EBV) is an oncogenic virus infecting more than 95% of the world’s population. After primary infection—responsible for infectious mononucleosis in young adults—the virus persists lifelong in the infected host, especially in memory B cells. Viral persistence is usually without clinical consequences, although it can lead to EBV-associated cancers such as lymphoma or carcinoma. Recent reports also suggest a link between EBV infection and multiple sclerosis. In the absence of vaccines, research efforts have focused on virological markers applicable in clinical practice for the management of patients with EBV-associated diseases. Nasopharyngeal carcinoma is an EBV-associated malignancy for which serological and molecular markers are widely used in clinical practice. Measuring blood EBV DNA load is additionally, useful for preventing lymphoproliferative disorders in transplant patients, with this marker also being explored in various other EBV-associated lymphomas. New technologies based on next-generation sequencing offer the opportunity to explore other biomarkers such as the EBV DNA methylome, strain diversity, or viral miRNA. Here, we review the clinical utility of different virological markers in EBV-associated diseases. Indeed, evaluating existing or new markers in EBV-associated malignancies or immune-mediated inflammatory diseases triggered by EBV infection continues to be a challenge.
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Affiliation(s)
- Julien Lupo
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
- Laboratoire de Virologie, CHU Grenoble Alpes, CS 10217, CEDEX 09, 38043 Grenoble, France
- Correspondence:
| | - Aurélie Truffot
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
- Laboratoire de Virologie, CHU Grenoble Alpes, CS 10217, CEDEX 09, 38043 Grenoble, France
| | - Julien Andreani
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
- Laboratoire de Virologie, CHU Grenoble Alpes, CS 10217, CEDEX 09, 38043 Grenoble, France
| | - Mohammed Habib
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
| | - Olivier Epaulard
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
- Service de Maladies Infectieuses, CHU Grenoble Alpes, CS 10217, CEDEX 09, 38043 Grenoble, France
| | - Patrice Morand
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
- Laboratoire de Virologie, CHU Grenoble Alpes, CS 10217, CEDEX 09, 38043 Grenoble, France
| | - Raphaële Germi
- Institut de Biologie Structurale, Université Grenoble Alpes, UMR 5075 CEA/CNRS/UGA, 71 Avenue des Martyrs, 38000 Grenoble, France
- Laboratoire de Virologie, CHU Grenoble Alpes, CS 10217, CEDEX 09, 38043 Grenoble, France
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15
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Hou F, Sun XD, Deng ZY. Diagnostic value of cell-free DNA in thyroid cancer: A systematic review and meta-analysis. Medicine (Baltimore) 2023; 102:e32928. [PMID: 36800605 PMCID: PMC9935987 DOI: 10.1097/md.0000000000032928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/19/2023] Open
Abstract
OBJECTIVE An increasing number of studies have shown the potential diagnostic value of cell-free DNA (cfDNA) as a new biomarker in the management of thyroid cancer (TC); however, the accuracy of research results is inconsistent. This meta-analysis is the first to synthesize published results and evaluate the application value of circulating cfDNA in the diagnosis of TC. METHODS A search strategy was developed according to PICO (P: Patient; I: Intervention; C: Comparison; O: Outcome) principles. We searched 5 databases until October 2022. Original studies that examined cfDNA for the diagnosis of TC and used pathology as the gold standard were included in this meta-analysis. A random-effects model was used to pool the data extracted from individual studies, including the number of patients and the numbers of true positives, false positives, true negatives, and false negatives. RESULTS A total of 622 patients with TC, 547 patients with benign thyroid nodules, and 98 healthy individuals were included in 20 studies reported in 14 articles. The types of cfDNA included in the research include specific mutations of cfDNA, methylation of cfDNA, the content of cfDNA, and cfDNA index. After rigorous statistical analysis, the pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver operating characteristic curve were 0.76 (95% confidence interval [CI] 0.62-0.85), 0.87 (95% CI 0.78-0.93), 5.08 (95% CI 3.3-10.3), 0.28 (95% CI 0.17-0.46), 21 (95% CI 9-49), and 0.89 (95% CI 0.86-0.91), respectively. The meta-regression results showed that the number of cfDNAs, cfDNA methylation status, and sample size were the sources of heterogeneity in the specificity of the study. A subgroup analysis showed that the quantitative analysis group (cfDNA level) had a higher diagnostic accuracy than that of the qualitative analysis group (cfDNA methylation, mutation, or integrity index), with a sensitivity of 0.84, specificity of 0.89, and area under the curve of 0.91. CONCLUSIONS The results of this meta-analysis suggest that cfDNA has value as an adjunct for the diagnosis of TC. Quantitative detection of cfDNA can achieve relatively high diagnostic accuracy. However, due to heterogeneity, the test results based on cfDNA for TC should be interpreted with caution.
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Affiliation(s)
- Fei Hou
- Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
| | - Xiao-Dan Sun
- Publicity Department, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
| | - Zhi-Yong Deng
- Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming, China
- * Correspondence: Zhi-Yong Deng, Department of Nuclear Medicine, Yunnan Cancer Hospital (The Third Affiliated Hospital of Kunming Medical University), Kunming 650118, China (e-mail: )
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Dai Y, Chen W, Huang J, Xie L, Lin J, Chen Q, Jiang G, Huang C. Identification of key pathways and genes in nasopharyngeal carcinoma based on WGCNA. Auris Nasus Larynx 2023; 50:126-133. [PMID: 35659152 DOI: 10.1016/j.anl.2022.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 05/17/2022] [Accepted: 05/19/2022] [Indexed: 01/28/2023]
Abstract
OBJECTIVE We aim to identify the potential genes and signaling pathways associated with the nasopharyngeal carcinoma (NPC) prognosis using Weighted Gene Co-Expression Network Analysis (WGCNA). METHODS Gene Expression Omnibus (GEO) query was utilized to download two NPC mRNA microarray data. WGCNA was conducted on differentially expressed genes (DEGs) to obtain tumor-associated gene modules. Genes in core modules were intersected with DEGs for gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional enrichment analysis. GSE102349 dataset was devoted to identifying prognostic hub genes by survival analysis and the results were confirmed by quantitative polymerase chain reaction (qPCR). RESULTS Co-expression networks were built, and we detected 12 gene modules. The Brown module and Magenta module were extremely associated with NPC samples. GO functional analysis and KEGG pathway analysis was carried out to the genes in the Brown and Magenta modules. Our data indicated that DEGs in Brown module and Magenta module were correlated with the biological regulation, metabolic process, reproduction, and cellular proliferation. Twenty-six hub genes were obtained and were considered to be closely related to NPC. GSE102349 dataset was devoted to identifying prognostic hub genes by survival analysis. The expression of IL33, MPP3 and SLC16A7 in GSE102349 dataset was significantly correlated with the progression-free survival (PFS). The results of qPCR indicated a strong correlation between SLC16A7 expression and the overall survival (OS). CONCLUSIONS WGCNA contributed to the detection of gene modules and identification of hub genes and crucial genes. These crucial genes might be potential targets for pharmaceutic therapies with potential clinical significance.
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Affiliation(s)
- Yongmei Dai
- Departments of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou 350001, China.
| | - Wenhan Chen
- The Second Clinical Medical College of Fujian Medical University, Fujian 362000, China; Department of Clinical Medicine, Fujian Medical University, Fujian 350122, China
| | - Junpeng Huang
- Departments of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou 350001, China
| | - Li Xie
- Departments of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou 350001, China
| | - Jianfang Lin
- Departments of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou 350001, China
| | - Qianshun Chen
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou 350001, China
| | - Guicheng Jiang
- Departments of Oncology, Shengli Clinical Medical College of Fujian Medical University & Fujian Provincial Hospital, Fuzhou 350001, China
| | - Chen Huang
- Department of Thoracic Surgery, Fujian Provincial Hospital, Shengli Clinical College of Fujian Medical University, Fuzhou 350001, China
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17
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Schroers-Martin JG, Alig S, Garofalo A, Tessoulin B, Sugio T, Alizadeh AA. Molecular Monitoring of Lymphomas. ANNUAL REVIEW OF PATHOLOGY 2023; 18:149-180. [PMID: 36130071 DOI: 10.1146/annurev-pathol-050520-044652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Molecular monitoring of tumor-derived alterations has an established role in the surveillance of leukemias, and emerging nucleic acid sequencing technologies are likely to similarly transform the clinical management of lymphomas. Lymphomas are well suited for molecular surveillance due to relatively high cell-free DNA and circulating tumor DNA concentrations, high somatic mutational burden, and the existence of stereotyped variants enabling focused interrogation of recurrently altered regions. Here, we review the clinical scenarios and key technologies applicable for the molecular monitoring of lymphomas, summarizing current evidence in the literature regarding molecular subtyping and classification, evaluation of treatment response, the surveillance of active cellular therapies, and emerging clinical trial strategies.
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Affiliation(s)
- Joseph G Schroers-Martin
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Stefan Alig
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Andrea Garofalo
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Benoit Tessoulin
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA; .,Current affiliation: Clinical Hematology Department, Nantes University Hospital, Nantes, France
| | - Takeshi Sugio
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA;
| | - Ash A Alizadeh
- Department of Medicine, Divisions of Hematology and Oncology, Stanford University Medical Center, Stanford, California, USA; .,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, California, USA.,Stanford Cancer Institute, Stanford University, Stanford, California, USA
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18
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Paudel S, Warner BE, Wang R, Adams-Haduch J, Reznik AS, Dou J, Huang Y, Gao YT, Koh WP, Bäckerholm A, Yuan JM, Shair KHY. Serologic Profiling Using an Epstein-Barr Virus Mammalian Expression Library Identifies EBNA1 IgA as a Prediagnostic Marker for Nasopharyngeal Carcinoma. Clin Cancer Res 2022; 28:5221-5230. [PMID: 36165913 PMCID: PMC9722633 DOI: 10.1158/1078-0432.ccr-22-1600] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/22/2022] [Accepted: 09/22/2022] [Indexed: 01/24/2023]
Abstract
PURPOSE The favorable prognosis of stage I and II nasopharyngeal carcinoma (NPC) has motivated a search for biomarkers for the early detection and risk assessment of Epstein-Barr virus (EBV)-associated NPC. Although EBV seropositivity is ubiquitous among adults, a spike in antibodies against select EBV proteins is a harbinger of NPC. A serologic survey would likely reveal which EBV antibodies could discriminate those at risk of developing NPC. EXPERIMENTAL DESIGN Lysates from a new EBV mammalian expression library were used in a denaturing multiplex immunoblot assay to survey antibodies against EBV in sera collected from healthy individuals who later developed NPC (incident cases) in a prospective cohort from Singapore and validated in an independent cohort from Shanghai, P.R. China. RESULTS We show that IgA against EBV nuclear antigen 1 (EBNA1) discriminated incident NPC cases from matched controls with 100% sensitivity and 100% specificity up to 4 years before diagnosis in both Singapore and Shanghai cohorts. Incident NPC cases had a greater IgG repertoire against lytic-classified EBV proteins, and the assortment of IgA against EBV proteins detected by the immunoblot assay increased closer to diagnosis. CONCLUSIONS Although NPC tumors consistently harbor latent EBV, the observed heightened systemic and mucosal immunity against lytic-classified antigens years prior to clinical diagnosis is consistent with enhanced lytic transcription. We conclude that an expanding EBV mucosal reservoir (which can be latent and/or lytic) is a risk factor for NPC. This presents an opportunity to identify those at risk of developing NPC using IgA against EBNA1 as a biomarker.
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Affiliation(s)
- Sarita Paudel
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Benjamin E Warner
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Renwei Wang
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jennifer Adams-Haduch
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Alex S Reznik
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jason Dou
- Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yufei Huang
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Electrical and Computer Engineering, Swanson School of Engineering, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Yu-Tang Gao
- Department of Epidemiology, Shanghai Cancer Institute, Renji Hospital, Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Woon-Puay Koh
- Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Alan Bäckerholm
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Jian-Min Yuan
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Division of Cancer Control and Population Sciences, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Kathy H Y Shair
- Cancer Virology Program, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA.,Corresponding author: Kathy H Y Shair, UPMC Hillman Cancer Center, 5117 Centre Avenue, Suite 1.8, Pittsburgh, PA 15213,Tel: 412-623 7717,
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Abstract
Cell-free DNA (cfDNA) is nonrandomly fragmented and contains a wealth of molecular information useful for noninvasive prenatal testing and cancer detection. cfDNA fragmentomics contains information beyond genetics, such as gene expression inference. However, the feasibility of using cfDNA fragmentomics for deducing cfDNA methylomics remains unexplored. This study demonstrated the possibility of using cfDNA fragmentation patterns to deduce the methylation patterns of cfDNA molecules, breaking free from the limitation of bisulfite sequencing. By using cfDNA cleavage profiles surrounding a cytosine-phosphate-guanine (CpG) site, we determined the methylation status ranging from a particular region down to a single CpG assisted by a deep learning algorithm. Both genetic and epigenetic information of cfDNA can therefore be obtained in a single nondestructive assay. Cell-free DNA (cfDNA) fragmentation patterns contain important molecular information linked to tissues of origin. We explored the possibility of using fragmentation patterns to predict cytosine-phosphate-guanine (CpG) methylation of cfDNA, obviating the use of bisulfite treatment and associated risks of DNA degradation. This study investigated the cfDNA cleavage profile surrounding a CpG (i.e., within an 11-nucleotide [nt] window) to analyze cfDNA methylation. The cfDNA cleavage proportion across positions within the window appeared nonrandom and exhibited correlation with methylation status. The mean cleavage proportion was ∼twofold higher at the cytosine of methylated CpGs than unmethylated ones in healthy controls. In contrast, the mean cleavage proportion rapidly decreased at the 1-nt position immediately preceding methylated CpGs. Such differential cleavages resulted in a characteristic change in relative presentations of CGN and NCG motifs at 5′ ends, where N represented any nucleotide. CGN/NCG motif ratios were correlated with methylation levels at tissue-specific methylated CpGs (e.g., placenta or liver) (Pearson’s absolute r > 0.86). cfDNA cleavage profiles were thus informative for cfDNA methylation and tissue-of-origin analyses. Using CG-containing end motifs, we achieved an area under a receiver operating characteristic curve (AUC) of 0.98 in differentiating patients with and without hepatocellular carcinoma and enhanced the positive predictive value of nasopharyngeal carcinoma screening (from 19.6 to 26.8%). Furthermore, we elucidated the feasibility of using cfDNA cleavage patterns to deduce CpG methylation at single CpG resolution using a deep learning algorithm and achieved an AUC of 0.93. FRAGmentomics-based Methylation Analysis (FRAGMA) presents many possibilities for noninvasive prenatal, cancer, and organ transplantation assessment.
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20
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Lv J, Wu C, Li J, Chen F, He S, He Q, Zhou G, Ma J, Sun Y, Wei D, Lin L. Improving on-treatment risk stratification of cancer patients with refined response classification and integration of circulating tumor DNA kinetics. BMC Med 2022; 20:268. [PMID: 35996151 PMCID: PMC9396864 DOI: 10.1186/s12916-022-02463-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Significant intertumoral heterogeneity exists as antitumor treatment is introduced. Heterogeneous therapeutic responses are conventionally evaluated by imaging examinations based on Response Evaluation Criteria in Solid Tumors (RECIST); nevertheless, there are increasing recognitions that they do not fully capture patient clinical benefits. Currently, there is a paucity of data regarding the clinical implication of biological responses assessed by liquid biopsy of on-treatment circulating tumor DNA (ctDNA). Here, we investigated whether biological response evaluated by ctDNA kinetics added critical information to the RECIST, and whether integrating on-treatment biological response information refined risk stratification of cancer patients. METHODS In this population-based cohort study, we included 821 patients with Epstein-Barr virus (EBV)-associated nasopharynx of head and neck cancer (NPC) receiving sequential neoadjuvant chemotherapy (NAC) and chemoradiotherapy (CRT), who had pretreatment and on-treatment cfEBV DNA and magnetic resonance imaging (MRI) surveillance. Biological responses evaluated by cfEBV DNA were profiled and compared with conventional MRI-based RECIST evaluation. The inverse probability weighting (IPW)-adjusted survival analysis was performed for major survival endpoints. The Cox proportional hazard regression [CpH]-based model was developed to predict the on-treatment ctDNA-based individualized survival. RESULTS Of 821 patients, 71.4% achieved complete biological response (cBR) upon NAC completion. RECIST-based response evaluations had 25.3% discordance with ctDNA-based evaluations. IPW-adjusted survival analysis revealed that cfEBV DNApost-NAC was a preferential prognosticator for all endpoints, especially for distant metastasis. In contrast, radiological response was more preferentially associated with locoregional recurrence. Intriguingly, cfEBV DNApost-NAC further stratified RECIST-responsive and non-responsive patients; RECIST-based non-responsive patients with cBR still derived substantial clinical benefits. Moreover, detectable cfEBV DNApost-NAC had 83.6% prediction sensitivity for detectable post-treatment ctDNA, which conferred early determination of treatment benefits. Finally, we established individualized risk prediction models and demonstrated that introducing on-treatment ctDNA significantly refined risk stratification. CONCLUSIONS Our study helps advance the implementation of ctDNA-based testing in therapeutic response evaluation for a refined risk stratification. The dynamic and refined risk profiling would tailor future liquid biopsy-based risk-adapted personalized therapy.
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Affiliation(s)
- Jiawei Lv
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China. .,State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Chenfei Wu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Junyan Li
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Foping Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Shiwei He
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Qingmei He
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China
| | - Guanqun Zhou
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Jun Ma
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China
| | - Ying Sun
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.
| | - Denghui Wei
- State Key Laboratory of Oncology in Southern China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-sen University Cancer Center, Guangzhou, China.
| | - Li Lin
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, the State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Center for Precision Medicine of Sun Yat-sen University, Guangzhou, 510060, People's Republic of China.
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21
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Miller JA, Sahoo MK, Yamamoto F, Huang C, Wang H, Zehnder JL, Le QT, Pinsky BA. Multiplex Epstein-Barr virus BALF2 genotyping detects high-risk variants in plasma for population screening of nasopharyngeal carcinoma. Mol Cancer 2022; 21:154. [PMID: 35902864 PMCID: PMC9330640 DOI: 10.1186/s12943-022-01625-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 07/04/2022] [Indexed: 11/10/2022] Open
Abstract
Background Epstein-Barr Virus (EBV)-associated nasopharyngeal carcinoma (NPC) exhibits unusual geographic restriction despite ubiquitous lifelong infection. Screening programs can detect most NPC cases at an early stage, but existing EBV diagnostics are limited by false positives and low positive predictive value (PPV), leading to excess screening endoscopies, MRIs, and repeated testing. Recent EBV genome-wide association studies (GWAS) suggest that EBV BALF2 variants account for more than 80% of attributable NPC risk. We therefore hypothesized that high-risk BALF2 variants could be readily detected in plasma for once-lifetime screening triage. Methods We designed and validated a multiplex genotyping assay to detect EBV BALF2 polymorphisms in human plasma. Targeted next-generation sequencing was used to validate this assay, conduct association studies with clinical phenotype, and longitudinally genotype plasma to assess within-host haplotype stability. We examined the association between NPC and BALF2 haplotypes in a large non-endemic population and three prior EBV GWAS. Finally, we estimated NPC mortality reduction, resource utilization, and cost-effectiveness of BALF2 variant-informed screening using a previously-validated cohort model. Results Following analytical validation, the BALF2 genotyping assay had 99.3% concordance with sequencing in a cohort of 24 NPC cases and 155 non-NPC controls. BALF2 haplotype was highly associated with NPC in this non-endemic population (I613V: odds ratio [OR] 7.9; V317M: OR 178.8). No other candidate BALF2 polymorphisms were significantly associated with NPC or hematologic disorders. Longitudinal genotyping revealed 97.8% within-host haplotype concordance, indicative of lifelong latent infection. In a meta-analysis of 755 NPC cases and 981 non-NPC controls, BALF2 I613V and V317M were significantly associated with NPC in both endemic and non-endemic populations. Modeled variant-informed screening strategies achieved a 46% relative increase in PPV with 7% decrease in effective screening sensitivity, thereby averting nearly half of screening endoscopies/MRIs among endemic populations in east/southeast Asia. Conclusions EBV BALF2 haplotypes are temporally stable within hosts and can be readily detected in plasma via an inexpensive multiplex genotyping assay that offers near-perfect sequencing concordance. In endemic and non-endemic populations, I613V and V317M were highly associated with NPC and could be leveraged to develop variant-informed screening programs that mitigate false positives with small reductions in screening sensitivity. Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01625-6.
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Affiliation(s)
- Jacob A Miller
- Department of Radiation Oncology, Stanford University School of Medicine, 875 Blake Wilbur Drive, Palo Alto, CA, 94304, USA
| | - Malaya K Sahoo
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - Fumiko Yamamoto
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - ChunHong Huang
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - Hannah Wang
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - James L Zehnder
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University School of Medicine, 875 Blake Wilbur Drive, Palo Alto, CA, 94304, USA
| | - Benjamin A Pinsky
- Department of Pathology, Stanford University School of Medicine, 3375 Hillview Avenue, Palo Alto, CA, 94304, USA. .,Division of Infectious Diseases and Geographic Medicine, Department of Medicine, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA, 94305, USA.
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22
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The roles of DNA methylation on the promotor of the Epstein–Barr virus (EBV) gene and the genome in patients with EBV-associated diseases. Appl Microbiol Biotechnol 2022; 106:4413-4426. [PMID: 35763069 PMCID: PMC9259528 DOI: 10.1007/s00253-022-12029-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 06/11/2022] [Accepted: 06/13/2022] [Indexed: 11/22/2022]
Abstract
Abstract Epstein–Barr virus (EBV) is an oncogenic virus that is closely associated with several malignant and lymphoproliferative diseases. Studies have shown that the typical characteristic of EBV-associated diseases is aberrant methylation of viral DNA and the host genome. EBV gene methylation helps EBV escape from immune monitoring and persist in host cells. EBV controls viral gene promoter methylation by hijacking host epigenetic machinery to regulate the expression of viral genes. EBV proteins also interact with host epigenetic regulatory factors to mediate the methylation of the host’s important tumour suppressor gene promoters, thereby participating in the occurrence of tumorigenesis. Since epigenetic modifications, including DNA methylation, are reversible in nature, drugs that target DNA methylation can be developed for epigenetic therapy against EBV-associated tumours. Various methylation modes in the host and EBV genomes may also be of diagnostic and prognostic value. This review summarizes the regulatory roles of DNA methylation on the promotor of EBV gene and host genome in EBV-associated diseases, proposes the application prospect of DNA methylation in early clinical diagnosis and treatment, and provides insight into methylation-based strategies against EBV-associated diseases. Key points • Methylation of both the host and EBV genomes plays an important role in EBV-associateddiseases. • The functions of methylation of the host and EBV genomes in the occurrence and development of EBV-associated diseases are diverse. • Methylation may be a therapeutic target or biomarker in EBV-associated diseases.
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23
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Manara F, Jay A, Odongo GA, Mure F, Maroui MA, Diederichs A, Sirand C, Cuenin C, Granai M, Mundo L, Hernandez-Vargas H, Lazzi S, Khoueiry R, Gruffat H, Herceg Z, Accardi R. Epigenetic Alteration of the Cancer-Related Gene TGFBI in B Cells Infected with Epstein-Barr Virus and Exposed to Aflatoxin B1: Potential Role in Burkitt Lymphoma Development. Cancers (Basel) 2022; 14:1284. [PMID: 35267594 PMCID: PMC8909323 DOI: 10.3390/cancers14051284] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 01/25/2023] Open
Abstract
Burkitt lymphoma (BL) is a malignant B cell neoplasm that accounts for almost half of pediatric cancers in sub-Saharan African countries. Although the BL endemic prevalence is attributable to the combination of Epstein-Barr virus (EBV) infection with malaria and environmental carcinogens exposure, such as the food contaminant aflatoxin B1 (AFB1), the molecular determinants underlying the pathogenesis are not fully understood. Consistent with the role of epigenetic mechanisms at the interface between the genome and environment, AFB1 and EBV impact the methylome of respectively leukocytes and B cells specifically. Here, we conducted a thorough investigation of common epigenomic changes following EBV or AFB1 exposure in B cells. Genome-wide DNA methylation profiling identified an EBV-AFB1 common signature within the TGFBI locus, which encodes for a putative tumor suppressor often altered in cancer. Subsequent mechanistic analyses confirmed a DNA-methylation-dependent transcriptional silencing of TGFBI involving the recruitment of DNMT1 methyltransferase that is associated with an activation of the NF-κB pathway. Our results reveal a potential common mechanism of B cell transformation shared by the main risk factors of endemic BL (EBV and AFB1), suggesting a key determinant of disease that could allow the development of more efficient targeted therapeutic strategies.
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Affiliation(s)
- Francesca Manara
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Antonin Jay
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Grace Akinyi Odongo
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Fabrice Mure
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Universite Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, 69007 Lyon, France; (F.M.); (M.A.M.)
| | - Mohamed Ali Maroui
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Universite Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, 69007 Lyon, France; (F.M.); (M.A.M.)
| | - Audrey Diederichs
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Cecilia Sirand
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Cyrille Cuenin
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Massimo Granai
- Department of Medical Biotechnology, Section of Pathology, University of Siena, 53100 Siena, Italy; (M.G.); (S.L.)
| | - Lucia Mundo
- Health Research Institute, University of Limerick, V94 T9PX Limerick, Ireland;
| | | | - Stefano Lazzi
- Department of Medical Biotechnology, Section of Pathology, University of Siena, 53100 Siena, Italy; (M.G.); (S.L.)
| | - Rita Khoueiry
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Henri Gruffat
- CIRI, Centre International de Recherche en Infectiologie, RNA Expression in Viruses and Eukaryotes Group, Universite Claude Bernard Lyon I, INSERM U1111, CNRS UMR5308, ENS Lyon, 69007 Lyon, France; (F.M.); (M.A.M.)
| | - Zdenko Herceg
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
| | - Rosita Accardi
- International Agency for Research on Cancer, World Health Organization, 69000 Lyon, France; (F.M.); (A.J.); (G.A.O.); (A.D.); (C.S.); (C.C.); (R.K.)
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24
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Mishra V, Singh A, Chen X, Rosenberg AJ, Pearson AT, Zhavoronkov A, Savage PA, Lingen MW, Agrawal N, Izumchenko E. Application of liquid biopsy as multi-functional biomarkers in head and neck cancer. Br J Cancer 2022; 126:361-370. [PMID: 34876674 PMCID: PMC8810877 DOI: 10.1038/s41416-021-01626-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 10/25/2021] [Accepted: 11/01/2021] [Indexed: 02/06/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a molecularly heterogeneous disease, with a 5-year survival rate that still hovers at ~60% despite recent advancements. The advanced stage upon diagnosis, limited success with effective targeted therapy and lack of reliable biomarkers are among the key factors underlying the marginally improved survival rates over the decades. Prevention, early detection and biomarker-driven treatment adaptation are crucial for timely interventions and improved clinical outcomes. Liquid biopsy, analysis of tumour-specific biomarkers circulating in bodily fluids, is a rapidly evolving field that may play a striking role in optimising patient care. In recent years, significant progress has been made towards advancing liquid biopsies for non-invasive early cancer detection, prognosis, treatment adaptation, monitoring of residual disease and surveillance of recurrence. While these emerging technologies have immense potential to improve patient survival, numerous methodological and biological limitations must be overcome before their implementation into clinical practice. This review outlines the current state of knowledge on various types of liquid biopsies in HNSCC, and their potential applications for diagnosis, prognosis, grading treatment response and post-treatment surveillance. It also discusses challenges associated with the clinical applicability of liquid biopsies and prospects of the optimised approaches in the management of HNSCC.
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Affiliation(s)
- Vasudha Mishra
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alka Singh
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Xiangying Chen
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Ari J Rosenberg
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | - Alexander T Pearson
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA
| | | | - Peter A Savage
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Mark W Lingen
- Department of Pathology, University of Chicago, Chicago, IL, USA
| | - Nishant Agrawal
- Department of Surgery, Section of Otolaryngology-Head and Neck Surgery, University of Chicago, Chicago, IL, USA.
| | - Evgeny Izumchenko
- Department of Medicine, Section of Hematology and Oncology, University of Chicago, Chicago, IL, USA.
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25
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Lyu M, Yi X, Huang Z, Chen Y, Ai Z, Liang Y, Feng Q, Xiang Z. A transcriptomic analysis based on aberrant methylation levels revealed potential novel therapeutic targets for nasopharyngeal carcinoma. ANNALS OF TRANSLATIONAL MEDICINE 2022; 10:47. [PMID: 35282089 PMCID: PMC8848444 DOI: 10.21037/atm-21-6628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 01/05/2022] [Indexed: 12/24/2022]
Abstract
Background This study aimed to identify potential novel therapeutic targets for nasopharyngeal carcinoma (NPC) by identifying aberrantly methylated-differentially expressed genes (DEGs) and pathways based on a comprehensive bioinformatics analysis. Methods Eight gene expression data sets and 2 methylation microarray data sets that included NPC and control groups from the Gene Expression Omnibus were identified. Meta-analyses of the DEGs were performed using the online analysis database “NetworkAnalyst”. Aberrantly methylated gene loci were obtained from the GEO2R. Aberrantly methylated DEGs were obtained from Venn diagrams. The enrichment analysis was carried out on the “Metascape” website, and the protein-protein interaction (PPI) network construction, network analysis, and visualization of the analysis results were carried out on the “String” website using “Cytoscape” software. Results In total, 544 hypomethylation high-expression genes and 164 hypermethylation low-expression genes were obtained. The enrichment and PPI network analyses suggested that several pathways and hub genes with abnormal gene expression accompanied by methylation change, including inositol-trisphosphate 3-kinase B (ITPKB), G protein subunit beta 5 (GNB5), FYN proto-oncogene, Src family tyrosine kinase (FYN), LCK proto-oncogene, Src family tyrosine kinase (LCK), nuclear factor of activated T cells 1 (NFATC1), GNAS complex locus (GNAS), protein kinase C beta (PRKCB), zeta chain of T cell receptor associated protein kinase 70 (ZAP70), lysophosphatidic acid receptor 1 (LPAR1), protein kinase C epsilon (PRKCE), tumor protein p53 (TP53), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), fibronectin 1 (FN1), cyclin D1 (CCND1), vascular endothelial growth factor A (VEGFA), HRas proto-oncogene, GTPase (HRAS), signal transducer and activator of transcription 3 (STAT3), fibroblast growth factor 2 (FGF2), amyloid beta precursor protein (APP), and matrix metallopeptidase 2 (MMP2), may be related to the occurrence of nasopharyngeal carcinoma . Conclusions The identification of novel and important pathways and hub genes and their roles in the occurrence and development of NPC will guide clinical research and the development of pharmaceutical targets.
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Affiliation(s)
- Mo Lyu
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,School of Life Sciences, South China Normal University, Guangzhou, China
| | - Xinzhu Yi
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhiwei Huang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Yirong Chen
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China.,Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Zhu Ai
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Yuying Liang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
| | - Qili Feng
- School of Life Sciences, South China Normal University, Guangzhou, China
| | - Zhiming Xiang
- Department of Radiology, Guangzhou Panyu Central Hospital, Guangzhou, China
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26
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Zhu QY, Zhao GX, Li Y, Talakatta G, Mai HQ, Le QT, Young LS, Zeng MS. Advances in pathogenesis and precision medicine for nasopharyngeal carcinoma. MedComm (Beijing) 2021; 2:175-206. [PMID: 34766141 PMCID: PMC8491203 DOI: 10.1002/mco2.32] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Revised: 07/28/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a squamous carcinoma with apparent geographical and racial distribution, mostly prevalent in East and Southeast Asia, particularly concentrated in southern China. The epidemiological trend over the past decades has suggested a substantial reduction in the incidence rate and mortality rate due to NPC. These results may reflect changes in lifestyle and environment, and more importantly, a deeper comprehension of the pathogenic mechanism of NPC, leading to much progress in the preventing, screening, and treating for this cancer. Herein, we present the recent advances on the key signal pathways involved in pathogenesis of NPC, the mechanism of Epstein‐Barr virus (EBV) entry into the cell, and the progress of EBV vaccine and screening biomarkers. We will also discuss in depth the development of various therapeutic approaches including radiotherapy, chemotherapy, surgery, targeted therapy, and immunotherapy. These research advancements have led to a new era of precision medicine in NPC.
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Affiliation(s)
- Qian-Ying Zhu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center (SYSUCC) Guangzhou China
| | - Ge-Xin Zhao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center (SYSUCC) Guangzhou China
| | - Yan Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center (SYSUCC) Guangzhou China
| | - Girish Talakatta
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center (SYSUCC) Guangzhou China
| | - Hai-Qiang Mai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center (SYSUCC) Guangzhou China
| | - Quynh-Thu Le
- Department of Radiation Oncology Stanford California
| | - Lawrence S Young
- Warwick Medical School University of Warwick Coventry United Kingdom
| | - Mu-Sheng Zeng
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy Sun Yat-sen University Cancer Center (SYSUCC) Guangzhou China
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27
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Wong KCW, Hui EP, Lo KW, Lam WKJ, Johnson D, Li L, Tao Q, Chan KCA, To KF, King AD, Ma BBY, Chan ATC. Nasopharyngeal carcinoma: an evolving paradigm. Nat Rev Clin Oncol 2021; 18:679-695. [PMID: 34194007 DOI: 10.1038/s41571-021-00524-x] [Citation(s) in RCA: 192] [Impact Index Per Article: 64.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2021] [Indexed: 02/06/2023]
Abstract
The past three decades have borne witness to many advances in the understanding of the molecular biology and treatment of nasopharyngeal carcinoma (NPC), an Epstein-Barr virus (EBV)-associated cancer endemic to southern China, southeast Asia and north Africa. In this Review, we provide a comprehensive, interdisciplinary overview of key research findings regarding NPC pathogenesis, treatment, screening and biomarker development. We describe how technological advances have led to the advent of proton therapy and other contemporary radiotherapy approaches, and emphasize the relentless efforts to identify the optimal sequencing of chemotherapy with radiotherapy through decades of clinical trials. Basic research into the pathogenic role of EBV and the genomic, epigenomic and immune landscape of NPC has laid the foundations of translational research. The latter, in turn, has led to the development of new biomarkers and therapeutic targets and of improved approaches for individualizing immunotherapy and targeted therapies for patients with NPC. We provide historical context to illustrate the effect of these advances on treatment outcomes at present. We describe current preclinical and clinical challenges and controversies in the hope of providing insights for future investigation.
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Affiliation(s)
- Kenneth C W Wong
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Edwin P Hui
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Wai Kei Jacky Lam
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - David Johnson
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Lili Li
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Qian Tao
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Kwan Chee Allen Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ka-Fai To
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Ann D King
- Department of Diagnostic Imaging and Interventional Radiology, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR
| | - Brigette B Y Ma
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR.
| | - Anthony T C Chan
- State Key Laboratory of Translational Oncology, Sir YK Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute, The Chinese University of Hong Kong, Hong Kong, Hong Kong SAR.
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28
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Rathod A, Rathod R, Zhang H, Rahimabad PK, Karmaus W, Arshad H. Association of Asthma and Rhinitis with Epigenetics of Coronavirus Related Genes. Epigenet Insights 2021; 14:25168657211039224. [PMID: 34604700 PMCID: PMC8485269 DOI: 10.1177/25168657211039224] [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: 03/22/2021] [Accepted: 07/23/2021] [Indexed: 12/15/2022] Open
Abstract
Introduction: Susceptibility factors for coronavirus disease 2019 (COVID-19) include sex and medical conditions such as asthma and rhinitis. DNA methylation (DNAm) is associated with asthma, rhinitis, and several viruses. We examined associations of asthma/rhinitis with DNAm at CpGs located on coronavirus related genes, and if these associations were sex-specific. Methods: In total, n = 242 subjects aged 26 years from the Isle of Wight Birth Cohort were included in the study. Linear regressions were used to examine sex specific and non-specific associations of DNAm at CpGs on coronavirus related genes with asthma/rhinitis status. Associations of DNAm with gene expression in blood were assessed for functional relevance of identified CpGs. Results: Statistically significant interaction effects of asthma or rhinitis with sex were identified at 40 CpGs for asthma and 27 CpGs for rhinitis. At 21 CpGs, DNAm was associated with asthma, and at 45 CpGs with rhinitis, regardless of sex. Assessment of functional relevance of the identified CpGs indicated a potential of epigenetic regulatory functionality on gene activity at 14 CpGs for asthma and 17 CpGs for rhinitis, and of those 6 CpGs for asthma and 7 CpGs for rhinitis were likely to be sex-specific. Conclusion: Subjects with asthma/rhinitis may have altered susceptibility to COVID-19 due to changes in their DNAm associated with these conditions. Sex specificity on association of asthma/rhinitis with DNAm at certain CpGs, and on the association of DNAm at asthma/rhinitis-linked CpGs with gene expression have the potential to explain the reported sex-specificity in COVID-19 morbidity and mortality.
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Affiliation(s)
- Aniruddha Rathod
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Rutu Rathod
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hongmei Zhang
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Parnian Kheirkhah Rahimabad
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Wilfried Karmaus
- Division of Epidemiology, Biostatistics, and Environmental Health Sciences, School of Public Health, University of Memphis, Memphis, TN, USA
| | - Hasan Arshad
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, UK.,David Hide Asthma and Allergy Research Centre, Isle of Wight, UK.,NIHR Southampton Biomedical Research Center, University Hospital Southampton, Southampton, UK
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29
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Clinical analysis of 12 patients with primary lymphoepithelial carcinoma of the parotid gland. Eur Arch Otorhinolaryngol 2021; 279:2003-2008. [PMID: 34379180 DOI: 10.1007/s00405-021-06947-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/10/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND AND PURPOSE The WHO recently designated salivary gland lymphoepithelial carcinoma as a unique malignant tumor that most commonly occurs in the parotid gland. This is a rare cancer and there are few reports in the literature. Among 854 patients with parotid gland tumors who were admitted to our institution, we diagnosed 12 patients (1.41%) with parotid lymphoepithelial carcinoma. METHODS Retrospective analysis of 12 patients with parotid lymphoepithelial carcinoma diagnosed by the Department of Pathology, Xiangya Hospital of Central South University. RESULTS All 12 patients had unilateral parotid gland disease and 8 had cervical lymph node metastasis. Five patients received PCR testing for the Epstein-Barr virus and two were positive. All patients received surgical treatment, two received surgical resection alone, nine received surgery and postoperative radiotherapy and chemotherapy, and one received surgery and postoperative chemotherapy. The postoperative follow-up time ranged from 13 to 77 months. As of the last follow-up, eight patients were tumor-free, one patient was lost to follow-up, and three patients died. The main cause of death was local tumor recurrence and multiple metastases throughout the body. CONCLUSION Parotid lymphoepithelial carcinoma is a malignant neoplasm characterized by proliferation, invasion, and inclusion of poorly differentiated or undifferentiated carcinoma, and a high rate of metastasis to ipsilateral cervical lymph nodes. The comprehensive treatment method consists of radical resection combined with postoperative radiotherapy and chemotherapy. After this comprehensive treatment, the 1-year, 3-year, and 5-year overall survival rates of our patients were 100%, 78.8%, and 39.4%.
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30
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Burgener JM, Zou J, Zhao Z, Zheng Y, Shen SY, Huang SH, Keshavarzi S, Xu W, Liu FF, Liu G, Waldron JN, Weinreb I, Spreafico A, Siu LL, de Almeida JR, Goldstein DP, Hoffman MM, De Carvalho DD, Bratman SV. Tumor-Naïve Multimodal Profiling of Circulating Tumor DNA in Head and Neck Squamous Cell Carcinoma. Clin Cancer Res 2021; 27:4230-4244. [PMID: 34158359 PMCID: PMC9401560 DOI: 10.1158/1078-0432.ccr-21-0110] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 03/16/2021] [Accepted: 05/28/2021] [Indexed: 01/07/2023]
Abstract
PURPOSE Circulating tumor DNA (ctDNA) enables personalized treatment strategies in oncology by providing a noninvasive source of clinical biomarkers. In patients with low ctDNA abundance, tumor-naïve methods are needed to facilitate clinical implementation. Here, using locoregionally confined head and neck squamous cell carcinoma (HNSCC) as an example, we demonstrate tumor-naïve detection of ctDNA by simultaneous profiling of mutations and methylation. EXPERIMENTAL DESIGN We conducted CAncer Personalized Profiling by deep Sequencing (CAPP-seq) and cell-free Methylated DNA ImmunoPrecipitation and high-throughput sequencing (cfMeDIP-seq) for detection of ctDNA-derived somatic mutations and aberrant methylation, respectively. We analyzed 77 plasma samples from 30 patients with stage I-IVA human papillomavirus-negative HNSCC as well as plasma samples from 20 risk-matched healthy controls. In addition, we analyzed leukocytes from patients and controls. RESULTS CAPP-seq identified mutations in 20 of 30 patients at frequencies similar to that of The Tumor Genome Atlas (TCGA). Differential methylation analysis of cfMeDIP-seq profiles identified 941 ctDNA-derived hypermethylated regions enriched for CpG islands and HNSCC-specific methylation patterns. Both methods demonstrated an association between ctDNA abundance and shorter fragment lengths. In addition, mutation- and methylation-based ctDNA abundance was highly correlated (r > 0.85). Patients with detectable pretreatment ctDNA by both methods demonstrated significantly worse overall survival (HR = 7.5; P = 0.025) independent of clinical stage, with lack of ctDNA clearance post-treatment strongly correlating with recurrence. We further leveraged cfMeDIP-seq profiles to validate a prognostic signature identified from TCGA samples. CONCLUSIONS Tumor-naïve detection of ctDNA by multimodal profiling may facilitate biomarker discovery and clinical use in low ctDNA abundance applications.
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Affiliation(s)
- Justin M. Burgener
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
| | - Jinfeng Zou
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Zhen Zhao
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Yangqiao Zheng
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Shao Hui Huang
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Deparment of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Sareh Keshavarzi
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Wei Xu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John N. Waldron
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada
| | - Ilan Weinreb
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Anna Spreafico
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Lillian L. Siu
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Division of Medical Oncology and Hematology, Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - John R. de Almeida
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - David P. Goldstein
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Deparment of Otolaryngology – Head and Neck Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Michael M. Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Department of Computer Science, University of Toronto, Toronto, Ontario, Canada.,Vector Institute, Toronto, Ontario, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Scott V. Bratman, Medical Biophysics, Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-946-2121; E-mail: ; and Daniel D. De Carvalho,
| | - Scott V. Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Deparment of Radiation Oncology, University of Toronto, Toronto, Ontario, Canada.,Corresponding Authors: Scott V. Bratman, Medical Biophysics, Princess Margaret Cancer Centre, University Health Network, 101 College Street, Toronto, ON M5G 1L7, Canada. Phone: 416-946-2121; E-mail: ; and Daniel D. De Carvalho,
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31
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Barefoot ME, Loyfer N, Kiliti AJ, McDeed AP, Kaplan T, Wellstein A. Detection of Cell Types Contributing to Cancer From Circulating, Cell-Free Methylated DNA. Front Genet 2021; 12:671057. [PMID: 34386036 PMCID: PMC8353442 DOI: 10.3389/fgene.2021.671057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/17/2021] [Indexed: 12/24/2022] Open
Abstract
Detection of cellular changes in tissue biopsies has been the basis for cancer diagnostics. However, tissue biopsies are invasive and limited by inaccuracies due to sampling locations, restricted sampling frequency, and poor representation of tissue heterogeneity. Liquid biopsies are emerging as a complementary approach to traditional tissue biopsies to detect dynamic changes in specific cell populations. Cell-free DNA (cfDNA) fragments released into the circulation from dying cells can be traced back to the tissues and cell types they originated from using DNA methylation, an epigenetic regulatory mechanism that is highly cell-type specific. Decoding changes in the cellular origins of cfDNA over time can reveal altered host tissue homeostasis due to local cancer invasion and metastatic spread to distant organs as well as treatment responses. In addition to host-derived cfDNA, changes in cancer cells can be detected from cell-free, circulating tumor DNA (ctDNA) by monitoring DNA mutations carried by cancer cells. Here, we will discuss computational approaches to identify and validate robust biomarkers of changed tissue homeostasis using cell-free, methylated DNA in the circulation. We highlight studies performing genome-wide profiling of cfDNA methylation and those that combine genetic and epigenetic markers to further identify cell-type specific signatures. Finally, we discuss opportunities and current limitations of these approaches for implementation in clinical oncology.
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Affiliation(s)
- Megan E. Barefoot
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
| | - Netanel Loyfer
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Amber J. Kiliti
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, United States
| | - A. Patrick McDeed
- Department of Biostatistics, Bioinformatics, and Biomathematics, Georgetown University, Washington, DC, United States
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Anton Wellstein
- Department of Oncology, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, United States
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32
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Vasudevan HN, Yom SS. Nasopharyngeal Carcinoma and Its Association with Epstein-Barr Virus. Hematol Oncol Clin North Am 2021; 35:963-971. [PMID: 34187713 DOI: 10.1016/j.hoc.2021.05.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Nasopharyngeal carcinoma (NPC) is caused by Epstein-Barr virus (EBV) infection, yet incorporating measurement of EBV DNA levels into clinical practice remains a challenge. Here, we summarize the relationship between NPC and EBV infection before describing the use of cell-free DNA as a plasma biomarker in cancer. We then compare conventional polymerase chain reaction methods and emerging next-generation sequencing approaches for EBV viral load detection emphasizing their prognostic and predictive utility. We conclude by considering how assay standardization, novel molecular approaches, and alternative clinical specimens may be leveraged to bring EBV testing into the routine care of patients with NPC.
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Affiliation(s)
- Harish N Vasudevan
- Department of Radiation Oncology, University of California San Francisco, Helen Diller Cancer Research Building, 1450 3rd street, HD403, San Francisco, CA 94158, USA
| | - Sue S Yom
- Department of Radiation Oncology, University of California San Francisco, Precision Cancer Medicine Building, 1825 4th Street, Suite L1101, San Francisco, CA 94158, USA.
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33
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CpG methylation in cell-free Epstein-Barr virus DNA in patients with EBV-Hodgkin lymphoma. Blood Adv 2021; 4:1624-1627. [PMID: 32311011 DOI: 10.1182/bloodadvances.2020001511] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 02/26/2020] [Indexed: 12/13/2022] Open
Abstract
Epstein-Barr virus (EBV) is associated with a variety of tumors and nonmalignant conditions. Latent EBV genomes in cells, including tumor cells, are often CpG methylated, whereas virion DNA is not CpG methylated. We demonstrate that methyl CpG binding magnetic beads can be used to fractionate among sources of EBV DNA (DNA extracted from laboratory-purified virions vs DNA extracted from latently infected cell lines). We then applied the technique to plasma specimens and showed that this technique can distinguish EBV DNA from patients with EBV-associated tumors (nasopharyngeal carcinoma, Hodgkin lymphoma) and viral DNA from patients without EBV-associated tumors, including immunocompromised patients and patients with EBV(-) Hodgkin lymphoma.
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34
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Abstract
Oligometastasis represents an intermediate disease stage between localized and widely metastatic cancer. Efficient identification of patients with oligometastasis remains a barrier for accrual on clinical trials of oligometastasis-directed therapy. Here we review the prospect of circulating tumor DNA-based monitoring to promote sensitive, specific, and cost-efficient detection of cancer recurrence during posttreatment surveillance. Thus, an impetus for the development and implementation of clinical-grade circulating tumor DNA assays should be for the positive impact they will have on clinical investigations of oligometastasis-directed therapy.
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Affiliation(s)
- David Routman
- Department of Radiation Oncology, Mayo Clinic, Rochester, MN
| | - Bhishamjit S. Chera
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
| | - Gaorav P. Gupta
- Department of Radiation Oncology, Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
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35
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Lo YMD, Han DSC, Jiang P, Chiu RWK. Epigenetics, fragmentomics, and topology of cell-free DNA in liquid biopsies. Science 2021; 372:372/6538/eaaw3616. [PMID: 33833097 DOI: 10.1126/science.aaw3616] [Citation(s) in RCA: 238] [Impact Index Per Article: 79.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 02/08/2021] [Indexed: 12/14/2022]
Abstract
Liquid biopsies that analyze cell-free DNA in blood plasma are used for noninvasive prenatal testing, oncology, and monitoring of organ transplant recipients. DNA molecules are released into the plasma from various bodily tissues. Physical and molecular features of cell-free DNA fragments and their distribution over the genome bear information about their tissues of origin. Moreover, patterns of DNA methylation of these molecules reflect those of their tissue sources. The nucleosomal organization and nuclease content of the tissue of origin affect the fragmentation profile of plasma DNA molecules, such as fragment size and end motifs. Besides double-stranded linear fragments, other topological forms of cell-free DNA also exist-namely circular and single-stranded molecules. Enhanced by these features, liquid biopsies hold promise for the noninvasive detection of tissue-specific pathologies with a range of clinical applications.
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Affiliation(s)
- Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China. .,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory in Translational Oncology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Diana S C Han
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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36
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Cao Y, Xie L, Shi F, Tang M, Li Y, Hu J, Zhao L, Zhao L, Yu X, Luo X, Liao W, Bode AM. Targeting the signaling in Epstein-Barr virus-associated diseases: mechanism, regulation, and clinical study. Signal Transduct Target Ther 2021; 6:15. [PMID: 33436584 PMCID: PMC7801793 DOI: 10.1038/s41392-020-00376-4] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2020] [Accepted: 10/15/2020] [Indexed: 12/11/2022] Open
Abstract
Epstein–Barr virus-associated diseases are important global health concerns. As a group I carcinogen, EBV accounts for 1.5% of human malignances, including both epithelial- and lymphatic-originated tumors. Moreover, EBV plays an etiological and pathogenic role in a number of non-neoplastic diseases, and is even involved in multiple autoimmune diseases (SADs). In this review, we summarize and discuss some recent exciting discoveries in EBV research area, which including DNA methylation alterations, metabolic reprogramming, the changes of mitochondria and ubiquitin-proteasome system (UPS), oxidative stress and EBV lytic reactivation, variations in non-coding RNA (ncRNA), radiochemotherapy and immunotherapy. Understanding and learning from this advancement will further confirm the far-reaching and future value of therapeutic strategies in EBV-associated diseases.
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Affiliation(s)
- Ya Cao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China. .,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China. .,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China. .,Research Center for Technologies of Nucleic Acid-Based Diagnostics and Therapeutics Hunan Province, 410078, Changsha, China. .,Molecular Imaging Research Center of Central South University, 410008, Changsha, Hunan, China. .,National Joint Engineering Research Center for Genetic Diagnostics of Infectious Diseases and Cancer, 410078, Changsha, China. .,Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.
| | - Longlong Xie
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Feng Shi
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Min Tang
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China.,Molecular Imaging Research Center of Central South University, 410008, Changsha, Hunan, China
| | - Yueshuo Li
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Jianmin Hu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Lin Zhao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Luqing Zhao
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China
| | - Xinfang Yu
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China
| | - Xiangjian Luo
- Key Laboratory of Carcinogenesis and Invasion, Chinese Ministry of Education, Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China.,Cancer Research Institute and School of Basic Medical Science, Xiangya School of Medicine, Central South University, 410078, Changsha, China.,Key Laboratory of Carcinogenesis, Chinese Ministry of Health, 410078, Changsha, China.,Molecular Imaging Research Center of Central South University, 410008, Changsha, Hunan, China
| | - Weihua Liao
- Department of Radiology, Xiangya Hospital, Central South University, 410078, Changsha, China
| | - Ann M Bode
- The Hormel Institute, University of Minnesota, Austin, MN, 55912, USA
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37
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Dudley JC, Diehn M. Detection and Diagnostic Utilization of Cellular and Cell-Free Tumor DNA. ANNUAL REVIEW OF PATHOLOGY-MECHANISMS OF DISEASE 2020; 16:199-222. [PMID: 33228464 DOI: 10.1146/annurev-pathmechdis-012419-032604] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Because cancer is caused by an accumulation of genetic mutations, mutant DNA released by tumors can be used as a highly specific biomarker for cancer. Although this principle was described decades ago, the advent and falling costs of next-generation sequencing have made the use of tumor DNA as a biomarker increasingly practical. This review surveys the use of cellular and cell-free DNA for the detection of cancer, with a focus on recent technological developments and applications to solid tumors. It covers (a) key principles and technology enabling the highly sensitive detection of tumor DNA; (b) assessment of tumor DNA in plasma, including for genotyping, minimal residual disease detection, and early detection of localized cancer; (c) detection of tumor DNA in body cavity fluids, such as urine or cerebrospinal fluid; and (d) challenges posed to the use of tumor DNA as a biomarker by the phenomenon of benign clonal expansions.
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Affiliation(s)
- Jonathan C Dudley
- Ludwig Center, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, USA
| | - Maximilian Diehn
- Department of Radiation Oncology, Stanford Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, California 94305, USA;
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38
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Lam WKJ, Ji L, Tse OYO, Cheng SH, Jiang P, Lee PHP, Lin SV, Hui EP, Ma BBY, Chan ATC, Chan KCA, Chiu RWK, Lo YMD. Sequencing Analysis of Plasma Epstein-Barr Virus DNA Reveals Nasopharyngeal Carcinoma-Associated Single Nucleotide Variant Profiles. Clin Chem 2020; 66:598-605. [PMID: 32191318 DOI: 10.1093/clinchem/hvaa027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 01/14/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is strongly associated with Epstein-Barr virus (EBV) infection. Plasma EBV DNA is a validated screening tool for NPC. In screening, there are some individuals who do not have NPC but carry EBV DNA in plasma. Currently it is not known from screening if there may be any genotypic differences in EBV isolates from NPC and non-NPC subjects. Also, low concentrations of EBV DNA in plasma could pose challenge to such EBV genotypic analysis through plasma DNA sequencing. METHODS In a training dataset comprised of plasma DNA sequencing data of NPC and non-NPC subjects, we studied the difference in the EBV single nucleotide variant (SNV) profiles between the two groups. The most differentiating SNVs across the EBV genome were identified. We proposed an NPC risk score to be derived from the genotypic patterns over these SNV sites. We subsequently analyzed the NPC risk scores in a testing set. RESULTS A total of 661 significant SNVs across the EBV genome were identified from the training set. In the testing set, NPC plasma samples were shown to have high NPC risk scores, which suggested the presence of NPC-associated EBV SNV profiles. Among the non-NPC samples, there was a wide range of NPC risk scores. These results support the presence of diverse SNV profiles of EBV isolates from non-NPC subjects. CONCLUSION EBV genotypic analysis is feasible through plasma DNA sequencing. The NPC risk score may be used to inform the cancer risk based on the EBV genome-wide SNV profile.
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Affiliation(s)
- W K Jacky Lam
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Lu Ji
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - O Y Olivia Tse
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Suk Hang Cheng
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Peiyong Jiang
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - P H Patrick Lee
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - S Vivien Lin
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Edwin P Hui
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Brigette B Y Ma
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - Anthony T C Chan
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Clinical Oncology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China
| | - K C Allen Chan
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Rossa W K Chiu
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
| | - Y M Dennis Lo
- Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China.,Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong SAR, China
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Tan R, Phua SKA, Soong YL, Oon LLE, Chan KS, Lucky SS, Mong J, Tan MH, Lim CM. Clinical utility of Epstein-Barr virus DNA and other liquid biopsy markers in nasopharyngeal carcinoma. Cancer Commun (Lond) 2020; 40:564-585. [PMID: 32989921 PMCID: PMC7668470 DOI: 10.1002/cac2.12100] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/14/2020] [Indexed: 12/22/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a malignant epithelial tumor ubiquitously associated with the Epstein-Barr virus (EBV), which is highly prevalent in South China, Southeast Asia, and North Africa. Despite being a highly radio-sensitive and treatable cancer, a majority of NPC patients are diagnosed in their advanced stage, and locoregional and distant relapses following definitive treatment contribute largely to cancer-specific mortality among these patients. Given that EBV-driven NPC is the predominant variant seen in endemic regions, various EBV detection methods have been developed and are utilized in screening, prognostication, and post-treatment surveillance of NPC patients. While the Immunoglobulin A (IgA) serology assay is the most extensively studied EBV detection method, the detection of plasma EBV DNA released during replication or cellular apoptosis has shown superior outcomes in endemic population screening, prognostication, and detection of distant relapse. Furthermore, there is emerging evidence on the use of circulating tumor cells, microRNAs, DNA hypermethylation, and combination assays in various clinical scenarios. Herein, this paper provides a comprehensive overview of the relevant studies using various EBV detection techniques in the management of NPC. Specifically, the recent advances, clinical evidence, and challenges associated with the clinical application of EBV liquid biopsies in population screening, prognostication, and surveillance of NPC are presented.
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Affiliation(s)
- Rong Tan
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore117599Singapore
| | - Sean Kean Ann Phua
- Yong Loo Lin School of MedicineNational University of SingaporeSingapore117599Singapore
| | - Yoke Lim Soong
- Department of Radiation OncologyNational Cancer CenterSingapore169608Singapore
| | - Lynette Lin Ean Oon
- Department of Molecular PathologySingapore General HospitalSingapore169608Singapore
| | - Kian Sing Chan
- Department of Molecular PathologySingapore General HospitalSingapore169608Singapore
| | | | - Jamie Mong
- Institute of Bioengineering and NanotechnologySingapore138669Singapore
| | - Min Han Tan
- Institute of Bioengineering and NanotechnologySingapore138669Singapore
- Lucence DiagnosticsSingapore159552Singapore
| | - Chwee Ming Lim
- Institute of Bioengineering and NanotechnologySingapore138669Singapore
- Department of Otorhinolaryngology‐Head and Neck SurgerySingapore General HospitalSingapore169608Singapore
- Surgery Academic Clinical ProgrammeDuke‐NUS Graduate Medical SchoolSingapore169857Singapore
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40
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Ma BBY, Chen YP, Hui EP, Liu X, Chan AKC, Chan ATC, Ma J. Recent Advances in the Development of Biomarkers and Chemoradiotherapeutic Approaches for Nasopharyngeal Carcinoma. Am Soc Clin Oncol Educ Book 2020; 40:1-11. [PMID: 32191137 DOI: 10.1200/edbk_280747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Epstein-Barr virus (EBV) associated nasopharyngeal carcinoma (NPC) is endemic in Southern China, and the prognosis of this cancer has improved in part due to advances in radiotherapy (RT) techniques, broadened therapeutic options, and more precise prognostic stratification of patients. RT is the primary curative treatment of NPC, and the incorporation of chemotherapy (induction, concurrent, adjuvant) to RT has contributed to improved survival in patients with locoregionally advanced NPC. Concurrent chemoradiotherapy (CCRT) in combination with adjuvant or induction chemotherapy is now the standard treatment of locoregionally advanced NPC, but the ideal CCRT therapeutic strategy for NPC remains controversial. Plasma EBV DNA is the archetypal tumor-derived DNA in NPC, and three generations of studies have gradually expanded its clinical applications. Recently, the advent of whole exome/genome sequencing of NPC and the promising clinical activity of immune checkpoint inhibitors have also spurred interest in the development of newer biomarkers. This review will focus on two clinical advances in NPC research that have made substantial impact on the contemporary management of NPC: (1) The integration of plasma EBV DNA in an expanding spectrum of clinical indications, and the development of promising immune-related biomarkers; (2) the current development of CCRT with special emphasis on the use of induction and adjuvant chemotherapy, as well as the potential applications of metronomic chemotherapy and immune checkpoint inhibitors in the treatment of locoregionally advanced NPC.
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Affiliation(s)
- Brigette B Y Ma
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Yu-Pei Chen
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, People's Republic of China
| | - Edwin P Hui
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Xu Liu
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, People's Republic of China
| | - Allen K C Chan
- Department of Chemical Pathology, The Chinese University of Hong Kong. Hong Kong SAR, People's Republic of China
| | - Anthony T C Chan
- State Key Laboratory of Translational Oncology, Sir Y.K. Pao Centre for Cancer, Department of Clinical Oncology, Hong Kong Cancer Institute and Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Hong Kong SAR, People's Republic of China
| | - Jun Ma
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Guangzhou, People's Republic of China
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41
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Tang Z, Chen W, Xu Y, Lin X, Liu X, Li Y, Liu Y, Luo Z, Liu Z, Fang W, Zhao M. miR-4721, Induced by EBV-miR-BART22, Targets GSK3β to Enhance the Tumorigenic Capacity of NPC through the WNT/β-catenin Pathway. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 22:557-571. [PMID: 33230457 PMCID: PMC7566007 DOI: 10.1016/j.omtn.2020.09.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Accepted: 09/17/2020] [Indexed: 12/12/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is prevalent in East and Southeast Asia. In a previous study, Epstein-Barr virus (EBV)-miR-BART22 induces tumor metastasis and stemness and is significantly involved in NPC progression. In the present study, we observed that miR-4721 is induced by EBV-miR-BART22 through phosphatidylinositol 3-kinase (PI3K)/AKT/c-JUN/Sp1 signaling to promote its transcription. In a subsequent study, we observed that miR-4721 serves as a potential oncogenic factor promoting NPC cell cycle progression and cell proliferation in vitro and in vivo. Mechanism analysis indicated that miR-4721 directly targetes GSK3β and reduces its expression, which therefore elevates β-catenin intra-nuclear aggregation and activates its downstream cell cycle factors, including CCND1 and c-MYC. In clinical samples, miR-4721 and GSK3β are respectively observed to be upregulated and downregulated in NPC progression. Elevated expression of miR-4721 is positively associated with clinical progression and poor prognosis. Our study first demonstrated that miR-4721 as an oncogene is induced by EBV-miR-BART22 via modulating PI3K/AKT/c-JUN/Sp1 signaling to target GSK3β, which thus activates the WNT/β-catenin-stimulated cell cycle signal and enhances the tumorigenic capacity in NPC. miR-4721 may be a potential biomarker or therapeutic target in NPC treatment in the future.
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Affiliation(s)
- ZiBo Tang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - WeiFeng Chen
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - Yan Xu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - Xian Lin
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - Xiong Liu
- Department of Otolaryngology, Head and Neck Surgery, Nanfang Hospital, Southern Medical University, 510515 Guangzhou, China
| | - YongHao Li
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - YiYi Liu
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - ZhiJian Luo
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - Zhen Liu
- Key Laboratory of Protein Modification and Degradation, School of Basic Medical Sciences, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, 511436 Guangzhou, China
| | - WeiYi Fang
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China
| | - MengYang Zhao
- Cancer Center, Integrated Hospital of Traditional Chinese Medicine, Southern Medical University, 510315 Guangzhou, China.,Department of Oncology, The People's Hospital of Zhengzhou University, 450003 Zhengzhou, China
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42
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Lam WKJ. Circulating Tumor DNA in Cancer Management: A Value Proposition. J Appl Lab Med 2020; 5:1017-1026. [PMID: 32830269 DOI: 10.1093/jalm/jfaa112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Accepted: 06/21/2020] [Indexed: 11/14/2022]
Abstract
BACKGROUND Analysis of circulating tumor DNA (ctDNA) allows the noninvasive molecular profiling of tumor, and such analysis has gained popularity for the detection of mutations with therapeutic implications. A value-based assessment would be useful for an objective evaluation of the benefits of ctDNA testing. CONTENT The value proposition approach was used to evaluate the benefits of implementing ctDNA testing to inform treatment decisions of targeted therapy. The ctDNA testing was shown to complement tumor biopsy testing for the detection of mutations that are predictive of treatment response. It might be particularly useful for tracking resistance mechanisms among patients who experience disease progression despite treatment. SUMMARY Patients, clinicians, and laboratory medicine specialists would benefit from the implementation of appropriate ctDNA testing in routine clinical care.
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Affiliation(s)
- Wai Kei Jacky Lam
- Department of Chemical Pathology, Prince of Wales Hospital, and Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong, Hong Kong SAR, China; State Key Laboratory of Translational Oncology, Sir Y.K. Pao Center for Cancer, Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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43
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Guo D, Yang L, Yang J, Shi K. Plasma cell-free DNA methylation combined with tumor mutation detection in prognostic prediction of patients with non-small cell lung cancer (NSCLC). Medicine (Baltimore) 2020; 99:e20431. [PMID: 32590728 PMCID: PMC7328949 DOI: 10.1097/md.0000000000020431] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 01/28/2020] [Accepted: 04/25/2020] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Lung Cancer is one of the most common cancers with high degree of malignancy, is a devastating disease with a poor prognosis worldwide. prognostic prediction for patients with non small-cell lung cancer (NSCLC) is still challenge. MATERIAL AND METHODS The cohort consisted of 64 consecutive patients with NSCLC identified from June1, 2014, to June 30, 2018. Liquid biopsy samples were collected. Genomic mutation DNA was calculated by including all substitutions and indels over the entire somatic, coding, sequencing length. statistical evaluations were carried out using SPSS software. RESULTS Quantity of total ctDNA was successfully determined in all 64 patients from whom baseline circulating DNA was available. ctDNA concentration ranged from 4000 to 3,562,000 genome equivalents per milliliter. Treatments induced a significant decrease in cancer specific markers in most patients with response to treatments, while the methylated DNA demonstrated favorable prediction efficiency regardless of the response status. Patients with ctDNA mutation and methylated DNA decreasing have favorable overall survival (P < .05). combination of genetic and methylated DNA decreasing had high reliability in predicting overall survival of patients with NSCLC. CONCLUSIONS We have detected both tumor mutations and methylated DNA in plasma of patients with NSCLC. Combined genetic and methylated DNA decreasing after treatment was an independent risk factor for prognosis of patients with NSCLC. Meanwhile, it had favorable predict value and had potential to be defined as a novel biomarker for patients with NSCLC.
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Affiliation(s)
| | - Liang Yang
- Department of Microbiology and Immunology and Medicine, Henan Medical College
| | - Jianwei Yang
- PET-CT Center, Henan Tumor Hospital, Affiliated Cancer Hospital of Zhengzhou University
| | - Ke Shi
- Department of Biochemistry and Molecular Biology, Henan Medical College, Henan, China
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44
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45
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Zhang J, Xie T, Zhong X, Jiang HL, Li R, Wang BY, Huang XT, Cen BH, Yuan YW. Melatonin reverses nasopharyngeal carcinoma cisplatin chemoresistance by inhibiting the Wnt/β-catenin signaling pathway. Aging (Albany NY) 2020; 12:5423-5438. [PMID: 32203052 PMCID: PMC7138577 DOI: 10.18632/aging.102968] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2019] [Accepted: 03/16/2020] [Indexed: 01/12/2023]
Abstract
Cisplatin (DDP)-based concurrent chemo-radiotherapy is a standard approach to treat locoregionally advanced nasopharyngeal carcinoma (NPC). However, many patients eventually develop recurrence and/or distant metastasis due to chemoresistance. In this study, we aimed to elucidate the effects of melatonin on DDP chemoresistance in NPC cell lines in vitro and vivo, and we explored potential chemoresistance mechanisms. We found that DDP chemoresistance in NPC cells is mediated through the Wnt/β-catenin signaling pathway. Melatonin not only reversed DDP chemoresistance, but also enhanced DDP antitumor activity by suppressing the nuclear translocation of β-catenin, and reducing expression of Wnt/β-catenin response genes in NPC cells. In vivo, combined treatment with DDP and melatonin reduced tumor burden to a greater extent than single drug-treatments in an orthotopic xenograft mouse model. Our findings provide novel evidence that melatonin inhibits the Wnt/β-catenin pathway in NPC, and suggest that melatonin could be applied in combination with DDP to treat NPC.
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Affiliation(s)
- Jian Zhang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Tao Xie
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xi Zhong
- Department of Radiology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Hua-Li Jiang
- Department of Cardiovascularology, Tungwah Hospital of Sun Yat-Sen University, Dongguan, P.R. China
| | - Rong Li
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Bai-Yao Wang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Xiao-Ting Huang
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Bo-Hong Cen
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
| | - Ya-Wei Yuan
- Department of Radiation Oncology, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, State Key Laboratory of Respiratory Diseases, Guangzhou Institute of Respiratory Disease, Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, P. R. China
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46
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Liu W, Luo B. The impact of EBV on the epigenetics of gastric carcinoma. Future Virol 2020. [DOI: 10.2217/fvl-2019-0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
EBV is an important human tumor virus and is closely related to the occurrence of a variety of tumors, involving 10% of gastric cancer. In EBV-associated gastric carcinoma (EBVaGC), EBV expresses restrict viral genes including EBV nuclear antigen 1, EBV encoded small RNAs, Bam HI-A rightward transcripts, latent membrane protein 2A and miRNAs. The role of EBV in gastric carcinogenesis has received increasing attention and is considered to be another pathogenic factor in addition to Helicobacter pylori. A typical characteristic of EBVaGC is the extensive methylation of viral and host genome. Combined with other epigenetic mechanisms, EBV infection acts as an epigenetic driver of EBVaGC oncogenesis. In this review we discuss recent findings of EBV effect on host epigenetic alterations in EBVaGC and its role in oncogenic process.
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Affiliation(s)
- Wen Liu
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, PR China
| | - Bing Luo
- Department of Pathogenic Biology, School of Basic Medicine, Qingdao University, Qingdao, PR China
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47
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Mohammed EM. Environmental Influencers, MicroRNA, and Multiple Sclerosis. J Cent Nerv Syst Dis 2020; 12:1179573519894955. [PMID: 32009827 PMCID: PMC6971968 DOI: 10.1177/1179573519894955] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 11/25/2019] [Indexed: 02/06/2023] Open
Abstract
Multiple sclerosis (MS) is a complex neurological disorder characterized by an aberrant immune system that affects patients' quality of life. Several environmental factors have previously been proposed to associate with MS pathophysiology, including vitamin D deficiency, Epstein-Barr virus (EBV) infection, and cigarette smoking. These factors may influence cellular molecularity, interfering with cellular proliferation, differentiation, and apoptosis. This review argues that small noncoding RNA named microRNA (miRNA) influences these factors' mode of action. Dysregulation in the miRNAs network may deeply impact cellular hemostasis, thereby possibly resulting in MS pathogenicity. This article represents a literature review and an author's theory of how environmental factors may induce dysregulations in the miRNAs network, which could ultimately affect MS pathogenicity.
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48
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Smyth LJ, Kilner J, Maxwell AP, McKnight AJ. Comparison of methylation patterns generated from genomic and cell-line derived DNA using the Illumina Infinium MethylationEPIC BeadChip array. BMC Res Notes 2019; 12:821. [PMID: 31864401 PMCID: PMC6925854 DOI: 10.1186/s13104-019-4853-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 12/10/2019] [Indexed: 01/09/2023] Open
Abstract
Objectives Genomic DNA (gDNA) is the optimal source of DNA for methylation analysis. This study compared methylation patterns in gDNA derived from blood with cell-line derived DNA (clDNA) from the same individuals. The clDNA had been generated via an Epstein-Barr virus transformation of the participant’s lymphocytes. This analysis sought to determine whether clDNA has the potential to be utilised in lieu of finite/unavailable gDNA in methylation analyses using Illumina Infinium MethylationEPIC BeadChip arrays that assess 862,927 CpG sites. Results DNA samples were divided into two groups with eight gDNA and eight matched clDNA samples compared in each group (n = 16 individuals with 32 samples in total). Methylation patterns for gDNA samples generated for both groups were compared to the clDNA equivalent samples using Partek® Genomics Suite® to assess whether the significantly different CpG sites were consistent between both groups. In total, 28,632 CpG sites with significantly different levels of methylation (p < ×10−8) were common to both groups while 828,072 CpG sites assessed by the MethylationEPIC array were not significantly different in either group. This indicates that there is potential for clDNA to be used as a replacement for finite gDNA samples when absolutely necessary in DNA methylation studies.
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Affiliation(s)
- L J Smyth
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK.
| | - J Kilner
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - A P Maxwell
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
| | - A J McKnight
- Molecular Epidemiology Research Group, Centre for Public Health, Queen's University of Belfast, Belfast, UK
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49
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Tsang CM, Lui VWY, Bruce JP, Pugh TJ, Lo KW. Translational genomics of nasopharyngeal cancer. Semin Cancer Biol 2019; 61:84-100. [PMID: 31521748 DOI: 10.1016/j.semcancer.2019.09.006] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Revised: 09/11/2019] [Accepted: 09/11/2019] [Indexed: 12/26/2022]
Abstract
Nasopharyngeal carcinoma (NPC), also named the Cantonese cancer, is a unique cancer with strong etiological association with infection of the Epstein-Barr virus (EBV). With particularly high prevalence in Southeast Asia, the involvement of EBV and genetic aberrations contributive to NPC tumorigenesis have remained unclear for decades. Recently, genomic analysis of NPC has defined it as a genetically homogeneous cancer, driven largely by NF-κB signaling caused by either somatic aberrations of NF-κB negative regulators or by overexpression of the latent membrane protein 1 (LMP1), an EBV viral oncoprotein. This represents a landmark finding of the NPC genome. Exome and RNA sequencing data from new EBV-positive NPC models also highlight the importance of PI3K pathway aberrations in NPC. We also realize for the first time that NPC mutational burden, mutational signatures, MAPK/PI3K aberrations, and MHC Class I gene aberrations, are prognostic for patient outcome. Together, these multiple genomic discoveries begin to shape the focus of NPC therapy development. Given the challenge of NF-κB targeting in human cancers, more innovative drug discovery approaches should be explored to target the unique atypical NF-κB activation feature of NPC. Our next decade of NPC research should focus on further identification of the -omic landscapes of recurrent and metastatic NPC, development of gene-based precision medicines, as well as large-scale drug screening with the newly developed and well-characterized EBV-positive NPC models. Focused preclinical and clinical investigations on these major directions may identify new and effective targeting strategies to further improve survival of NPC patients.
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Affiliation(s)
- Chi Man Tsang
- Department of Anatomical and cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Vivian Wai Yan Lui
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, ON, M5G 1L7, Canada; Ontario Institute for Cancer Research, Toronto, ON, M5G 1L7, Canada
| | - Kwok Wai Lo
- Department of Anatomical and cellular Pathology and State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
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