1
|
Li D, Wang X, Lu S, Wang P, Wang X, Yin W, Zhu W, Li S. Integrated analysis revealing genome-wide chromosomal copy number variation in supraglottic laryngeal squamous cell carcinoma. Oncol Lett 2020; 20:1201-1212. [PMID: 32724360 PMCID: PMC7377034 DOI: 10.3892/ol.2020.11653] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/27/2020] [Indexed: 01/22/2023] Open
Abstract
Laryngeal squamous cell carcinoma (LSCC) is a genetically complex tumor type and one of the leading causes of cancer-associated disability and mortality. Genetic instability, such as chromosomal instability, is associated with the tumorigenesis of LSCC. Copy number variations (CNVs) have been demonstrated to contribute to the genetic diversity of tumor pathogenesis. Comparative genomic hybridization (CGH) has emerged as a high-throughput genomic technology that facilitates the aggregation of high-resolution data of cancer-associated genomic imbalances. In the present study, a total of 38 primary supraglottic LSCC cases were analyzed by high-resolution array-based CGH (aCGH) to improve the understanding of the genetic alterations in LSCC. Additionally, integration with bioinformatic analysis of microarray expression profiling data from the Gene Expression Omnibus (GEO) database provided a fundamental method for the identification of putative target genes. Genomic CNVs were detected in all cases. The size of net genomic imbalances per case ranged between a loss of 682.3 Mb (~24% of the genome) and a gain of 1,958.6 Mb (~69% of the genome). Recurrent gains included 2pter-q22.1, 3q26.1-qter, 5pter-p12, 7p22.3p14.1, 8p12p11.22, 8q24.13q24.3, 11q13.2q13.4, 12pter-p12.2, 18pter-p11.31 and 20p13p12.1, whereas recurrent losses included 3pter-p21.32, 4q28.1-q35.2, 5q13.2-qter, 9pter-p21.3 and monosomy 13. Gains of 3q26.1-qter were associated with tumor stage, poor differentiation and smoking history. Additionally, through integration with bioinformatic analysis of data from the GEO database, putative target oncogenes, including sex-determining region Y-box 2, eukaryotic translation initiation factor 4 gamma 1, fragile X-related gene 1, disheveled segment polarity protein 3, defective n cullin neddylation 1 domain containing 1, insulin like growth factor 2 mRNA binding protein 2 and CCDC26 long non-coding RNA, and tumor suppressor genes, such as CUB and sushi multiple domains 1, cyclin dependent kinase inhibitor 2A, protocadherin 20, serine peptidase inhibitor Kazal type 5 and Nei like DNA glycosylase 3, were identified in supraglottic LSCC. Supraglottic LSCC is a genetically complex tumor type and aCGH was demonstrated to be effective in the determination of molecular profiles with higher resolution. The present results enable the identification of putative target oncogenes and tumor suppressor gene mapping in supraglottic LSCC.
Collapse
Affiliation(s)
- Dongjie Li
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xianfu Wang
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| | - Shunfei Lu
- Department of Clinical Medicine, Lishui College of Medicine, Lishui, Zhejiang 323000, P.R. China
| | - Ping Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Xin Wang
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wanzhong Yin
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Wei Zhu
- Department of Otorhinolaryngology, Head and Neck Surgery, The First Hospital of Jilin University, Changchun, Jilin 130021, P.R. China
| | - Shibo Li
- Department of Pediatrics, Genetics Laboratory, University of Oklahoma Health Sciences Center, Oklahoma, OK 73104, USA
| |
Collapse
|
2
|
Ribeiro IP, Caramelo F, Ribeiro M, Machado A, Miguéis J, Marques F, Carreira IM, Melo JB. Upper aerodigestive tract carcinoma: Development of a (epi)genomic predictive model for recurrence and metastasis. Oncol Lett 2020; 19:3459-3468. [PMID: 32269619 PMCID: PMC7115117 DOI: 10.3892/ol.2020.11459] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2019] [Accepted: 12/31/2019] [Indexed: 12/02/2022] Open
Abstract
Despite the increased molecular knowledge and the diagnostic and therapeutic improvements, the survival of patients with upper aerodigestive tract carcinoma remains poor. The identification of early diagnostic and prognostic biomarkers and the development of molecular models to distinguish patients that will recur and/or develop metastasis after treatment as well as to benefit with target therapies can be important to decrease mortality, improve survival rates and improve the quality of life of these patients. The current study analyzed 21 upper aerodigestive tract carcinomas through array comparative genomic hybridization and methylation-specific multiplex ligation-dependent probe amplification techniques. A number of chromosomal regions and genes were observed with copy number alterations and methylation. A predictive (epi)genomic model that comprises the 3p chromosomal region and WT1, VHL and THBS1 genes was built, highlighting a molecular signature with possible clinical use. The current study may aid in the development of a more individualized patient management and targeted drug design. The power of this genomic and epigenetic model to predict the recurrence and metastasis development should be evaluated and validated in future larger cohort study.
Collapse
Affiliation(s)
- Ilda Patrícia Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| | - Francisco Caramelo
- iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal.,Laboratory of Biostatistics and Medical Informatics, IBILI-Institute for Biomedical Imaging and Life Sciences, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Margarida Ribeiro
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal
| | - Ana Machado
- Department of Otorhinolaryngology-Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Jorge Miguéis
- Department of Otorhinolaryngology-Head and Neck Surgery, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Francisco Marques
- iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal.,Department of Dentistry, Faculty of Medicine, University of Coimbra, 3000-075 Coimbra, Portugal.,Stomatology Unit, Coimbra Hospital and University Centre, CHUC-Coimbra Hospital and University Centre, EPE, 3000-075 Coimbra, Portugal
| | - Isabel Marques Carreira
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| | - Joana Barbosa Melo
- Cytogenetics and Genomics Laboratory, Faculty of Medicine, University of Coimbra, 3000-354 Coimbra, Portugal.,iCBR-CIMAGO-Coimbra Institute for Clinical and Biomedical Research/Center of Investigation on Environment Genetics and Oncobiology-Faculty of Medicine, University of Coimbra, 3001-301 Coimbra, Portugal
| |
Collapse
|
3
|
Yang J, Chen Y, Luo H, Cai H. The Landscape of Somatic Copy Number Alterations in Head and Neck Squamous Cell Carcinoma. Front Oncol 2020; 10:321. [PMID: 32226775 PMCID: PMC7080958 DOI: 10.3389/fonc.2020.00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/24/2020] [Indexed: 02/05/2023] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common malignancy worldwide. Somatic copy number alterations (CNAs) play a significant role in the development of this lethal cancer. In this study, we present a meta-analysis of CNAs for a total of 1,395 HNSCC samples. Publicly available R packages and in-house scripts were used for genomic array data processing, including normalization, segmentation and CNA calling. We detected 125 regions of significant gains or losses using GISTIC algorithm and found several potential driver genes in these regions. The incidence of chromothripsis in HNSCC was estimated to be 6%, and the chromosome pulverization hotspot regions were detected. We determined 323 genomic locations significantly enriched for breakpoints, which indicate HNSCC-specific genomic instability regions. Unsupervised clustering of genome-wide CNA data revealed a sub-cluster predominantly composed of nasopharynx tumors and presented a large proportion of HPV-positive samples. These results will facilitate the discovery of therapeutic candidates and extend our molecular understanding of HNSCC.
Collapse
Affiliation(s)
- Jian Yang
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Yi Chen
- Department of Gastrointestinal Surgery, West China Hospital, Sichuan University, Chengdu, China
| | - Hong Luo
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| | - Haoyang Cai
- Center of Growth, Metabolism, and Aging, Key Laboratory of Bio-Resources and Eco-Environment, College of Life Sciences, Sichuan University, Chengdu, China
| |
Collapse
|
4
|
Combined deletion and DNA methylation result in silencing of FAM107A gene in laryngeal tumors. Sci Rep 2017; 7:5386. [PMID: 28710449 PMCID: PMC5511162 DOI: 10.1038/s41598-017-05857-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/05/2017] [Indexed: 12/13/2022] Open
Abstract
Larynx squamous cell carcinoma (LSCC) is characterized by complex genotypes, with numerous abnormalities in various genes. Despite the progress in diagnosis and treatment of this disease, 5-year survival rates remain unsatisfactory. Therefore, the extended studies are conducted, with the aim to find genes, potentially implicated in this cancer. In this study, we focus on the FAM107A (3p14.3) gene, since we found its significantly reduced expression in LSCC by microarray profiling (Affymetrix U133 Plus 2.0 array). By RT-PCR we have confirmed complete FAM107A downregulation in laryngeal cancer cell lines (15/15) and primary tumors (21/21) and this finding was further supported by FAM107A protein immunohistochemistry (15/15). We further demonstrate that a combined two hit mechanism including loss of 3p and hypermethylation of FAM107A promoter region (in 9/15 cell lines (p < 0.0001) and in 15/21 primary tumors (p < 0.0001)) prevails in the gene transcriptional loss. As a proof of principle, we show that Decitabine - a hypomethylating agent – restores FAM107A expression (5 to 6 fold increase) in the UT-SCC-29 cell line, characterized by high DNA methylation. Therefore, we report the recurrent inactivation of FAM107A in LSCC, what may suggest that the gene is a promising tumor suppressor candidate involved in LSCC development.
Collapse
|
5
|
Vaidyanathan V, Naidu V, Kao CHJ, Karunasinghe N, Bishop KS, Wang A, Pallati R, Shepherd P, Masters J, Zhu S, Goudie M, Krishnan M, Jabed A, Marlow G, Narayanan A, Ferguson LR. Environmental factors and risk of aggressive prostate cancer among a population of New Zealand men - a genotypic approach. MOLECULAR BIOSYSTEMS 2017; 13:681-698. [PMID: 28252132 DOI: 10.1039/c6mb00873a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Prostate cancer is one of the most significant health concerns for men worldwide. Numerous researchers carrying out molecular diagnostics have indicated that genetic interactions with biological and behavioral factors play an important role in the overall risk and prognosis of this disease. Single nucleotide polymorphisms (SNPs) are increasingly becoming strong biomarker candidates to identify susceptibility to prostate cancer. We carried out a gene × environment interaction analysis linked to aggressive and non-aggressive prostate cancer (PCa) with a number of SNPs. By using this method, we identified the susceptible alleles in a New Zealand population, and examined the interaction with environmental factors. We have identified a number of SNPs that have risk associations both with and without environmental interaction. The results indicate that certain SNPs are associated with disease vulnerability based on behavioral factors. The list of genes with SNPs identified as being associated with the risk of PCa in a New Zealand population is provided in the graphical abstract.
Collapse
Affiliation(s)
- Venkatesh Vaidyanathan
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Vijay Naidu
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Chi Hsiu-Juei Kao
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | | | - Karen S Bishop
- Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Alice Wang
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Radha Pallati
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Phillip Shepherd
- Sequenom Facility, Liggins Institute, University of Auckland, Auckland 1023, New Zealand.
| | - Jonathan Masters
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Shuotun Zhu
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| | - Megan Goudie
- Urology Department, Auckland District Health Board, Auckland, New Zealand.
| | - Mohanraj Krishnan
- Department of Obstetrics and Gynaecology, FMHS, University of Auckland, Auckland 1023, New Zealand.
| | - Anower Jabed
- Department of Molecular Medicine and Pathology, FM & HS, University of Auckland, Auckland 1023, New Zealand.
| | - Gareth Marlow
- Experimental Cancer Medicine Centre, Cardiff University, Cardiff, CF14 4XN, UK.
| | - Ajit Narayanan
- School of Engineering, Computer and Mathematical Sciences, Auckland University of Technology, Auckland 1010, New Zealand.
| | - Lynnette R Ferguson
- Discipline of Nutrition and Dietetics, FM & HS, University of Auckland, Auckland 1023, New Zealand. and Auckland Cancer Society Research Centre, Auckland 1023, New Zealand.
| |
Collapse
|
6
|
Singchat W, Hitakomate E, Rerkarmnuaychoke B, Suntronpong A, Fu B, Bodhisuwan W, Peyachoknagul S, Yang F, Koontongkaew S, Srikulnath K. Genomic Alteration in Head and Neck Squamous Cell Carcinoma (HNSCC) Cell Lines Inferred from Karyotyping, Molecular Cytogenetics, and Array Comparative Genomic Hybridization. PLoS One 2016; 11:e0160901. [PMID: 27501229 PMCID: PMC4976893 DOI: 10.1371/journal.pone.0160901] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 07/26/2016] [Indexed: 02/06/2023] Open
Abstract
Genomic alteration in head and neck squamous cell carcinoma (HNSCC) was studied in two cell line pairs (HN30-HN31 and HN4-HN12) using conventional C-banding, multiplex fluorescence in situ hybridization (M-FISH), and array comparative genomic hybridization (array CGH). HN30 and HN4 were derived from primary lesions in the pharynx and base of tongue, respectively, and HN31 and HN12 were derived from lymph-node metastatic lesions belonging to the same patients. Gain of chromosome 1, 7, and 11 were shared in almost all cell lines. Hierarchical clustering revealed that HN31 was closely related to HN4, which shared eight chromosome alteration cases. Large C-positive heterochromatins were found in the centromeric region of chromosome 9 in HN31 and HN4, which suggests complex structural amplification of the repetitive sequence. Array CGH revealed amplification of 7p22.3p11.2, 8q11.23q12.1, and 14q32.33 in all cell lines involved with tumorigenesis and inflammation genes. The amplification of 2p21 (SIX3), 11p15.5 (H19), and 11q21q22.3 (MAML2, PGR, TRPC6, and MMP family) regions, and deletion of 9p23 (PTPRD) and 16q23.1 (WWOX) regions were identified in HN31 and HN12. Interestingly, partial loss of PTPRD (9p23) and WWOX (16q23.1) genes was identified in HN31 and HN12, and the level of gene expression tended to be the down-regulation of PTPRD, with no detectable expression of the WWOX gene. This suggests that the scarcity of PTPRD and WWOX genes might have played an important role in progression of HNSCC, and could be considered as a target for cancer therapy or a biomarker in molecular pathology.
Collapse
Affiliation(s)
- Worapong Singchat
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Ekarat Hitakomate
- Faculty of Dentistry, Thammasart University, Pathum Thani, 12121, Thailand
| | - Budsaba Rerkarmnuaychoke
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, 10400, Thailand
| | - Aorarat Suntronpong
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Beiyuan Fu
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | - Winai Bodhisuwan
- Department of Statistics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand
| | - Surin Peyachoknagul
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU, Thailand)
| | - Fengtang Yang
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, United Kingdom
| | | | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics, Department of Genetics, Faculty of Science, Kasetsart University, 50 Ngamwongwan, Chatuchak, Bangkok, 10900, Thailand.,Center of Advanced Studies in Tropical Natural Resources, National Research University-Kasetsart University, Kasetsart University, Thailand (CASTNAR, NRU-KU, Thailand)
| |
Collapse
|
7
|
Bodnar M, Luczak M, Bednarek K, Szylberg L, Marszalek A, Grenman R, Szyfter K, Jarmuz-Szymczak M, Giefing M. Proteomic profiling identifies the inorganic pyrophosphatase (PPA1) protein as a potential biomarker of metastasis in laryngeal squamous cell carcinoma. Amino Acids 2016; 48:1469-76. [PMID: 26948660 PMCID: PMC4875942 DOI: 10.1007/s00726-016-2201-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 02/12/2016] [Indexed: 01/29/2023]
Abstract
Relapse and metastasis are the main causes of unfavorable outcome in head and neck cancers. Whereas, understanding of the molecular background of these processes is far from being complete. Therefore, in this study we aimed to identify potential biomarker candidates of relapse and metastasis in laryngeal squamous cell carcinoma (LSCC) by combining the 2D electrophoresis based protein screen and immunohistochemical analysis of candidate proteins. We screened three groups of LSCC cell lines derived from primary tumors, recurrent tumors and metastases and identified seven proteins that differed significantly in relative abundance between the analyzed groups. Among the identified proteins were the heat shock proteins HSP60 and HSP70 that were significantly downregulated both in recurrences- and metastases-derived cell lines but not in primary tumor-derived cell lines. Moreover, we identified significant upregulation of the annexin V, calreticulin and the inorganic pyrophosphatase (PPA1) exclusively in the metastases-derived cell lines. As these upregulated proteins could potentially become novel biomarkers of metastasis, we have compared their abundance in primary tumor LSCC N(0) cases, primary tumor LSCC N(+) cases as well as in LSCC metastases N(+). Our results show an intense increase of cytoplasmic PPA1 abundance in the N(+) (p = 0.000042) compared to the N(0) group. In summary, we show a group of proteins deregulated in recurrences and metastases of LSCC. Moreover, we suggest the PPA1 protein as a potential new biomarker for metastasis in this cancer.
Collapse
Affiliation(s)
- Magdalena Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Magdalena Luczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.,Institute of Chemical Technology and Engineering, Poznan University of Technology, Poznan, Poland
| | - Kinga Bednarek
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Lukasz Szylberg
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland
| | - Andrzej Marszalek
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Torun, Bydgoszcz, Poland.,Chair of Oncologic Pathology and Epidemiology, Poznan University of Medical Sciences and Greater Poland Cancer Center, Poznan, Poland
| | - Reidar Grenman
- Department of Otorhinolaryngology, Head and Neck Surgery, Turku University Hospital and University of Turku, Turku, Finland.,Department of Medical Biochemistry, Turku University Hospital and University of Turku, Turku, Finland
| | - Krzysztof Szyfter
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Audiology and Phoniatrics, Poznan University of Medical Sciences, Poznan, Poland
| | - Malgorzata Jarmuz-Szymczak
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland.,Department of Hematology and Bone Marrow Transplantation, Poznan University of Medical Sciences, Poznan, Poland
| | - Maciej Giefing
- Department of Cancer Genetics, Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland. .,Department of Otolaryngology and Laryngeal Oncology, Poznan University of Medical Sciences, Poznan, Poland.
| |
Collapse
|
8
|
Bednarek K, Kiwerska K, Szaumkessel M, Bodnar M, Kostrzewska-Poczekaj M, Marszalek A, Janiszewska J, Bartochowska A, Jackowska J, Wierzbicka M, Grenman R, Szyfter K, Giefing M, Jarmuz-Szymczak M. Recurrent CDK1 overexpression in laryngeal squamous cell carcinoma. Tumour Biol 2016; 37:11115-26. [PMID: 26912061 PMCID: PMC4999469 DOI: 10.1007/s13277-016-4991-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 02/11/2016] [Indexed: 12/12/2022] Open
Abstract
In this study, we analyzed the expression profile of four genes (CCNA2, CCNB1, CCNB2, and CDK1) in laryngeal squamous cell carcinoma (LSCC) cell lines and tumor samples. With the application of microarray platform, we have shown the overexpression of these genes in all analyzed LSCC samples in comparison to non-cancer controls from head and neck region. We have selected CDK1 for further analysis, due to its leading role in cell cycle regulation. It is a member of the Ser/Thr protein kinase family of proven oncogenic properties. The results obtained for CDK1 were further confirmed with the application of reverse transcription quantitative polymerase chain reaction (RT-qPCR) technique, Western blot, and immunohistochemistry (IHC). The observed upregulation of CDK1 in laryngeal squamous cell carcinoma has encouraged us to analyze for genetic mechanisms that can be responsible this phenomenon. Therefore, with the application of array-CGH, sequencing analysis and two methods for epigenetic regulation analysis (DNA methylation and miRNA expression), we tried to identify such potential mechanisms. Our attempts to identify the molecular mechanisms responsible for observed changes failed as we did not observe significant alterations neither in the DNA sequence nor in the gene copy number that could underline CDK1 upregulation. Similarly, the pyrosequencing and miRNA expression analyses did not reveal any differences in methylation level and miRNA expression, respectively; thus, these mechanisms probably do not contribute to elevation of CDK1 expression in LSCC. However, our results suggest that alteration of CDK1 expression on both mRNA and protein level probably appears on the very early step of carcinogenesis.
Collapse
Affiliation(s)
- K Bednarek
- Department of Cancer Genetics, Institute of Human Genetics, PAS, Poznan, Poland
| | - K Kiwerska
- Department of Cancer Genetics, Institute of Human Genetics, PAS, Poznan, Poland
| | - M Szaumkessel
- Department of Cancer Genetics, Institute of Human Genetics, PAS, Poznan, Poland
| | - M Bodnar
- Department of Clinical Pathomorphology, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland
| | | | - A Marszalek
- Department of Clinical Pathomorphology, Collegium Medicum, Nicolaus Copernicus University, Bydgoszcz, Poland.,Department of Oncologic Pathology, Greater Poland Cancer Centre, Poznan, Poland
| | - J Janiszewska
- Department of Cancer Genetics, Institute of Human Genetics, PAS, Poznan, Poland
| | - A Bartochowska
- Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - J Jackowska
- Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - M Wierzbicka
- Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - R Grenman
- Department of Otorhinolaryngology-Head and Neck Surgery and Department of Medical Biochemistry, Turku University Hospital and University of Turku, Turku, Finland
| | - K Szyfter
- Department of Audiology and Phoniatry, University of Medical Sciences, Poznan, Poland
| | - M Giefing
- Department of Cancer Genetics, Institute of Human Genetics, PAS, Poznan, Poland.,Department of Otolaryngology and Laryngological Oncology, University of Medical Sciences, Poznan, Poland
| | - M Jarmuz-Szymczak
- Department of Cancer Genetics, Institute of Human Genetics, PAS, Poznan, Poland. .,Department of Hematology, University of Medical Sciences, Poznan, Poland.
| |
Collapse
|
9
|
Reddy RB, Bhat AR, James BL, Govindan SV, Mathew R, DR R, Hedne N, Illiayaraja J, Kekatpure V, Khora SS, Hicks W, Tata P, Kuriakose MA, Suresh A. Meta-Analyses of Microarray Datasets Identifies ANO1 and FADD as Prognostic Markers of Head and Neck Cancer. PLoS One 2016; 11:e0147409. [PMID: 26808319 PMCID: PMC4726811 DOI: 10.1371/journal.pone.0147409] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Accepted: 01/04/2016] [Indexed: 01/18/2023] Open
Abstract
The head and neck squamous cell carcinoma (HNSCC) transcriptome has been profiled extensively, nevertheless, identifying biomarkers that are clinically relevant and thereby with translational benefit, has been a major challenge. The objective of this study was to use a meta-analysis based approach to catalog candidate biomarkers with high potential for clinical application in HNSCC. Data from publically available microarray series (N = 20) profiled using Agilent (4X44K G4112F) and Affymetrix (HGU133A, U133A_2, U133Plus 2) platforms was downloaded and analyzed in a platform/chip-specific manner (GeneSpring software v12.5, Agilent, USA). Principal Component Analysis (PCA) and clustering analysis was carried out iteratively for segregating outliers; 140 normal and 277 tumor samples from 15 series were included in the final analysis. The analyses identified 181 differentially expressed, concordant and statistically significant genes; STRING analysis revealed interactions between 122 of them, with two major gene clusters connected by multiple nodes (MYC, FOS and HSPA4). Validation in the HNSCC-specific database (N = 528) in The Cancer Genome Atlas (TCGA) identified a panel (ECT2, ANO1, TP63, FADD, EXT1, NCBP2) that was altered in 30% of the samples. Validation in treatment naïve (Group I; N = 12) and post treatment (Group II; N = 12) patients identified 8 genes significantly associated with the disease (Area under curve>0.6). Correlation with recurrence/re-recurrence showed ANO1 had highest efficacy (sensitivity: 0.8, specificity: 0.6) to predict failure in Group I. UBE2V2, PLAC8, FADD and TTK showed high sensitivity (1.00) in Group I while UBE2V2 and CRYM were highly sensitive (>0.8) in predicting re-recurrence in Group II. Further, TCGA analysis showed that ANO1 and FADD, located at 11q13, were co-expressed at transcript level and significantly associated with overall and disease-free survival (p<0.05). The meta-analysis approach adopted in this study has identified candidate markers correlated with disease outcome in HNSCC; further validation in a larger cohort of patients will establish their clinical relevance.
Collapse
Affiliation(s)
- Ram Bhupal Reddy
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Division of Medical Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, Tamil Nadu, India
| | - Anupama Rajan Bhat
- Strand Life Sciences, Kirloskar Business Park, Bangalore, Karnataka, India
| | - Bonney Lee James
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| | | | - Rohit Mathew
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| | - Ravindra DR
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| | - Naveen Hedne
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| | - Jeyaram Illiayaraja
- Department of Clinical Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| | - Vikram Kekatpure
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| | - Samanta S. Khora
- Division of Medical Biotechnology, School of Biosciences and Technology, Vellore Institute of Technology University, Vellore, Tamil Nadu, India
| | - Wesley Hicks
- Department of Head and Neck/Plastic & Reconstructive Surgery, Roswell Park Cancer Institute, Buffalo, New York, United States of America
- Mazumdar Shaw Medical Centre-Roswell Park Collaboration Program, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Pramila Tata
- Strand Life Sciences, Kirloskar Business Park, Bangalore, Karnataka, India
| | - Moni A. Kuriakose
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Mazumdar Shaw Medical Centre-Roswell Park Collaboration Program, Roswell Park Cancer Institute, Buffalo, New York, United States of America
| | - Amritha Suresh
- Integrated Head and Neck Oncology Program, Mazumdar Shaw Centre for Translational Research, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
- Head and Neck Oncology, Mazumdar Shaw Medical Centre, Narayana Health, Bangalore, Karnataka, India
| |
Collapse
|
10
|
Cheng C, Cui H, Zhang L, Jia Z, Song B, Wang F, Li Y, Liu J, Kong P, Shi R, Bi Y, Yang B, Wang J, Zhao Z, Zhang Y, Hu X, Yang J, He C, Zhao Z, Wang J, Xi Y, Xu E, Li G, Guo S, Chen Y, Yang X, Chen X, Liang J, Guo J, Cheng X, Wang C, Zhan Q, Cui Y. Genomic analyses reveal FAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma. Gigascience 2016; 5:1. [PMID: 26759717 PMCID: PMC4709967 DOI: 10.1186/s13742-015-0107-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/23/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is the sixth most lethal cancer worldwide and the fourth most lethal cancer in China. Genomic characterization of tumors, particularly those of different stages, is likely to reveal additional oncogenic mechanisms. Although copy number alterations and somatic point mutations associated with the development of ESCC have been identified by array-based technologies and genome-wide studies, the genomic characterization of ESCCs from different stages of the disease has not been explored. Here, we have performed either whole-genome sequencing or whole-exome sequencing on 51 stage I and 53 stage III ESCC patients to characterize the genomic alterations that occur during the various clinical stages of ESCC, and further validated these changes in 36 atypical hyperplasia samples. RESULTS Recurrent somatic amplifications at 8q were found to be enriched in stage I tumors and the deletions of 4p-q and 5q were particularly identified in stage III tumors. In particular, the FAM84B gene was amplified and overexpressed in preclinical and ESCC tumors. Knockdown of FAM84B in ESCC cell lines significantly reduced in vitro cell growth, migration and invasion. Although the cancer-associated genes TP53, PIK3CA, CDKN2A and their pathways showed no significant difference between stage I and stage III tumors, we identified and validated a prevalence of mutations in NOTCH1 and in the NOTCH pathway that indicate that they are involved in the preclinical and early stages of ESCC. CONCLUSIONS Our results suggest that FAM84B and the NOTCH pathway are involved in the progression of ESCC and may be potential diagnostic targets for ESCC susceptibility.
Collapse
Affiliation(s)
- Caixia Cheng
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Pathology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Heyang Cui
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Ling Zhang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Zhiwu Jia
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Bin Song
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Fang Wang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Yaoping Li
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Jing Liu
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Pengzhou Kong
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Ruyi Shi
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Yanghui Bi
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Bin Yang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Juan Wang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Zhenxiang Zhao
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Yanyan Zhang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Xiaoling Hu
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Jie Yang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Chanting He
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Zhiping Zhao
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Jinfen Wang
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Yanfeng Xi
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Enwei Xu
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Guodong Li
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Shiping Guo
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Yunqing Chen
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Xiaofeng Yang
- />Department of Urology Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Xing Chen
- />Department of Endoscopy, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi 030001 China
| | - Jianfang Liang
- />Department of Pathology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Jiansheng Guo
- />Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Xiaolong Cheng
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Chuangui Wang
- />Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620 China
| | - Qimin Zhan
- />Cancer Institute and Cancer Hospital, State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Yongping Cui
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| |
Collapse
|
11
|
Li M, Cui X, Shen Y, Dong H, Liang W, Chen Y, Hu J, Li S, Kong J, Li H, Zhao J, Li F. ORAOV1 overexpression in esophageal squamous cell carcinoma and esophageal dysplasia: a possible biomarker of progression and poor prognosis in esophageal carcinoma. Hum Pathol 2015; 46:707-15. [PMID: 25732110 DOI: 10.1016/j.humpath.2015.01.009] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Revised: 01/11/2015] [Accepted: 01/21/2015] [Indexed: 12/18/2022]
Abstract
Oral cancer overexpressed 1 (ORAOV1) has been reported to exhibit high amplification levels in esophageal squamous cell cancer (ESCC) and in premalignant lesions. However, ORAOV1 protein expression levels in ESCC and esophageal squamous intraepithelial neoplasia (ESIN) have not yet been reported. We have explored the relationship of ORAOV1 protein expression with ESCC and ESIN by immunohistochemically analyzing tissue microarrays containing esophageal samples from patients with various clinical features and prognoses. The percentage of ESCC, high-grade ESIN (HGESIN), low-grade ESIN (LGESIN), and nontumoral control patients overexpressing ORAOV1 were 70.63% (101/143), 77.36% (41/53), 48.96% (47/96), and 5.79% (7/121), respectively. ORAOV1 overexpression also appears to be significantly higher in ESCC, HGESIN, and LGESIN than in the controls (all P < .001), and the levels observed for ESCC and HGESIN were also significantly higher than that in LGESIN (both P = .001). These results corresponded to high sensitivity and specificity values in ESCC, HGESIN, and LGESIN tissues. Furthermore, the increased expression of ORAOV1 is significantly associated with lymph node metastasis (P = .001) and an advanced TNM stage (III + IV) (P = .014), and patients with ORAOV1 overexpression experienced shorter overall survival time compared with those with lower ORAOV1 (χ(2) = 11.505, P = .001). This study provides the first evidence of ORAOV1 overexpression in ESCC and ESIN and demonstrates a potential role in tumor progression and metastasis. ORAOV1 overexpression could, therefore, be used as a novel biomarker of poor prognosis in patients with ESCC.
Collapse
Affiliation(s)
- Man Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Xiaobin Cui
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yaoyuan Shen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Hongchao Dong
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Weihua Liang
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Yunzhao Chen
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Jianming Hu
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Shugang Li
- Department of Preventive Medicine, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Jing Kong
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Hongan Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China
| | - Jin Zhao
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China.
| | - Feng Li
- Department of Pathology and Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Pathology, The First Affiliated Hospital, Shihezi University School of Medicine, Shihezi 832002, Xinjiang, China; Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
| |
Collapse
|
12
|
Szyfter K, Wierzbicka M, Hunt JL, Rinaldo A, Rodrigo JP, Takes RP, Ferlito A. Frequent chromosomal aberrations and candidate genes in head and neck squamous cell carcinoma. Eur Arch Otorhinolaryngol 2014; 273:537-45. [PMID: 25355032 DOI: 10.1007/s00405-014-3339-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Accepted: 10/14/2014] [Indexed: 12/21/2022]
Abstract
The knowledge of the biology of head and neck squamous cell carcinoma (HNSCC) has had relatively little impact on the improvement in oncologic outcome up to date. However, the identification of oncogenes and tumor suppressor genes (TSGs) involved in cancer progression contributes to the understanding of the molecular pathways involved in oncogenesis and could contribute to individual risk assessment and provide tools for improvement of treatment and targets for therapy based on the alterations in these pathways. The aim of this article is to review the chromosomal aberrations commonly found in HNSCC, to identify the genes in these chromosomal regions suggested to act as (candidate) oncogenes or TSGs, and to discuss the molecular mechanisms modulating their expression.
Collapse
Affiliation(s)
- Krzysztof Szyfter
- Institute of Human Genetics, Polish Academy of Sciences, Poznan, Poland
| | - Malgorzata Wierzbicka
- Department of Otolaryngology and Laryngeal Oncology, K. Marcinkowski University of Medical Sciences, Poznan, Poland
| | - Jennifer L Hunt
- Department of Pathology and Laboratory Services, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Juan P Rodrigo
- Department of Otolaryngology, Hospital Universitario Central de Asturias, Oviedo, Spain.,Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Robert P Takes
- Department of Otolaryngology Head and Neck Surgery, Radboud University Medicine Center, Nijmegen, The Netherlands
| | - Alfio Ferlito
- University of Udine School of Medicine, Udine, Italy.
| |
Collapse
|
13
|
Roy D, Calaf GM. Allelic loss at chromosome 11q13 alters FGF3 gene expression in a human breast cancer progression model. Oncol Rep 2014; 32:2445-52. [PMID: 25333703 DOI: 10.3892/or.2014.3502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 08/26/2014] [Indexed: 11/06/2022] Open
Abstract
Identification of markers with the potential to predict tumorigenic behavior is important in breast cancer, due to the variability in clinical disease progression. Genetic alterations during neoplastic progression may appear as changes in total DNA content, single genes, or gene expression. Oncogenic alterations are thought to be prognostic indices for patients with breast cancer. Breast cancer deregulation can occur in the normal cellular process and can be measured by microsatellite instability (MSI)/loss of heterozygosity (LOH). Chromosome 11 is unique in this respect, as three regions of MSI/LOH have been identified (11p15-p15.5, 11q13-q13.3 and 11q23-q24). There are many important families of genes, such as FGF, CCND1, FADD, BAD and GAD2, that are located on chromosome 11 and these play a crucial role in breast cancer progression. Among them, different members of the fibroblast growth factor (FGF) family of genes are clustered around human chromosome 11q13 amplicon, which are constantly altering during breast cancer progression. Therefore, in this study, locus 11q13 and FGF3 gene (11q13) function were investigated in a radiation and estrogen breast cancer model induced by high-LET (α-particle) radiation and estrogen exposure. To assess the effect of ionizing radiation and estrogen at chromosome 11q13 loci and the subsequent role of FGF3 gene expression, various microsatellite markers were chosen in this region, and allelic loses (~20-45%) were identified by PCR-SSCP analysis. Results showed an increase in FGF3 protein expression and a 6- to 8-fold change in gene expression of FGF3 and associated genes. These deregulations could be utilized as an appropriate target for therapeutic intervention in breast cancer.
Collapse
Affiliation(s)
- Debasish Roy
- Department of Natural Sciences, Hostos College of the City University of New York, Bronx, NY, USA
| | - Gloria M Calaf
- Instituto de Alta Investigación, Universidad de Tarapacá, Arica, Chile
| |
Collapse
|
14
|
Choi EJ, Yun JA, Jabeen S, Jeon EK, Won HS, Ko YH, Kim SY. Prognostic significance of TMEM16A, PPFIA1, and FADD expression in invasive ductal carcinoma of the breast. World J Surg Oncol 2014; 12:137. [PMID: 24886289 PMCID: PMC4028009 DOI: 10.1186/1477-7819-12-137] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2013] [Accepted: 04/20/2014] [Indexed: 01/01/2023] Open
Abstract
Background 11q13 region is a frequently amplified locus in human malignancies. Among the genes located in this region, FADD is one of the alleged driving genes. Because amplification is not generally confined to a single gene and amplified genes may not show increased expression, we need to evaluate clinical significance of changes occurring in 11q13 region to understand their roles in carcinogenesis. Therefore, we screened expressions of FADD and closely located genes (PPFIA1 and TMEM16A) and evaluated the expressions to find clinical significance in invasive ductal carcinoma of the breast. Methods Ninety-eight cases of invasive ductal carcinoma of the breast were collected. Using archival tissues resected from the cases, we built a tissue microarray and used it in immunohistochemistry. We evaluated the association of FADD, PPFIA1, and TMEM16A expression scores with clinicopathological parameters, including disease-free survival. Results FADD expression was associated with T stage (P = 0.046). The combined score of FADD, PPFIA1, and TMEM16A gene expressions was associated with perineural invasion (P = 0.022). Although individual gene expressions of TMEM16A, FADD, and PPFIA1 failed to show significant association with disease-free survival, combined gene expression scores did show association with disease-free survival (P = 0.034). Conclusions FADD, TMEM16A, and PPFIA1 gene expressions as a whole were associated with disease-free survival in breast cancer.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Su Young Kim
- Department of Pathology, The Catholic University of Korea, School of Medicine, Seochogu Banpodaero 222, Seoul 137-701, South Korea.
| |
Collapse
|
15
|
Paluszczak J, Hemmerling D, Kostrzewska-Poczekaj M, Jarmuż-Szymczak M, Grenman R, Wierzbicka M, Baer-Dubowska W. Frequent hypermethylation of WNT pathway genes in laryngeal squamous cell carcinomas. J Oral Pathol Med 2014; 43:652-7. [PMID: 24762262 DOI: 10.1111/jop.12178] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/03/2014] [Indexed: 12/24/2022]
Abstract
BACKGROUND Aberrations in the function of the WNT signaling pathway have been recently implicated in the pathogenesis of head and neck cancer, and the hypermethylation of several WNT cascade inhibitors were shown to be useful in disease prognosis. However, the extent of deregulation of WNT pathway by DNA hypermethylation has not been studied in detail in laryngeal cancer so far. The aim of this study was to establish the frequency of methylation of WNT pathway negative regulators in laryngeal squamous cell carcinomas and evaluate its prognostic significance. METHODS Twenty-six laryngeal squamous cell carcinoma cell lines and samples obtained from twenty-eight primary laryngeal carcinoma patients were analyzed. The methylation status of DKK1, LKB1, PPP2R2B, RUNX3, SFRP1, SFRP2, and WIF-1 was assessed using the methylation-specific polymerase chain reaction. RESULTS Frequent hypermethylation of DKK1, PPP2R2B, SFRP1, SFRP2, and WIF-1 was detected, and a high methylation index was usually observed. Half of the cell lines analyzed and seventy percent of primary laryngeal carcinoma cases were characterized by the methylation of at least four genes. The hypermethylation of PPP2R2B or WIF-1 was associated with longer survival in laryngeal carcinoma cell lines. Moreover, the concurrent methylation of PPP2R2B and SFRP1 differentiated primary from recurrent laryngeal carcinoma cell lines. CONCLUSIONS Frequent hypermethylation of WNT pathway negative regulators is observed in laryngeal squamous cell carcinomas. The possible prognostic significance of the methylation of DKK1, PPP2R2B, and SFRP1 needs to be evaluated in further prospective studies.
Collapse
Affiliation(s)
- Jarosław Paluszczak
- Department of Pharmaceutical Biochemistry, Poznań University of Medical Sciences, Poznań, Poland
| | | | | | | | | | | | | |
Collapse
|