1
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Yu KHO, Shi CH, Wang B, Chow SHC, Chung GTY, Lung RWM, Tan KE, Lim YY, Tsang ACM, Lo KW, Yip KY. Quantifying full-length circular RNAs in cancer. Genome Res 2021; 31:2340-2353. [PMID: 34663689 PMCID: PMC8647826 DOI: 10.1101/gr.275348.121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 10/12/2021] [Indexed: 01/22/2023]
Abstract
Circular RNAs (circRNAs) are abundantly expressed in cancer. Their resistance to exonucleases enables them to have potentially stable interactions with different types of biomolecules. Alternative splicing can create different circRNA isoforms that have different sequences and unequal interaction potentials. The study of circRNA function thus requires knowledge of complete circRNA sequences. Here we describe psirc, a method that can identify full-length circRNA isoforms and quantify their expression levels from RNA sequencing data. We confirm the effectiveness and computational efficiency of psirc using both simulated and actual experimental data. Applying psirc on transcriptome profiles from nasopharyngeal carcinoma and normal nasopharynx samples, we discover and validate circRNA isoforms differentially expressed between the two groups. Compared with the assumed circular isoforms derived from linear transcript annotations, some of the alternatively spliced circular isoforms have 100 times higher expression and contain substantially fewer microRNA response elements, showing the importance of quantifying full-length circRNA isoforms.
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Affiliation(s)
- Ken Hung-On Yu
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Christina Huan Shi
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Bo Wang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Savio Ho-Chit Chow
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Grace Tin-Yun Chung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Raymond Wai-Ming Lung
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Ke-En Tan
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Yat-Yuen Lim
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur 50603, Malaysia
| | - Anna Chi-Man Tsang
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Bioinformatics Centre, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
- Hong Kong Institute of Diabetes and Obesity, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong
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2
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Bruce JP, To KF, Lui VWY, Chung GTY, Chan YY, Tsang CM, Yip KY, Ma BBY, Woo JKS, Hui EP, Mak MKF, Lee SD, Chow C, Velapasamy S, Or YYY, Siu PK, El Ghamrasni S, Prokopec S, Wu M, Kwan JSH, Liu Y, Chan JYK, van Hasselt CA, Young LS, Dawson CW, Paterson IC, Yap LF, Tsao SW, Liu FF, Chan ATC, Pugh TJ, Lo KW. Whole-genome profiling of nasopharyngeal carcinoma reveals viral-host co-operation in inflammatory NF-κB activation and immune escape. Nat Commun 2021; 12:4193. [PMID: 34234122 PMCID: PMC8263564 DOI: 10.1038/s41467-021-24348-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 05/19/2021] [Indexed: 02/07/2023] Open
Abstract
Interplay between EBV infection and acquired genetic alterations during nasopharyngeal carcinoma (NPC) development remains vague. Here we report a comprehensive genomic analysis of 70 NPCs, combining whole-genome sequencing (WGS) of microdissected tumor cells with EBV oncogene expression to reveal multiple aspects of cellular-viral co-operation in tumorigenesis. Genomic aberrations along with EBV-encoded LMP1 expression underpin constitutive NF-κB activation in 90% of NPCs. A similar spectrum of somatic aberrations and viral gene expression undermine innate immunity in 79% of cases and adaptive immunity in 47% of cases; mechanisms by which NPC may evade immune surveillance despite its pro-inflammatory phenotype. Additionally, genomic changes impairing TGFBR2 promote oncogenesis and stabilize EBV infection in tumor cells. Fine-mapping of CDKN2A/CDKN2B deletion breakpoints reveals homozygous MTAP deletions in 32-34% of NPCs that confer marked sensitivity to MAT2A inhibition. Our work concludes that NPC is a homogeneously NF-κB-driven and immune-protected, yet potentially druggable, cancer.
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Affiliation(s)
- Jeff P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ka-Fai To
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China.,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Vivian W Y Lui
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Grace T Y Chung
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuk-Yu Chan
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chi Man Tsang
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Kevin Y Yip
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Brigette B Y Ma
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - John K S Woo
- Department of Otorhinolaryngology, Head and Neck Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Edwin P Hui
- State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China.,Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Hong Kong SAR, China.,Department of Clinical Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Michael K F Mak
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sau-Dan Lee
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Chit Chow
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Sharmila Velapasamy
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yvonne Y Y Or
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Pui Kei Siu
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Samah El Ghamrasni
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Stephenie Prokopec
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Man Wu
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Johnny S H Kwan
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yuchen Liu
- School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Jason Y K Chan
- Department of Otorhinolaryngology, Head and Neck Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - C Andrew van Hasselt
- Department of Otorhinolaryngology, Head and Neck Surgery, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China
| | | | | | - Ian C Paterson
- Department of Oral & Craniofacial Sciences and Oral Cancer Research and Coordinating Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Lee-Fah Yap
- Department of Oral & Craniofacial Sciences and Oral Cancer Research and Coordinating Centre, University of Malaya, Kuala Lumpur, Malaysia
| | - Sai-Wah Tsao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Fei-Fei Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Radiation Oncology, University of Toronto, Toronto, ON, Canada
| | - Anthony T C Chan
- Department of Computer Science and Engineering, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada. .,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada. .,Ontario Institute for Cancer Research, Toronto, ON, Canada.
| | - Kwok-Wai Lo
- Department of Anatomical and cellular Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China. .,State Key Laboratory of Translational Oncology, The Chinese University of Hong Kong, Hong Kong SAR, China.
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3
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Pontoriero F, Silverman AM, Pascasio JM, Bajaj R. Nonkeratinizing Nasopharyngeal Carcinoma, Undifferentiated Type With Trisomy 2: A Case Report and Short Review of Cytogenetic and Molecular Literature. Pediatr Dev Pathol 2020; 23:448-452. [PMID: 32755442 DOI: 10.1177/1093526620945861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Carcinoma originating from the surface epithelium of the nasopharynx is classified by the World Health Organization (WHO) as nasopharyngeal carcinoma (NPC) and has 3 main types: keratinizing squamous cell carcinoma (WHO type 1) and nonkeratinizing carcinoma, differentiated (WHO type II), and undifferentiated (WHO type III). Nonkeratinizing NPC is strongly associated with prior Epstein-Barr virus (EBV) infection. These tumors may be divided into differentiated and undifferentiated carcinoma. Histologically, the tumor is characterized by syncytia of large malignant cells with vesicular nuclei, conspicuous nucleoli, and easily observed mitotic figures. We report a case of a 14-year-old boy diagnosed with EBV and human papillomavirus (HPV)-positive NPC (WHO type 3) with cytogenetics showing the presence of mosaic trisomy 2. This case report brings to light a rare cytogenetic aberration to our knowledge only reported once before in the literature in a xenograft model.
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Affiliation(s)
- Francesco Pontoriero
- St. Christopher's Hospital for Children-Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania
| | - Ayaka M Silverman
- St. Christopher's Hospital for Children-Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania
| | - Judy M Pascasio
- St. Christopher's Hospital for Children-Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania
| | - Renu Bajaj
- St. Christopher's Hospital for Children-Department of Pathology and Laboratory Medicine, Philadelphia, Pennsylvania
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4
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Yip YL, Lin W, Deng W, Jia L, Lo KW, Busson P, Vérillaud B, Liu X, Tsang CM, Lung ML, Tsao SW. Establishment of a nasopharyngeal carcinoma cell line capable of undergoing lytic Epstein-Barr virus reactivation. J Transl Med 2018; 98:1093-1104. [PMID: 29769697 DOI: 10.1038/s41374-018-0034-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 12/22/2017] [Accepted: 01/10/2018] [Indexed: 01/30/2023] Open
Abstract
Epstein-Barr virus (EBV) infects more than 90% of the adult human population. Undifferentiated nasopharyngeal carcinoma (NPC) is common in Southeast Asia, with a particularly high incidence among southern Chinese. The EBV genome can be detected in practically all cancer cells in undifferentiated NPC. The role of EBV in pathogenesis of undifferentiated NPC remains elusive. NPC cell lines are known to be difficult to establish in culture. The EBV+ve NPC cell lines, even if established in culture, rapidly lost their EBV episomes upon prolonged propagation. At present, the C666-1 NPC cell line, which is defective in lytic EBV reactivation, is the only EBV+ve NPC cell line available for NPC and EBV research. The need to establish new and representative NPC cell lines is eminent for NPC and EBV research. In this study, we report the use of the Rho-associated kinase inhibitor (Y-27632) has facilitated the establishment of a new EBV+ve NPC cell line from an earlier established NPC xenograft, C17. The C17 cell line was tumorigenic in immune-deficient mice (NOD/SCID). It retained the EBV episomes and could be induced to undergo productive lytic reactivation of EBV to generate infectious virus particles. The C17 cell line represents a new investigative tool for NPC and EBV studies. The ability of C17 to undergo lytic reactivation is unique and opens up the opportunity to examine regulation of latent and lytic infection of EBV and their contributions to NPC pathogenesis.
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Affiliation(s)
- Yim Ling Yip
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Weitao Lin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Wen Deng
- School of Nursing, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, Shatin, Hong Kong
| | - Pierre Busson
- Laboratoire de Biologie des Tumeurs Humaines, Institut Gustave Roussy, Villejuif, France
| | - Benjamin Vérillaud
- Laboratoire de Biologie des Tumeurs Humaines, Institut Gustave Roussy, Villejuif, France
| | - Xuefeng Liu
- Department of Pathology and Center for Cellular Reprogramming, Georgetown University Medical Center, Washington, DC, USA.,Cancer Hospital, Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Chi Man Tsang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Maria Li Lung
- Department of Clinical Oncology, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China
| | - Sai Wah Tsao
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, University of Hong Kong, Hong Kong SAR, China.
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5
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Liu JQ, Mai WY, Wang SB, Lou YJ, Yan SX, Jin J, Xu WL. Central nervous system leukemia in a patient with concurrent nasopharyngeal carcinoma and acute myeloid leukaemia: A case report. Medicine (Baltimore) 2017; 96:e9199. [PMID: 29384905 PMCID: PMC6393157 DOI: 10.1097/md.0000000000009199] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
RATIONALE Concurrent case of nasopharyngeal carcinoma (NPC) and acute myeloid leukemia (AML) has not been reported. Here, we report a case of NPC, who was concurrently suffered from AML one mother after the NPC diagnosis. PATIENT CONCERNS The patient was a 45-year-old male who presented with a mass on his right side neck. DIAGNOSES The patient was diagnosed with Epstein-Barr virus negative type-2 non-keratinizing carcinoma with clivus involvement and unilateral metastasis to the cervical lymph node. INTERVENTIONS He was treated with one cycle of cisplatin and 69.76 Gy of concurrent external-beam radiation. OUTCOMES Three months after completion of chemo-radiotherapy, the patient was diagnosed as acute myeloid leukemia, which achieved complete remission after one course induction chemotherapy. Two months later, however, the patient was diagnosed as central nervous system leukemia. He ultimately died of relapsed leukemia. The overall survival of the patient was 10 months. LESSONS The co-occurrence of NPC and AML is rare and prognosis is poor. Radiotherapy in NPC can disrupt the blood-brain barrier, which may contribute to the pathogenesis of central nervous system leukemia. Early alert and prevention of central nervous system leukemia following radiotherapy in NPC patient is recommended.
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Affiliation(s)
- Jun-Qing Liu
- Department of Radiation Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Wen-Yuan Mai
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University; Key Laboratory of Hematologic Malignancies of Zhejiang Province, Hangzhou
| | - Si-Ben Wang
- Department of Radiation Oncology, Shaoxing Second Hospital, Shaoxing, Zhejiang, China
| | - Yin-Jun Lou
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University; Key Laboratory of Hematologic Malignancies of Zhejiang Province, Hangzhou
| | - Sen-Xiang Yan
- Department of Radiation Oncology, The First Affiliated Hospital, College of Medicine, Zhejiang University
| | - Jie Jin
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University; Key Laboratory of Hematologic Malignancies of Zhejiang Province, Hangzhou
| | - Wei-Lai Xu
- Department of Hematology, The First Affiliated Hospital, College of Medicine, Zhejiang University; Key Laboratory of Hematologic Malignancies of Zhejiang Province, Hangzhou
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6
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Chung GT, Lung RW, Hui AB, Yip KY, Woo JK, Chow C, Tong CY, Lee SD, Yuen JW, Lun SW, Tso KK, Wong N, Tsao SW, Yip TT, Busson P, Kim H, Seo JS, O'Sullivan B, Liu FF, To KF, Lo KW. Identification of a recurrent transforming UBR5-ZNF423 fusion gene in EBV-associated nasopharyngeal carcinoma. J Pathol 2013; 231:158-67. [PMID: 23878065 PMCID: PMC4166696 DOI: 10.1002/path.4240] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Revised: 06/23/2013] [Accepted: 07/15/2013] [Indexed: 11/30/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a distinct type of head and neck cancer which is prevalent in southern China, south-east Asia and northern Africa. The development and stepwise progression of NPC involves accumulation of multiple gross genetic changes during the clonal expansion of Epstein–Barr virus (EBV)-infected nasopharyngeal epithelial cell population. Here, using paired-end whole-transcriptome sequencing, we discovered a number of chimeric fusion transcripts in a panel of EBV-positive tumour lines. Among these transcripts, a novel fusion of ubiquitin protein ligase E3 component n-recognin 5 (UBR5) on 8q22.3 and zinc finger protein 423 (ZNF423) on 16q12.1, identified from the NPC cell line C666-1, was recurrently detected in 12/144 (8.3%) of primary tumours. The fusion gene contains exon 1 of UBR5 and exons 7–9 of ZNF423 and produces a 94 amino acid chimeric protein including the original C-terminal EBF binding domain (ZF29-30) of ZNF423. Notably, the growth of NPC cells with UBR5–ZNF423 rearrangement is dependent on expression of this fusion protein. Knock-down of UBR5–ZNF423 by fusion-specific siRNA significantly inhibited the cell proliferation and colony-forming ability of C666-1 cells. The transforming ability of UBR5–ZNF423 fusion was also confirmed in NIH3T3 fibroblasts. Constitutive expression of UBR5–ZNF423 in NIH3T3 fibroblasts significantly enhanced its anchorage-independent growth in soft agar and induced tumour formation in a nude mouse model. These findings suggest that expression of UBR5–ZNF423 protein might contribute to the transformation of a subset of NPCs, possibly by altering the activity of EBFs (early B cell factors). Identification of the oncogenic UBR5–ZNF423 provides new potential opportunities for therapeutic intervention in NPC. © 2013 The Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Grace Ty Chung
- Department of Anatomical and Cellular Pathology, State Key Laboratory in Oncology in South China, Prince of Wales Hospital, The Chinese University of Hong Kong, SAR; Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, SAR
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7
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Lo KW, Chung GTY, To KF. Acquired Genetic and Epigenetic Alterations in Nasopharyngeal Carcinoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2013. [DOI: 10.1007/978-1-4614-5947-7_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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8
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Lo KW, Chung GTY, To KF. Deciphering the molecular genetic basis of NPC through molecular, cytogenetic, and epigenetic approaches. Semin Cancer Biol 2012; 22:79-86. [PMID: 22245473 DOI: 10.1016/j.semcancer.2011.12.011] [Citation(s) in RCA: 153] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2011] [Revised: 12/21/2011] [Accepted: 12/22/2011] [Indexed: 12/12/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is consistently associated with EBV infection and prevalence in southern China and Southeast Asia. In addition to EBV, the development of NPC involves cumulative genetic and epigenetic changes influenced by predisposing genetic factors and environmental carcinogens. Over the past two decades, knowledge of genetic and epigenetic alterations of NPC has rapidly accumulated. Multiple chromosomal abnormalities (e.g. copy number changes on chromosomes 3p, 9p, 11q, 12p, and 14q), gene alterations (e.g. p16 deletion and LTBR amplification), and epigenetic changes (e.g. RASSF1A and TSLC1 methylation) have been identified by various genome-wide approaches, such as allelotyping, CGH, and microarray analysis. In this review, we will discuss the critical genetic events that contribute to the initiation and progression of NPC. Studies on the precancerous lesions and in vitro immortalized nasopharyngeal epithelial cell models provide important evidence for the involvement of genetic alterations and EBV infection in early development of this cancer. A hypothetical model describing the role of EBV latent infection and multiple genetic changes in NPC tumorigenesis is proposed.
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Affiliation(s)
- Kwok-Wai Lo
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, The Chinese University of Hong Kong, Hong Kong SAR, China.
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9
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The progress on genetic analysis of nasopharyngeal carcinoma. Comp Funct Genomics 2010:57513. [PMID: 18288251 PMCID: PMC2233780 DOI: 10.1155/2007/57513] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2007] [Accepted: 12/09/2007] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy in most parts of the world, but is one of the most common cancers in Southeast Asia. Both genetic and environmental factors contribute to the tumorigenesis of NPC, most notably the consumption of certain salted food items and Epstein-Barr virus infection. This review will focus on the current progress of the genetic analysis of NPC (genetic susceptibilities and somatic alterations). We will review the current advances in genomic technologies and their shaping of the future direction of NPC research.
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10
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Rodriguez S, Khabir A, Keryer C, Perrot C, Drira M, Ghorbel A, Jlidi R, Bernheim A, Valent A, Busson P. Conventional and array-based comparative genomic hybridization analysis of nasopharyngeal carcinomas from the Mediterranean area. ACTA ACUST UNITED AC 2005; 157:140-7. [PMID: 15721635 DOI: 10.1016/j.cancergencyto.2004.08.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2004] [Revised: 08/02/2004] [Accepted: 08/03/2004] [Indexed: 11/30/2022]
Abstract
Nasopharyngeal carcinoma (NPC) occurs with a high incidence in Southeast Asia and to a lesser extent in the Mediterranean area, especially in Tunisia, Algeria, and Morocco. Cellular gene alterations combined with latent Epstein-Barr virus infection are thought to be essential for NPC oncogenesis. To date, chromosome analysis with comparative genomic hybridization (CGH) has been reported exclusively for NPCs from Southeast Asia. Although NPCs from the Mediterranean area have several distinct clinical and epidemiological features, CGH investigations have been lacking. Chromosome analysis was therefore undertaken on a series of NPC xenografts and biopsies derived from patients of Mediterranean origin. Four xenografts were investigated with a combination of conventional CGH, array-based CGH, and comparative expressed sequence hybridization. In addition, 23 fresh NPC biopsies were analyzed with conventional CGH. Data obtained from xenografts and fresh biopsies were consistent, except that amplification of genes at 18p was observed only in xenografts derived from metastatic tissues. Frequent gains associated with gene overexpression were detected at 1q25 approximately qter (64%) and 12p13 (50%). Losses were noticed mainly at 11q14 approximately q23 (50%), 13q12 approximately q31 (50%), 14q24 approximately q31 (43%), and 3p13 approximately p23 (43%). Comparison with previous reports suggests that Mediterranean NPCs have higher frequencies of gains at 1q and losses at 13q than their Asian counterparts.
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Affiliation(s)
- S Rodriguez
- Laboratoire des Interactions Moléculaires et Cancer, UMR 8126 CNRS-PR1, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif cedex, France
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11
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Czepulkowski B, Saunders K, Pocock C, Sadullah S. Mosaic trisomy 2 in myelodysplastic syndromes and acute myeloblastic leukemias. CANCER GENETICS AND CYTOGENETICS 2003; 145:78-81. [PMID: 12885468 DOI: 10.1016/s0165-4608(03)00030-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We present a short report here of two more patients with trisomy 2 as the sole chromosomal abnormality in a hematologic malignancy. Although trisomy 2 is a recognized abnormality in neoplasms, particularly hepatoblastomas, to the best of our knowledge only three other cases have been reported with trisomy 2, in patients with a hematologic malignancy. The two cases presented here of myelodysplastic syndrome transforming to acute myeloblastic leukemia and chronic myelomonocytic leukemia showed trisomy 2 as the sole abnormality.
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Affiliation(s)
- B Czepulkowski
- Department of Cytogenetics, The Rayne Institute, King's College Hospital, London, UK.
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12
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Vicat JM, Ardila-Osorio H, Khabir A, Brezak MC, Viossat I, Kasprzyk P, Jlidi R, Opolon P, Ooka T, Prevost G, Huang DP, Busson P. Apoptosis and TRAF-1 cleavage in Epstein-Barr virus-positive nasopharyngeal carcinoma cells treated with doxorubicin combined with a farnesyl-transferase inhibitor. Biochem Pharmacol 2003; 65:423-33. [PMID: 12527335 DOI: 10.1016/s0006-2952(02)01449-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Epstein-Barr virus (EBV)-associated nasopharyngeal carcinomas (NPC) are much more sensitive to chemotherapy than other head and neck carcinomas. Spectacular regressions are frequently observed after induction chemotherapy. However, these favorable responses are difficult to predict and often of short duration. So far there have been only few experiments to investigate the mechanisms which underline the cytotoxic effects of anti-neoplastic drugs against NPC cells. In addition, these studies were performed almost entirely on EBV-negative cell lines therefore not truly representative of NPC cells. For the first time, we have used two EBV-positive NPC tumor lines derived from a North African (C15) and a Chinese (C666-1) patient as in vitro targets for a panel of anti-neoplastic agents. Doxorubicin, taxol and in a lesser extent cis-platinum efficiently inhibited NPC cell proliferation at clinically relevant concentrations, but all three agents failed to induce apoptosis. However, massive apoptosis of C15 cells was achieved when doxorubicin (1 microM) was combined with a farnesyl-transferase inhibitor, BIM 2001 (5 microM). Moreover, this apoptotic process was associated with a caspase-dependent early cleavage of the TNF-receptor associated factor 1 (TRAF-1) molecule, a signaling adaptor which is specifically expressed in latently EBV-infected cells. TRAF-1 cleavage might become a useful indicator of chemo-induced apoptosis in EBV-associated NPCs.
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Affiliation(s)
- Jean Michel Vicat
- UMR 1598, Institut Gustave Roussy, 39 rue Camille Desmoulins, 94805 Villejuif, France
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13
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Wong N, Hui ABY, Fan B, Lo KW, Pang E, Leung SF, Huang DP, Johnson PJ. Molecular cytogenetic characterization of nasopharyngeal carcinoma cell lines and xenografts by comparative genomic hybridization and spectral karyotyping. CANCER GENETICS AND CYTOGENETICS 2003; 140:124-32. [PMID: 12645650 DOI: 10.1016/s0165-4608(02)00657-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Nasopharyngeal carcinoma (NPC) cell lines and xenografts represent valuable models for functional and therapeutic studies on this common malignancy in Southeast Asia. The karyotypic information in most NPC cell lines and xenografts, however, remains largely unclear to date. We have characterized the chromosomal aberrations in six commonly used human NPC cell lines and xenografts using the molecular cytogenetic technique of comparative genomic hybridization (CGH). Genomic imbalances identified in cell lines were further correlated with structural abnormalities indicated from spectral karyotyping (SKY) analysis. CGH revealed consistent overrepresentations of 8q (six out of six cases) with a smallest overlapping region identified on 8q21.1 approximately q22. Other common gains included 7p (4/6 cases), 7q (4/6 cases), 12q (4/6), and 20q (4/6 cases), where minimal overlapping regions were suggested on 7p15 approximately p14, 7q11.2 approximately q21, and 12q22 approximately q24.1. Common losses were detected on 3p12 approximately p21 (4/6 cases) and 11q14 approximately qter (4/6 cases). Although SKY analysis on cell lines revealed predominantly unbalanced rearrangements, reciprocal translocations that involved chromosome 2 [i.e., t(1;2), t(2;3), and t(2;4)] were suggested. Furthermore, SKY examination illustrated additional breakpoints on a number of apparently balanced chromosomes. These breakpoints included 3p21, 3q26, 5q31, 6p21.1 approximately p25, 7p14 approximately p22, and 8q22. Our finding of regional gains and losses and breakpoints represents information that may contribute to NPC studies in vitro.
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Affiliation(s)
- Nathalie Wong
- Department of Clinical Oncology, Sir Y. K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, N.T., Hong Kong, China.
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14
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Cheng Y, Stanbridge EJ, Kong H, Bengtsson U, Lerman MI, Lung ML. A functional investigation of tumor suppressor gene activities in a nasopharyngeal carcinoma cell line HONE1 using a monochromosome transfer approach. Genes Chromosomes Cancer 2000; 28:82-91. [PMID: 10738306 DOI: 10.1002/(sici)1098-2264(200005)28:1<82::aid-gcc10>3.0.co;2-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Monochromosome transfers of selected chromosomes into a nasopharyngeal carcinoma (NPC) cell line were performed to determine if tumor suppressing activity for NPC mapped to chromosomes 9, 11, and 17. Current information from cytogenetic and molecular allelotyping studies indicate that these chromosomes may harbor potential tumor suppressor genes vital to NPC. The present results show the importance of CDKN2A on chromosome 9 in NPC development. There was no functional suppression of tumor development in nude mice with microcell hybrids harboring the newly transferred chromosome 9 containing an interstitial deletion at 9p21, whereas transfection of CDKN2A into the NPC HONE1 cells resulted in obvious growth suppression. Whereas intact chromosome 17 transfers into HONE1 cells showed no functional suppression of tumor formation, chromosome 11 was able to do so. Molecular analysis of chromosome 11 tumor segregants indicated that at least two tumor suppressive regions mapping to 11q13 and 11q22-23 may be critical for the development of NPC.
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MESH Headings
- Animals
- Chromosomes, Human, Pair 11/genetics
- Chromosomes, Human, Pair 17/genetics
- Chromosomes, Human, Pair 9/genetics
- Cyclin-Dependent Kinase Inhibitor p16/genetics
- Female
- Gene Transfer Techniques
- Genes, Tumor Suppressor/genetics
- Humans
- Mice
- Mice, Inbred BALB C
- Mice, Nude
- Nasopharyngeal Neoplasms/genetics
- Transfection
- Tumor Cells, Cultured
- Tumor Stem Cell Assay
- Tumor Suppressor Protein p53/biosynthesis
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Y Cheng
- Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong, China
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15
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Fan CS, Wong N, Leung SF, To KF, Lo KW, Lee SW, Mok TS, Johnson PJ, Huang DP. Frequent c-myc and Int-2 overrepresentations in nasopharyngeal carcinoma. Hum Pathol 2000; 31:169-78. [PMID: 10685630 DOI: 10.1016/s0046-8177(00)80216-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a commonly occurring tumor in southern China. Although several causative factors have now been recognized, the genetic basis underlying its tumorigenesis is still unclear. To identify potential chromosomal aberrations for further investigations, comparative genomic hybridization (CGH) analysis was applied to the study of genomic imbalances in 10 NPC biopsy specimens. Before CGH analysis, the tumor cell content within the biopsy specimens was enriched by tissue microdissection, and universal genome amplification was performed on the recovered DNA. Recurrent chromosomal gains were detected on 1q (6 of 10 cases), 2q (5 of 10 cases), 3q (7 of 10 cases), 6p (8 of 10 cases), 6q (5 of 10 cases), 7q11.2 (4 of 10 cases), 8q (6 of 10 cases), 11q13, 12, and 15q (8 of 10 cases each), 17q (6 of 10 cases), and 20q (5 of 10 cases). Common losses were identified on 3p (5 of 10 cases), 9p (5 of 10 cases), 11q14-qter (8 of 10 cases), and 14q (5 of 10 cases). Among these aberrations, 7, 8, and 11 gains were further investigated on a series of NPC tissue samples, by interphase fluorescent in situ hybridization (FISH), for the incidence of alpha-satellites: 7, 8, and 11 c-myc and Int-2. Low-level increases of alpha-satellite 7 (9 of 34 cases; 26.5%), alpha-satellite 8 (15 of 34 cases; 44%), and alpha-satellite 11 (8 of 32 cases; 25%) were detected, whereas high-level copy gains of c-myc (21 of 34 cases; 62%) and Int-2 (26 of 34 cases; 76.5%) were more frequently found. Our series is the first to identify genomic overrepresentations of c-myc and Int-2 in NPC. The high incidence of Int-2 amplifications strongly suggests a role of this proto-oncogene in the pathogenesis of NPC.
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Affiliation(s)
- C S Fan
- Department of Clinical Oncology at the Sir Y.K. Pao Centre for Cancer, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, NT, SAR
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16
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Tsang YS, Lo KW, Leung SF, Choi PH, Fong Y, Lee JC, Huang DP. Two distinct regions of deletion on chromosome 13q in primary nasopharyngeal carcinoma. Int J Cancer 1999; 83:305-8. [PMID: 10495420 DOI: 10.1002/(sici)1097-0215(19991029)83:3<305::aid-ijc3>3.0.co;2-d] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is rare in most parts of the world, but prevalent in Southern China. Although this disease poses a serious health problem in our population, the genetic alterations that lead to the development of NPC have yet to be defined. In a comparative genomic hybridization (CGH) study on NPC by our group, loss of the long arm of chromosome 13 has been identified as a frequent event. To investigate further the involvement of this genetic alteration in NPC tumorigenesis, we examined 31 primary NPC tumours by LOH analysis with a panel of 13 microsatellite polymorphic markers distributed along the long arm of chromosome 13. It was found that 19/31 tumours (60%) showed LOH for markers on chromosome 13q. The highest frequency of LOH was found at loci D13S133 (53.6%) on 13q14.3 and D13S796 (38.5%) on 13q32-34. Two distinct smallest deletion regions were delineated: the first region between D13S133 and D13S119 at 13q14.3-22, and the second region between D13S317 and D13S285 at 13q31-34. Our findings show that LOH of 13q is a common event in NPC and that at least 2 putative tumour-suppressor loci may be present on 13q. Mapping of the critical regions of these loci suggests that some candidate tumour-suppressor genes on 13q, other than Rb and BRCA2, may be involved in the development of NPC.
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Affiliation(s)
- Y S Tsang
- Department of Anatomical Pathology, The Chinese University of Hong Kong, Hong Kong SAR, China
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17
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Hui AB, Lo KW, Leung SF, Teo P, Fung MK, To KF, Wong N, Choi PH, Lee JC, Huang DP. Detection of recurrent chromosomal gains and losses in primary nasopharyngeal carcinoma by comparative genomic hybridisation. Int J Cancer 1999; 82:498-503. [PMID: 10404061 DOI: 10.1002/(sici)1097-0215(19990812)82:4<498::aid-ijc5>3.0.co;2-s] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a common cancer in Southern China but rare in Western countries. To search for genetic alterations in NPC, we examined a series of 20 primary tumours with comparative genomic hybridisation. The identified common chromosomal alterations included gain of chromosomes 1q, 8, 12, 19 and 20 as well as loss of chromosomes 1p, 3p, 9p, 9q, 11q, 13q, 14q and 16q. In concordance with our previous loss of heterozygosity studies in primary NPC, a high incidence of loss was detected on chromosomes 3p (75%), 11q (70%) and 14q (65%). Losses of 9q (60%), 13q (50%) and 16q (40%) were also identified. Novel chromosomal gains were observed on chromosome 12, with a high frequency (70%). Current analysis has revealed a comprehensive profile of the chromosomal regions showing losses and gains in primary NPC. Our findings may provide an entry point for conducting further investigations to locate the putative tumour-suppresser genes and oncogenes that may be involved in the tumourigenesis of NPC.
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Affiliation(s)
- A B Hui
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, the Chinese University of Hong Kong, Shatin, Hong Kong, People's Republic of China
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18
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Liao SK, Perng YP, Shen YC, Chung PJ, Chang YS, Wang CH. Chromosomal abnormalities of a new nasopharyngeal carcinoma cell line (NPC-BM1) derived from a bone marrow metastatic lesion. CANCER GENETICS AND CYTOGENETICS 1998; 103:52-8. [PMID: 9595045 DOI: 10.1016/s0165-4608(97)00416-0] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An epithelial cell line, NPC-BM1, was established from a bone marrow biopsy of a female Taiwanese patient with nasopharyngeal carcinoma (NPC). Histopathology of the bone marrow biopsy and xenografts grown in severe combined immunodeficiency mice showed that the tumor was a nonkeratinizing, poorly differentiated carcinoma. NPC-BM1 cells grown as monolayers had a doubling time of 28.5 hours. Chromosome analysis showed that NPC-BM1 had the following features: 1) hypotetraploidy with a modal chromosome number of 87 (84-90); 2) numerically and structurally normal chromosomes 18; 3) numerical abnormalities without apparent structural alterations on chromosomes 14, 16, 17, 19, and 20; 4) ten structural abnormalities, t(1;9)(p11;q11), t(3;?;4)(p13;?;q13), add(4p),del(6p), i(8) [corrected] (q10),der(?)t(?;12),(?;p12),[corrected] add(21)(p11), del(X)(q24), add(X)(q22), and marker 1 (M1), in all metaphases examined, which were found to be present in two to five cell lines from primary NPC tumors reported previously; and 5) four other abnormalities, t(2;?;2)(p11.2;?;q21),t(11;22)(q11;q11),i(22)(q10), and marker 2 (M2), unique to this metastatic cell line. To the best of our knowledge, NPC-BM1 is the first NPC cell line derived from a distant metastatic site. Further evaluation of this cell line and additional metastatic NPC cell lines as well as primary NPC cell lines with respect to relations between the timing, karyotypic anomalies, and immunobiological characteristics in NPC progression and metastasis is warranted.
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Affiliation(s)
- S K Liao
- Graduate Institute of Clinical Medicine, College of Medicine, Chang Gung University, Taoyuan, Taiwan, Republic of China
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19
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Hui AB, Cheung ST, Fong Y, Lo KW, Huang DP. Characterization of a new EBV-associated nasopharyngeal carcinoma cell line. CANCER GENETICS AND CYTOGENETICS 1998; 101:83-8. [PMID: 9494607 DOI: 10.1016/s0165-4608(97)00231-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Only a few reports exist of cytogenetic studies in nasopharyngeal carcinoma (NPC), probably because of the technical limitations of culturing solid tumors. We established a cell line (cell-666) that was derived from an NPC xenograft growing in athymic nude mice. Epstein-Barr virus (EBV) infection is one of the important etiologic factors of NPC. This cell line has been shown to have the consistent presence of EBV by Epstein-Barr virus encoded RNAs (EBER) in situ hybridization. Furthermore, aberrant methylation of 5'CpG island of p16 gene was detected. Thus, this cell line represents a valuable model for the study of NPC tumorigenecity. The karyotype of this newly established cell line is: 45,X,del(X)(q24),-5der(5)(5pter-->5q31::5q13-->+ ++5q31::5p12-->5pter),der(6;?) (q10;p10),add(7)(p22), + 9, del(11)(q13),add(12)(p13),-14,-18,-21, + 2mar. Fluorescence in situ hybridization analyses were performed using whole chromosome painting probes of chromosomes 5, 6, 11, and 12.
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Affiliation(s)
- A B Hui
- Department of Anatomical and Cellular Pathology, Prince of Wales Hospital, Chinese University of Hong Kong, Shatin, N.T., People's Republic of China
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