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Erkizan HV, Sukhadia S, Natarajan TG, Marino G, Notario V, Lichy JH, Wadleigh RG. Exome sequencing identifies novel somatic variants in African American esophageal squamous cell carcinoma. Sci Rep 2021; 11:14814. [PMID: 34285259 PMCID: PMC8292420 DOI: 10.1038/s41598-021-94064-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
Esophageal cancer has a strikingly low survival rate mainly due to the lack of diagnostic markers for early detection and effective therapies. In the U.S., 75% of individuals diagnosed with esophageal squamous cell carcinoma (ESCC) are of African descent. African American ESCC (AA ESCC) is particularly aggressive, and its biological underpinnings remain poorly understood. We sought to identify the genomic abnormalities by conducting whole exome sequencing of 10 pairs of matched AA esophageal squamous cell tumor and control tissues. Genomic analysis revealed diverse somatic mutations, copy number alterations (SCNAs), and potential cancer driver genes. Exome variants created two subgroups carrying either a high or low tumor mutation burden. Somatic mutational analysis based on the Catalog of Somatic Mutations in Cancer (COSMIC) detected SBS16 as the prominent signature in the high mutation rate group suggesting increased DNA damage. SBS26 was also detected, suggesting possible defects in mismatch repair and microsatellite instability. We found SCNAs in multiple chromosome segments, encoding MYC on 8q24.21, PIK3CA and SOX2 on 3q26, CCND1, SHANK2, CTTN on 11q13.3, and KRAS on 12p12. Amplifications of EGFRvIII and EGFRvIVa mutants were observed in two patients, representing a novel finding in ESCC that has potential clinical relevance. This present exome sequencing, which to our knowledge, represents the first comprehensive exome analysis exclusively in AA ESCC, and highlights novel mutated loci that might explain the aggressive nature of AA ESCC and lead to the development of diagnostic and prognostic markers as well as therapeutic targets.
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Affiliation(s)
- Hayriye Verda Erkizan
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.
| | | | | | - Gustavo Marino
- Hepatology and Gastroenterology, Veterans Affairs Medical Center, Washington, DC, USA
| | - Vicente Notario
- Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Jack H Lichy
- Pathology and Laboratory Service, Veterans Affairs Medical Center, Washington, DC, USA
| | - Robert G Wadleigh
- Institute for Clinical Research, Veterans Affairs Medical Center, Washington, DC, USA.,Hematology and Medical Oncology, Veterans Affairs Medical Center, Washington, DC, USA
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2
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Wang M, Liu B, Li D, Wu Y, Wu X, Jiao S, Xu C, Yu S, Wang S, Yang J, Li Y, Wang Q, Luo S, Tang H. Upregulation of IBSP Expression Predicts Poor Prognosis in Patients With Esophageal Squamous Cell Carcinoma. Front Oncol 2019; 9:1117. [PMID: 31709184 PMCID: PMC6823256 DOI: 10.3389/fonc.2019.01117] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC), which is characterized by invasiveness and poor prognosis, is the sixth most common leading cause of cancer-related death worldwide. Despite advances in multimodality therapy, ESCC mortality remains high, and an understanding of the molecular changes that lead to ESCC development and progression remains limited. In the present study, Integrin Binding Sialoprotein (IBSP) upregulation was found in 182 of 269 (67.7%) primary ESCC cells at the mRNA level by quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, IHC staining further demonstrated that IBSP was upregulated in ESCC patients and IBSP protein upregulation was significantly related to the lymph node metastasis (P = 0.017), clinicopathologic stage (P = 0.001) and poor disease survival (P = 0.002). Moreover, functional studies illustrated that the IBSP gene can promote the proliferation and metastasis of ESCC cells. Furthermore, IBSP was found to regulate epithelial-mesenchymal transition (EMT), which promotes tumor cell metastasis. In conclusion, our study suggests that IBSP may be a valuable prognostic marker for ESCC patients.
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Affiliation(s)
- Mingyue Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Baoxing Liu
- Department of Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Dan Li
- Department of Surgery, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yufeng Wu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Xuan Wu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Shuyue Jiao
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Cong Xu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Sheng Yu
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Shuai Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Jianwei Yang
- Department of Radiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Yanmei Li
- Department of Radiology, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Qiming Wang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Suxia Luo
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
| | - Hong Tang
- Department of Internal Medicine, Affiliated Cancer Hospital of Zhengzhou University, Henan Cancer Hospital, Zhengzhou, China
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Comen EA, Bowman RL, Kleppe M. Underlying Causes and Therapeutic Targeting of the Inflammatory Tumor Microenvironment. Front Cell Dev Biol 2018; 6:56. [PMID: 29946544 PMCID: PMC6005853 DOI: 10.3389/fcell.2018.00056] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 05/11/2018] [Indexed: 12/13/2022] Open
Abstract
Historically, the link between chronic inflammation and cancer has long been speculated. Only more recently, pre-clinical and epidemiologic data as well as clinical evidence all point to the role of the tumor microenvironment as inextricably connected to the neoplastic process. The tumor microenvironment (TME), a complex mix of vasculature, inflammatory cells, and stromal cells is the essential "soil" helping to modulate tumor potential. Increasingly, evidence suggests that chronic inflammation modifies the tumor microenvironment, via a host of mechanisms, including the production of cytokines, pro-inflammatory mediators, angiogenesis, and tissue remodeling. Inflammation can be triggered by a variety of different pressures, such as carcinogen exposure, immune dysfunction, dietary habits, and obesity, as well as genetic alterations leading to oncogene activation or loss of tumor suppressors. In this review, we examine the concept of the tumor microenvironment as related to both extrinsic and intrinsic stimuli that promote chronic inflammation and in turn tumorigenesis. Understanding the common pathways inherent in an inflammatory response and the tumor microenvironment may shed light on new therapies for both primary and metastatic disease. The concept of personalized medicine has pushed the field of oncology to drill down on the genetic changes of a cancer, in the hopes of identifying individually targeted agents. Given the complexities of the tumor microenvironment, it is clear that effective oncologic therapies will necessitate targeting not only the cancer cells, but their dynamic relationship to the tumor microenvironment as well.
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Affiliation(s)
- Elizabeth A. Comen
- Breast Cancer Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Robert L. Bowman
- Center for Hematopoietic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Maria Kleppe
- Center for Hematopoietic Malignancies, Memorial Sloan Kettering Cancer Center, New York, NY, United States
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States
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4
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Alaei S, Sadeghi B, Najafi A, Masoudi-Nejad A. LncRNA and mRNA integration network reconstruction reveals novel key regulators in esophageal squamous-cell carcinoma. Genomics 2018; 111:76-89. [PMID: 29317304 DOI: 10.1016/j.ygeno.2018.01.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2017] [Revised: 01/05/2018] [Accepted: 01/05/2018] [Indexed: 12/19/2022]
Abstract
Many experimental and computational studies have identified key protein coding genes in initiation and progression of esophageal squamous cell carcinoma (ESCC). However, the number of researches that tried to reveal the role of long non-coding RNAs (lncRNAs) in ESCC has been limited. LncRNAs are one of the important regulators of cancers which are transcribed dominantly in the genome and in various conditions. The main goal of this study was to use a systems biology approach to predict novel lncRNAs as well as protein coding genes associated with ESCC and assess their prognostic values. By using microarray expression data for mRNAs and lncRNAs from a large number of ESCC patients, we utilized "Weighted Gene Co-expression Network Analysis" (WGCNA) method to make a big coding-non-coding gene co-expression network, and discovered important functional modules. Gene set enrichment and pathway analysis revealed major biological processes and pathways involved in these modules. After selecting some protein coding genes involved in biological processes and pathways related to cancer, we used "LncTar", a computational tool to predict potential interactions between these genes and lncRNAs. By combining interaction results with Pearson correlations, we introduced some novel lncRNAs with putative key regulatory roles in the network. Survival analysis with Kaplan-Meier estimator and Log-rank test statistic confirmed that most of the introduced genes are associated with poor prognosis in ESCC. Overall, our study reveals novel protein coding genes and lncRNAs associated with ESCC, along with their predicted interactions. Based on the promising results of survival analysis, these genes can be used as good estimators of patients' survival, or even can be analyzed further as new potential signatures or targets for the therapy of ESCC disease.
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Affiliation(s)
- Shervin Alaei
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Balal Sadeghi
- Food Hygiene and Public Health Department, Faculty of Veterinary Medicine, Shahid Bahonar University of Kerman, Kerman, Iran
| | - Ali Najafi
- Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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Wang J, Du Q, Li C. Bioinformatics analysis of gene expression profiles to identify causal genes in luminal B2 breast cancer. Oncol Lett 2017; 14:7880-7888. [PMID: 29250180 PMCID: PMC5727610 DOI: 10.3892/ol.2017.7256] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/03/2017] [Indexed: 12/15/2022] Open
Abstract
Patients with the luminal B subtype of breast cancer exhibit a poor prognosis, high metastatic risk and high incidence of chemotherapy resistance. Luminal B breast cancer is sub-classified into B1 and B2. The pathophysiological mechanism of luminal B2 breast cancer (LB2BC) progression has yet to be characterized. Therefore, the present study aimed to identify the genes involved in the pathogenesis of LB2BC. The data of 117 LB2BC expression profiles were downloaded from The Cancer Genome Atlas (TCGA) and differentially expressed genes (DEGs) were identified by comparison with non-tumor tissue expression profiles. Gene Ontology enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis and protein-protein interaction (PPI) networks were used to obtain insight into the functions of DEGs. Reverse transcription-quantitative polymerase chain reaction (RT-qPCR) analysis was performed to validate the expression level of DEGs in tissue samples. A total of 2,251 DEGs, including 759 upregulated and 1,492 downregulated genes, were identified between LB2BC and non-tumor tissues. The top 15 upregulated and downregulated genes were used to construct a PPI network: Epidermal growth factor receptor (EGFR), fibronectin-1 (FN1) and Polo-like kinase-1 had the highest connectivity degrees. KEGG analysis identified that DEGs were most significantly enriched in 'focal adhesion', 'pathways in cancer' and 'ECM-receptor interaction' pathways. The results of RT-qPCR demonstrated that EGFR was significantly downregulated in LB2BC, whereas FN1 was significantly upregulated, whereas neurotrophic receptor tyrosine kinase 2 (NTRK2) trended towards downregulation. In conclusion, the DEGs identified in the present study, including NTRK2, FN1 and EGFR, may serve pivotal roles in the tumorigenesis of LB2BC by affecting the 'focal adhesion', 'pathways in cancer' and 'ECM-receptor interaction' KEGG pathways.
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Affiliation(s)
- Jinguang Wang
- Department of Thyroid and Breast Surgery, Linyi People's Hospital, Linyi, Shandong 272100, P.R. China
| | - Qi Du
- Department of Prevention and Health Care, Lanshan District Center for Disease Control and Prevention, Linyi, Shandong 276000, P.R. China
| | - Chen Li
- Department of General Surgery, Linyi People's Hospital, Linyi, Shandong 272100, P.R. China
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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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7
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Somatic mutations in ZFHX4 gene are associated with poor overall survival of Chinese esophageal squamous cell carcinoma patients. Sci Rep 2017; 7:4951. [PMID: 28694483 PMCID: PMC5504002 DOI: 10.1038/s41598-017-04221-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/10/2017] [Indexed: 01/05/2023] Open
Abstract
Recent genome-sequencing studies have revealed dozens of genes frequently mutated in esophageal squamous cell carcinoma, but few genes are associated with patients’ clinical outcomes. Novel prognostic biomarkers are urgently needed in the clinic. We collected both somatic mutations and clinical information of 442 Chinese esophageal squamous cell carcinoma patients from four published studies. Survival analysis was performed to reveal the clinical significance of the mutated genes. Dysregulation of the mutated genes was observed from public gene-expression data sets and its effects on cell migration and invasion were investigated with siRNA-mediated silencing. Our integrated analysis revealed 26 genes significantly and frequently mutated in esophageal squamous cell carcinoma. Importantly, mutations in ZFHX4, SPHKAP, NRXN1, KIAA1109, DNAH5 and KCNH7 were associated with poor survival. In addition, ZFHX4 was overexpressed in tumor tissues compared to normal controls, and knockdown of ZFHX4 in vitro significantly inhibited cell migration and invasion. Mutations in ZFHX4 were strongly associated with poor prognosis and the down-regulation of ZFHX4 inhibits the progression of esophageal squamous cell carcinoma. Further investigation is warranted to confirm the prognostic values of ZFHX4 in a prospective study.
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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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Wang Q, Bai J, Abliz A, Liu Y, Gong K, Li J, Shi W, Pan Y, Liu F, Lai S, Yang H, Lu C, Zhang L, Chen W, Xu R, Cai H, Ke Y, Zeng C. An Old Story Retold: Loss of G1 Control Defines A Distinct Genomic Subtype of Esophageal Squamous Cell Carcinoma. GENOMICS PROTEOMICS & BIOINFORMATICS 2015; 13:258-70. [PMID: 26386145 PMCID: PMC4610972 DOI: 10.1016/j.gpb.2015.06.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 06/03/2015] [Accepted: 06/19/2015] [Indexed: 01/12/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) has a high mortality rate. To determine the molecular basis of ESCC development, this study sought to identify characteristic genome-wide alterations in ESCC, including exonic mutations and structural alterations. The clinical implications of these genetic alterations were also analyzed. Exome sequencing and verification were performed for nine pairs of ESCC and the matched blood samples, followed by validation with additional samples using Sanger sequencing. Whole-genome SNP arrays were employed to detect copy number alteration (CNA) and loss of heterozygosity (LOH) in 55 cases, including the nine ESCC samples subjected to exome sequencing. A total of 108 non-synonymous somatic mutations (NSSMs) in 102 genes were verified in nine patients. The chromatin modification process was found to be enriched in our gene ontology (GO) analysis. Tumor genomes with TP53 mutations were significantly more unstable than those without TP53 mutations. In terms of the landscape of genomic alterations, deletion of 9p21.3 covering CDKN2A/2B (30.9%), amplification of 11q13.3 covering CCND1 (30.9%), and TP53 point mutation (50.9%) occurred in two-thirds of the cases. These results suggest that the deregulation of the G1 phase during the cell cycle is a key event in ESCC. Furthermore, six minimal common regions were found to be significantly altered in ESCC samples and three of them, 9p21.3, 7p11.2, and 3p12.1, were associated with lymph node metastasis. With the high correlation of TP53 mutation and genomic instability in ESCC, the amplification of CCND1, the deletion of CDKN2A/2B, and the somatic mutation of TP53 appear to play pivotal roles via G1 deregulation and therefore helps to classify this cancer into different genomic subtypes. These findings provide clinical significance that could be useful in future molecular diagnoses and therapeutic targeting.
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Affiliation(s)
- Qiyan Wang
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China; Beijing University of Chinese Medicine, Beijing 100029, China
| | - Jian Bai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Amir Abliz
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China
| | - Ying Liu
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China
| | - Kenan Gong
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jingjing Li
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China
| | - Wenjie Shi
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Yaqi Pan
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China
| | - Fangfang Liu
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China
| | - Shujuan Lai
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Haijun Yang
- Anyang Cancer Hospital, Anyang 455000, China
| | | | - Lixin Zhang
- Anyang Cancer Hospital, Anyang 455000, China
| | - Wei Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Ruiping Xu
- Anyang Cancer Hospital, Anyang 455000, China
| | - Hong Cai
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China.
| | - Yang Ke
- MOE Key Laboratory of Carcinogenesis and Translational Research, Laboratory of Genetics, Peking University, Cancer Hospital & Institute, Beijing 100142, China.
| | - Changqing Zeng
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China.
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Hao JJ, Yao HQ, Dai GY, Kang W, Jia XM, Xu X, Cai Y, Zhan QM, Wang GQ, Wang MR. Chromosomal aneuploidies and combinational fluorescence in situ hybridization probe panels are useful for predicting prognosis for esophageal squamous cell carcinoma. J Gastroenterol 2015; 50:155-66. [PMID: 24816430 DOI: 10.1007/s00535-014-0961-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Accepted: 04/08/2014] [Indexed: 02/07/2023]
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is a common cancer type in China. In this study, we aimed to develop aneuploidy markers for diagnosis and prognosis of ESCC. METHODS Chromosomal aneuploidies were detected in 493 primary tumors and 61 precancerous lesions by fluorescence in situ hybridization with chromosome enumeration probes (CEP), and cut-off values were set by receiver operating characteristic (ROC) curves. RESULTS According to the cut-off values, chromosomes 3, 8, 10, 12, 17 and 20 presented frequent gains, with rates of 70.1, 69.7, 58.9, 66.9, 67.5 and 77.2 % in tumors and of 32.1, 26.8, 33.9, 41.2, 44.0 and 42.0 % in precancerous lesions. Loss of chromosome Y was detected in 72.0 % of male patients. An optimal four-probe panel CEP3/12/17/20 was established for detecting ESCC (sensitivity: 86.1 %), and CEP3/10/12/20 for precancerous lesions (sensitivity: 48.0 %). Gain of CEP8 was significantly correlated with lymph node metastasis (LNM) and late stages (P = 0.002 and 0.001), and loss of CEPY with age (P = 0.002, male). Kaplan-Meier survival curves indicated that patients with positive CEP10/17 (pT1 + T2, P = 0.041) and CEP8/17 (stages IIb + III + IV, P = 0.002) had poor overall survival. Combinations of LNM/stage and CEP panels could divide patients into more subgroups, including LNM + CEP3/17, LNM + CEP10/17, LNM + CEP3/10/17, stage + CEP3/17, stage + CEP10/17 and stage + CEP3/10/17 (P = 0.0004, 0.0003, 0.0001, 0.005, 0.001 and 0.0008, respectively). Multivariate Cox regression analysis confirmed that the above combinational models were independent prognostic factors. CONCLUSIONS Our data suggest that the combinational probe sets may have potential for detection and prognostic prediction of ESCC.
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Affiliation(s)
- Jia-Jie Hao
- State Key Laboratory of Molecular Oncology, Cancer Institute/Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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Shen Y, Tantai J, Zhao H. Ranking candidate genes of esophageal squamous cell carcinomas based on differentially expressed genes and the topological properties of the co-expression network. Eur J Med Res 2014; 19:52. [PMID: 25358439 PMCID: PMC4223754 DOI: 10.1186/s40001-014-0052-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Accepted: 09/22/2014] [Indexed: 11/18/2022] Open
Abstract
Background The aim of this study was to identify the candidate genes of esophageal squamous cell carcinoma (ESCC). Methods Gene expression profiling of 17 ESCC samples and 17 adjacent normal samples, GSE20347, was downloaded from Gene Expression Omnibus database. The raw data were preprocessed, and the differentially expressed genes (DEGs) between ESCC and normal samples were identified by using SAM software (false discovery rate <0.001). Then, the co-expression network of DEGs was constructed based on Pearson’s correlation test (r-value ≥0.8). Furthermore, the topological properties of the co-expression network were analyzed through NetworkAnalyzer (default settings) of Cytoscape. The expression fold changes of DEGs and topological properties were utilized to identify the candidate genes of ESCC (Crin score >4), which were further analyzed based on DAVID functional enrichment analysis (P-value <0.05). Results A total of 1,063 DEGs were identified, including 490 up-regulated and 573 down-regulated DEGs. Then, the co-expression network of DEGs was constructed, containing 999 nodes and 46,323 edges. Based on the expression fold changes of DEGs and the topological properties of the co-expression network, DEGs were ranked, and the top 24 genes were candidate genes of ESCC, such as CRISP3, EREG, CXCR2, and CRNN. Furthermore, the 24 genes were significantly enriched in bio-functions regarding cell differentiation, glucan biosynthetic process and immune response. Conclusion The present study suggested that CRISP3, EREG, CXCR2, and CRNN might be causative genes of ESCC, and play vital roles in the development of ESCC. However, further experimental studies are needed to confirm our results. Electronic supplementary material The online version of this article (doi:10.1186/s40001-014-0052-x) contains supplementary material, which is available to authorized users.
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12
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PTPLAD2 is a tumor suppressor in esophageal squamous cell carcinogenesis. FEBS Lett 2014; 588:981-9. [DOI: 10.1016/j.febslet.2014.01.058] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Revised: 01/27/2014] [Accepted: 01/30/2014] [Indexed: 11/19/2022]
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13
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Sun Y, Shi N, Lu H, Zhang J, Ma Y, Qiao Y, Mao Y, Jia K, Han L, Liu F, Li H, Lin Z, Li X, Zhao X. ABCC4copy number variation is associated with susceptibility to esophageal squamous cell carcinoma. Carcinogenesis 2014; 35:1941-50. [DOI: 10.1093/carcin/bgu043] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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14
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Wang J, Min A, Gao S, Tang Z. Genetic regulation and potentially therapeutic application of cancer-associated fibroblasts in oral cancer. J Oral Pathol Med 2013; 43:323-34. [PMID: 23782231 DOI: 10.1111/jop.12098] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/16/2013] [Indexed: 12/22/2022]
Affiliation(s)
- Jingyi Wang
- School of Stomatology; Central South University; Changsha China
- Department of Oral and Maxillofacial Surgery; Xiangya Stomatological Hospital; Central South University; Changsha China
| | - Anjie Min
- Department of Oral and Maxillofacial Surgery; Xiangya Hospital; Central South University; Changsha China
| | - Shan Gao
- The Interdisciplinary Nanoscience Center (iNANO); Department of Molecular Biology; University of Aarhus; Aarhus C Denmark
- School of Stomatology; Tianjin Medical University; Tianjin China
| | - Zhangui Tang
- School of Stomatology; Central South University; Changsha China
- Department of Oral and Maxillofacial Surgery; Xiangya Stomatological Hospital; Central South University; Changsha China
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Yan W, Shih J, Rodriguez-Canales J, Tangrea MA, Player A, Diao L, Hu N, Goldstein AM, Wang J, Taylor PR, Lippman SM, Wistuba II, Emmert-Buck MR, Erickson HS. Three-dimensional mRNA measurements reveal minimal regional heterogeneity in esophageal squamous cell carcinoma. THE AMERICAN JOURNAL OF PATHOLOGY 2012; 182:529-39. [PMID: 23219752 DOI: 10.1016/j.ajpath.2012.10.028] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Revised: 09/24/2012] [Accepted: 10/15/2012] [Indexed: 12/11/2022]
Abstract
The classic tumor clonal evolution theory postulates that cancers change over time to produce unique molecular subclones within a parent neoplasm, presumably including regional differences in gene expression. More recently, however, this notion has been challenged by studies showing that tumors maintain a relatively stable transcript profile. To examine these competing hypotheses, we microdissected discrete subregions containing approximately 3000 to 8000 cells (500 to 1500 μm in diameter) from ex vivo esophageal squamous cell carcinoma (ESCC) specimens and analyzed transcriptomes throughout three-dimensional tumor space. Overall mRNA profiles were highly similar in all 59 intratumor comparisons, in distinct contrast to the markedly different global expression patterns observed in other dissected cell populations. For example, normal esophageal basal cells contained 1918 and 624 differentially expressed genes at a greater than twofold level (95% confidence level of <5% false positives), compared with normal differentiated esophageal cells and ESCC, respectively. In contrast, intratumor regions had only zero to four gene changes at a greater than twofold level, with most tumor comparisons showing none. The present data indicate that, when analyzed using a standard array-based method at this level of histological resolution, ESCC contains little regional mRNA heterogeneity.
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Affiliation(s)
- Wusheng Yan
- Pathogenetics Unit, National Institutes of Health, Bethesda, Maryland 20892, USA
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Yan W, Shih JH, Rodriguez-Canales J, Tangrea MA, Ylaya K, Hipp J, Player A, Hu N, Goldstein AM, Taylor PR, Emmert-Buck MR, Erickson HS. Identification of unique expression signatures and therapeutic targets in esophageal squamous cell carcinoma. BMC Res Notes 2012; 5:73. [PMID: 22280838 PMCID: PMC3283499 DOI: 10.1186/1756-0500-5-73] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 01/26/2012] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC), the predominant histological subtype of esophageal cancer, is characterized by high mortality. Previous work identified important mRNA expression differences between normal and tumor cells; however, to date there are limited ex vivo studies examining expression changes occurring during normal esophageal squamous cell differentiation versus those associated with tumorigenesis. In this study, we used a unique tissue microdissection strategy and microarrays to measure gene expression profiles associated with cell differentiation versus tumorigenesis in twelve cases of patient-matched normal basal squamous epithelial cells (NB), normal differentiated squamous epithelium (ND), and squamous cell cancer. Class comparison and pathway analysis were used to compare NB versus tumor in a search for unique therapeutic targets. RESULTS As a first step towards this goal, gene expression profiles and pathways were evaluated. Overall, ND expression patterns were markedly different from NB and tumor; whereas, tumor and NB were more closely related. Tumor showed a general decrease in differentially expressed genes relative to NB as opposed to ND that exhibited the opposite trend. FSH and IgG networks were most highly dysregulated in normal differentiation and tumorigenesis, respectively. DNA repair pathways were generally elevated in NB and tumor relative to ND indicating involvement in both normal and pathological growth. PDGF signaling pathway and 12 individual genes unique to the tumor/NB comparison were identified as therapeutic targets, and 10 associated ESCC gene-drug pairs were identified. We further examined the protein expression level and the distribution patterns of four genes: ODC1, POSTN, ASPA and IGF2BP3. Ultimately, three genes (ODC1, POSTN, ASPA) were verified to be dysregulated in the same pattern at both the mRNA and protein levels. CONCLUSIONS These data reveal insight into genes and molecular pathways mediating ESCC development and provide information potentially useful in designing novel therapeutic interventions for this tumor type.
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Affiliation(s)
- Wusheng Yan
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, USA.
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Ashida S, Orloff MS, Bebek G, Zhang L, Zheng P, Peehl DM, Eng C. Integrated Analysis Reveals Critical Genomic Regions in Prostate Tumor Microenvironment Associated with Clinicopathologic Phenotypes. Clin Cancer Res 2012; 18:1578-87. [DOI: 10.1158/1078-0432.ccr-11-2535] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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18
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Rumiato E, Pasello G, Montagna M, Scaini MC, De Salvo GL, Parenti A, Cagol M, Ruol A, Ancona E, Amadori A, Saggioro D. DNA copy number profile discriminates between esophageal adenocarcinoma and squamous cell carcinoma and represents an independent prognostic parameter in esophageal adenocarcinoma. Cancer Lett 2011; 310:84-93. [PMID: 21757289 DOI: 10.1016/j.canlet.2011.06.017] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2011] [Revised: 06/01/2011] [Accepted: 06/12/2011] [Indexed: 11/17/2022]
Abstract
We report multiplex ligation-dependent probe amplification analysis (MLPA) of DNA copy number alterations in 59 esophageal cancer samples, stratified by histotype. Results showed that squamous cell carcinoma (SCC) samples present clustered abnormalities with several genes altered at high frequency. Instead, esophageal adenocarcinoma (ADC) samples are characterized by a more widespread genomic instability, and in these patients total DNA copy number alterations resulted to be an independent prognostic factor. The detection of characteristic molecular changes represents a step towards a better understanding of the molecular basis of esophageal tumorigenesis, and might offer the potential for the discovery of tumor-specific biomarkers.
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Affiliation(s)
- Enrica Rumiato
- Immunology and Molecular Oncology Unit, Veneto Institute of Oncology IOV--IRCCS, Padova, Italy
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19
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Hu N, Clifford RJ, Yang HH, Wang C, Goldstein AM, Ding T, Taylor PR, Lee MP. Genome wide analysis of DNA copy number neutral loss of heterozygosity (CNNLOH) and its relation to gene expression in esophageal squamous cell carcinoma. BMC Genomics 2010; 11:576. [PMID: 20955586 PMCID: PMC3091724 DOI: 10.1186/1471-2164-11-576] [Citation(s) in RCA: 137] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Accepted: 10/18/2010] [Indexed: 12/14/2022] 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 using the Affymetrix GeneChip Human Mapping 500K array in 30 cases from a high-risk region of China. In the current study we focused on copy number neutral (CN = 2) LOH (CNNLOH) and its relation to gene expression in ESCC. Results Overall we found that 70% of all LOH observed was CNNLOH. Ninety percent of ESCCs showed CNNLOH (median frequency in cases = 60%) and this was the most common type of LOH in two-thirds of cases. CNNLOH occurred on all 39 autosomal chromosome arms, with highest frequencies on 19p (100%), 5p (96%), 2p (95%), and 20q (95%). In contrast, LOH with CN loss represented 19% of all LOH, occurred in just half of ESCCs (median frequency in cases = 0%), and was most frequent on 3p (56%), 5q (47%), and 21q (41%). LOH with CN gain was 11% of all LOH, occurred in 93% of ESCCs (median frequency in cases = 13%), and was most common on 20p (82%), 8q (74%), and 3q (42%). To examine the effect of genomic instability on gene expression, we evaluated RNA profiles from 17 pairs of matched normal and tumor samples (a subset of the 30 ESCCs) using Affymetrix U133A 2.0 arrays. In CN neutral regions, expression of 168 genes (containing 1976 SNPs) differed significantly in tumors with LOH versus tumors without LOH, including 101 genes that were up-regulated and 67 that were down-regulated. Conclusion Our results indicate that CNNLOH has a profound impact on gene expression in ESCC, which in turn may affect tumor development.
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Affiliation(s)
- Nan Hu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, Maryland, USA
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20
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Huang YJ, Niu J, Wei S, Yin M, Liu Z, Wang LE, Sturgis EM, Wei Q. A novel functional DEC1 promoter polymorphism -249T>C reduces risk of squamous cell carcinoma of the head and neck. Carcinogenesis 2010; 31:2082-90. [PMID: 20935061 DOI: 10.1093/carcin/bgq198] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Human DEC1 (deleted in esophageal cancer 1) gene is located on chromosome 9q, a region frequently deleted in various types of human cancers, including squamous cell carcinoma of the head and neck (SCCHN). However, only one epidemiological study has evaluated the association between DEC1 polymorphisms and cancer risk. In this hospital-based case-control study, four potentially functional single-nucleotide polymorphisms -1628 G>A (rs1591420), -606 T>C [rs4978620, in complete linkage disequilibrium with -249T>C (rs2012775) and -122 G>A(rs2012566)], c.179 C>T p.Ala60Val (rs2269700) and 3' untranslated region-rs3750505 as well as the TP53 tumor suppressor gene codon 72 (Arg72Pro, rs1042522) polymorphism were genotyped in 1111 non-Hispanic Whites SCCHN patients and 1130 age-and sex-matched cancer-free controls. After adjustment for age, sex and smoking and drinking status, the variant -606CC (i.e. -249CC) homozygotes had a significantly reduced SCCHN risk (adjusted odds ratio = 0.71, 95% confidence interval = 0.52-0.99) compared with the -606TT homozygotes. Stratification analyses showed that a reduced risk associated with the -606CC genotype was more pronounced in subgroups of non-smokers, non-drinkers, younger subjects (defined as ≤57 years), carriers of the TP53 Arg/Arg (rs1042522) genotype, patients with oropharyngeal cancer or late-stage SCCHN. Further in silico analysis revealed that the -249 T-to-C change led to a gain of a transcription factor-binding site. Additional functional analysis showed that the -249T-to-C change significantly enhanced transcriptional activity of the DEC1 promoter and the DNA-protein-binding activity. We conclude that the DEC1 promoter -249 T>C (rs2012775) polymorphism is functional, modulating susceptibility to SCCHN among non-Hispanic Whites.
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Affiliation(s)
- Yu-Jing Huang
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
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21
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Yang HH, Hu N, Wang C, Ding T, Dunn BK, Goldstein AM, Taylor PR, Lee MP. Influence of genetic background and tissue types on global DNA methylation patterns. PLoS One 2010; 5:e9355. [PMID: 20186319 PMCID: PMC2826396 DOI: 10.1371/journal.pone.0009355] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Accepted: 02/03/2010] [Indexed: 12/31/2022] Open
Abstract
Recent studies have shown a genetic influence on gene expression variation, chromatin, and DNA methylation. However, the effects of genetic background and tissue types on DNA methylation at the genome-wide level have not been characterized extensively. To study the effect of genetic background and tissue types on global DNA methylation, we performed DNA methylation analysis using the Affymetrix 500K SNP array on tumor, adjacent normal tissue, and blood DNA from 30 patients with esophageal squamous cell carcinoma (ESCC). The use of multiple tissues from 30 individuals allowed us to evaluate variation of DNA methylation states across tissues and individuals. Our results demonstrate that blood and esophageal tissues shared similar DNA methylation patterns within the same individual, suggesting an influence of genetic background on DNA methylation. Furthermore, we showed that tissue types are important contributors of DNA methylation states.
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Affiliation(s)
- Howard H. Yang
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Nan Hu
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Chaoyu Wang
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, People's Republic of China
| | - Barbara K. Dunn
- Basic Prevention Science Research Group, Division of Cancer Prevention, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Alisa M. Goldstein
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
| | - Philip R. Taylor
- Genetic Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: (PRT); (MPL)
| | - Maxwell P. Lee
- Laboratory of Population Genetics, Center for Cancer Research, National Cancer Institute, Bethesda, Maryland, United States of America
- * E-mail: (PRT); (MPL)
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Chattopadhyay I, Singh A, Phukan R, Purkayastha J, Kataki A, Mahanta J, Saxena S, Kapur S. Genome-wide analysis of chromosomal alterations in patients with esophageal squamous cell carcinoma exposed to tobacco and betel quid from high-risk area in India. Mutat Res 2010; 696:130-8. [PMID: 20083228 DOI: 10.1016/j.mrgentox.2010.01.001] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 01/04/2010] [Accepted: 01/10/2010] [Indexed: 01/19/2023]
Abstract
Genomic alterations such as chromosomal amplifications, deletions and loss of heterozygosity play an important role in the pathogenesis and progression of cancer. Environmental risk factors contribute to the development and progression of tumors by facilitating the loss of tumor suppressor genes and amplification of oncogenes. In this current study, Affymetrix 10K single nucleotide polymorphism (SNP) arrays were used to evaluate genomic alterations in 20 pairs of matched germ-line and tumor DNA obtained from patients with esophageal squamous cell carcinoma (ESCC) from high-risk area of India where tobacco, betel quid and alcohol use are widespread. Twenty-two amplified regions and 16 deleted regions identified across chromosomal arms were biologically relevant. The candidate genes located at amplified regions of chromosomes or low-level gain regions such as PLA2G5 (1p36-p34), COL11A1 (1p21), KCNK2 (1q41), S100A3 (1q21), ENAH (1q42.12), RGS1 (1q31), KCNH1 (1q32-q41), INSIG2 (2q14.1), FGF12 (3q28), TRIO (5p15.2), RNASEN (5p15.2), FGF10 (5p13-p12), EDN1(6p24.1-p22.3), SULF1 (8q13.2-13.3), TLR4 (9q32-q33), TNC (9q33), NTRK2 (9q22.1), CD44 (11p13), NCAM1 (11q23.1), TRIM29 (11q22-q23), PAK1 (11q13-q14) and RAB27A (15q15-q21.1), are found to be associated with cellular migration and proliferation, tumor cell metastasis and invasion, anchorage independent growth and inhibition of apoptosis. The candidate genes located at deleted regions of chromosomes, such as FBLN2 (3p25.1), WNT7A (3p25), DLC1 (8p22), LZTS1 (8p22), CDKN2A (9p21), COL4A1 (13q34), CDK8 (13q12) and DCC (18q21.3), are found to be associated with the suppression of tumor. The suggested candidate genes were mostly involved in potential signaling pathways such as focal adhesion (COL4A1), tight junction (CLDN10), MAPK signaling pathway (FGF12) and neuroactive ligand receptor interaction pathway (CCKAR). Expression of FGF12 and COL4A1 was validated by tissue microarray. These unique copy number alteration profiles should be taken into consideration when developing biomarkers for the early detection of ESCC in high-risk areas of India in association with tobacco and betel quid use.
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Jeon JP, Shim SM, Jung JS, Nam HY, Lee HJ, Oh BS, Kim K, Kim HL, Han BG. A comprehensive profile of DNA copy number variations in a Korean population: identification of copy number invariant regions among Koreans. Exp Mol Med 2010; 41:618-28. [PMID: 19478558 DOI: 10.3858/emm.2009.41.9.068] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
To examine copy number variations among the Korean population, we compared individual genomes with the Korean reference genome assembly using the publicly available Korean HapMap SNP 50 k chip data from 90 individuals. Korean individuals exhibited 123 copy number variation regions (CNVRs) covering 27.2 mb, equivalent to 1.0% of the genome in the copy number variation (CNV) analysis using the combined criteria of P value (P<0.01) and standard deviation of copy numbers (SD>or= 0.25) among study subjects. In contrast, when compared to the Affymetrix reference genome assembly from multiple ethnic groups, considerably more CNVRs (n=643) were detected in larger proportions (5.0%) of the genome covering 135.1 mb even by more stringent criteria (P<0.001 and SD>or=0.25), reflecting ethnic diversity of structural variations between Korean and other populations. Some CNVRs were validated by the quantitative multiplex PCR of short fluorescent fragment (QMPSF) method, and then copy number invariant regions were detected among the study subjects. These copy number invariant regions would be used as good internal controls for further CNV studies. Lastly, we demonstrated that the CNV information could stratify even a single ethnic population with a proper reference genome assembly from multiple heterogeneous populations.
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Affiliation(s)
- Jae Pil Jeon
- Division of Biobank for Health Sciences, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Seoul 122-701, Korea
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Hu SP, Zhou GB, Luan JA, Chen YP, Xiao DW, Deng YJ, Huang LQ, Cai KL. Polymorphisms of HLA-A and HLA-B genes in genetic susceptibility to esophageal carcinoma in Chaoshan Han Chinese. Dis Esophagus 2010; 23:46-52. [PMID: 19392852 DOI: 10.1111/j.1442-2050.2009.00965.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Esophageal carcinoma (EC) occurs at high rate in Chaoshan region of southern China. Human leukocyte antigen (HLA) polymorphism has been implicated in risk for various cancers. To investigate the impact of HLA-A and HLA-B polymorphisms on susceptibility to EC, a case-control study was conducted among 206 patients with esophageal squamous cell carcinoma and 524 controls from Chaoshan Han population. HLA-A and HLA-B polymorphisms were genotyped by polymerase chain reaction-sequence-specific primers. Genotypic association tests for dominant, recessive, and additive models, and haplotypic association were calculated using unconditional logistic regression. A*11 was identified in a recessive model as an only allele strongly associated with EC risk (odds ratios [OR]=2.10, 95% confidence interval [CI]=1.33-3.31) even after correction for multiple test. The haplotypes A*02-B*46 (OR=1.53, 95% CI=1.04-2.24) and A*11-B*51 (OR=2.29, 95% CI=1.20-4.40) showed association with increased risk for EC, whereas A*11-B*58 (OR=0.00, 95% CI=0.00-0.82) was associated with decreased risk, though the significance of these haplotypes was lost after correction. This is a first association study at genetic level identifying HLA-A and HLA-B-related variations in genetic susceptibility to EC among Chaoshan population. The variation pattern is likely to be EC-specific because it is different from that observed for nasopharyngeal carcinoma in the same study population and might, at least in part, explain the high rate of EC in this ethnic group.
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Affiliation(s)
- Sheng-Ping Hu
- Department of Thoracic Surgery, First Affiliated Hospital, and Center for Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, China.
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Li J, Yang T, Wang L, Yan H, Zhang Y, Guo Y, Pan F, Zhang Z, Peng Y, Zhou Q, He L, Zhu X, Deng H, Levy S, Papasian CJ, Drees BM, Hamilton JJ, Recker RR, Cheng J, Deng HW. Whole genome distribution and ethnic differentiation of copy number variation in Caucasian and Asian populations. PLoS One 2009; 4:e7958. [PMID: 19956714 PMCID: PMC2776354 DOI: 10.1371/journal.pone.0007958] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2008] [Accepted: 07/03/2009] [Indexed: 12/16/2022] Open
Abstract
Although copy number variation (CNV) has recently received much attention as a form of structure variation within the human genome, knowledge is still inadequate on fundamental CNV characteristics such as occurrence rate, genomic distribution and ethnic differentiation. In the present study, we used the Affymetrix GeneChip® Mapping 500K Array to discover and characterize CNVs in the human genome and to study ethnic differences of CNVs between Caucasians and Asians. Three thousand and nineteen CNVs, including 2381 CNVs in autosomes and 638 CNVs in X chromosome, from 985 Caucasian and 692 Asian individuals were identified, with a mean length of 296 kb. Among these CNVs, 190 had frequencies greater than 1% in at least one ethnic group, and 109 showed significant ethnic differences in frequencies (p<0.01). After merging overlapping CNVs, 1135 copy number variation regions (CNVRs), covering approximately 439 Mb (14.3%) of the human genome, were obtained. Our findings of ethnic differentiation of CNVs, along with the newly constructed CNV genomic map, extend our knowledge on the structural variation in the human genome and may furnish a basis for understanding the genomic differentiation of complex traits across ethnic groups.
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Affiliation(s)
- Jian Li
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Tielin Yang
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Liang Wang
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Han Yan
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Yinping Zhang
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Yan Guo
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Feng Pan
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Zhixin Zhang
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Yumei Peng
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Qi Zhou
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Lina He
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Xuezhen Zhu
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
| | - Hongyi Deng
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Shawn Levy
- Vanderbilt Microarray Shared Resource, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Christopher J. Papasian
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Betty M. Drees
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - James J. Hamilton
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
| | - Robert R. Recker
- Osteoporosis Research Center, Creighton University, Omaha, Nebraska, United States of America
| | - Jing Cheng
- National Engineering Research Center for Beijing Biochip Technology, Changping District, Beijing, People's Republic of China
| | - Hong-Wen Deng
- School of Medicine, University of Missouri Kansas City, Kansas City, Missouri, United States of America
- The Key Laboratory of Biomedical Information Engineering of Ministry of Education and Institute of Molecular Genetics, School of Life Science and Technology, Xi'an Jiaotong University, Xi'an, Shanxi, People's Republic of China
- Laboratory of Molecular and Statistical Genetics, College of Life Sciences, Hunan Normal University, Changsha, Hunan, People's Republic of China
- * E-mail:
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26
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Affiliation(s)
- Charis Eng
- Genomic Medicine Institute, Lerner Research Institute and Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio 44195, USA.
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Warnecke-Eberz U, Vallböhmer D, Alakus H, Kütting F, Lurje G, Bollschweiler E, Wienand-Dorweiler A, Drebber U, Hölscher AH, Metzger R. ERCC1 and XRCC1 gene polymorphisms predict response to neoadjuvant radiochemotherapy in esophageal cancer. J Gastrointest Surg 2009; 13:1411-21. [PMID: 19421825 DOI: 10.1007/s11605-009-0881-z] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2009] [Accepted: 03/24/2009] [Indexed: 01/31/2023]
Abstract
INTRODUCTION Neoadjuvant treatment strategies have been developed to improve survival of patients with locally advanced esophageal cancer. Since only patients with major histopathological response benefit from this therapy, predictive markers are needed. We examined a panel of selected gene polymorphisms to predict response to neoadjuvant radiochemotherapy (cisplatin, 5-fluorouracil, 36 Gy) in esophageal cancer patients. MATERIALS AND METHOD Genomic DNA was extracted from paraffin-embedded tissues of 52 patients. Allelic genotyping was performed by real-time polymerase chain reaction using allele-specific TaqMan probes and correlated with therapy response. RESULTS Single-nucleotide polymorphism ERCC1 C118T was predictive for therapy response (p < 0.003). Within the TT genotype group of 25 patients, 20 (80%) did not respond to chemoradiation. Of 20 patients with heterogeneous C/T genotype, 14 (70%) were major responders. The CC genotype (seven patients) was not of predictive importance. ERCC1 polymorphism was significantly (p < 0.02) associated with formation of lymph node metastases. Predominant GG genotype of XRCC1 A194G was not predictive; however, the rarely occurring AA genotype was response-associated and the A/G variant was associated with nonresponse. Fifteen additionally analyzed polymorphisms did not show any correlation. CONCLUSION Our data support the role of ERCC1 as a predictive marker for therapy response. Single-nucleotide polymorphisms of ERCC1 and XRCC1 could be applied to further individualize treatment strategies.
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Affiliation(s)
- Ute Warnecke-Eberz
- Department of General, Visceral, and Cancer Surgery, Center for Integrated Oncology, University Hospital of Cologne, Kerpener Str. 62, 50937, Cologne, Germany.
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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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Zheng YL, Hu N, Sun Q, Wang C, Taylor PR. Telomere attrition in cancer cells and telomere length in tumor stroma cells predict chromosome instability in esophageal squamous cell carcinoma: a genome-wide analysis. Cancer Res 2009; 69:1604-14. [PMID: 19190333 DOI: 10.1158/0008-5472.can-08-3028] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Previous studies showed that chromosomal instability was common in esophageal squamous cell carcinoma (ESCC); however, the mechanisms underlying this instability are unknown. Individuals with deficiencies in telomere maintenance are susceptible to enhanced telomere loss during cell proliferation; such deficiencies could result in telomere dysfunction and genomic instability. We investigated the association between genome-wide chromosomal changes in cancer cells and telomere length/attrition in cancer/stroma cells in 47 ESCC patients. Genome-wide detection of loss of heterozygosity was performed using the Affymetrix GeneChip single nucleotide polymorphism arrays. Telomere length was assessed separately for cancer cells, carcinoma-associated fibroblasts (CAF), infiltrative lymphocytes, and adjacent normal epithelial cells by quantitative fluorescent in situ hybridization using paraffin-embedded sections. Telomere length differed significantly among cell types, such that length in infiltrative lymphocytes > CAFs > cancer cells. Shortened telomeres were observed in cancer cells in 44 of 47 (94%) of the tumors examined. Telomere length in CAFs was significantly associated with chromosomal instability on 4q and 13q and lymphocyte telomere length was significantly associated with instability on chromosomal arms 15q. Although telomere length in cancer cells was not associated with chromosome arm instability, telomere attrition in cancer cells, defined as the telomere length in CAFs minus the telomere length in cancer cells, was significantly associated with chromosomal instability on 13q and 15q. This study provides evidence that telomere shortening is a common genetic alteration in ESCC and that chromosome arm instability is related to both telomere attrition in cancer cells and telomere length in tumor stroma cells.
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Affiliation(s)
- Yun-Ling Zheng
- Cancer Genetics and Epidemiology Program, Lombardi Comprehensive Cancer Center, Georgetown University, Washington, District of Columbia 20057, USA.
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Kuga D, Mizoguchi M, Guan Y, Hata N, Yoshimoto K, Shono T, Suzuki SO, Kukita Y, Tahira T, Nagata S, Sasaki T, Hayashi K. Prevalence of copy-number neutral LOH in glioblastomas revealed by genomewide analysis of laser-microdissected tissues. Neuro Oncol 2008; 10:995-1003. [PMID: 18697953 DOI: 10.1215/15228517-2008-064] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
We have employed a laser-capture microdissection technique and single-nucleotide polymorphism arrays to characterize genomic alterations associated with the development of glioblastoma multiforme (GBM). Combined analysis of loss of heterozygosity (LOH) and copy number revealed that more than half (56.3%) of the 254 identified LOH loci showed no copy-number alteration, indicating the presence of copy-number neutral LOH (cnLOH). Furthermore, we found a GBM case that showed cnLOH in 18 of the 22 autosomes. These results were confirmed by quantitative real-time PCR, microsatellite analysis, and fluorescence in situ hybridization. The high rate of cnLOH suggests that epigenetic abnormalities of many genes are involved in the development and progression of GBMs.
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Affiliation(s)
- Daisuke Kuga
- Department of Neurosurgery, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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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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Assié G, LaFramboise T, Platzer P, Bertherat J, Stratakis CA, Eng C. SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples. Am J Hum Genet 2008; 82:903-15. [PMID: 18355774 DOI: 10.1016/j.ajhg.2008.01.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2007] [Revised: 01/28/2008] [Accepted: 01/29/2008] [Indexed: 11/17/2022] Open
Abstract
SNP arrays provide reliable genotypes and can detect chromosomal aberrations at a high resolution. However, tissue heterogeneity is currently a major limitation for somatic tissue analysis. We have developed SOMATICs, an original program for accurate analysis of heterogeneous tissue samples. Fifty-four samples (42 tumors and 12 normal tissues) were processed through Illumina Beadarrays and then analyzed with SOMATICs. We demonstrate that tissue heterogeneity-related limitations not only can be overcome but can also be turned into an advantage. First, admixture of normal cells with tumor can be used as an internal reference, thereby enabling highly sensitive detection of somatic deletions without having corresponding normal tissue. Second, the presence of normal cells allows for discrimination of somatic from germline aberrations, and the proportion of cells in the tissue sample that are harboring the somatic events can be assessed. Third, relatively early versus late somatic events can also be distinguished, assuming that late events occur only in subsets of cancer cells. Finally, admixture by normal cells allows inference of germline genotypes from a cancer sample. All this information can be obtained from any cancer sample containing a proportion of 40-75% of cancer cells. SOMATICs is a ready-to-use open-source program that integrates all of these features into a simple format, comprehensively describing each chromosomal event.
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Affiliation(s)
- Guillaume Assié
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio 44195, USA
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Heaphy CM, Bisoffi M, Griffith JK. Diagnostic significance of allelic imbalance in cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2007; 1:159-68. [PMID: 23489303 DOI: 10.1517/17530059.1.2.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Allelic imbalance (AI), a deviation from the normal 1:1 ratio of maternal and paternal alleles, occurs in virtually all solid and blood-borne malignancies. The frequency and spectrum of AI in a tumor cell reflects the karyotypic complexity of the cancer genome. Hence, many investigations have assessed the extent of AI to analyze differences between normal and tumor tissues in a variety of different organs. In this review, the authors describe established and emerging technologies used to assess the extent of AI in human tissues, and their application in the diagnosis of cancer. The four major methods to be reviewed represent powerful and widely used tools for the identification of allelic imbalances accompanying cancer initiation and progression. These are fluorescent in situ hybridization, comparative genomic hybridization, single nucleotide polymorphism arrays and the use of microsatellite markers. For each method, the authors provide a brief description of the approach and elaborate on specific studies that highlight its utility in the diagnosis of human cancers.
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Affiliation(s)
- Christopher M Heaphy
- Graduate Research Assistant, University of New Mexico School of Medicine, Department of Biochemistry and Molecular Biology, MSC08 4670, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA +1 505 272 5090 ; +1 505 272 6587 ;
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