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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.
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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
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2
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Jacobsen F, Kohsar J, Gebauer F, Kluth M, Hube-Magg C, Simon R, Bockhorn M, Hinsch A, Burandt E, Lübke AM, Steurer S, Tachezy M, Sauter G, Izbicki JR, Wilczak W, Melling N. Loss of p16 and high Ki67 labeling index is associated with poor outcome in esophageal carcinoma. Oncotarget 2020; 11:1007-1016. [PMID: 32256975 PMCID: PMC7105162 DOI: 10.18632/oncotarget.27507] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 01/13/2020] [Indexed: 02/06/2023] Open
Abstract
The p16 tumor suppressor is coded by CDKN2A (9p21) and plays an important role during carcinogenesis and tumor progression in numerous tumor entities. The aim of our study was to evaluate the prognostic role of p16 expression and CDKN2A deletion in esophageal cancer (EC). Therefore, we analyzed p16 and KI67 expression by immunohistochemistry and 9p21 deletion by fluorescence in-situ hybridization on a tissue microarray including 398 adenocarcinomas (AC) and 293 squamous cell carcinomas (SCC) with clinical follow up-data. p16 positivity was found in 30.2% of AC and 13.9% of SCC and CDKN2A deletion in 32.1% of AC and 33.5% of SCC. In SCC p16 immunostaining correlated with low tumor stage (P = 0.014). In AC Ki67 positivity was associated with high tumor stage (P = 0.001), presence of lymph node metastasis (P = 0.009), high UICC stage (P = 0.001) and poor grading (P = 0.005). Overall survival (OS) was shorter for patients with high Ki67 labeling index (Ki67LI; P = 0.009) and negative p16 immunostaining (P = 0.026). In both histological tumor types, CDKN2A deletion showed no association with phenotype or outcome. Proportional cox-regression modeling revealed patients' age, tumor stage, lymph node metastasis and Ki67 labeling index as independent prognostic markers in AC. In SCC, only patients' age and tumor stage proved to be independent prognosticators. In summary, our study shows that loss of p16 expression and high Ki67LI is linked to shortened OS in AC. CDKN2A deletion shows no relevant association with tumor phenotype and patient outcome.
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Affiliation(s)
- Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,These authors contributed equally to this work
| | - Jacob Kohsar
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,These authors contributed equally to this work
| | - Florian Gebauer
- Department of Surgery, University Hospital Cologne, Cologne, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Maximilian Bockhorn
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andrea Hinsch
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Eike Burandt
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Andreas M Lübke
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Stefan Steurer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Michael Tachezy
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jacob R Izbicki
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Wildemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Nathaniel Melling
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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3
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van der Wilk BJ, Noordman BJ, Atmodimedjo PN, Dinjens WNM, Laheij RJF, Wagner A, Wijnhoven BPL, van Lanschot JJB. Development of esophageal squamous cell cancer in patients with FAMMM syndrome: Two clinical reports. Eur J Med Genet 2020; 63:103840. [PMID: 31923587 DOI: 10.1016/j.ejmg.2020.103840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 12/10/2019] [Accepted: 01/05/2020] [Indexed: 12/20/2022]
Abstract
Familial atypical multiple mole melanoma (FAMMM) syndrome is a hereditary syndrome characterized by multiple dysplastic nevi and melanoma. Patients with FAMMM may have a heterozygous, inactivating, pathogenic germline variant in the CDKN2A gene, especially the NM_000077.4: c.225_243del19 (p.p75fs) variant, also known as p16-Leiden variant. Patients with this variant are at high risk for developing melanomas and pancreatic cancer due to somatic inactivation of the wild-type CDKN2A allele. The combination of an inactivating germline CDKN2A mutation and somatic inactivation of the wild-type CDKN2A allele in the same cell results in tumor formation. It has been suggested that carriers of a germline CDKN2A mutation are also at increased risk for several other cancer types, including esophageal cancer. Here, we describe two unrelated patients with the p16-Leiden variant who developed esophageal squamous cell cancer. Evidence of loss of the wild-type CDKN2A allele was obtained in the tumor tissue of both patients indicating biallelic inactivation of p16 in the tumor cells. These results suggest that these patients developed esophageal squamous cell cancer in the context of FAMMM syndrome.
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Affiliation(s)
- Berend J van der Wilk
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands.
| | - Bo J Noordman
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands
| | - Peggy N Atmodimedjo
- Department of Pathology, Erasmus MC Cancer Institute - Erasmus University Medical Center Rotterdam, the Netherlands
| | - Winand N M Dinjens
- Department of Pathology, Erasmus MC Cancer Institute - Erasmus University Medical Center Rotterdam, the Netherlands
| | - Robert J F Laheij
- Department of Gastroenterology and Hepatology, Elisabeth - Tweesteden Hospital, Tilburg, the Netherlands
| | - Anja Wagner
- Department of Clinical Genetics, Erasmus MC Cancer Institute - Erasmus University Medical Center Rotterdam, the Netherlands
| | - Bas P L Wijnhoven
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands
| | - J Jan B van Lanschot
- Department of Surgery, Erasmus MC - University Medical Center, Rotterdam, the Netherlands
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4
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Pennathur A, Godfrey TE, Luketich JD. The Molecular Biologic Basis of Esophageal and Gastric Cancers. Surg Clin North Am 2019; 99:403-418. [PMID: 31047032 DOI: 10.1016/j.suc.2019.02.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Esophageal cancer and gastric cancer are leading causes of cancer-related mortality worldwide. In this article, the authors discuss the molecular biology of esophageal and gastric cancer with a focus on esophageal adenocarcinoma. They review data from The Cancer Genome Atlas project and advances in the molecular stratification and classification of esophageal carcinoma and gastric cancer. They also summarize advances in microRNA, molecular staging, gene expression profiling, tumor microenvironment, and detection of circulating tumor DNA. Finally, the authors summarize some of the implications of understanding the molecular basis of esophageal cancer and future directions in the management of esophageal cancer.
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Affiliation(s)
- Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, The University of Pittsburgh School of Medicine, University of Pittsburgh, 200 Lothrop St. Suite C-800, Pittsburgh, PA 15213, USA.
| | - Tony E Godfrey
- Department of Surgery, Boston University School of Medicine, 700 Albany St, Boston, MA 02118, USA
| | - James D Luketich
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, The University of Pittsburgh School of Medicine, University of Pittsburgh, 200 Lothrop St. Suite C-800, Pittsburgh, PA 15213, USA
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5
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Su Z, Zou GR, Mao YP, OuYang PY, Cao XL, Xie FY, Li Q. Prognostic impact of family history of cancer in Southern Chinese patients with esophageal squamous cell cancer. J Cancer 2019; 10:1349-1357. [PMID: 31031844 PMCID: PMC6485237 DOI: 10.7150/jca.26511] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 12/05/2018] [Indexed: 12/30/2022] Open
Abstract
Background: First degree family history of cancer is associated with developing esophageal cancer and sparse data is about the impact on poor survival among established esophageal squamous cell cancer (ESCC) patients. In this study, we investigated the prognoses of patients with ESCC with a family history. Methods: A total of 479 ESCC patients were retrospectively enrolled from a Southern Chinese institution. A positive family history was defined as having malignant cancer among parents and siblings. Kaplan-Meier plots and Cox proportional hazards regressions were applied for overall survival (OS) and progression-free survival (PFS). Results: Among 479 patients, 119 (24.8%) and 68 (14.2%) reported a first-degree family history of cancer and digestive tract cancer, respectively. Compared with patients without a family history of cancer, the adjusted hazard ratios (HR) among those with it were 1.40 (95% CI, 1.08-1.82, p=0.011) for death, 1.36 (95% CI, 1.05-1.76, p=0.018) for progression. Similar results were observed in those with a family history of digestive tract cancer (HR=1.69, 95%CI, 1.24-1.98, p=0.001 for death and HR=1.77, 95%CI, 1.30-2.37, p<0.001 for progression, respectively). Furthermore, there was a trend for increasing risk of overall mortality (p=0.021, p=0.004, respectively), and progression (p=0.022, p=0.001, respectively) with an increasing number of affected family members. Conclusion: A first-degree family history of cancer, especially digestive tract cancer is associated with poor survival for established ESCC patients and plays an important role in prognosis. The patients with a family history of cancer might need a greater intensity of treatment and more frequent follow-up.
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Affiliation(s)
- Zhen Su
- Panyu central hospital, Cancer Institute of Panyu, Guangzhou, China
| | - Guo-Rong Zou
- Panyu central hospital, Cancer Institute of Panyu, Guangzhou, China
| | - Yan-Ping Mao
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Pu-Yun OuYang
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Xiao-Long Cao
- Panyu central hospital, Cancer Institute of Panyu, Guangzhou, China
| | - Fang-Yun Xie
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
| | - Qun Li
- Department of Radiation Oncology, Sun Yat-sen University Cancer Center; State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangzhou 510060, China
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6
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Ghobadi N, Mehramiz M, ShahidSales S, Rezaei Brojerdi A, Anvari K, Khazaei M, Rezayi M, Sadegh Khorrami M, Joudi‐Mashhad M, Ramshini H, Ahmadi‐Simab S, Moradi A, Hassanian SM, Ghayour‐Mobarhan M, Boroushaki MT, Ferns GA, Avan A. A genetic variant in
CDKN2A/2B
locus was associated with poor prognosis in patients with esophageal squamous cell carcinoma. J Cell Physiol 2018; 234:5070-5076. [PMID: 30238987 DOI: 10.1002/jcp.27310] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Accepted: 08/02/2018] [Indexed: 12/13/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is among the leading causes of cancer related death. Despite of extensive efforts in identifying valid cancer prognostic biomarkers, only a very small number of markers have been identified. Several genetic variants in the 9p21 region have been identified that are associated with the risk of multiple cancers. Here, we explored the association of two genetic variants in the 9p21 region, CDKN2A/B, rs10811661, and rs1333049 for the first time in 273 subjects with, or without ESCC. We observed that the patients with ESCC had a higher frequency of a TT genotype for rs10811661 than individuals in the control group, and this polymorphism was also associated with tumor size. Moreover, a CC genotype for the rs1333049 polymorphism was associated with a reduced overall survival (OS) of patients with ESCC. In particular, patients with a CC (rs1333049) genotype had a significantly shorter OS (CC genotype: 34.5 ± 8.9 months vs. CG+GG: 47.7 ± 5.9 months; p value = 0.03). We have also shown the association of a novel genetic variant in CDKN2B gene with clinical outcome of patients with ESCC. Further investigations are warranted in a larger population to explore the value of emerging markers as a risk stratification marker in ESCC.
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Affiliation(s)
- Niloofar Ghobadi
- Department of Biochemistry Faculty of Sciences, Payam‐e Noor University of Mashhad Mashhad Iran
- Department of Biology Payam e Noor University, Branch of Sabzevar Sabzevar Iran
| | - Mehrane Mehramiz
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | | | | | - Kazem Anvari
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Majid Khazaei
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | - Majid Rezayi
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
| | - Mohammad Sadegh Khorrami
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Mona Joudi‐Mashhad
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Hassan Ramshini
- Department of Biology Payam e Noor University, Branch of Sabzevar Sabzevar Iran
| | | | - Ali Moradi
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
| | - Seyed Mahdi Hassanian
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Medical Biochemistry School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | | | - Mohammad Taher Boroushaki
- Department of Pharmacology and Pharmacological Research Center of Medicinal Plants Faculty of Medicine, Mashhad University of Medical Sciences Mashhad Iran
| | - Gordon A. Ferns
- Division of Medical Education Brighton & Sussex Medical School Brighton Sussex UK
| | - Amir Avan
- Metabolic syndrome Research center, Mashhad University of Medical Sciences Mashhad Iran
- Cancer Research Center, Mashhad University of Medical Sciences Mashhad Iran
- Department of Modern Sciences and Technologies School of Medicine, Mashhad University of Medical Sciences Mashhad Iran
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7
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Thibodeau ML, Bonakdar M, Zhao E, Mungall KL, Reisle C, Zhang W, Bye MH, Thiessen N, Bleile D, Mungall AJ, Ma YP, Jones MR, Renouf DJ, Lim HJ, Yip S, Ng T, Ho C, Laskin J, Marra MA, Schrader KA, Jones SJM. Whole genome and whole transcriptome genomic profiling of a metastatic eccrine porocarcinoma. NPJ Precis Oncol 2018; 2:8. [PMID: 29872726 PMCID: PMC5871832 DOI: 10.1038/s41698-018-0050-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Revised: 01/26/2018] [Accepted: 02/01/2018] [Indexed: 12/31/2022] Open
Abstract
Eccrine porocarcinomas (EPs) are rare malignant tumours of the intraepidermic sweat gland duct and most often arise from benign eccrine poromas. Some recurrent somatic genomic events have been identified in these malignancies, but very little is known about the complexity of their molecular pathophysiology. We describe the whole genome and whole transcriptome genomic profiling of a metastatic EP in a 66-year-old male patient with a previous history of localized porocarcinoma of the scalp. Whole genome and whole transcriptome genomic profiling was performed on the metastatic EP. Whole genome sequencing was performed on blood-derived DNA in order to allow a comparison between germline and somatic events. We found somatic copy losses of several tumour suppressor genes including APC, PTEN and CDKN2A, CDKN2B and CDKN1A. We identified a somatic hemizygous CDKN2A pathogenic splice site variant. De novo transcriptome assembly revealed abnormal splicing of CDKN2A p14ARF and p16INK4a. Elevated expression of oncogenes EGFR and NOTCH1 was noted and no somatic mutations were found in these genes. Wnt pathway somatic alterations were also observed. In conclusion, our results suggest that the molecular pathophysiology of malignant EP features high complexity and subtle interactions of multiple key genes. Cell cycle dysregulation and CDKN2A loss of function was found to be a new potential driver in EP tumourigenesis. Moreover, the combination of somatic copy number variants and abnormal gene expression perhaps partly related to epigenetic mechanisms, all likely contribute to the development of this rare malignancy in our patient.
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Affiliation(s)
- My Linh Thibodeau
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Melika Bonakdar
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Eric Zhao
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Karen L. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Caralyn Reisle
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Wei Zhang
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Morgan H. Bye
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Nina Thiessen
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Dustin Bleile
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Yussanne P. Ma
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Martin R. Jones
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Daniel J. Renouf
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Howard J. Lim
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Tony Ng
- Department of Pathology & Laboratory Medicine, Vancouver General Hospital, 910 West 10th Avenue, Vancouver, BC V5Z 1M9 Canada
| | - Cheryl Ho
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Janessa Laskin
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
- Department of Medical Oncology, British Columbia Cancer Agency, 600 West 10th Avenue, Vancouver, BC V5Z 4E6 Canada
| | - Marco A. Marra
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
| | - Kasmintan A. Schrader
- Hereditary Cancer Program, Department of Medical Genetics, British Columbia Cancer Agency, 614–750 West Broadway, Vancouver, BC V5Z 1H5 Canada
| | - Steven J. M. Jones
- Department of Medical Genetics, University of British Columbia, C201–4500 Oak Street, Vancouver, BC V6H 3N1 Canada
- Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, 100–570 West 7th Avenue, Vancouver, BC V5Z 4S6 Canada
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8
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Song Q, Jiang D, Wang H, Huang J, Liu Y, Xu C, Hou Y. Chromosomal and Genomic Variations in Esophageal Squamous Cell Carcinoma: A Review of Technologies, Applications, and Prospections. J Cancer 2017; 8:2492-2500. [PMID: 28900487 PMCID: PMC5595079 DOI: 10.7150/jca.19601] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 05/30/2017] [Indexed: 12/14/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignant tumors with poor prognosis worldwide. The poor prognosis is due to the advanced stage at the time of diagnosis and the limited clinical staging lacking significant molecular biomarkers to effectively stratify patients for treatment options. As cancer is a disease of genome instability and a resulting of accumulation of genetic alteration, mounting chromosomal and genomic technologies were developed and progressed rapidly which could be used for characterizing patients in genomics level. In this review, we summarized applications of multiple technologies and research progress at chromosomal and genomic level in ESCC.
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Affiliation(s)
- Qi Song
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Dongxian Jiang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Haixing Wang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Jie Huang
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Yalan Liu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Chen Xu
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
| | - Yingyong Hou
- Department of Pathology, Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
- Department of Pathology, School of Basic Medical Sciences & Zhongshan Hospital, Fudan University, Shanghai 200032, P. R. China
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9
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Donner I, Katainen R, Tanskanen T, Kaasinen E, Aavikko M, Ovaska K, Artama M, Pukkala E, Aaltonen LA. Candidate susceptibility variants for esophageal squamous cell carcinoma. Genes Chromosomes Cancer 2017; 56:453-459. [PMID: 28165652 DOI: 10.1002/gcc.22448] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 01/20/2017] [Accepted: 01/30/2017] [Indexed: 01/01/2023] Open
Abstract
Esophageal cancer is common worldwide, and often fatal. The major histological subtype is esophageal squamous cell carcinoma (ESCC). ESCC shows familial aggregation and high heritability. Mutations in RHBDF2 cause tylosis, a very rare disorder characterized by high life-time risk of ESCC, but no other well-established predisposition genes have been identified. To identify candidate susceptibility variants for ESCC we utilized the Population Information System and the Finnish cancer registry to find study materials by clustering ESCC patients by family name at birth and municipality at birth. We collected archival tissue material and exome sequenced a total of 30 ESCC cases. We prioritized shared, deleterious and rare variants that were significantly enriched in our sample set compared to Finnish and population subset specific controls. Six variants passed filtering, the most frequent being a nonsense mutation in DNAH9 (p.Tyr1573Ter) found in four unrelated patients. DNAH9 has been reported to be frequently lost in ESCC tumors. In this study, one patient's tumor showed loss of the wild type allele of DNAH9 suggesting a tumor suppressive function. A missense variant in GKAP1 was shared by three patients, and missense variants in BAG1, NFX1, FUK, and DDOST by two each. EP300 which has previously been implicated in the genesis of ESCC had a missense variant segregating in three affected individuals in a single family. If validated in independent patient sets, these variants could serve as a tool towards prevention and early diagnosis of ESCC.
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Affiliation(s)
- Iikki Donner
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Riku Katainen
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Tomas Tanskanen
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Eevi Kaasinen
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Kristian Ovaska
- Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Miia Artama
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Eero Pukkala
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Genome Scale Biology Research Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
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10
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Nariman-Saleh-Fam Z, Bastami M, Somi MH, Samadi N, Abbaszadegan MR, Behjati F, Ghaedi H, Tavakkoly-Bazzaz J, Masotti A. In silico dissection of miRNA targetome polymorphisms and their role in regulating miRNA-mediated gene expression in esophageal cancer. Cell Biochem Biophys 2016; 74:483-497. [PMID: 27518186 DOI: 10.1007/s12013-016-0754-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 07/09/2016] [Indexed: 12/14/2022]
Abstract
Esophageal cancer is the eighth most common cancer worldwide. Also middle-aged obese adults with higher body mass index during childhood have a greater risk to develop esophageal cancer. The contribution of microRNAs to esophageal cancer has been extensively studied and it became clear that these noncoding RNAs may play crucial roles in pathogenesis, diagnosis and prognosis of the disease. Increasing evidences have suggested that polymorphisms perturbing microRNA targetome (i.e., the compendium of all microRNA target sites) are associated with cancers including esophageal cancer. However, the extent to which such variants contribute to esophageal cancer is still unclear. In this study, we applied an in silico approach to systematically identify polymorphisms perturbing microRNA targetome in esophageal cancer and performed various analyses to predict the functional consequences of the occurrence of these variants. The computational results were integrated to provide a prioritized list of the most potentially disrupting esophageal cancer-implicated microRNA targetome polymorphisms along with the in silico insight into the mechanisms with which such variations may modulate microRNA-mediated regulation. The results of this study will be valuable for future functional experiments aimed at dissecting the roles of microRNA targetome polymorphisms in the onset and progression of esophageal cancer.
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Affiliation(s)
- Ziba Nariman-Saleh-Fam
- Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Milad Bastami
- Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Hossein Somi
- Liver and Gastrointestinal Disease Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Naser Samadi
- Faculty of Advanced Biomedical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry and Medical Laboratories, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Abbaszadegan
- Division of Human Genetics, Immunology Research Center, Avicenna Research Institute, Mashhad University of Medical Sciences, Mashhad, 9196773117, Iran
| | - Farkhondeh Behjati
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hamid Ghaedi
- Medical Genetics Department, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Javad Tavakkoly-Bazzaz
- Medical Genetics Department, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran.
| | - Andrea Masotti
- Bambino Gesù Children's Hospital-IRCCS, Gene Expression - Microarrays Laboratory, Viale di San Paolo 15, Rome, 00146, Italy.
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11
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Kishino T, Niwa T, Yamashita S, Takahashi T, Nakazato H, Nakajima T, Igaki H, Tachimori Y, Suzuki Y, Ushijima T. Integrated analysis of DNA methylation and mutations in esophageal squamous cell carcinoma. Mol Carcinog 2016; 55:2077-2088. [PMID: 26756304 DOI: 10.1002/mc.22452] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 12/01/2015] [Accepted: 12/15/2015] [Indexed: 12/12/2022]
Abstract
The recent development of next-generation sequencing technology for extensive mutation analysis, and beadarray technology for genome-wide DNA methylation analysis has made it possible to obtain integrated pictures of genetic and epigenetic alterations, using the same cancer samples. In this study, we aimed to characterize such a picture in esophageal squamous cell carcinomas (ESCCs). Base substitutions of 55 cancer-related genes and copy number alterations (CNAs) of 28 cancer-related genes were analyzed by targeted sequencing. Forty-four of 57 ESCCs (77%) had 64 non-synonymous somatic mutations, and 24 ESCCs (42%) had 35 CNAs. A genome-wide DNA methylation analysis using an Infinium HumanMethylation450 BeadChip array showed that the CpG island methylator phenotype was unlikely to be present in ESCCs, a different situation from gastric and colon cancers. Regarding individual pathways affected in ESCCs, the WNT pathway was activated potentially by aberrant methylation of its negative regulators, such as SFRP1, SFRP2, SFRP4, SFRP5, SOX17, and WIF1 (33%). The p53 pathway was inactivated by TP53 mutations (70%), and potentially by aberrant methylation of its downstream genes. The cell cycle was deregulated by mutations of CDKN2A (9%), deletions of CDKN2A and RB1 (32%), and by aberrant methylation of CDKN2A and CHFR (9%). In conclusion, ESCCs had unique methylation profiles different from gastric and colon cancers. The genes involved in the WNT pathway were affected mainly by epigenetic alterations, and those involved in the p53 pathway and cell cycle regulation were affected mainly by genetic alterations. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Takayoshi Kishino
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan.,Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Tohru Niwa
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Satoshi Yamashita
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Takamasa Takahashi
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Hidetsugu Nakazato
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan.,Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Takeshi Nakajima
- Division of Endoscopy, National Cancer Center Hospital, Tokyo, Japan
| | - Hiroyasu Igaki
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yuji Tachimori
- Division of Esophageal Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yasuyuki Suzuki
- Department of Gastroenterological Surgery, Kagawa University, Kagawa, Japan
| | - Toshikazu Ushijima
- Division of Epigenomics, National Cancer Center Research Institute, Tokyo, Japan
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12
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Hu X, Moon JW, Li S, Xu W, Wang X, Liu Y, Lee JY. Amplification and overexpression of CTTN and CCND1 at chromosome 11q13 in Esophagus squamous cell carcinoma (ESCC) of North Eastern Chinese Population. Int J Med Sci 2016; 13:868-874. [PMID: 27877079 PMCID: PMC5118758 DOI: 10.7150/ijms.16845] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 09/01/2016] [Indexed: 12/13/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) is a genetically complex tumor type and is a major cause of cancer-related mortality. The combination of genetics, diet, behavior, and environment plays an important role in the carcinogenesis of ESCC. To characterize the genomic aberrations of this disease, we investigated the genomic imbalances in 19 primary ESCC cases using high-resolution array comparative genomic hybridization (CGH). All cases showed either loss or gain of whole chromosomes or segments of chromosome(s) with variable genomic sizes. The copy number alterations per case affected the median 34% (~ 1,034Mb/3,000Mb) of the whole genome. Recurrent gains were 1q21.3-qter, 3q13.11-qter, 5pter-p11, 7pter-p15.3, 7p12.1-p11.2, 7q11-q11.2, 8p12-qter, 11q13.2-q13.3, 12pter-p13.31, 17q24.2, 20q11.21-qter, and 22q11.21-q11.22 whereas the recurrent losses were 3pter-p11.1, 4pter-p12, 4q28.3-q31.22, 4q31.3-q32.1, 9pter-p12, 11q22.3-qter and 13q12.11-q22.1. Amplification of 11q13 resulting in overexpression of CTTN/CCND1 was the most prominent finding, which was observed in 13 of 19 ESCC cases. These unique profiles of copy number alteration should be validated by further studies and need to be taken into consideration when developing biomarkers for early detection of ESCC.
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Affiliation(s)
- Xiaoxia Hu
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA; Department of Clinical Medicine, College of Medicine and Health, Lishui University, Zhejiang, 323000, P.R. China
| | - Ji Wook Moon
- Department of Pathology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Shibo Li
- Department of Pediatrics, University of Oklahoma Health Sciences Center, Oklahoma City, OK 73104 USA
| | - Weihong Xu
- Department of Pathology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Xianfu Wang
- Department of Pathology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
| | - Yuanyuan Liu
- Department of Internal Medicine, the First Hospital of Jilin University, Jilin, 130021, P.R. China
| | - Ji-Yun Lee
- Department of Pathology, Korea University College of Medicine, Seoul, 02841, Republic of Korea
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13
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Hu N, Wang C, Clifford RJ, Yang HH, Su H, Wang L, Wang Y, Xu Y, Tang ZZ, Ding T, Zhang T, Goldstein AM, Giffen C, Lee MP, Taylor PR. Integrative genomics analysis of genes with biallelic loss and its relation to the expression of mRNA and micro-RNA in esophageal squamous cell carcinoma. BMC Genomics 2015; 16:732. [PMID: 26409826 PMCID: PMC4584010 DOI: 10.1186/s12864-015-1919-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 09/11/2015] [Indexed: 12/11/2022] Open
Abstract
Background Genomic instability plays an important role in human cancers. We previously characterized genomic instability in esophageal squamous cell carcinomas (ESCC) in terms of loss of heterozygosity (LOH) and copy number (CN) changes in tumors. In the current study we focus on biallelic loss and its relation to expression of mRNA and miRNA in ESCC using results from 500K SNP, mRNA, and miRNA arrays in 30 cases from a high-risk region of China. Results (i) Biallelic loss was uncommon but when it occurred it exhibited a consistent pattern: only 77 genes (<0.5 %) showed biallelic loss in at least 10 % of ESCC samples, but nearly all of these genes were concentrated on just four chromosomal arms (ie, 42 genes on 3p, 14 genes on 9p, 10 genes on 5q, and seven genes on 4p). (ii) Biallelic loss was associated with lower mRNA expression: 52 of the 77 genes also had RNA expression data, and 41 (79 %) showed lower expression levels in cases with biallelic loss compared to those without. (iii) The relation of biallelic loss to miRNA expression was less clear but appeared to favor higher miRNA levels: of 60 miRNA-target gene pairs, 34 pairs (57 %) had higher miRNA expression with biallelic loss than without, while 26 pairs (43 %) had lower miRNA expression. (iv) Finally, the effect of biallelic loss on the relation between miRNA and mRNA expression was complex. Biallelic loss was most commonly associated with a pattern of elevated miRNA and reduced mRNA (43 %), but a pattern of both reduced miRNA and mRNA was also common (35 %). Conclusion Our results indicate that biallelic loss in ESCC is uncommon, but when it occurs it is localized to a few specific chromosome regions and is associated with reduced mRNA expression of affected genes. The effect of biallelic loss on miRNA expression and on the relation between miRNA and mRNA expressions was complex. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1919-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Nan Hu
- Genetic Epidemiology Branch, DCEG, NCI, 9609 Medical Center Drive, Rm 6E444 MSC 9769, Bethesda, MD, 20892-9769, USA.
| | - Chaoyu Wang
- Genetic Epidemiology Branch, DCEG, NCI, 9609 Medical Center Drive, Rm 6E444 MSC 9769, Bethesda, MD, 20892-9769, USA.
| | - Robert J Clifford
- High-dimension Data Analysis Group, Basic Research Laboratory, Center for Cancer Research, 9609 Medical Center Drive, Rm 1W586, Bethesda, MD, 20892, USA.
| | - Howard H Yang
- High-dimension Data Analysis Group, Basic Research Laboratory, Center for Cancer Research, 9609 Medical Center Drive, Rm 1W586, Bethesda, MD, 20892, USA.
| | - Hua Su
- Genetic Epidemiology Branch, DCEG, NCI, 9609 Medical Center Drive, Rm 6E444 MSC 9769, Bethesda, MD, 20892-9769, USA.
| | - Lemin Wang
- Genetic Epidemiology Branch, DCEG, NCI, 9609 Medical Center Drive, Rm 6E444 MSC 9769, Bethesda, MD, 20892-9769, USA.
| | - Yuan Wang
- Shanxi Cancer Hospital, Taiyuan, Shanxi, 030013, People's Republic of China.
| | - Yi Xu
- Shanxi Cancer Hospital, Taiyuan, Shanxi, 030013, People's Republic of China.
| | - Ze-Zhong Tang
- Shanxi Cancer Hospital, Taiyuan, Shanxi, 030013, People's Republic of China.
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, 030013, People's Republic of China.
| | - Tongwu Zhang
- Laboratory of Translational Genomics, DCEG, NCI, Bethesda, MD, 20892, USA.
| | - Alisa M Goldstein
- Genetic Epidemiology Branch, DCEG, NCI, 9609 Medical Center Drive, Rm 6E444 MSC 9769, Bethesda, MD, 20892-9769, USA.
| | - Carol Giffen
- Information Management Services, Inc., Silver Spring, Bethesda, MD, 20904, USA.
| | - Maxwell P Lee
- High-dimension Data Analysis Group, Basic Research Laboratory, Center for Cancer Research, 9609 Medical Center Drive, Rm 1W586, Bethesda, MD, 20892, USA.
| | - Philip R Taylor
- Genetic Epidemiology Branch, DCEG, NCI, 9609 Medical Center Drive, Rm 6E444 MSC 9769, Bethesda, MD, 20892-9769, USA.
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14
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Li WQ, Pfeiffer RM, Hyland PL, Shi J, Gu F, Wang Z, Bhattacharjee S, Luo J, Xiong X, Yeager M, Deng X, Hu N, Taylor PR, Albanes D, Caporaso NE, Gapstur SM, Amundadottir L, Chanock SJ, Chatterjee N, Landi MT, Tucker MA, Goldstein AM, Yang XR. Genetic polymorphisms in the 9p21 region associated with risk of multiple cancers. Carcinogenesis 2014; 35:2698-705. [PMID: 25239644 DOI: 10.1093/carcin/bgu203] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The chromosome 9p21 region has been implicated in the pathogenesis of multiple cancers. We analyzed 9p21 single nucleotide polymorphisms (SNPs) from eight genome-wide association studies (GWAS) with data deposited in dbGaP, including studies of esophageal squamous cell carcinoma (ESCC), gastric cancer (GC), pancreatic cancer, renal cell carcinoma (RCC), lung cancer (LC), breast cancer (BrC), bladder cancer (BC) and prostate cancer (PrC). The number of subjects ranged from 2252 (PrC) to 7619 (LC). SNP-level analyses for each cancer were conducted by logistic regression or random-effects meta-analysis. A subset-based statistical approach (ASSET) was performed to combine SNP-level P values across multiple cancers. We calculated gene-level P values using the adaptive rank truncated product method. We identified that rs1063192 and rs2157719 in the CDKN2A/2B region were significantly associated with ESCC and rs2764736 (3' of TUSC1) was associated with BC (P ≤ 2.59 × 10(-6)). ASSET analyses identified four SNPs significantly associated with multiple cancers: rs3731239 (CDKN2A intronic) with ESCC, GC and BC (P = 3.96 × 10(-) (4)); rs10811474 (3' of IFNW1) with RCC and BrC (P = 0.001); rs12683422 (LINGO2 intronic) with RCC and BC (P = 5.93 × 10(-) (4)) and rs10511729 (3' of ELAVL2) with LC and BrC (P = 8.63 × 10(-) (4)). At gene level, CDKN2B, CDKN2A and CDKN2B-AS1 were significantly associated with ESCC (P ≤ 4.70 × 10(-) (5)). Rs10511729 and rs10811474 were associated with cis-expression of 9p21 genes in corresponding cancer tissues in the expression quantitative trait loci analysis. In conclusion, we identified several genetic variants in the 9p21 region associated with the risk of multiple cancers, suggesting that this region may contribute to a shared susceptibility across different cancer types.
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Affiliation(s)
- Wen-Qing Li
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Department of Dermatology, Warren Alpert Medical School, Brown University, Providence, RI, USA,
| | - Ruth M Pfeiffer
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Paula L Hyland
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Fangyi Gu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Zhaoming Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | | | - Jun Luo
- Information Management Services, Inc., Calverton, MD, USA and
| | - Xiaoqin Xiong
- Information Management Services, Inc., Calverton, MD, USA and
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Xiang Deng
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA, Cancer Genomics Research Laboratory, NCI-Frederick, SAIC-Frederick Inc., Frederick, MD, USA
| | - Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Demetrius Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Neil E Caporaso
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Susan M Gapstur
- Epidemiology Research Program, American Cancer Society, Atlanta, GA, USA
| | - Laufey Amundadottir
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Nilanjan Chatterjee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Maria Teresa Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Margaret A Tucker
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
| | - Xiaohong R Yang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institute of Health, Bethesda, MD, USA
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15
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Kawano H, Saeki H, Kitao H, Tsuda Y, Otsu H, Ando K, Ito S, Egashira A, Oki E, Morita M, Oda Y, Maehara Y. Chromosomal instability associated with global DNA hypomethylation is associated with the initiation and progression of esophageal squamous cell carcinoma. Ann Surg Oncol 2014; 21 Suppl 4:S696-702. [PMID: 24898425 DOI: 10.1245/s10434-014-3818-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Indexed: 02/01/2023]
Abstract
BACKGROUND Global DNA hypomethylation is associated with increased chromosomal instability and plays an important role in tumorigenesis. The methylation status of the long interspersed nuclear element-1 (LINE-1) element is a useful surrogate marker for global DNA methylation. Although LINE-1 hypomethylation is recognized as a poor prognostic marker, the correlation of LINE-1 methylation level with tumor suppressor gene mutation, chromosomal instability, and clinical significance in esophageal squamous cell carcinoma (ESCC) remains unclear. METHODS Using resected tumor tissues and the corresponding normal esophageal mucosa from 105 patients with ESCC, bisulfite pyrosequencing analysis was performed to quantify the LINE-1 methylation levels. p53 mutations in exons two to ten were detected by polymerase chain reaction direct sequencing. Chromosomal instability was assessed by single nucleotide polymorphism array comparative genomic hybridization analysis. RESULTS The LINE-1 methylation level of ESCC was significantly lower than matched normal mucosa. LINE-1 methylation levels of normal mucosa from the esophagus had a significant inverse correlation with both cigarette smoking and alcohol consumption of the study subjects. LINE-1 hypomethylation of ESCC was significantly associated with lymph node metastasis, lymphovascular invasion, the frequency of p53 mutation and poor survivability. The LINE-1 methylation levels in ESCC had a significant inverse association with the percentage of copy number alterations in the whole genome, mirroring chromosomal instability. CONCLUSIONS Our results suggested that whole genome hypomethylation caused by chronic inflammation could initiate carcinogenesis of esophageal squamous cells through chromosomal instability. In addition, chromosomal instability associated with the global hypomethylation might correlate highly with the progression of ESCC.
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Affiliation(s)
- Hiroyuki Kawano
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Fukuoka, Japan
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16
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Ko JM, Zhang P, Law S, Fan Y, Song YQ, Zhao XK, Wong EHW, Tang S, Song X, Lung ML, Wang LD. Identity-by-descent approaches identify regions of importance for genetic susceptibility to hereditary esophageal squamous cell carcinoma. Oncol Rep 2014; 32:860-70. [PMID: 24890309 DOI: 10.3892/or.2014.3222] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2014] [Accepted: 04/30/2014] [Indexed: 11/05/2022] Open
Abstract
Worldwide, the highest prevalence of esophageal cancer (EC) occurs in Northern China. High-density SNP arrays allow identification of identity-by-descent (IBD) segments in genomic DNAs representative of shared common ancestral regions. We utilized IBD approaches to map susceptibility loci associated with low-penetrance SNPs in high-risk Henan hereditary esophageal squamous cell carcinoma (ESCC) patients. Affymetrix GeneChip Human mapping SNP array IBD analysis was performed in 32 Henan family history-positive (FH+) ESCC patients, 18 Henan healthy unrelated individuals, and 45 Chinese individuals from a CHB HapMap dataset using PLink (scoring IBD segments individually) and Beagle (scoring of shared IBD segments among case/case vs. control/control pairs) software. Both analyses identified longer IBD segment lengths associated with FH+ ESCC compared to controls. However, there was no strong evidence for a genetic founder effect. Pairing IBD analysis with BEAGLE identified 8 critical IBD segments residing at 2q32.1-q32.2, 3p22.3-p22.2, 4q21.1-q21.21, 7p22.2, 8q23.2-q23.3, 10q23.33-q24.1, 14q24.3 and 16q11.2-q12.1, which were more significantly shared among case/case compared to control/control. The shared IBD segments in FH+ ESCC samples with no overlap with control/CHB Hapmap may encompass potential cancer susceptibility loci. Selected targeted genes, PLCE1, GPT2, SIAH1 and CYP2C-18, residing within the IBD segments at 10q23.33-q24.1 and 16q11.2-q12.1, had statistically significant differential expression in primary ESCC tissues and are likely involved in ESCC carcinogenesis. The importance of these IBD segments to the etiology and development of ESCC in high-risk areas requires further study with expanded sample sizes. This is the first report employing the pairing IBD approach for elucidation of the genetic basis of hereditary ESCC in Henan by applying high throughput SNP array analysis.
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Affiliation(s)
- Josephine My Ko
- Department of Clinical Oncology, University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Peng Zhang
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Simon Law
- Department of Surgery, University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Yanhui Fan
- Department of Biochemistry, University of Hong Kong, Hong Kong, SAR, P.R. China
| | - You-Qiang Song
- Department of Biochemistry, University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Xue Ke Zhao
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Elibe H W Wong
- Department of Clinical Oncology, University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Sa Tang
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Xin Song
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, P.R. China
| | - Maria Li Lung
- Department of Clinical Oncology, University of Hong Kong, Hong Kong, SAR, P.R. China
| | - Li Dong Wang
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated Hospital, Zhengzhou University, Zhengzhou, Henan, P.R. China
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Hou JZ, Feng J, Hou ZJ. Relationship between the nm23 gene and prognosis of esophageal carcinoma. Shijie Huaren Xiaohua Zazhi 2013; 21:3356-3362. [DOI: 10.11569/wcjd.v21.i31.3356] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The occurrence and development of esophageal cancer are the result of multiple gene interactions, and the nm23 gene is involved in the regulation of tumor cell metastasis and can inhibit lymph node metastasis. The detection of the change in the nm23 gene can help predict the presence of lymph node metastasis or not in esophageal carcinoma. Moreover, nm23 is an important indicator for prognosis evaluation in esophageal carcinoma.
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Pennathur A, Xi L, Litle VR, Gooding WE, Krasinskas A, Landreneau RJ, Godfrey TE, Luketich JD. Gene expression profiles in esophageal adenocarcinoma predict survival after resection. J Thorac Cardiovasc Surg 2013; 145:505-12; discussion 512-3. [PMID: 23321130 DOI: 10.1016/j.jtcvs.2012.10.031] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Revised: 09/28/2012] [Accepted: 10/22/2012] [Indexed: 01/22/2023]
Abstract
OBJECTIVE The incidence of esophageal adenocarcinoma is rapidly increasing in the western population. Despite aggressive treatment, survival after esophagectomy is suboptimal. The main objective of the present study was to evaluate the gene expression profiles in esophageal adenocarcinoma and determine their association with survival after resection. METHODS We conducted a prospective National Institutes of Health/National Cancer Institute funded study to evaluate the prognostic significance of gene expression in patients with esophageal adenocarcinoma undergoing esophagectomy. Gene expression in tumor tissue was analyzed using high-throughput oligonucleotide arrays. The association of gene expression and overall survival was analyzed using the tail-strength statistic and Cox regression analysis. Gene signatures were constructed with semisupervised methods using principal components. A cross-validated risk score was devised by conducting 10-fold cross-validation, 100 times. RESULTS We evaluated the gene expression in 64 patients with esophageal adenocarcinoma who underwent esophagectomy. The median overall survival was 27 months (95% confidence interval 22 to not reached). After filtering, 10,214 probe sets were used for survival analysis. The tail-strength statistic for these probe sets (0.318) indicated a significant association with overall survival. Patients were classified into high- and low-risk groups, according to the gene signature. High-risk patients had a predicted median survival of 19 months, but the median was not reached for the low-risk group (P < .05). On multivariate analysis, the gene signature was independently associated with survival (hazard ratio, 2.22; P = .04). CONCLUSIONS Global gene expression levels were significantly associated with overall survival after esophagectomy. Furthermore, individual genes could be successfully combined into a strongly predictive, internally cross-validated gene signature. If validated further, these results could help direct additional clinical trials of neoadjuvant and adjuvant therapies for esophageal adenocarcinoma.
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Affiliation(s)
- Arjun Pennathur
- Department of Cardiothoracic Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA
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Achyut BR, Bader DA, Robles AI, Wangsa D, Harris CC, Ried T, Yang L. Inflammation-mediated genetic and epigenetic alterations drive cancer development in the neighboring epithelium upon stromal abrogation of TGF-β signaling. PLoS Genet 2013; 9:e1003251. [PMID: 23408900 PMCID: PMC3567148 DOI: 10.1371/journal.pgen.1003251] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2012] [Accepted: 12/02/2012] [Indexed: 12/14/2022] Open
Abstract
Deletion of tumor suppressor genes in stromal fibroblasts induces epithelial cancer development, suggesting an important role of stroma in epithelial homoeostasis. However, the underlying mechanisms remain to be elucidated. Here we report that deletion of the gene encoding TGFβ receptor 2 (Tgfbr2) in the stromal fibroblasts (Tgfbr2fspKO) induces inflammation and significant DNA damage in the neighboring epithelia of the forestomach. This results in loss or down-regulation of cyclin-dependent kinase inhibitors p15, p16, and p21, which contribute to the development of invasive squamous cell carcinoma (SCC). Anti-inflammation treatment restored p21 expression, delayed tumorigenesis, and increased survival of Tgfbr2fspKO mice. Our data demonstrate for the first time that inflammation is a critical player in the epigenetic silencing of p21 in tumor progression. Examination of human esophageal SCC showed a down-regulation of TGFβ receptor 2 (TβRII) in the stromal fibroblasts, as well as increased inflammation, DNA damage, and loss or decreased p15/p16 expression. Our study suggests anti-inflammation may be a new therapeutic option in treating human SCCs with down-regulation of TβRII in the stroma. Cancer is no longer regarded as a problem of solely cancer cells. The development and metastasis of cancers clearly involves many aspects of the host. We sought to identify the molecular mechanisms underlying epithelial cancer development due to alterations in stromal cells. Using an animal model in which TGF-β signaling is deleted in stromal fibroblasts, we found that inflammation and DNA damage are induced in the epithelial compartment and are responsible for the loss of cell cycle–dependent kinase inhibitors, leading to the compromise of epithelial cell cycle control. These results are important in understanding the stromal-tumor cross talk which has been an important focus in cancer biology in recent years. Our findings suggest that careful examination of the stromal compartment is important and that anti-inflammation therapy may be a new chemoprevention option for epithelial cancer development.
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Affiliation(s)
- B. R. Achyut
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David A. Bader
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, United States of America
| | - Ana I. Robles
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Darawalee Wangsa
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Curtis C. Harris
- Laboratory of Human Carcinogenesis, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
| | - Li Yang
- Laboratory of Cancer Biology and Genetics, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, United States of America
- * E-mail:
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Abstract
BACKGROUND The chromosome 9p21.3 region has been implicated in the pathogenesis of multiple cancers. METHODS We systematically examined up to 203 tagging SNPs of 22 genes on 9p21.3 (19.9-32.8 Mb) in eight case-control studies: thyroid cancer, endometrial cancer (EC), renal cell carcinoma, colorectal cancer (CRC), colorectal adenoma (CA), oesophageal squamous cell carcinoma (ESCC), gastric cardia adenocarcinoma and osteosarcoma (OS). We used logistic regression to perform single SNP analyses for each study separately, adjusting for study-specific covariates. We combined SNP results across studies by fixed-effect meta-analyses and a newly developed subset-based statistical approach (ASSET). Gene-based P-values were obtained by the minP method using the Adaptive Rank Truncated Product program. We adjusted for multiple comparisons by Bonferroni correction. RESULTS Rs3731239 in cyclin-dependent kinase inhibitors 2A (CDKN2A) was significantly associated with ESCC (P=7 × 10(-6)). The CDKN2A-ESCC association was further supported by gene-based analyses (Pgene=0.0001). In the meta-analyses by ASSET, four SNPs (rs3731239 in CDKN2A, rs615552 and rs573687 in CDKN2B and rs564398 in CDKN2BAS) showed significant associations with ESCC and EC (P<2.46 × 10(-4)). One SNP in MTAP (methylthioadenosine phosphorylase) (rs7023329) that was previously associated with melanoma and nevi in multiple genome-wide association studies was associated with CRC, CA and OS by ASSET (P=0.007). CONCLUSION Our data indicate that genetic variants in CDKN2A, and possibly nearby genes, may be associated with ESCC and several other tumours, further highlighting the importance of 9p21.3 genetic variants in carcinogenesis.
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Abstract
Tumor suppressor genes (TSGs) are guardian genes that play important roles in controlling cell proliferation processes such as cell-cycle checkpoints and inducing apoptosis. Identification of these genes and understanding their functions are critical for further investigation of tumorigenesis. So far, many studies have identified numerous TSGs and illustrated their functions in various types of tumors or normal samples. Furthermore, accumulating evidence has shown that non-coding RNAs can act as TSGs to prevent the tumorigenesis processes. Therefore, there is a growing demand to integrate TSGs with large-scale experimental evidence (e.g. gene expression and epigenetic signatures) to provide a comprehensive resource for further investigation of TSGs and their molecular mechanisms in cancer. To achieve this goal, we first developed a comprehensive literature-based database called TSGene (tumor suppressor gene database), freely available at http://bioinfo.mc.vanderbilt.edu/TSGene/. In the current release, TSGene contains 716 human (637 protein-coding and 79 non-coding genes), 628 mouse and 567 rat TSGs curated from UniProtKB, the Tumor Associated Gene database and 5795 PubMed abstracts. Additionally, the TSGene provides detailed annotations for each TSG, such as cancer mutations, gene expressions, methylation sites, TF regulations and protein–protein interactions.
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Affiliation(s)
- Min Zhao
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37232, USA
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22
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[Chromosomal and genomic aberrations in esophageal squamous cell carcinoma]. YI CHUAN = HEREDITAS 2012; 34:519-25. [PMID: 22659423 DOI: 10.3724/sp.j.1005.2012.00519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies with poor prognosis in China. Patients with ESCC may present with vague symptoms in early stage and most of the cases are diagnosed at advanced stage, without the chance of optimal therapy. In the development and progression of ESCC, cytogenetic and molecular aberrations are frequently observed. This review is to summarize the advances in the chromosomal and genomic alterations of ESCC reported recently.
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Su H, Hu N, Yang HH, Wang C, Takikita M, Wang QH, Giffen C, Clifford R, Hewitt SM, Shou JZ, Goldstein AM, Lee MP, Taylor PR. Global gene expression profiling and validation in esophageal squamous cell carcinoma and its association with clinical phenotypes. Clin Cancer Res 2011; 17:2955-66. [PMID: 21385931 DOI: 10.1158/1078-0432.ccr-10-2724] [Citation(s) in RCA: 162] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC will enable identification of molecular subtypes and provide potential targets for early detection and therapy. EXPERIMENTAL DESIGN We followed up a previous array study with additional discovery and confirmatory studies in new ESCC cases by using alternative methods. We profiled global gene expression for discovery and confirmation, and validated selected dysregulated genes with additional RNA and protein studies. RESULTS A total of 159 genes showed differences with extreme statistical significance (P < E-15) and 2-fold differences or more in magnitude (tumor/normal RNA expression ratio, N = 53 cases), including 116 upregulated and 43 downregulated genes. Of 41 genes dysregulated in our prior array study, all but one showed the same fold change directional pattern in new array studies, including 29 with 2-fold changes or more. Alternative RNA expression methods validated array results: more than two thirds of 51 new cases examined by real-time PCR (RT-PCR) showed 2-fold differences or more for all seven genes assessed. Immunohistochemical protein expression results in 275 cases which were concordant with RNA for five of six genes. CONCLUSION We identified an expanded panel of genes dysregulated in ESCC and confirmed previously identified differentially expressed genes. Microarray-based gene expression results were confirmed by RT-PCR and protein expression studies. These dysregulated genes will facilitate molecular categorization of tumor subtypes and identification of their risk factors, and serve as potential targets for early detection, outcome prediction, and therapy.
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Affiliation(s)
- Hua Su
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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24
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Su H, Hu N, Yang HH, Wang C, Takikita M, Wang QH, Giffen C, Clifford R, Hewitt SM, Shou JZ, Goldstein AM, Lee MP, Taylor PR, Kaempgen E, Van Gool SW, Helms W, Keegan P, Pazdur R. Global gene expression profiling and validation in esophageal squamous cell carcinoma and its association with clinical phenotypes. Clin Cancer Res 2011. [PMID: 29950348 DOI: 10.1158/1078-0432] [Citation(s) in RCA: 402] [Impact Index Per Article: 30.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE Esophageal squamous cell carcinoma (ESCC) is an aggressive tumor with poor prognosis. Understanding molecular changes in ESCC will enable identification of molecular subtypes and provide potential targets for early detection and therapy. EXPERIMENTAL DESIGN We followed up a previous array study with additional discovery and confirmatory studies in new ESCC cases by using alternative methods. We profiled global gene expression for discovery and confirmation, and validated selected dysregulated genes with additional RNA and protein studies. RESULTS A total of 159 genes showed differences with extreme statistical significance (P < E-15) and 2-fold differences or more in magnitude (tumor/normal RNA expression ratio, N = 53 cases), including 116 upregulated and 43 downregulated genes. Of 41 genes dysregulated in our prior array study, all but one showed the same fold change directional pattern in new array studies, including 29 with 2-fold changes or more. Alternative RNA expression methods validated array results: more than two thirds of 51 new cases examined by real-time PCR (RT-PCR) showed 2-fold differences or more for all seven genes assessed. Immunohistochemical protein expression results in 275 cases which were concordant with RNA for five of six genes. CONCLUSION We identified an expanded panel of genes dysregulated in ESCC and confirmed previously identified differentially expressed genes. Microarray-based gene expression results were confirmed by RT-PCR and protein expression studies. These dysregulated genes will facilitate molecular categorization of tumor subtypes and identification of their risk factors, and serve as potential targets for early detection, outcome prediction, and therapy.
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Affiliation(s)
- Hua Su
- Genetic Epidemiology Branch, DCEG, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Whitney Helms
- Office of Hematology and Oncology Products, Office of New Drugs, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Patricia Keegan
- Office of Hematology and Oncology Products, Office of New Drugs, U.S. Food and Drug Administration, Silver Spring, Maryland
| | - Richard Pazdur
- Office of Biostatistics, Office of Translational Sciences, U.S. Food and Drug Administration, Silver Spring, Maryland
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Koshiol J, Kreimer AR. Lessons from Australia: human papillomavirus is not a major risk factor for esophageal squamous cell carcinoma. Cancer Epidemiol Biomarkers Prev 2010; 19:1889-92. [PMID: 20696658 DOI: 10.1158/1055-9965.epi-10-0506] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Affiliation(s)
- Jill Koshiol
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 6120 Executive Boulevard, Rockville, MD 20852-7248, USA.
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Hu N, Wang C, Ng D, Clifford R, Yang HH, Tang ZZ, Wang QH, Han XY, Giffen C, Goldstein AM, Taylor PR, Lee MP. Genomic characterization of esophageal squamous cell carcinoma from a high-risk population in China. Cancer Res 2009; 69:5908-17. [PMID: 19584285 DOI: 10.1158/0008-5472.can-08-4622] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Genomic instability plays an important role in most human cancers. To characterize genomic instability in esophageal squamous cell carcinoma (ESCC), we examined loss of heterozygosity (LOH), copy number (CN) loss, CN gain, and gene expression using the Affymetrix GeneChip Human Mapping 500K (n = 30 cases) and Human U133A (n = 17 cases) arrays in ESCC cases from a high-risk region of China. We found that genomic instability measures varied widely among cases and separated them into two groups: a high-frequency instability group (two-thirds of all cases with one or more instability category of > or =10%) and a low-frequency instability group (one-third of cases with instability of <10%). Genomic instability also varied widely across chromosomal arms, with the highest frequency of LOH on 9p (33% of informative single nucleotide polymorphisms), CN loss on 3p (33%), and CN gain on 3q (48%). Twenty-two LOH regions were identified: four on 9p, seven on 9q, four on 13q, two on 17p, and five on 17q. Three CN loss regions-3p12.3, 4p15.1, and 9p21.3-were detected. Twelve CN gain regions were found, including six on 3q, one on 7q, four on 8q, and one on 11q. One of the most gene-rich of these CN gain regions was 11q13.1-13.4, where 26 genes also had RNA expression data available. CN gain was significantly correlated with increased RNA expression in over 80% of these genes. Our findings show the potential utility of combining CN analysis and gene expression data to identify genes involved in esophageal carcinogenesis.
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Affiliation(s)
- Nan Hu
- Division of Cancer Epidemiology and Genetics, Center for Cancer Research, National Cancer Institute, NIH, Department of Health and Human Services, Bethesda, Maryland 20892-7236, USA
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Chen J, Guo L, Peiffer DA, Zhou L, Chan OTM, Bibikova M, Wickham-Garcia E, Lu SH, Zhan Q, Wang-Rodriguez J, Jiang W, Fan JB. Genomic profiling of 766 cancer-related genes in archived esophageal normal and carcinoma tissues. Int J Cancer 2008; 122:2249-54. [PMID: 18241037 DOI: 10.1002/ijc.23397] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We employed the BeadArraytrade mark technology to perform a genetic analysis in 33 formalin-fixed, paraffin-embedded (FFPE) human esophageal carcinomas, mostly squamous-cell-carcinoma (ESCC), and their adjacent normal tissues. A total of 1,432 single nucleotide polymorphisms (SNPs) derived from 766 cancer-related genes were genotyped with partially degraded genomic DNAs isolated from these samples. This directly targeted genomic profiling identified not only previously reported somatic gene amplifications (e.g., CCND1) and deletions (e.g., CDKN2A and CDKN2B) but also novel genomic aberrations. Among these novel targets, the most frequently deleted genomic regions were chromosome 3p (including tumor suppressor genes FANCD2 and CTNNB1) and chromosome 5 (including tumor suppressor gene APC). The most frequently amplified genomic region was chromosome 3q (containing DVL3, MLF1, ABCC5, BCL6, AGTR1 and known oncogenes TNK2, TNFSF10, FGF12). The chromosome 3p deletion and 3q amplification occurred coincidently in nearly all of the affected cases, suggesting a molecular mechanism for the generation of somatic chromosomal aberrations. We also detected significant differences in germline allele frequency between the esophageal cohort of our study and normal control samples from the International HapMap Project for 10 genes (CSF1, KIAA1804, IL2, PMS2, IRF7, FLT3, NTRK2, MAP3K9, ERBB2 and PRKAR1A), suggesting that they might play roles in esophageal cancer susceptibility and/or development. Taken together, our results demonstrated the utility of the BeadArray technology for high-throughput genetic analysis in FFPE tumor tissues and provided a detailed genetic profiling of cancer-related genes in human esophageal cancer.
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Affiliation(s)
- Jing Chen
- Illumina Inc., San Diego, CA 92121, USA
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Kramar F, Zemanova Z, Michalova K, Babicka L, Ransdorfova S, Hrabal P, Kozler P. Cytogenetic analyses in 81 patients with brain gliomas: correlation with clinical outcome and morphological data. J Neurooncol 2007; 84:201-11. [PMID: 17569001 DOI: 10.1007/s11060-007-9358-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2006] [Accepted: 02/16/2007] [Indexed: 11/27/2022]
Abstract
Specific gene mutations, loss of heterozygosity, deletions and/or amplifications of entire chromosomal regions and gene silencing have been described in gliomas. 82 samples from 81 patients were investigated to detect the deletion of TP53, RB1, CDKN2A genes, deletion of 1p36 and 19q13.3 region, amplification of EGFR gene, trisomy of chromosome 7 and monosomy of chromosome 10 in glial cells. Dual-colour interphase fluorescence in situ hybridization (I-FISH) with locus-specific and/or chromosome enumeration DNA probes were used for cytogenetic analyses. In the study, molecular cytogenetic analyses were successfully performed in 74 patients (91.3%) and were uninformative in 7 only (8.7%). The cytogenetic analyses were correlated with morphological data and clinical outcome. I-FISH was the essential part of diagnostics. In comparison with the clinical data, the patients' age seems to be a factor more important for the overall survival, rather than cytogenetic findings in glial tumours. The combined deletion of 1p36 and 19q13.3 chromosomal regions predicts longer overall survival for patients with oligodendroglial tumours.
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Affiliation(s)
- Filip Kramar
- Department of Neurosurgery, 1st Faculty of Medicine, Charles University and Central Military Hospital, Prague 16902, Czech Republic.
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Li J, Liu Z, Wang Y, Yu Z, Wang M, Zhan Q, Liu Z. Allelic imbalance of chromosome 1q in esophageal squamous cell carcinomas from China: a novel region of allelic loss and significant association with differentiation. Cancer Lett 2005; 220:221-30. [PMID: 15766597 DOI: 10.1016/j.canlet.2004.07.032] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2004] [Revised: 07/23/2004] [Accepted: 07/26/2004] [Indexed: 12/11/2022]
Abstract
Our previous work has shown that a number of genes locating on 1q21 were down-regulated in esophageal squamous cell carcinomas (ESCC) and they may involve in carcinogenesis. To determine whether chromosome 1q LOH occurs in ESCC, we analyzed LOH in 61 ESCCs using 18 microsatellite markers on chromosome 1q. Forty-six of 61 (75.4%) tumors presented LOH at one or more loci. A significant association was found between chromosome 1q LOH and histopathological grade. LOH on D1S3466 had a negative correlation with family history, whereas LOH on D1S2777 positively correlated with smoking. These results suggest this region harbor putative tumor suppressor gene(s) contributing to tumorigenesis and differentiation in ESCC.
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Affiliation(s)
- Jie Li
- National Lab of Molecular Oncology, Cancer Institute, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, People's Republic of China
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30
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N/A. N/A. Shijie Huaren Xiaohua Zazhi 2004; 12:1476-1478. [DOI: 10.11569/wcjd.v12.i6.1476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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