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Shou J, Zhang C, Zheng X, Li Y, Wu P, Chen L, Wei X. LncRNA HCP5 Facilitates the Progression of Ovarian Cancer by Interacting with the PTBP1 Protein. Biochem Genet 2024; 62:3136-3154. [PMID: 38071681 PMCID: PMC11289333 DOI: 10.1007/s10528-023-10558-8] [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: 07/14/2023] [Accepted: 10/22/2023] [Indexed: 07/31/2024]
Abstract
Ovarian cancer (OC) is a major gynecological malignancy with an annually increasing morbidity that poses a significant threat to the health of women worldwide. Most OC patients are diagnosed at an advanced stage. It is an urgent task to search for biomarkers for the diagnosis and treatment of OC. The lncRNA HCP5 (HCP5) was recently identified as an oncogene in several malignant tumors. However, the function of HCP5 in OC has rarely been reported. Herein, the levels of HCP5 and PTBP1 were found to be markedly increased in malignant OC tumor tissues and OC cell lines. In HCP5-silenced SKOV-3 and HEY cells, cell viability was markedly decreased, and the apoptosis rate was significantly increased, with more cells exhibiting G0/G1 arrest and increased expression of cleaved caspase-3 and cleaved caspase-9. Furthermore, the number of migrated cells, number of invaded cells, and migration distance were notably decreased by the knockdown of HCP5 in SKOV-3 cells and HEY cells. In the xenograft model established with SKOV-3 cells, the number of lung metastases, tumor growth, and Ki67 expression in tumor tissues were markedly decreased by the knockdown of HCP5, accompanied by an increased percentage of TUNEL-positive cells. HCP5 was found to be localized in the nucleus, and the interaction between HCP5 and PTBP1 was verified by RNA pull-down and RNA immunoprecipitation assays. Furthermore, in HCP5-overexpressing OC cells, the impacts of HCP5 on cell proliferation and apoptosis were significantly attenuated by the knockdown of PTBP1. Collectively, these results indicate that HCP5 facilitates the progression of OC by interacting with the PTBP1 protein.
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Affiliation(s)
- Jian Shou
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China
| | - Chuanling Zhang
- Department of Translational Medicine Laboratory, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China
| | - Xiaoyu Zheng
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China
| | - Yaowei Li
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China
| | - Peng Wu
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China
| | - Long Chen
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China
| | - XiuJun Wei
- Department of Gynecology, Affiliated Xiaoshan Hospital, Hangzhou Normal University, No. 728, North Yucai Road, Beigan Street, Xiaoshan District, Hangzhou, 311200, Zhejiang, China.
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Li S, Dai W, Kam NW, Zhang J, Lee VHF, Ren X, Kwong DLW. The Role of Natural Killer Cells in the Tumor Immune Microenvironment of EBV-Associated Nasopharyngeal Carcinoma. Cancers (Basel) 2024; 16:1312. [PMID: 38610990 PMCID: PMC11011204 DOI: 10.3390/cancers16071312] [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: 02/23/2024] [Revised: 03/23/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
Endemic nasopharyngeal carcinoma (NPC) is closely associated with the Epstein-Barr virus (EBV), which contributes to tumor development and influences the tumor immune microenvironment (TIME) in NPC. Natural killer (NK) cells, as part of the innate immune system, play a crucial role in responding to viral infections and malignant cell transformations. Notably, NK cells possess a unique ability to target tumor cells independent of major histocompatibility complex class I (MHC I) expression. This means that MHC I-deficient tumor cells, which can escape from effective T cell attack, are susceptible to NK-cell-mediated killing. The activation of NK cells is determined by the signals generated through inhibitory and activating receptors expressed on their surface. Understanding the role of NK cells in the complex TIME of EBV+ NPC is of utmost importance. In this review, we provide a comprehensive summary of the current understanding of NK cells in NPC, focusing on their subpopulations, interactions, and cytotoxicity within the TIME. Moreover, we discuss the potential translational therapeutic applications of NK cells in NPC. This review aims to enhance our knowledge of the role of NK cells in NPC and provide valuable insights for future investigations.
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Affiliation(s)
- Shuzhan Li
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China; (S.L.); (J.Z.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Wei Dai
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (W.D.); (N.-W.K.); (V.H.F.L.)
| | - Ngar-Woon Kam
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (W.D.); (N.-W.K.); (V.H.F.L.)
- Laboratory for Synthetic Chemistry and Chemical Biology Limited, Hong Kong Science Park, New Territories, Hong Kong 999077, China
| | - Jiali Zhang
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China; (S.L.); (J.Z.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Victor H. F. Lee
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (W.D.); (N.-W.K.); (V.H.F.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
| | - Xiubao Ren
- Department of Biotherapy, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Tianjin 300060, China; (S.L.); (J.Z.)
- Tianjin’s Clinical Research Center for Cancer, Tianjin 300060, China
- Key Laboratory of Cancer Immunology and Biotherapy, Tianjin 300060, China
| | - Dora Lai-Wan Kwong
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China; (W.D.); (N.-W.K.); (V.H.F.L.)
- Clinical Oncology Center, The University of Hong Kong-Shenzhen Hospital, Shenzhen 518053, China
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3
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Klussmeier A, Putke K, Klasberg S, Kohler M, Sauter J, Schefzyk D, Schöfl G, Massalski C, Schäfer G, Schmidt AH, Roers A, Lange V. High population frequencies of MICA copy number variations originate from independent recombination events. Front Immunol 2023; 14:1297589. [PMID: 38035108 PMCID: PMC10684724 DOI: 10.3389/fimmu.2023.1297589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 10/24/2023] [Indexed: 12/02/2023] Open
Abstract
MICA is a stress-induced ligand of the NKG2D receptor that stimulates NK and T cell responses and was identified as a key determinant of anti-tumor immunity. The MICA gene is located inside the MHC complex and is in strong linkage disequilibrium with HLA-B. While an HLA-B*48-linked MICA deletion-haplotype was previously described in Asian populations, little is known about other MICA copy number variations. Here, we report the genotyping of more than two million individuals revealing high frequencies of MICA duplications (1%) and MICA deletions (0.4%). Their prevalence differs between ethnic groups and can rise to 2.8% (Croatia) and 9.2% (Mexico), respectively. Targeted sequencing of more than 70 samples indicates that these copy number variations originate from independent nonallelic homologous recombination events between segmental duplications upstream of MICA and MICB. Overall, our data warrant further investigation of disease associations and consideration of MICA copy number data in oncological study protocols.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Axel Roers
- Institute for Immunology, Medical Faculty Carl Gustav Carus, University of Technology (TU) Dresden, Dresden, Germany
- Institute for Immunology, University Hospital Heidelberg, Heidelberg, Germany
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4
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Qiao JL, Levinson RT, Chen B, Engelter ST, Erhart P, Gaynor BJ, McArdle PF, Schlicht K, Krawczak M, Stenman M, Lindgren AG, Cole JW, Grond-Ginsbach C. A novel scatterplot-based method to detect copy number variation (CNV). Front Genet 2023; 14:1166972. [PMID: 37485343 PMCID: PMC10359988 DOI: 10.3389/fgene.2023.1166972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 06/23/2023] [Indexed: 07/25/2023] Open
Abstract
Objective: Most methods to detect copy number variation (CNV) have high false positive rates, especially for small CNVs and in real-life samples from clinical studies. In this study, we explored a novel scatterplot-based method to detect CNVs in microarray samples. Methods: Illumina SNP microarray data from 13,254 individuals were analyzed with scatterplots and by PennCNV. The data were analyzed without the prior exclusion of low-quality samples. For CNV scatterplot visualization, the median signal intensity of all SNPs located within a CNV region was plotted against the median signal intensity of the flanking genomic region. Since CNV causes loss or gain of signal intensities, carriers of different CNV alleles pop up in clusters. Moreover, SNPs within a deletion are not heterozygous, whereas heterozygous SNPs within a duplication show typical 1:2 signal distribution between the alleles. Scatterplot-based CNV calls were compared with standard results of PennCNV analysis. All discordant calls as well as a random selection of 100 concordant calls were individually analyzed by visual inspection after noise-reduction. Results: An algorithm for the automated scatterplot visualization of CNVs was developed and used to analyze six known CNV regions. Use of scatterplots and PennCNV yielded 1019 concordant and 108 discordant CNV calls. All concordant calls were evaluated as true CNV-findings. Among the 108 discordant calls, 7 were false positive findings by the scatterplot method, 80 were PennCNV false positives, and 21 were true CNVs detected by the scatterplot method, but missed by PennCNV (i.e., false negative findings). Conclusion: CNV visualization by scatterplots allows for a reliable and rapid detection of CNVs in large studies. This novel method may thus be used both to confirm the results of genome-wide CNV detection software and to identify known CNVs in hitherto untyped samples.
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Affiliation(s)
- Jia-Lu Qiao
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Rebecca T. Levinson
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University Hospital, Heidelberg, Germany
- Department of General Internal Medicine and Psychosomatics, University Hospital Heidelberg, Heidelberg, Germany
| | - Bowang Chen
- National Center for Cardiovascular Diseases, Beijing, China
| | - Stefan T. Engelter
- Neurorehabilitation Unit, University of Basel and University Center for Medicine of Aging Felix Platter Hospital, Basel, Switzerland
| | - Philipp Erhart
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Brady J. Gaynor
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Patrick F. McArdle
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Kristina Schlicht
- Institute of Diabetes and Clinical Metabolic Research, University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Michael Krawczak
- Institute of Medical Informatics and Statistics, Kiel University Medical Center Schleswig-Holstein, Kiel, Germany
| | - Martin Stenman
- Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
- Department of Neurology, Lund University, Skåne University Hospital, Lund, Sweden
| | - Arne G. Lindgren
- Department of Clinical Sciences Lund, Lund University, Skåne University Hospital, Lund, Sweden
| | - John W. Cole
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD, United States
- Veterans Affairs Maryland Healthcare System, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Caspar Grond-Ginsbach
- Department of Vascular and Endovascular Surgery, University Hospital Heidelberg, Heidelberg, Germany
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5
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Association of Inherited Copy Number Variation in ADAM3A and ADAM5 Pseudogenes with Oropharynx Cancer Risk and Outcome. Genes (Basel) 2022; 13:genes13122408. [PMID: 36553675 PMCID: PMC9778539 DOI: 10.3390/genes13122408] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/01/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Inherited copy number variations (CNVs) can provide valuable information for cancer susceptibility and prognosis. However, their association with oropharynx squamous cell carcinoma (OPSCC) is still poorly studied. Using microarrays analysis, we identified three inherited CNVs associated with OPSCC risk, of which one was validated in 152 OPSCC patients and 155 controls and related to pseudogene-microRNA-mRNA interaction. Individuals with three or more copies of ADAM3A and ADAM5 pseudogenes (8p11.22 chromosome region) were under 6.49-fold increased risk of OPSCC. ADAM5 shared a highly homologous sequence with the ADAM9 3'-UTR, predicted to be a binding site for miR-122b-5p. Individuals carrying more than three copies of ADAM3A and ADAM5 presented higher ADAM9 expression levels. Moreover, patients with total deletion or one copy of pseudogenes and with higher expression of miR-122b-5p presented worse prognoses. Our data suggest, for the first time, that ADAM3A and ADAM5 pseudogene-inherited CNV could modulate OPSCC occurrence and prognosis, possibly through the interaction of ADAM5 pseudogene transcript, miR-122b-5p, and ADAM9.
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Wang K, Cadzow M, Bixley M, Leask MP, Merriman ME, Yang Q, Li Z, Takei R, Phipps-Green A, Major TJ, Topless R, Dalbeth N, King F, Murphy R, Stamp LK, Zoysa J, Wang Z, Shi Y, Merriman TR. A Polynesian-specific copy number variant encompassing the MHC Class I Polypeptide-related Sequence A (MICA) gene associates with gout. Hum Mol Genet 2022; 31:3757-3768. [PMID: 35451026 PMCID: PMC9616569 DOI: 10.1093/hmg/ddac094] [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: 01/16/2022] [Revised: 04/01/2022] [Accepted: 04/19/2022] [Indexed: 12/04/2022] Open
Abstract
Gout is of particularly high prevalence in the Māori and Pacific (Polynesian) populations of Aotearoa New Zealand (NZ). Here, we investigated the contribution of common population-specific copy number variation (CNV) to gout in the Aotearoa NZ Polynesian population. Microarray-generated genome-wide genotype data from Aotearoa NZ Polynesian individuals with (n = 1196) and without (n = 1249) gout were analyzed. Comparator population groups were 552 individuals of European ancestry and 1962 of Han Chinese ancestry. Levels of circulating major histocompatibility complex (MHC) class I polypeptide-related sequence A (MICA) were measured by enzyme-linked immunosorbent assay. Fifty-four CNV regions (CNVRs) appearing in at least 10 individuals were detected, of which seven common (>2%) CNVRs were specific to or amplified in Polynesian people. A burden test of these seven revealed associations of insertion/deletion with gout (odds ratio (OR) 95% confidence interval [CI] = 1.80 [1.01; 3.22], P = 0.046). Individually testing of the seven CNVRs for association with gout revealed nominal association of CNVR1 with gout in Western Polynesian (Chr6: 31.36–31.45 Mb, OR = 1.72 [1.03; 2.92], P = 0.04), CNVR6 in the meta-analyzed Polynesian sample sets (Chr1: 196.75–196.92 Mb, OR = 1.86 [1.16; 3.00], P = 0.01) and CNVR9 in Western Polynesian (Chr1: 189.35–189.54 Mb, OR = 2.75 [1.15; 7.13], P = 0.03). Analysis of European gout genetic association data demonstrated a signal of association at the CNVR1 locus that was an expression quantitative trait locus for MICA. The most common CNVR (CNVR1) includes deletion of the MICA gene, encoding an immunomodulatory protein. Expression of MICA was reduced in the serum of individuals with the deletion. In summary, we provide evidence for the association of CNVR1 containing MICA with gout in Polynesian people, implicating class I MHC-mediated antigen presentation in gout.
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Affiliation(s)
- Ke Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China.,Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Murray Cadzow
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Matt Bixley
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Megan P Leask
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Qiangzhen Yang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Zhiqiang Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China.,Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Riku Takei
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States
| | | | - Tanya J Major
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Ruth Topless
- Department of Biochemistry, University of Otago, Dunedin, New Zealand
| | - Nicola Dalbeth
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Frances King
- Ngati Porou Hauora Charitable Trust, Te Puia Springs, New Zealand
| | - Rinki Murphy
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Lisa K Stamp
- Department of Medicine, University of Otago, Christchurch, New Zealand
| | - Janak Zoysa
- Department of Medicine, University of Auckland, Auckland, New Zealand
| | - Zhuo Wang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China
| | - Yongyong Shi
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Collaborative Innovation Center for Brain Science, Shanghai Jiao Tong University, Shanghai 200030, People's Republic of China.,Biomedical Sciences Institute of Qingdao University (Qingdao Branch of SJTU Bio-X Institutes), Qingdao University, Qingdao, 266003, China
| | - Tony R Merriman
- Department of Biochemistry, University of Otago, Dunedin, New Zealand.,Division of Clinical Immunology and Rheumatology, University of Alabama at Birmingham, Birmingham, Alabama, United States
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Lo Faro V, Ten Brink JB, Snieder H, Jansonius NM, Bergen AA. Genome-wide CNV investigation suggests a role for cadherin, Wnt, and p53 pathways in primary open-angle glaucoma. BMC Genomics 2021; 22:590. [PMID: 34348663 PMCID: PMC8336345 DOI: 10.1186/s12864-021-07846-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/18/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND To investigate whether copy number variations (CNVs) are implicated in molecular mechanisms underlying primary open-angle glaucoma (POAG), we used genotype data of POAG individuals and healthy controls from two case-control studies, AGS (n = 278) and GLGS-UGLI (n = 1292). PennCNV, QuantiSNP, and cnvPartition programs were used to detect CNV. Stringent quality controls at both sample and marker levels were applied. The identified CNVs were intersected in CNV region (CNVR). After, we performed burden analysis, CNV-genome-wide association analysis, gene set overrepresentation and pathway analysis. In addition, in human eye tissues we assessed the expression of the genes lying within significant CNVRs. RESULTS We reported a statistically significant greater burden of CNVs in POAG cases compared to controls (p-value = 0,007). In common between the two cohorts, CNV-association analysis identified statistically significant CNVRs associated with POAG that span 11 genes (APC, BRCA2, COL3A1, HLA-DRB1, HLA-DRB5, HLA-DRB6, MFSD8, NIPBL, SCN1A, SDHB, and ZDHHC11). Functional annotation and pathway analysis suggested the involvement of cadherin, Wnt signalling, and p53 pathways. CONCLUSIONS Our data suggest that CNVs may have a role in the susceptibility of POAG and they can reveal more information on the mechanism behind this disease. Additional genetic and functional studies are warranted to ascertain the contribution of CNVs in POAG.
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Affiliation(s)
- Valeria Lo Faro
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands.,Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Jacoline B Ten Brink
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Nomdo M Jansonius
- Department of Ophthalmology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Arthur A Bergen
- Departments of Clinical Genetics and Ophthalmology, Amsterdam University Medical Center (AMC), Location AMC K2-217
- AMC-UvA, P.O.Box 22700, 1100 DE, Amsterdam, The Netherlands. .,Department of Ophthalmology, Amsterdam UMC, Location AMC, Amsterdam, The Netherlands. .,Netherlands Institute for Neuroscience (NIN-KNAW), Amsterdam, The Netherlands.
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8
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Ning L, Ko JMY, Yu VZ, Ng HY, Chan CKC, Tao L, Lam SY, Leong MML, Ngan RKC, Kwong DLW, Lee AWM, Ng WT, Cheng A, Tung S, Lee VHF, Lam KO, Kwan CK, Li WS, Yau S, Bei JX, Lung ML. Nasopharyngeal carcinoma MHC region deep sequencing identifies HLA and novel non-HLA TRIM31 and TRIM39 loci. Commun Biol 2020; 3:759. [PMID: 33311639 PMCID: PMC7733486 DOI: 10.1038/s42003-020-01487-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/14/2020] [Indexed: 12/13/2022] Open
Abstract
Despite pronounced associations of major histocompatibility complex (MHC) regions with nasopharyngeal carcinoma (NPC), causal variants underlying NPC pathogenesis remain elusive. Our large-scale comprehensive MHC region deep sequencing study of 5689 Hong Kong Chinese identifies eight independent NPC-associated signals and provides mechanistic insight for disrupted transcription factor binding, altering target gene transcription. Two novel protective variants, rs2517664 (Trs2517664 = 4.6%, P = 6.38 × 10−21) and rs117495548 (Grs117495548 = 3.0%, P = 4.53 × 10−13), map near TRIM31 and TRIM39/TRIM39-RPP21; multiple independent protective signals map near HLA-B including a previously unreported variant, rs2523589 (P = 1.77 × 10−36). The rare HLA-B*07:05 allele (OR < 0.015, P = 5.83 × 10−21) is absent in NPC, but present in controls. The most prevalent haplotype lacks seven independent protective alleles (OR = 1.56) and the one with additional Asian-specific susceptibility rs9391681 allele (OR = 2.66) significantly increased NPC risk. Importantly, this study provides new evidence implicating two non-human leukocyte antigen (HLA) genes, E3 ubiquitin ligases, TRIM31 and TRIM39, impacting innate immune responses, with NPC risk reduction, independent of classical HLA class I/II alleles. Here the authors report a major histocompatibility complex (MHC) association analysis for nasopharyngeal carcinoma in Chinese individuals from Hong Kong, finding 8 independent associated loci associated with lower risk for developing nasopharyngeal carcinoma. Two non-human leukocyte antigen (HLA) genes are E3 ubiquitin ligases, TRIM31 and TRIM39, having a role in the innate immune response and implicating the importance of host Epstein-Barr virus interactions in this cancer.
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Affiliation(s)
- Lvwen Ning
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Josephine Mun-Yee Ko
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.
| | - Valen Zhuoyou Yu
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Hoi Yan Ng
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Candy King-Chi Chan
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Lihua Tao
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Shiu-Yeung Lam
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Merrin Man-Long Leong
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Roger Kai-Cheong Ngan
- Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Dora Lai-Wan Kwong
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Anne Wing-Mui Lee
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Wai-Tong Ng
- Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Department of Clinical Oncology, Pamela Youde Nethersole Eastern Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Ashley Cheng
- Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Department of Oncology, Princess Margaret Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Stewart Tung
- Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Department of Clinical Oncology, Tuen Mun Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Victor Ho-Fun Lee
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Ka-On Lam
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.,Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China
| | - Chung-Kong Kwan
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Wing-Sum Li
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Stephen Yau
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong (Special Administrative Region), People's Republic of China
| | - Jin-Xin Bei
- Sun Yat-sen University Cancer Centre, State Key Laboratory of Oncology in South China, Collaborative Innovation Centre for Cancer Medicine, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, 510060, Guangzhou, People's Republic of China
| | - Maria Li Lung
- Department of Clinical Oncology, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China. .,Center for Nasopharyngeal Carcinoma Research, University of Hong Kong, Hong Kong (Special Administrative Region), People's Republic of China.
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9
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Lopes-Ramos CM, Quackenbush J, DeMeo DL. Genome-Wide Sex and Gender Differences in Cancer. Front Oncol 2020; 10:597788. [PMID: 33330090 PMCID: PMC7719817 DOI: 10.3389/fonc.2020.597788] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Despite their known importance in clinical medicine, differences based on sex and gender are among the least studied factors affecting cancer susceptibility, progression, survival, and therapeutic response. In particular, the molecular mechanisms driving sex differences are poorly understood and so most approaches to precision medicine use mutational or other genomic data to assign therapy without considering how the sex of the individual might influence therapeutic efficacy. The mandate by the National Institutes of Health that research studies include sex as a biological variable has begun to expand our understanding on its importance. Sex differences in cancer may arise due to a combination of environmental, genetic, and epigenetic factors, as well as differences in gene regulation, and expression. Extensive sex differences occur genome-wide, and ultimately influence cancer biology and outcomes. In this review, we summarize the current state of knowledge about sex-specific genetic and genome-wide influences in cancer, describe how differences in response to environmental exposures and genetic and epigenetic alterations alter the trajectory of the disease, and provide insights into the importance of integrative analyses in understanding the interplay of sex and genomics in cancer. In particular, we will explore some of the emerging analytical approaches, such as the use of network methods, that are providing a deeper understanding of the drivers of differences based on sex and gender. Better understanding these complex factors and their interactions will improve cancer prevention, treatment, and outcomes for all individuals.
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Affiliation(s)
- Camila M Lopes-Ramos
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, United States.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States
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10
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Abstract
Sex is a key biological factor affecting the development of many cancer types. There are considerable differences between male and female subpopulations in terms of cancer incidence, prognosis and mortality. Recent studies have extensively characterized the sex-biased molecular changes in cancer patients. Further efforts should be made to develop sex-specific cancer prevention and therapeutic strategies.
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11
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CT Evaluation of Squamous Cell Carcinoma of the Nasopharynx. CURRENT HEALTH SCIENCES JOURNAL 2019; 45:79-86. [PMID: 31297267 PMCID: PMC6592665 DOI: 10.12865/chsj.45.01.11] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 03/10/2019] [Indexed: 12/11/2022]
Abstract
Squamous cell carcinoma is the most common type of neoplasia which affects the mucosa of the upper aero-digestive tract. Nasopharyngeal carcinoma is a unique disease with clinical behavior, epidemiology, and histopathology that is different from that of squamous cell carcinomas of the head and neck. For malignant tumors such as SCC, rapid growth may occur even though there are no previous clinical signs. Enlargement of a cervical lymph node, as the first presenting feature of neoplasia, is not uncommon, particularly with certain “silent” site, such as nasopharynx. Therefore, clinical examination must be complemented by radiological examination for the assessment of size, thickness and depth of the tumor, the degree of bone tissue invasion, and to detect the presence of enlarged lymph nodes. A total of 16 cases of patients were studied using CT, all diagnosed and operated with squamous cancer with localization in the nasopharynx.
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12
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Fan C, Tu C, Qi P, Guo C, Xiang B, Zhou M, Li X, Wu X, Li X, Li G, Xiong W, Zeng Z. GPC6 Promotes Cell Proliferation, Migration, and Invasion in Nasopharyngeal Carcinoma. J Cancer 2019; 10:3926-3932. [PMID: 31417636 PMCID: PMC6692608 DOI: 10.7150/jca.31345] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 05/07/2019] [Indexed: 12/14/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a highly metastatic tumor that occurs frequently in Southeast Asia, particularly including southern China. Epstein-Barr virus infection is well established as a primary cause of NPC; nevertheless, the mechanisms underlying NPC pathogenesis remain largely unknown. In our previous study, we conducted whole-genome sequencing to screen for genomic variations that were associated with NPC. Of the resultantly identified variations, glypican-6 (GPC6), was shown, for the first time, to be frequently mutated in NPC. In the present study, we verified this finding and conducted a series of functional experiments, which demonstrated that GPC6 promotes the migration, invasion, and proliferation of NPC cells in vitro. Thus, the present study identified novel biological functions for GPC6 in NPC, and thus, showed that GPC6 may be a promising potential therapeutic target for this disease.
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Affiliation(s)
- Chunmei Fan
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Chaofeng Tu
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Peng Qi
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Can Guo
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Bo Xiang
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Ming Zhou
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
| | - Xiayu Li
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Xu Wu
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Department of Chemistry, University of North Dakota, Grand Forks, North Dakota, USA
| | - Xiaoling Li
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Guiyuan Li
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Xiong
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhaoyang Zeng
- NHC Key Laboratory of Carcinogenesis (Central South University) and Hunan Key Laboratory of Translational Radiation Oncology, Hunan Cancer Hospital and The Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, Hunan, China
- The Key Laboratory of Carcinogenesis and Cancer Invasion of the Chinese Ministry of Education, Cancer Research Institute and Basic Medical Science, Central South University, Changsha, Hunan, China
- Hunan Key Laboratory of Nonresolving Inflammation and Cancer, Disease Genome Research Center, The Third Xiangya Hospital, Central South University, Changsha, Hunan, China
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13
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Nasopharyngeal cancer in Saudi Arabia: Epidemiology and possible risk factors. JOURNAL OF ONCOLOGICAL SCIENCES 2019. [DOI: 10.1016/j.jons.2019.01.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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14
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Clinical significance of germline copy number variation in susceptibility of human diseases. J Genet Genomics 2018; 45:3-12. [PMID: 29396143 DOI: 10.1016/j.jgg.2018.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 12/27/2017] [Accepted: 01/02/2018] [Indexed: 02/06/2023]
Abstract
Germline copy number variation (CNV) is considered to be an important form of human genetic polymorphisms. Previous studies have identified amounts of CNVs in human genome by advanced technologies, such as comparative genomic hybridization, single nucleotide genotyping, and high-throughput sequencing. CNV is speculated to be derived from multiple mechanisms, such as nonallelic homologous recombination (NAHR) and nonhomologous end-joining (NHEJ). CNVs cover a much larger genome scale than single nucleotide polymorphisms (SNPs), and may alter gene expression levels by means of gene dosage, gene fusion, gene disruption, and long-range regulation effects, thus affecting individual phenotypes and playing crucial roles in human pathogenesis. The number of studies linking CNVs with common complex diseases has increased dramatically in recent years. Here, we provide a comprehensive review of the current understanding of germline CNVs, and summarize the association of germline CNVs with the susceptibility to a wide variety of human diseases that were identified in recent years. We also propose potential issues that should be addressed in future studies.
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15
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Wang W, Tian W, Zhu F, Li L, Cai J, Wang F, Liu K, Jin H, Wang J. MICA Gene Deletion in 3411 DNA Samples from Five Distinct Populations in Mainland China and Lack of Association with Nasopharyngeal Carcinoma (NPC) in a Southern Chinese Han population. Ann Hum Genet 2017; 80:319-326. [PMID: 27870115 DOI: 10.1111/ahg.12175] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 09/23/2016] [Indexed: 12/20/2022]
Abstract
Deletion of major histocompatibility complex class I chain-related genes A (MICA*Del) was investigated in 3,411 DNA samples from two southern Chinese Han populations (Hunan Han, HNH; Guangdong Han, GDH), two northern Chinese populations (Inner Mongolia Han, IMH; Inner Mongolia Mongol, IMM) and one southeastern Chinese Han population (Fujian Han, FJH) using an in-house polymerase chain reaction-sequence specific priming (PCR-SSP) assay, which enables direct discrimination between heterozygote and homozygote for MICA*Del. MICA*Del showed a frequency ranging from 0.8% in FJH to 5.7% in IMM (Pcorrected < 0.05), indicating northward increase in frequency of MICA*Del in Chinese populations. In contrast to the association reported recently in a Taiwan Chinese population and a Malaysian Chinese cohort, MICA*Del distribution did not differ between 1,120 patients with nasopharyngeal carcinoma (NPC) and 1,483 normal controls in the HNH population (1.03% in NPC cases vs 1.18% in the controls, OR (95% CI) = 0.87 (0.51-1.47), p = 0.69). Further gender-stratified analysis also failed to disclose any male-specific association reported in a Taiwan Chinese population. Multi-locus typing of the 94 samples carrying MICA*Del revealed two new haplotypes, HLA-A*11:01-B*13:01-MICA*Del-MICB*009N-DRB1*04:06 and HLA-B*35:01-MICA*Del-MICB*009N-DRB1*15:01, in addition to HLA-B*48-MICA*Del. Unexpectedly, two samples with MICA*Del in the HNH population were each consistently found to have two distinct MICA alleles, indicating the existence of two MICA gene copies on certain HLA haplotypes. Based on the results from a sizeable case-control study, our data suggest that there is no association between MICA*Del and NPC in the southern Chinese Han population.
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Affiliation(s)
- WenYi Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Wei Tian
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - FaMing Zhu
- HLA Typing Laboratory, Blood Center of Zhejiang Province, Hangzhou, Zhejiang, People's Republic of China
| | - LiXin Li
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - JinHong Cai
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Fan Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - KangLong Liu
- Department of Nuclear Medicine, Hunan Cancer Hospital (the affiliated Cancer Hospital of XiangYa School of Medicine of Central South University), Changsha, Hunan, 410006, People's Republic of China
| | - HeKun Jin
- Department of Radiotherapy, Hunan Cancer Hospital (the affiliated Cancer Hospital of XiangYa School of Medicine of Central South University), Changsha, Hunan, 410006, People's Republic of China
| | - JunLong Wang
- Department of Laboratory Medicine, The 5th Hospital of Zhangzhou City, Zhangzhou, Fujian, People's Republic of China
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Wani SQ, Khan T, Wani SY, Mir LR, Lone MM, Malik TR, Najmi AM, Afroz F, Teli MA, Khan NA. Nasopharyngeal Carcinoma: A 15 Year Study with Respect to Clinicodemography and Survival Analysis. Indian J Otolaryngol Head Neck Surg 2016; 68:511-521. [PMID: 27833881 PMCID: PMC5083654 DOI: 10.1007/s12070-016-1018-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 08/31/2016] [Indexed: 11/25/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a rare malignancy in Kashmir with distinct pattern, hence we planned to study its clinicodemographic and survival profile. Kashmir has unique lifestyle and dietary habits which may be the source of carcinogenic compounds, most likely implicated in causation of NPC. A total of 148 patients of NPC registered from January 2000 to December 2014 were analyzed. The Mean ± SD age was 45.15 ± 17.092 years (range 11-85 years). The males were 72.3 % (N = 107) with male: female ratio of 2.61:1. Most of the patients were from rural area 81.90 % (N = 95) and non-smokers were 53.44 % (N = 62). Neck swelling was commonest presentation. WHO Type III NPC was commonest histopathological diagnosis 65.3 % (N = 92). Stage IV 36.1 % (N = 51) was commonest stage followed by stage III was 32 % (N = 46). Majority of the patients of NPC received CCRT 68.7 % (N = 78) followed by SCRT 13 % (N = 15) and Induction + CCRT 13 % (N = 15). The overall mean survival of NPC was 49.56 months. There was no significant correlation of age, gender, smoking, histopathology and treatment on the overall survival. However the stage was the only strong predictor of overall survival. Also the patients with intracranial extension had low survival which is turn depicts the advanced stage of disease. NPC survival is directly related to the stage of the disease irrespective of the treatment modality received. The negative EBV status in our patients implies that there are other risk factors involved in the causation of NPC for which further studies are needed to establish the etiological insult.
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Affiliation(s)
- Shaqul Qamar Wani
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Talib Khan
- Department of Anaesthesiology, Critical Care and Pain, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Saiful Yamin Wani
- Directorate of Health Services Kashmir, Government of Jammu and Kashmir, Srinagar, Jammu and Kashmir 190001 India
| | - Liza Rafiq Mir
- Directorate of Health Services Kashmir, Government of Jammu and Kashmir, Srinagar, Jammu and Kashmir 190001 India
| | - Mohammad Maqbool Lone
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Tariq Rasool Malik
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Arshad Manzoor Najmi
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Fir Afroz
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Mohammad Ashraf Teli
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
| | - Nazir Ahmad Khan
- Department of Radiation Oncology and Regional Cancer Centre, Sher-I- Kashmir Institute of Medical Sciences (SKIMS), Soura, Srinagar, Jammu and Kashmir 190011 India
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17
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Low JSY, Chin YM, Mushiroda T, Kubo M, Govindasamy GK, Pua KC, Yap YY, Yap LF, Subramaniam SK, Ong CA, Tan TY, Khoo ASB, Ng CC. A Genome Wide Study of Copy Number Variation Associated with Nasopharyngeal Carcinoma in Malaysian Chinese Identifies CNVs at 11q14.3 and 6p21.3 as Candidate Loci. PLoS One 2016; 11:e0145774. [PMID: 26730743 PMCID: PMC4701378 DOI: 10.1371/journal.pone.0145774] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 12/08/2015] [Indexed: 11/24/2022] Open
Abstract
Background Nasopharyngeal carcinoma (NPC) is a neoplasm of the epithelial lining of the nasopharynx. Despite various reports linking genomic variants to NPC predisposition, very few reports were done on copy number variations (CNV). CNV is an inherent structural variation that has been found to be involved in cancer predisposition. Methods A discovery cohort of Malaysian Chinese descent (NPC patients, n = 140; Healthy controls, n = 256) were genotyped using Illumina® HumanOmniExpress BeadChip. PennCNV and cnvPartition calling algorithms were applied for CNV calling. Taqman CNV assays and digital PCR were used to validate CNV calls and replicate candidate copy number variant region (CNVR) associations in a follow-up Malaysian Chinese (NPC cases, n = 465; and Healthy controls, n = 677) and Malay cohort (NPC cases, n = 114; Healthy controls, n = 124). Results Six putative CNVRs overlapping GRM5, MICA/HCP5/HCG26, LILRB3/LILRA6, DPY19L2, RNase3/RNase2 and GOLPH3 genes were jointly identified by PennCNV and cnvPartition. CNVs overlapping GRM5 and MICA/HCP5/HCG26 were subjected to further validation by Taqman CNV assays and digital PCR. Combined analysis in Malaysian Chinese cohort revealed a strong association at CNVR on chromosome 11q14.3 (Pcombined = 1.54x10-5; odds ratio (OR) = 7.27; 95% CI = 2.96–17.88) overlapping GRM5 and a suggestive association at CNVR on chromosome 6p21.3 (Pcombined = 1.29x10-3; OR = 4.21; 95% CI = 1.75–10.11) overlapping MICA/HCP5/HCG26 genes. Conclusion Our results demonstrated the association of CNVs towards NPC susceptibility, implicating a possible role of CNVs in NPC development.
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Affiliation(s)
- Joyce Siew Yong Low
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Translational Genomics Lab, High Impact Research Building (Level 2), University of Malaya, Kuala Lumpur, Malaysia
| | - Yoon Ming Chin
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Translational Genomics Lab, High Impact Research Building (Level 2), University of Malaya, Kuala Lumpur, Malaysia
| | - Taisei Mushiroda
- Laboratory for Pharmacogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | | | - Kin Choo Pua
- Department of Otorhinolaryngology, Hospital Pulau Pinang, Penang, Malaysia
| | - Yoke Yeow Yap
- Department of Surgery, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Kuala Lumpur, Malaysia
| | - Lee Fah Yap
- Department of Oral Biology & Biomedical Sciences and Oral Cancer Research & Coordinating Centre, Faculty of Dentistry, University of Malaya, Kuala Lumpur, Malaysia
| | - Selva Kumar Subramaniam
- Department of Otorhinolaryngology, Head and Neck Surgery, Sarawak General Hospital, Sarawak, Malaysia
| | - Cheng Ai Ong
- ENT Department, Hospital Queen Elizabeth, Karung Berkunci No. 2029, Kota Kinabalu, Sabah, Malaysia
| | - Tee Yong Tan
- Department of Otorhinolaryngology, Sarawak General Hospital, Kuching, Sarawak, Malaysia
| | - Alan Soo Beng Khoo
- Molecular Pathology Unit, Cancer Research Centre, Institute for Medical Research, Kuala Lumpur, Malaysia
| | - The Malaysian NPC Study Group
- The Malaysian Nasopharyngeal Carcinoma Study Group: Hospital Pulau Pinang, Hospital Kuala Lumpur/Universiti Putra Malaysia, University of Malaya, Institute for Medical Research, Cancer Research Initiatives Foundation, Sarawak General Hospital/Universiti Malaysia Sarawak, Queen Elizabeth Hospital and Hospital Universiti Sains, Malaysia
| | - Ching Ching Ng
- Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia
- Translational Genomics Lab, High Impact Research Building (Level 2), University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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18
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Yu H, Luo L, Wu L, Zheng M, Zhang L, Liu Y, Li H, Cao Q, Kijlstra A, Yang P. FASGene Copy Numbers are Associated with Susceptibility to Behçet Disease and VKH Syndrome in Han Chinese. Hum Mutat 2015; 36:1064-9. [PMID: 26136352 DOI: 10.1002/humu.22829] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2015] [Accepted: 06/23/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Hongsong Yu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Le Luo
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Lili Wu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Minming Zheng
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Lijun Zhang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Yunjia Liu
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Hua Li
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Qingfeng Cao
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
| | - Aize Kijlstra
- University Eye Clinic Maastricht; Maastricht The Netherlands
| | - Peizeng Yang
- The First Affiliated Hospital of Chongqing Medical University, Chongqing Key Laboratory of Ophthalmology and Chongqing Eye Institute; Chongqing P. R. China
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19
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Li L, Tian W, Wang W, Liu K, Wang J, Jin H, Cai J, Wang J. NKG2C copy number variations in five distinct populations in mainland China and susceptibility to nasopharyngeal carcinoma (NPC). Hum Immunol 2015; 76:90-4. [PMID: 25636564 DOI: 10.1016/j.humimm.2015.01.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2014] [Revised: 10/02/2014] [Accepted: 01/15/2015] [Indexed: 01/10/2023]
Abstract
In this study, copy number variation (CNV) of NKG2C gene was investigated in 1129 normal, unrelated individuals representing two southern Chinese Han populations (Hunan Han and Guangdong Han), two northern Chinese populations (Inner Mongolia Han and Inner Mongolia Mongol) and one southeastern Chinese Han population (Fujian Han) using polymerase chain reaction-sequence-specific priming (PCR-SSP) method. CNV of NKG2C gene did not vary significantly among the five Chinese populations, with NKG2C gene deletion showing a frequency ranging from 0.2031 to 0.2688. Compared with worldwide ethnic groups, very significant difference was observed between the five Chinese populations and the Mexican mestizos (all Pcorrected=0.0025), and between the Fujian Han population and the German population (Pcorrected=0.005). We further examined CNV of NKG2C and HLA-E allelic distribution in 653 patients afflicted with nasopharyngeal carcinoma (NPC) in Hunan province. Neither CNV of NKG2C nor HLA-E was associated with NPC. There was a trend of reduced NPC risk in individuals who were homozygous for both HLA-E(∗)01:03 and NKG2C deletion (0.46% vs. 2.51%, P=0.0076, Pcorrected=0.0684, OR (95% CI)=0.1794 (0.0473-0.6809)). Taken together, our results suggest that NKG2C deletion and HLA-E signalling pathway does not play a major role in determining genetic susceptibility to NPC.
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Affiliation(s)
- LiXin Li
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - Wei Tian
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China.
| | - WenYi Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - KangLong Liu
- Department of Nuclear Medicine, Hunan Cancer Hospital, The Affiliated Cancer Hospital of XiangYa Medical School of Central South University, Changsha, Hunan 410006, People's Republic of China
| | - JunLong Wang
- Department of Laboratory Medicine, The 5th Hospital of Zhangzhou City, Zhangzhou, Fujian, People's Republic of China
| | - HeKun Jin
- Department of Radiotherapy, Hunan Cancer Hospital, The Affiliated Cancer Hospital of XiangYa Medical School of Central South University, Changsha, Hunan 410006, People's Republic of China
| | - JinHong Cai
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China
| | - JunJie Wang
- Immunogenetics Research Group, Department of Immunology, College of Basic Medical Sciences, Central South University, Changsha, Hunan, People's Republic of China; Eight-Year Medical Educational Program, Central South University, School of Medicine, Changsha, Hunan, People's Republic of China
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Asnaghi L, Alkatan H, Mahale A, Othman M, Alwadani S, Al-Hussain H, Jastaneiah S, Yu W, Maktabi A, Edward DP, Eberhart CG. Identification of multiple DNA copy number alterations including frequent 8p11.22 amplification in conjunctival squamous cell carcinoma. Invest Ophthalmol Vis Sci 2014; 55:8604-13. [PMID: 25491297 DOI: 10.1167/iovs.14-14920] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
PURPOSE Little is known about the molecular alterations that drive formation and growth of conjunctival squamous cell carcinoma (cSCC). We therefore sought to identify genetic changes that could be used as diagnostic markers or therapeutic targets. METHODS The DNA extracted from 10 snap-frozen cSCC tumor specimens and 2 in situ carcinomas was analyzed using array-based comparative genomic hybridization (aCGH), and further examined with NanoString and quantitative PCR. RESULTS The number of regions of DNA loss ranged from 1 to 23 per tumor, whereas gains and amplifications ranged from 1 to 15 per tumor. Most large regions of chromosomal gain and loss were confirmed by NanoString karyotype analysis. The commonest alteration was amplification of 8p11.22 in 9 tumors (75%), and quantitative PCR analysis revealed 100-fold or greater overexpression of ADAM3A mRNA from 8p11.22 locus. In addition, recurring losses were observed at 14q13.2 and 22q11.23, both lost in 5 (42%) of the 12 tumors, and at 12p13.31, lost in 4 (33%) of the 12 samples. Of the eight loci associated with the DNA damage repair syndrome xeroderma pigmentosum, three showed loss of at least one allele in our aCGH analysis, including XPA (9q22.33, one tumor), XPE/DDB2 (11p11.2, one tumor) and XPG/ERCC5 (13q33.1, three tumors). CONCLUSIONS Conjunctival SCC contains a range of chromosomal alterations potentially important in tumor formation and growth. Amplification of 8p11.22 and overexpression of ADAM3A suggests a potential role for this protease. Our findings also suggest that defects in DNA repair loci are important in sporadic cSCC.
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Affiliation(s)
- Laura Asnaghi
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
| | - Hind Alkatan
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Alka Mahale
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Maha Othman
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Saeed Alwadani
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, King Saud University, Riyadh, Saudi Arabia
| | | | | | - Wayne Yu
- Microarray Core Facility, Sidney Kimmel Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
| | - Azza Maktabi
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia
| | - Deepak P Edward
- King Khaled Eye Specialist Hospital, Riyadh, Saudi Arabia Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
| | - Charles G Eberhart
- Department of Pathology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Ophthalmology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States Department of Oncology, Johns Hopkins University, School of Medicine, Baltimore, Maryland, United States
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21
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Li XL, Yu H, Wu GS. Investigating the genetic association ofHCP5,SPATA2,TNIP1,TNFAIP3andCOG6with psoriasis in Chinese population. Int J Immunogenet 2014; 41:503-7. [PMID: 25264125 DOI: 10.1111/iji.12150] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/28/2014] [Accepted: 08/11/2014] [Indexed: 02/05/2023]
Affiliation(s)
- X.-L. Li
- Department of Dermatology and Rheumatology; Affiliated Yan'an Hospital of Kunming Medical University; Yunnan China
| | - H. Yu
- College of Life Science; Foshan University; Guangdong China
| | - G.-S. Wu
- State Key Laboratory of Phytochemistry and Plant Resources in West China; Kunming Institute of Botany; Chinese Academy of Sciences; Yunnan China
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22
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Ding X, Tsang SY, Ng SK, Xue H. Application of Machine Learning to Development of Copy Number Variation-based Prediction of Cancer Risk. GENOMICS INSIGHTS 2014. [PMID: 26203258 PMCID: PMC4504076 DOI: 10.4137/gei.s15002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In the present study, recurrent copy number variations (CNVs) from non-tumor blood cell DNAs of Caucasian non-cancer subjects and glioma, myeloma, and colorectal cancer-patients, and Korean non-cancer subjects and hepatocellular carcinoma, gastric cancer, and colorectal cancer patients, were found to reveal for each of the two ethnic cohorts highly significant differences between cancer patients and controls with respect to the number of CN-losses and size-distribution of CN-gains, suggesting the existence of recurrent constitutional CNV-features useful for prediction of predisposition to cancer. Upon identification by machine learning, such CNV-features could extensively discriminate between cancer-patient and control DNAs. When the CNV-features selected from a learning-group of Caucasian or Korean mixed DNAs consisting of both cancer-patient and control DNAs were employed to make predictions on the cancer predisposition of an unseen test group of mixed DNAs, the average prediction accuracy was 93.6% for the Caucasian cohort and 86.5% for the Korean cohort.
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Affiliation(s)
- Xiaofan Ding
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Shui-Ying Tsang
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Siu-Kin Ng
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
| | - Hong Xue
- Applied Genomics Center and Division of Life Science, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong
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23
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Tsao SW, Yip YL, Tsang CM, Pang PS, Lau VMY, Zhang G, Lo KW. Etiological factors of nasopharyngeal carcinoma. Oral Oncol 2014; 50:330-8. [PMID: 24630258 DOI: 10.1016/j.oraloncology.2014.02.006] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 01/29/2014] [Accepted: 02/07/2014] [Indexed: 12/18/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is a common disease among southern Chinese. The major etiological factors proposed for NPC pathogenesis include genetic susceptibility, environment factors and EBV infection. In the high risk population, genetic susceptibility to NPC has been mapped to the HLA loci and adjacent genes in MHC region on chromosome 6p21. Consumption of preserved food including salted fish has been implicated in its etiology in earlier studies. Its contribution to pathogenesis of NPC remains to be determined. A decreasing trend of NPC incidence was observed in Hong Kong, Taiwan and Singapore in recent years which may be accounted by a change of dietary habits. A comprehensive epidemiological study will help to elucidate the relative importance of various risk factors in the pathogenesis of NPC. Despite the close association of EBV infection with NPC, the etiological role of EBV in NPC pathogenesis remains enigmatic. EBV infection in primary nasopharyngeal epithelial cells is uncommon and difficult to achieve. EBV does not transform primary nasopharyngeal epithelial cells into proliferative clones, which contrasts greatly with the well-documented ability of EBV to transform and immortalize primary B cells. Genetic alterations identified in premalignant nasopharyngeal epithelium may play crucial roles to support stable EBV infection. Subsequently, latent and lytic EBV gene products may drive clonal expansion and transformation of premalignant nasopharyngeal epithelial cells into cancer cells. Stromal inflammation in nasopharyngeal mucosa is believed to play an important role in modulating the growth and possibly drive the malignant transformation of EBV-infected nasopharyngeal epithelial cells. Furthermore, there are increasing evidences supporting a role of EBV infection to evade host immune surveillance. EBV-infected cells may have selective growth advantages in vivo by acquiring a stress-resistance phenotype. Understanding the etiological factors and pathogenesis of NPC will contribute effectively to the prevention and treatment of this disease.
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Affiliation(s)
- Sai Wah Tsao
- Department of Anatomy and Center for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region.
| | - Yim Ling Yip
- Department of Anatomy and Center for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Chi Man Tsang
- Department of Anatomy and Center for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Pei Shin Pang
- Department of Anatomy and Center for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Victoria Ming Yi Lau
- Department of Anatomy and Center for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Guitao Zhang
- Department of Anatomy and Center for Cancer Research, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Kwok Wai Lo
- Department of Anatomical and Cellular Pathology and Li Ka Shing Institute of Health Science, The Chinese University of Hong Kong, Hong Kong Special Administrative Region.
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24
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Su WH, Yao Shugart Y, Chang KP, Tsang NM, Tse KP, Chang YS. How genome-wide SNP-SNP interactions relate to nasopharyngeal carcinoma susceptibility. PLoS One 2013; 8:e83034. [PMID: 24376627 PMCID: PMC3871583 DOI: 10.1371/journal.pone.0083034] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 10/29/2013] [Indexed: 11/18/2022] Open
Abstract
This study is the first to use genome-wide association study (GWAS) data to evaluate the multidimensional genetic architecture underlying nasopharyngeal cancer. Since analysis of data from GWAS confirms a close and consistent association between elevated risk for nasopharyngeal carcinoma (NPC) and major histocompatibility complex class 1 genes, our goal here was to explore lesser effects of gene-gene interactions. We conducted an exhaustive genome-wide analysis of GWAS data of NPC, revealing two-locus interactions occurring between single nucleotide polymorphisms (SNPs), and identified a number of suggestive interaction loci which were missed by traditional GWAS analyses. Although none of the interaction pairs we identified passed the genome-wide Bonferroni-adjusted threshold for significance, using independent GWAS data from the same population (Stage 2), we selected 66 SNP pairs in 39 clusters with P<0.01. We identified that in several chromosome regions, multiple suggestive interactions group to form a block-like signal, effectively reducing the rate of false discovery. The strongest cluster of interactions involved the CREB5 gene and a SNP rs1607979 on chromosome 17q22 (P = 9.86×10(-11)) which also show trans-expression quantitative loci (eQTL) association in Chinese population. We then detected a complicated cis-interaction pattern around the NPC-associated HLA-B locus, which is immediately adjacent to copy-number variations implicated in male susceptibility for NPC. While it remains to be seen exactly how and to what degree SNP-SNP interactions such as these affect susceptibility for nasopharyngeal cancer, future research on these questions holds great promise for increasing our understanding of this disease's genetic etiology, and possibly also that of other gene-related cancers.
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Affiliation(s)
- Wen-Hui Su
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yin Yao Shugart
- Genomic Research Branch, Division of Neuroscience and Behavioral Sciences, National Institute of Mental Health, NIH, Bethesda, Maryland, United States of America
- Department of Gastroenterology, Johns Hopkins Medical School, Baltimore, Maryland, United States of America
| | - Kai-Ping Chang
- Department of Otolaryngology - Head and Neck Surgery, Chang Gung Memorial Hospital at Lin-Kou, Taoyuan, Taiwan
| | - Ngan-Ming Tsang
- Department of Radiation Oncology, Chang Gung Memorial Hospital at Lin-Kou, Taoyuan, Taiwan
| | - Ka-Po Tse
- Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yu-Sun Chang
- Chang Gung Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
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25
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Yang L, Liu B, Qiu F, Huang B, Li Y, Huang D, Yang R, Yang X, Deng J, Jiang Q, Zhou Y, Lu J. The effect of functional MAPKAPK2 copy number variation CNV-30450 on elevating nasopharyngeal carcinoma risk is modulated by EBV infection. Carcinogenesis 2013; 35:46-52. [PMID: 24056810 DOI: 10.1093/carcin/bgt314] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
UNLABELLED Mitogen-activated protein kinase-activated protein kinase 2 (MAPKAPK2) is recognized as oncogenic and simulative role on tumorigenesis by virtue of abnormal expression in cancer including nasopharyngeal carcinoma (NPC). We hypothesized that the copy number variation (CNV)-30450, which duplicates the MAPKAPK2 promoter, may affect MAPKAPK2 expression and be associated with NPC risk. In two independent case-control panels of southern and eastern Chinese with a total of 1590 NPC patients and 1979 cancer-free controls, we investigated the association between CNV-30450 and NPC risk by genotyping the CNV-30450 with the TaqMan assay, and tested its biological effect. Consistent findings were observed in the two populations, that the increased copy number of CNV-30450 was associated with increased risk of NPC (3/4-copy versus 2-copy: odds ratio = 1.28, 95% confidence interval = 1.10-1.49), in which lies a biological mechanism that the adverse genotypes enhanced the promoter activity of MAPKAPK2 and elevated MAPKAPK2 expression. Moreover, the CNV-30450 adverse genotypes significantly interacted with Epstein-Barr virus (EBV) infection on increasing NPC risk (P = 0.035), and the genotype-phenotype correlation was only significant in EBV-positive cases (P = 0.037) but not in EBV-negative ones (P = 0.366). These data suggest that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC. SUMMARY This case-control study suggests that the functional CNV-30450 in the MAPKAPK2 promoter elevates the NPC risk with a modulation by EBV infection, which may be an indicator of susceptibility to NPC.
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Affiliation(s)
- Lei Yang
- The Institute for Chemical Carcinogenesis, The State Key Lab of Respiratory Disease, Guangzhou Medical University, 195 Dongfengxi Road, Guangzhou 510182, People's Republic of China
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26
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Lo PHY, Urabe Y, Kumar V, Tanikawa C, Koike K, Kato N, Miki D, Chayama K, Kubo M, Nakamura Y, Matsuda K. Identification of a functional variant in the MICA promoter which regulates MICA expression and increases HCV-related hepatocellular carcinoma risk. PLoS One 2013; 8:e61279. [PMID: 23593449 PMCID: PMC3623965 DOI: 10.1371/journal.pone.0061279] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Accepted: 03/11/2013] [Indexed: 01/16/2023] Open
Abstract
Hepatitis C virus (HCV) infection is the major cause of hepatocellular carcinoma (HCC) in Japan. We previously identified the association of SNP rs2596542 in the 5' flanking region of the MHC class I polypeptide-related sequence A (MICA) gene with the risk of HCV-induced HCC. In the current study, we performed detailed functional analysis of 12 candidate SNPs in the promoter region and found that a SNP rs2596538 located at 2.8 kb upstream of the MICA gene affected the binding of a nuclear protein(s) to the genomic segment including this SNP. By electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP) assay, we identified that transcription factor Specificity Protein 1 (SP1) can bind to the protective G allele, but not to the risk A allele. In addition, reporter construct containing the G allele was found to exhibit higher transcriptional activity than that containing the A allele. Moreover, SNP rs2596538 showed stronger association with HCV-induced HCC (P = 1.82 × 10(-5) and OR = 1.34) than the previously identified SNP rs2596542. We also found significantly higher serum level of soluble MICA (sMICA) in HCV-induced HCC patients carrying the G allele than those carrying the A allele (P = 0.00616). In summary, we have identified a functional SNP that is associated with the expression of MICA and the risk for HCV-induced HCC.
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Affiliation(s)
- Paulisally Hau Yi Lo
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Yuji Urabe
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Departments of Medical and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
| | - Vinod Kumar
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Chizu Tanikawa
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuhiko Koike
- Department of Gastroenterology, Graduate School of Medicine, University of Tokyo, Tokyo, Japan
| | - Naoya Kato
- Unit of Disease Control Genome Medicine, The Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Daiki Miki
- Departments of Medical and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Center for Genomic Medicine, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Kazuaki Chayama
- Departments of Medical and Molecular Science, Division of Frontier Medical Science, Programs for Biomedical Research, Graduate School of Biomedical Sciences, Hiroshima University, Hiroshima, Japan
- Center for Genomic Medicine, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Michiaki Kubo
- Center for Genomic Medicine, The Institute of Physical and Chemical Research (RIKEN), Kanagawa, Japan
| | - Yusuke Nakamura
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Departments of Medicine and Surgery, and Center for Personalized Therapeutics, The University of Chicago, Chicago, Illinois, United States of America
| | - Koichi Matsuda
- Laboratory of Molecular Medicine, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
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Shadravan F. Sex bias in copy number variation of olfactory receptor gene family depends on ethnicity. Front Genet 2013; 4:32. [PMID: 23503716 PMCID: PMC3596775 DOI: 10.3389/fgene.2013.00032] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 02/26/2013] [Indexed: 12/22/2022] Open
Abstract
Gender plays a pivotal role in the human genetic identity and is also manifested in many genetic disorders particularly mental retardation. In this study its effect on copy number variation (CNV), known to cause genetic disorders was explored. As the olfactory receptor (OR) repertoire comprises the largest human gene family, it was selected for this study, which was carried out within and between three populations, derived from 150 individuals from the 1000 Genome Project. Analysis of 3872 CNVs detected among 791 OR loci, in which 307 loci showed CNV, revealed the following novel findings: Sex bias in CNV was significantly more prevalent in uncommon than common CNV variants of OR pseudogenes, in which the male genome showed more CNVs; and in one-copy number loss compared to complete deletion of OR pseudogenes; both findings implying a more recent evolutionary role for gender. Sex bias in copy number gain was also detected. Another novel finding was that the observed sex bias was largely dependent on ethnicity and was in general absent in East Asians. Using a CNV public database for sick children (International Standard Cytogenomic Array Consortium) the application of these findings for improving clinical molecular diagnostics is discussed by showing an example of sex bias in CNV among kids with autism. Additional clinical relevance is discussed, as the most polymorphic CNV-enriched OR cluster in the human genome, located on chr 15q11.2, is found near the Prader–Willi syndrome/Angelman syndrome bi-directionally imprinted region associated with two well-known mental retardation syndromes. As olfaction represents the primitive cognition in most mammals, arguably in competition with the development of a larger brain, the extensive retention of OR pseudogenes in females of this study, might point to a parent-of-origin indirect regulatory role for OR pseudogenes in the embryonic development of human brain. Thus any perturbation in the temporal regulation of olfactory system could lead to developmental delay disorders including mental retardation.
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Affiliation(s)
- Farideh Shadravan
- *Correspondence: Farideh Shadravan, 2584 San Jose Ave, San Francisco, CA 94112, USA. e-mail:
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28
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Yang L, Liu B, Huang B, Deng J, Li H, Yu B, Qiu F, Cheng M, Wang H, Yang R, Yang X, Zhou Y, Lu J. A functional copy number variation in the WWOX gene is associated with lung cancer risk in Chinese. Hum Mol Genet 2013; 22:1886-94. [DOI: 10.1093/hmg/ddt019] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Krepischi ACV, Pearson PL, Rosenberg C. Germline copy number variations and cancer predisposition. Future Oncol 2012; 8:441-50. [PMID: 22515447 DOI: 10.2217/fon.12.34] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
We present an overview of the role of germline copy number variations (CNVs) in cancer predisposition. CNVs represent a significant source of genetic diversity, although the mechanisms by which they influence cancer susceptibility still remain largely unknown. Approximately 100 highly penetrant germline mutant genes are now known to cause cancer predisposition inherited in a Mendelian fashion; in this review, we show that nearly half of these genes have also been observed as rare CNVs associated with cancer. However, these highly penetrant alleles seem to account for less than 5% of all familial cancers. We surmise that most of the genetic risk of cancer in the general population must largely involve genes of low or moderate penetrance. In the last 5 years, studies have demonstrated that although common low penetrant CNVs are modest contributors to cancer individually, their combined impact on cancer predisposition must be taken into account in estimating cancer risk.
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Zhang YW, Guan J, Zhang Y, Qiu YR, Chen LH. Role of an MDM4 polymorphism in the early age of onset of nasopharyngeal carcinoma. Oncol Lett 2012; 3:1115-1118. [PMID: 22783402 DOI: 10.3892/ol.2012.630] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2011] [Accepted: 02/24/2012] [Indexed: 12/22/2022] Open
Abstract
Mouse double minute 4 (MDM4) is a critical negative regulator of the tumor suppressor p53. The results of studies have revealed that an MDM4 polymorphism (rs1563828) may contribute to the earlier onset of several malignant diseases. However, the correlation between this polymorphism and nasopharyngeal carcinoma (NPC) susceptibility has not been explored. We performed a case-control study with 210 NPC patients and 200 healthy controls. Significant associations were found when comparing the age of onset of NPC according to the rs1563828 genotype (P=0.01). The average age of onset of NPC in patients with the TT, CC and CT genotypes was 39.3, 48.2 and 45.5 years, respectively. Homozygous variant (TT) carriers developed NPC at an earlier age than homozygous (CC) carriers, such that the age of onset was accelerated by 8.9 years (P=0.002). Our data suggest that rs1563828 is a modifier of the age of onset of NPC in the population studied. The age of onset for NPC with TT homozygotes was earlier than CC carriers.
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Affiliation(s)
- Yao Wei Zhang
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P.R. China
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31
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Al-Sukhni W, Joe S, Lionel AC, Zwingerman N, Zogopoulos G, Marshall CR, Borgida A, Holter S, Gropper A, Moore S, Bondy M, Klein AP, Petersen GM, Rabe KG, Schwartz AG, Syngal S, Scherer SW, Gallinger S. Identification of germline genomic copy number variation in familial pancreatic cancer. Hum Genet 2012; 131:1481-94. [PMID: 22665139 DOI: 10.1007/s00439-012-1183-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 05/23/2012] [Indexed: 12/20/2022]
Abstract
Adenocarcinoma of the pancreas is a significant cause of cancer mortality, and up to 10 % of cases appear to be familial. Heritable genomic copy number variants (CNVs) can modulate gene expression and predispose to disease. Here, we identify candidate predisposition genes for familial pancreatic cancer (FPC) by analyzing germline losses or gains present in one or more high-risk patients and absent in a large control group. A total of 120 FPC cases and 1,194 controls were genotyped on the Affymetrix 500K array, and 36 cases and 2,357 controls were genotyped on the Affymetrix 6.0 array. Detection of CNVs was performed by multiple computational algorithms and partially validated by quantitative PCR. We found no significant difference in the germline CNV profiles of cases and controls. A total of 93 non-redundant FPC-specific CNVs (53 losses and 40 gains) were identified in 50 cases, each CNV present in a single individual. FPC-specific CNVs overlapped the coding region of 88 RefSeq genes. Several of these genes have been reported to be differentially expressed and/or affected by copy number alterations in pancreatic adenocarcinoma. Further investigation in high-risk subjects may elucidate the role of one or more of these genes in genetic predisposition to pancreatic cancer.
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Affiliation(s)
- Wigdan Al-Sukhni
- Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada.
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Liu YT, Dai JJ, Xu CH, Lu YK, Fan YY, Zhang XL, Zhang CX, Chen YM. Greater intake of fruit and vegetables is associated with lower risk of nasopharyngeal carcinoma in Chinese adults: a case-control study. Cancer Causes Control 2012; 23:589-99. [PMID: 22392078 DOI: 10.1007/s10552-012-9923-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2011] [Accepted: 02/14/2012] [Indexed: 10/28/2022]
Abstract
PURPOSE The effect of fruit and vegetable intake on the risk of nasopharyngeal carcinoma (NPC) remains uncertain due to limited published evidence. We performed a matched case-control study to investigate the relationship between the intake of fruit and vegetables and the risk of NPC. METHODS Between July 2009 and March 2011, 600 (448 male, 152 female), NPC incident cases from a single hospital in Guangzhou, Guangdong Province, China, a high-incidence area, were enrolled in the study. 600 controls, matched by gender, age (± 3 years) and household type (urban/rural) were also enrolled. Face-to-face interviews were used to collect habitual dietary intakes and information on various covariates. RESULTS Multivariate conditional logistic regression analyses showed significant, dose-dependent inverse associations between the intake of vegetables, fruit or a combination of the two and the risk of NPC, even after adjustments for social-economic status, body mass index, dietary factors and other potential covariates. The adjusted odds ratios (95% confidence intervals) for NPC in the top quartile of vegetable intake, fruit intake or a combination of the two, as compared to the lowest quartile, were 0.33 (0.22-0.50), 0.70 (0.47-1.04) and 0.37 (0.25-0.55), respectively. Dark green leafy vegetables, carrots, peppers and tomatoes, citrus fruit and pome fruit showed much more pronounced benefits with regards to NPC than other types of fruit and vegetables. Interaction analyses demonstrated that the effects of total combined vegetable and fruit intake were much more significant in subjects with a higher education level (p interaction: 0.027), and the benefits of fruit were observed in males, but not in females (p interaction: 0.088). CONCLUSION Our findings suggest that a greater consumption of fruit and vegetables may lower the risk of NPC in Chinese adults.
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Affiliation(s)
- Yuan-Ting Liu
- Guangdong Provincial Key Laboratory of Food, Nutrition and Health, School of Public Health, Sun Yat-sen University, Guangzhou, 510080, People's Republic of China
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Krepischi AC, Achatz MIW, Santos EM, Costa SS, Lisboa BC, Brentani H, Santos TM, Gonçalves A, Nóbrega AF, Pearson PL, Vianna-Morgante AM, Carraro DM, Brentani RR, Rosenberg C. Germline DNA copy number variation in familial and early-onset breast cancer. Breast Cancer Res 2012; 14:R24. [PMID: 22314128 PMCID: PMC3496142 DOI: 10.1186/bcr3109] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2011] [Revised: 01/20/2012] [Accepted: 02/07/2012] [Indexed: 11/10/2022] Open
Abstract
Introduction Genetic factors predisposing individuals to cancer remain elusive in the majority of patients with a familial or clinical history suggestive of hereditary breast cancer. Germline DNA copy number variation (CNV) has recently been implicated in predisposition to cancers such as neuroblastomas as well as prostate and colorectal cancer. We evaluated the role of germline CNVs in breast cancer susceptibility, in particular those with low population frequencies (rare CNVs), which are more likely to cause disease." Methods Using whole-genome comparative genomic hybridization on microarrays, we screened a cohort of women fulfilling criteria for hereditary breast cancer who did not carry BRCA1/BRCA2 mutations. Results The median numbers of total and rare CNVs per genome were not different between controls and patients. A total of 26 rare germline CNVs were identified in 68 cancer patients, however, a proportion that was significantly different (P = 0.0311) from the control group (23 rare CNVs in 100 individuals). Several of the genes affected by CNV in patients and controls had already been implicated in cancer. Conclusions This study is the first to explore the contribution of germline CNVs to BRCA1/2-negative familial and early-onset breast cancer. The data suggest that rare CNVs may contribute to cancer predisposition in this small cohort of patients, and this trend needs to be confirmed in larger population samples.
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Affiliation(s)
- Ana Cv Krepischi
- National Institute of Science and Technology in Oncogenomics, AC Camargo Hospital, Rua Taguá 440, 01508-010, São Paulo, Brazil.
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Bei JX, Jia WH, Zeng YX. Familial and large-scale case-control studies identify genes associated with nasopharyngeal carcinoma. Semin Cancer Biol 2012; 22:96-106. [PMID: 22313875 DOI: 10.1016/j.semcancer.2012.01.012] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 01/21/2012] [Accepted: 01/24/2012] [Indexed: 12/17/2022]
Abstract
Nasopharyngeal carcinoma (NPC) is an epithelial malignancy and has a remarkable geographic distribution, which is highly prevalent in southern China, Southeast Asia, and North Africa. Although most of the NPC are sporadic cases, the familial clustering of NPC has been demonstrated worldwide. Accumulating studies have proposed that the etiology of NPC is multi-stage and multi-factorial, involving genetic lesions, Epstein-Barr virus infection, and environmental exposure. Genetic variations result in differences in gene function, which in turn lead to different susceptibility to disease. Many studies have been carried out to dissect the genetic variants that contribute to NPC susceptibility. This article reviews the current progress of genetic studies to identify genes associated with NPC, focusing on the familial linkage and large-scale case-control study designs.
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Affiliation(s)
- Jin-Xin Bei
- State Key Laboratory of Oncology in South China, Sun Yat-sen University Cancer Center, Guangzhou 510060, China
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