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Yu VZ, So SS, Lung BCC, Hou GZ, Wong CWY, Chow LKY, Chung MKY, Wong IYH, Wong CLY, Chan DKK, Chan FSY, Law BTT, Xu K, Tan ZZ, Lam KO, Lo AWI, Lam AKY, Kwong DLW, Ko JMY, Dai W, Law S, Lung ML. ΔNp63-restricted viral mimicry response impedes cancer cell viability and remodels tumor microenvironment in esophageal squamous cell carcinoma. Cancer Lett 2024; 595:216999. [PMID: 38823762 DOI: 10.1016/j.canlet.2024.216999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 05/10/2024] [Accepted: 05/27/2024] [Indexed: 06/03/2024]
Abstract
Tumor protein p63 isoform ΔNp63 plays roles in the squamous epithelium and squamous cell carcinomas (SCCs), including esophageal SCC (ESCC). By integrating data from cell lines and our latest patient-derived organoid cultures, derived xenograft models, and clinical sample transcriptomic analyses, we identified a novel and robust oncogenic role of ΔNp63 in ESCC. We showed that ΔNp63 maintains the repression of cancer cell endogenous retrotransposon expression and cellular double-stranded RNA sensing. These subsequently lead to a restricted cancer cell viral mimicry response and suppressed induction of tumor-suppressive type I interferon (IFN-I) signaling through the regulations of Signal transducer and activator of transcription 1, Interferon regulatory factor 1, and cGAS-STING pathway. The cancer cell ΔNp63/IFN-I signaling axis affects both the cancer cell and tumor-infiltrating immune cell (TIIC) compartments. In cancer cells, depletion of ΔNp63 resulted in reduced cell viability. ΔNp63 expression is negatively associated with the anticancer responses to viral mimicry booster treatments targeting cancer cells. In the tumor microenvironment, cancer cell TP63 expression negatively correlates with multiple TIIC signatures in ESCC clinical samples. ΔNp63 depletion leads to increased cancer cell antigen presentation molecule expression and enhanced recruitment and reprogramming of tumor-infiltrating myeloid cells. Similar IFN-I signaling and TIIC signature association with ΔNp63 were also observed in lung SCC. These results support the potential application of ΔNp63 as a therapeutic target and a biomarker to guide candidate anticancer treatments exploring viral mimicry responses.
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Affiliation(s)
- Valen Zhuoyou Yu
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Shan Shan So
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Bryan Chee-Chad Lung
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - George Zhaozheng Hou
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Carissa Wing-Yan Wong
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Larry Ka-Yue Chow
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Michael King-Yung Chung
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ian Yu-Hong Wong
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Claudia Lai-Yin Wong
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Desmond Kwan-Kit Chan
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Fion Siu-Yin Chan
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Betty Tsz-Ting Law
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kaiyan Xu
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Zack Zhen Tan
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Ka-On Lam
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Anthony Wing-Ip Lo
- Division of Anatomical Pathology, Queen Mary Hospital, Pokfulam, Hong Kong
| | - Alfred King-Yin Lam
- Divsion of Cancer Molecular Pathology, School of Medicine and Dentistry and Menzies Health Institute Queensland, Griffith University, Gold Coast, Australia
| | - Dora Lai-Wan Kwong
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Josephine Mun-Yee Ko
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Wei Dai
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Simon Law
- Department of Surgery, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Maria Li Lung
- Department of Clinical Oncology, Centre of Cancer Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong.
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Wang D, Dai J, Suo C, Wang S, Zhang Y, Chen X. Molecular subtyping of esophageal squamous cell carcinoma by large-scale transcriptional profiling: Characterization, therapeutic targets, and prognostic value. Front Genet 2022; 13:1033214. [DOI: 10.3389/fgene.2022.1033214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/28/2022] [Indexed: 11/11/2022] Open
Abstract
The tumor heterogeneity of the transcriptional profiles is independent of genetic variation. Several studies have successfully identified esophageal squamous cell carcinoma (ESCC) subtypes based on the somatic mutation profile and copy number variations on the genome. However, transcriptome-based classification is limited. In this study, we classified 141 patients with ESCC into three subtypes (Subtype 1, Subtype 2, and Subtype 3) via tumor sample gene expression profiling. Differential gene expression (DGE) analysis of paired tumor and normal samples for each subtype revealed significant difference among subtypes. Moreover, the degree of change in the expression levels of most genes gradually increased from Subtype 1 to Subtype 3. Gene set enrichment analysis (GSEA) identified the representative pathways in each subtype: Subtype 1, abnormal Wnt signaling pathway activation; Subtype 2, inhibition of glycogen metabolism; and Subtype 3, downregulation of neutrophil degranulation process. Weighted gene co-expression network analysis (WGCNA) was used to elucidate the finer regulation of biological pathways and discover hub genes. Subsequently, nine hub genes (CORO1A, CD180, SASH3, CD52, CD300A, CD14, DUSP1, KIF14, and MCM2) were validated to be associated with survival in ESCC based on the RNA sequencing (RNA-seq) data from The Cancer Genome Atlas (TCGA) database. The clustering analysis of ESCC granted better understanding of the molecular characteristics of ESCC and led to the discover of new potential therapeutic targets that may contribute to the clinical treatment of ESCC.
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Abstract
Esophageal squamous cell carcinoma (ESCC) is common in the developing world with decreasing incidence in developed countries and carries significant morbidity and mortality. Major risk factors for ESCC development include significant use of alcohol and tobacco. Screening for ESCC can be recommended in high-risk populations living in highly endemic regions. The treatment of ESCC ranges from endoscopic resection therapy or surgery in localized disease to chemoradiotherapy in metastatic disease, and prognosis is directly related to the stage at diagnosis. New immunotherapies and molecular targeted therapies may improve the dismal survival outcomes in patients with metastatic ESCC.
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Affiliation(s)
- D Chamil Codipilly
- Division of Gastroenterology and Hepatology, Mayo Clinic, SMH Campus, 6 Alfred GI Unit, 200 1st Street South West, Rochester MN 55905, USA
| | - Kenneth K Wang
- Division of Gastroenterology and Hepatology, Mayo Clinic, SMH Campus, 6 Alfred GI Unit, 200 1st Street South West, Rochester MN 55905, USA.
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Modified eQTL and Somatic DNA Segment Alterations in Esophageal Squamous Cell Carcinoma for Genes Related to Immunity, DNA Repair, and Inflammation. Cancers (Basel) 2022; 14:cancers14071629. [PMID: 35406404 PMCID: PMC8996990 DOI: 10.3390/cancers14071629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/21/2022] [Accepted: 03/21/2022] [Indexed: 01/27/2023] Open
Abstract
We integrated ESCC expression and GWAS genotyping, to investigate eQTL and somatic DNA segment alterations, including somatic copy number alteration, allelic imbalance (AI), and loss of heterozygosity (LOH) in ESCC. First, in eQTL analysis, we used a classical approach based on genotype data from GWAS and expression signals in normal tissue samples, and then used a modified approach based on fold change in the tumor vs. normal samples. We focused on the genes in three pathways: inflammation, DNA repair, and immunity. Among the significant (p < 0.05) SNP-probe pairs from classical and modified eQTL analyses, 24 genes were shared by the two approaches, including 18 genes that showed the same numbers of SNPs and probes and 6 genes that had the different numbers of SNPs and probes. For these 18 genes, we found 28 SNP−probe pairs were correlated in opposite directions in the two approaches, indicating an intriguing difference between the classical and modified eQTL approaches. Second, we analyzed the somatic DNA segment alterations. Across the 24 genes, abnormal gene expression on mRNA arrays was seen in 19−95% of cases and 26−78% showed somatic DNA segment alterations on Affymetrix GeneChip Human Mapping Arrays. The results suggested that this strategy could identify gene expression and somatic DNA segment alterations for biological markers (genes) by combining classical and modified eQTLs and somatic DNA evaluation on SNP arrays. Thus, this study approach may allow us to understand functionality indicative of potentially relevant biomarkers in ESCC.
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Wu Q, Liu F, Ge M, Laster KV, Wei L, Du R, Jiang M, Zhang J, Zhi Y, Jin G, Zhao S, Kim DJ, Dong Z, Liu K. BRD4 drives esophageal squamous cell carcinoma growth by promoting RCC2 expression. Oncogene 2022; 41:347-360. [PMID: 34750516 DOI: 10.1038/s41388-021-02099-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 10/18/2021] [Accepted: 10/25/2021] [Indexed: 12/24/2022]
Abstract
The low survival rate of esophageal squamous cell carcinoma patients is primarily attributed to technical limitations and a lack of insight regarding the molecular mechanisms contributing to its progression. Alterations in epigenetic modulators are critical to cancer development and prognosis. BRD4, a chromatin reader protein, plays an essential role in regulating oncogene expression. Here, we investigated the contributing role of BRD4 and its related mechanisms in the context of ESCC tumor progression. Our observations showed that BRD4 transcript and protein expression levels are significantly increased in ESCC patient tissues. Genetic or pharmacological inhibition of BRD4 suppressed ESCC cell proliferation in vitro and in vivo. Proteomic and transcriptomic analyses were subsequently used to deduce the potential targets of BRD4. Mechanistic studies showed that RCC2 is a downstream target of BRD4. Inhibition of either BRD4 or RCC2 resulted in decreased ESCC cell proliferation. The BRD4-TP73 interaction facilitated the binding of BRD4 complex to the promoter region of RCC2, and subsequently modulated RCC2 transcription. Furthermore, targeting BRD4 with inhibitors significantly decreased tumor volume in ESCC PDX models, indicating that BRD4 expression may contribute to tumor progression. Collectively, these findings suggest that BRD4 inhibition could be a promising strategy to treat ESCC by downregulating RCC2.
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Affiliation(s)
- Qiong Wu
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Fangfang Liu
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Mengmeng Ge
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | | | - Lixiao Wei
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Ruijuan Du
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Ming Jiang
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Jing Zhang
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Yafei Zhi
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China.,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China
| | - Guoguo Jin
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.,The Henan Luoyang Orthopedic Hospital, Zhengzhou, 450000, Henan, China
| | - Simin Zhao
- China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.,Affiliated Cancer Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Dong Joon Kim
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China. .,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China.
| | - Zigang Dong
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China. .,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China. .,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450000, Henan, China. .,Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, 450000, Henan, China.
| | - Kangdong Liu
- The Pathophysiology Department, The School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450000, China. .,China-US (Henan) Hormel Cancer Institute, Zhengzhou, 450000, China. .,State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou, 450000, Henan, China. .,Provincial Cooperative Innovation Center for Cancer Chemoprevention, Zhengzhou University, Zhengzhou, 450000, Henan, China. .,Cancer Chemoprevention International Collaboration Laboratory, Zhengzhou, 450000, Henan, China.
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6
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Wang X, Liu Y, Leng X, Cao K, Sun W, Zhu J, Ma J. UBE2T Contributes to the Prognosis of Esophageal Squamous Cell Carcinoma. Pathol Oncol Res 2021; 27:632531. [PMID: 34257599 PMCID: PMC8262217 DOI: 10.3389/pore.2021.632531] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
Background: The ubiquitin-conjugating enzyme E2 T (UBE2T) has been shown to contribute to several types of cancer. However, no publication has reported its implication in esophageal squamous cell cancer (ESCC). Methods: We explored several public databases, including The Cancer Genome Atlas (TCGA), Oncomine, and gene expression Omnibus (GEO). Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, and gene set enrichment analysis (GSEA) were adopted to explore involved signaling pathways. We used R software to develop prognostic gene signatures with the LASSO and stepwise Cox regression analysis, separately. Immunohistochemistry staining was performed to detect UBE2T in 90 ESCC patients, followed by survival analysis. We also used an R package pRRophetic to evaluate chemotherapy sensitivity for the TCGA–ESCC cohort. Results: We found significantly increased UBE2T transcript levels and DNA copy numbers in ESCC tissues. UBE2T was associated with the p53 signaling pathway, cell cycle, Fanconi anemia pathway, and DNA replication, as indicated by Go, KEGG pathway enrichment analysis. These pathways were also upregulated in ESCC. The prognostic signatures with UBE2T-associated genes could stratify ESCC patients into low- and high-risk groups with significantly different overall survival in the TCGA–ESCC cohort. We also validated the association of UBE2T with unfavorable survival in 90 ESCC patients recruited for this study. Moreover, we found that the low-risk group was significantly more sensitive to chemotherapy than the high-risk group. Conclusions: UBE2T is involved in the development of ESCC, and gene signatures derived from UBE2T-associated genes are predictive of prognosis in ESCC.
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Affiliation(s)
- Xiaoyuan Wang
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Yang Liu
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Xue Leng
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
| | - Kui Cao
- Department of Oncology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Wentao Sun
- Department of Radiology, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jinhong Zhu
- Department of Clinical Laboratory, Biobank, Harbin Medical University Cancer Hospital, Harbin, China
| | - Jianqun Ma
- Department of Thoracic Surgery, Harbin Medical University Cancer Hospital, Harbin, China
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7
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Grady WM, Yu M, Markowitz SD, Chak A. Barrett's Esophagus and Esophageal Adenocarcinoma Biomarkers. Cancer Epidemiol Biomarkers Prev 2020; 29:2486-2494. [PMID: 33093162 DOI: 10.1158/1055-9965.epi-20-0223] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/31/2020] [Accepted: 10/15/2020] [Indexed: 12/20/2022] Open
Abstract
Esophageal adenocarcinoma is a major cause of cancer-related morbidity and mortality in Western countries. The incidences of esophageal adenocarcinoma and its precursor Barrett's esophagus have increased substantially in the last four decades. Current care guidelines recommend that endoscopy be used for the early detection and monitoring of patients with Barrett's esophagus; however, the efficacy of this approach is unclear. To prevent the increasing morbidity and mortality from esophageal adenocarcinoma, there is a tremendous need for early detection and surveillance biomarker assays that are accurate, low-cost, and clinically feasible to implement. The last decade has seen remarkable advances in the development of minimally invasive molecular biomarkers, an effort led in large part by the Early Detection Research Network (EDRN). Advances in multi-omics analysis, the development of swallowable cytology collection devices, and emerging technology have led to promising assays that are likely to be implemented into clinical care in the next decade. In this review, an updated overview of the molecular pathology of Barrett's esophagus and esophageal adenocarcinoma and emerging molecular biomarker assays, as well as the role of EDRN in biomarker discovery and validation, will be discussed.See all articles in this CEBP Focus section, "NCI Early Detection Research Network: Making Cancer Detection Possible."
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Affiliation(s)
- William M Grady
- Department of Medicine, University of Washington School of Medicine, Seattle, Washington. .,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Ming Yu
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Sanford D Markowitz
- Oncology Division, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
| | - Amitabh Chak
- Gastroenterology Division, Case Western Reserve University and University Hospitals Cleveland Medical Center, Cleveland, Ohio
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8
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Pan X, Huang L, Mo D, Liang Y, Huang Z, Zhu B, Fang M. SNP rs2240688 in CD133 gene on susceptibility and clinicopathological features of hepatocellular carcinoma. Transl Cancer Res 2020; 9:5940-5948. [PMID: 35117206 PMCID: PMC8799249 DOI: 10.21037/tcr-19-2690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 08/21/2020] [Indexed: 01/30/2023]
Abstract
Background CD133 is one of the important cancer stem cells (CSCs) markers of hepatocellular carcinoma (HCC). The aim of this study was to explore the relationship between CD133 single-nucleotide polymorphisms (SNPs) and risk factors associated with HCC susceptibility and clinicopathological features in HCC cases and healthy controls from the Guangxi region of southern China. Methods A case control study was conducted, including 565 HCC patients and 561 control subjects. The genotyping of rs2240688 was performed using the SNaPshot method. Unconditional logistic regression was used to correct for gender, age, and other confounding factors. Odds ratio (OR) and its 95% confidence interval (CI) were calculated to analyze the relationship between allele and genotype frequency and the risk of HCC. Results The distribution frequencies of CD133 alleles and genotypes in the HCC case group and the control group were statistically significant (P<0.05). The CA heterozygous (P=0.003, OR =1.463, 95% CI: 1.134–1.887) and CC homozygous genotypes (P=0.036, OR =1.910, 95% CI: 1.044–3.493), as well as C carrier status (P=0.004, OR =1.465, 95% CI: 1.136–1.889) and C alleles (P=0.004, OR =1.465, 95% CI: 1.136–1.889), were associated with an increased risk of HCC. Additionally, in the subgroup analysis of CD133 rs2240688 polymorphism and clinical characteristics, the results showed that the genotype distribution of CD133 rs2240688 was significantly different in genotype distribution of metastasis and alanine aminotransferase (ALT). Conclusions the expression of miRNA binding site rs2240688 of tumor stem cell marker gene CD133 in HCC may be a promising marker for the prediction of HCC, but larger studies are still needed.
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Affiliation(s)
- Xiaolan Pan
- Department of Clinical Laboratory, Guangxi Medical University Affiliated Tumor Hospital, Nanning, China
| | - Lingsha Huang
- Department of Clinical Laboratory, Guangxi Medical University Affiliated Tumor Hospital, Nanning, China
| | - Dan Mo
- Department of Surgery, Maternal and Child Health Hospital of the Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yihua Liang
- Department of Clinical Laboratory, Guangxi Medical University Affiliated Tumor Hospital, Nanning, China
| | - Zhaodong Huang
- Department of Clinical Laboratory, Guangxi Medical University Affiliated Tumor Hospital, Nanning, China
| | - Bo Zhu
- Department of Clinical Laboratory, Guangxi Medical University Affiliated Tumor Hospital, Nanning, China
| | - Min Fang
- Department of Clinical Laboratory, Guangxi Medical University Affiliated Tumor Hospital, Nanning, China
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Brown J, Stepien AJ, Willem P. Landscape of copy number aberrations in esophageal squamous cell carcinoma from a high endemic region of South Africa. BMC Cancer 2020; 20:281. [PMID: 32252688 PMCID: PMC7137242 DOI: 10.1186/s12885-020-06788-3] [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: 10/09/2019] [Accepted: 03/26/2020] [Indexed: 02/08/2023] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is an aggressive cancer with one of the highest world incidences in the Eastern Cape region of South Africa. Several genome wide studies have been performed on ESCC cohorts from Asian countries, North America, Malawi and other parts of the world but none have been conducted on ESCC tumors from South Africa to date, where the molecular pathology and etiology of this disease remains unclear. We report here tumor associated copy number changes observed in 51 ESCC patients’ samples from the Eastern Cape province of South Africa. Methods We extracted tumor DNA from 51 archived ESCC specimens and interrogated tumor associated DNA copy number changes using Affymetrix® 500 K SNP array technology. The Genomic Identification of Significant Targets in Cancer (GISTIC 2.0) algorithm was applied to identify significant focal regions of gains and losses. Gains of the top recurrent cancer genes were validated by fluorescence in situ hybridization and their protein expression assessed by immunohistochemistry. Results Twenty-three significant focal gains were identified across samples. Gains involving the CCND1, MYC, EGFR and JAG1 loci recapitulated those described in studies on Asian and Malawian cohorts. The two most significant gains involved the chromosomal sub-bands 3q28, encompassing the TPRG1 gene and 11q13.3 including the CTTN, PPFIA1and SHANK2 genes. There was no significant homozygous loss and the most recurrent hemizygous deletion involved the B3GAT1 gene on chromosome 11q25. Focal gains on 11q13.3 in 37% of cases (19/51), consistently involved CTTN and SHANK2 genes. Twelve of these cases (23,5%), had a broader region of gain that also included the CCND1, FGF19, FGF4 and FGF3 genes. SHANK2 and CTTN are co-amplified in several cancers, these proteins interact functionally together and are involved in cell motility. Immunohistochemistry confirmed both Shank2 (79%) and cortactin (69%) protein overexpression in samples with gains of these genes. In contrast, cyclin D1 (65%) was moderately expressed in samples with CCND1 DNA gain. Conclusions This study reports copy number changes in a South African ESCC cohort and highlights similarities and differences with cohorts from Asia and Malawi. Our results strongly suggest a role for CTTN and SHANK2 in the pathogenesis of ESCC in South Africa.
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Affiliation(s)
- Jacqueline Brown
- School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Services, Johannesburg, South Africa.
| | - Andrzej J Stepien
- Department of Anatomical Pathology, School of Medicine, Faculty of Health Science, Walter Sisulu University, National Health Laboratory Services/NMAH, Mthatha, South Africa
| | - Pascale Willem
- School of Pathology, Department of Molecular Medicine and Haematology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg and the National Health Laboratory Services, Johannesburg, South Africa
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Wang L, Li K, Lin X, Yao Z, Wang S, Xiong X, Ning Z, Wang J, Xu X, Jiang Y, Liu D, Chen Y, Zhang D, Zhang H. Metformin induces human esophageal carcinoma cell pyroptosis by targeting the miR-497/PELP1 axis. Cancer Lett 2019; 450:22-31. [PMID: 30771436 DOI: 10.1016/j.canlet.2019.02.014] [Citation(s) in RCA: 145] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 02/01/2019] [Accepted: 02/08/2019] [Indexed: 02/05/2023]
Abstract
Evasion of apoptosis is a major contributing factor to the development of chemo- and radiotherapy resistance. Therefore, activation of non-apoptotic programmed cell death (PCD) could be an effective alternative against apoptosis-resistant cancers. In this study, we demonstrated in vitro and in vivo that metformin can induce pyroptosis, a non-apoptotic PCD, in esophageal squamous cell carcinoma (ESCC), a commonly known chemo-refractory cancer, especially at its advanced stages. Proline-, glutamic acid- and leucine-rich protein-1 (PELP1) is a scaffolding oncogene and upregulated PELP1 in advanced stages of ESCC is highly associated with cancer progression and patient outcomes. Intriguingly, metformin treatment leads to gasdermin D (GSDMD)-mediated pyroptosis, which is abrogated by forced expression of PELP1. Mechanistically, metformin induces pyroptosis of ESCC by targeting miR-497/PELP1 axis. Our findings suggest that metformin and any other pyroptosis-inducing reagents could serve as alternative treatments for chemo- and radiotherapy refractory ESCC or other cancers sharing the same pyroptosis mechanisms.
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Affiliation(s)
- Lu Wang
- Department of Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China; Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, China; Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Kai Li
- Department of Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China; Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, China; Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Xianjie Lin
- Department of Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China; Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Zhimeng Yao
- Department of Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China; Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Shuhong Wang
- Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiao Xiong
- Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Zhifeng Ning
- Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Jing Wang
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Xiaozheng Xu
- Cancer Research Centre, Shantou University Medical College, Shantou, Guangdong, China
| | - Yi Jiang
- Department of Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Ditian Liu
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yuping Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Dianzheng Zhang
- Department of Bio-Medical Sciences, Philadelphia College of Osteopathic Medicine, 4170 City Ave, Philadelphia, PA, 19131, USA
| | - Hao Zhang
- Institute of Precision Cancer Medicine and Pathology, Department of Pathology, Jinan University Medical College, Guangzhou, China; Research Centre of Translational Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou, Guangdong, China.
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11
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Li M, Gu MM, Tian X, Xiao BB, Lu S, Zhu W, Yu L, Shang ZF. Hydroxylated-Graphene Quantum Dots Induce DNA Damage and Disrupt Microtubule Structure in Human Esophageal Epithelial Cells. Toxicol Sci 2018; 164:339-352. [PMID: 29669094 PMCID: PMC6016703 DOI: 10.1093/toxsci/kfy090] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Graphene quantum dots (GQDs) have attracted significant interests due to their unique chemical and physical properties. In this study, we investigated the potential effects of hydroxyl-modified GQDs (OH-GQDs) on the human esophageal epithelial cell line HET-1A. Our data revealed significant cytotoxicity of OH-GQDs which decreased the viability of HET-1A in a dose and time-dependent manner. The moderate concentration (25 or 50 µg/ml) of OH-GQDs significantly blocked HET-1A cells in G0/G1 cell cycle phase. An increased percentage of γH2AX-positive and genomically unstable cells were also detected in cells treated with different doses of OH-GQDs (25, 50, and 100 µg/ml). Microarray data revealed that OH-GQDs treatment down-regulated genes related to DNA damage repair, cell cycle regulation and cytoskeleton signal pathways indicating a novel role of OH-GQDs. Consistent with the microarray data, OH-GQDs disrupted microtubule structure and inhibited microtubule regrowth around centrosomes in HET-1A cells. In conclusion, our findings provide important evidence for considering the application of OH-GQDs in biomedical fields.
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Affiliation(s)
- Ming Li
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
| | - Meng-Meng Gu
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
| | - Xin Tian
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
| | - Bei-Bei Xiao
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
| | - Siyuan Lu
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
| | - Wei Zhu
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
| | - Lan Yu
- Suzhou Digestive Diseases and Nutrition Research Center, Nanjing Medical University Affiliated Suzhou Hospital, North District of Suzhou Municipal Hospital, Suzhou 215000, People’s Republic of China
| | - Zeng-Fu Shang
- State Key Laboratory of Radiation Medicine and Protection, Department of Radiobiology, School of Radiation Medicine and Protection, Medical College of Soochow University, Suzhou 215123, People’s Republic of China
- Collaborative Innovation Center of Radiation Medicine of Jiangsu Higher Education Institutions, Soochow University, Suzhou 215123, People’s Republic of China
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12
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Wang P, Shan L, Xue L, Zheng B, Ying J, Lu N. Genome wide copy number analyses of superficial esophageal squamous cell carcinoma with and without metastasis. Oncotarget 2018; 8:5069-5080. [PMID: 27974698 PMCID: PMC5354893 DOI: 10.18632/oncotarget.13847] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 11/21/2016] [Indexed: 01/08/2023] Open
Abstract
Superficial esophageal squamous cell carcinoma (ESCC) is generally considered a subtype of less invasive ESCC. Yet a subset of these superficial ESCC would have metastasis after esophagostomy or endoscopic resection and lead to poor prognosis. The objective of this study is to determine biomarkers that can identify such subset of superficial ESCC that would have metastasis after surgery using genome wide copy number alteration (CNA) analyses. The CNAs of 38 cases of superficial ESCCs originated from radical surgery, including 19 without metastasis and 19 with metastasis within 5 years’ post-surgery, were analyzed using Affymetrix OncoScan™ FFPE Assay. A 39-gene signature was identified which characterized the subset of superficial ESCC with high risk of metastasis after surgery. In addition, recurrent CNAs of superficial ESCC were also investigated in the study. Amplification of 11q13.3 (FGF4) and deletion of 9p21.3 (CDKN2A) were found to be recurrent in all 38 superficial ESCCs analyzed. Notably amplifications of 3p26.33 (SOX2OT), 8q24.21 (MYC), 14q21.1 (FOXA1) and deletion of 3p12.1 (GBE1) were only found to be recurrent in metastaic superficial ESCCs. In conclusion, using CNAs analyses, we identify a 39-gene signature which characterizes the high risk metastatic superficial ESCCs and discover several recurrent CNAs that might be the driver alterations in metastasis among superficial ESCCs.
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Affiliation(s)
- Pengjiao Wang
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ling Shan
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Liyan Xue
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Bo Zheng
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Jianming Ying
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
| | - Ning Lu
- Department of Pathology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, P. R. China
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13
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Cui XB, Tian YX, Chun CP, Peng H, Liu CX, Yang L, Hu JM, Xin HH, Chen X, Wang N, Wei YT, Yin LB, Chen YZ, Li F. Genome-wide screening for genomic aberrations in Kazakh patients with esophageal squamous cell cancer by comparative genomic hybridization. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:427-437. [PMID: 31938128 PMCID: PMC6957937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 11/16/2017] [Indexed: 06/10/2023]
Abstract
Multiple chromosome aberrations are responsible for tumorigenesis of esophagus squamous cell carcinoma (ESCC). To characterize genetic alterations by comparative genomic hybridization (CGH) and their relation to ESCC, We enrolled 54 members with ESCC from Kazakh's patients. We found that the deletions of 3p (P = 0.032), 17p (P = 0.004), 22q (P = 0.000) and gains of 5p (P = 0.000), 11q (P = 0.000) were significantly correlated with the location of tumors. Losses of 1p (P = 0.005), 3p (P = 0.006), 22q (P = 0.024) and gains of 3q (P = 0.043), 8q (P = 0.038), 18q (P = 0.046) were also found more frequently in patients with larger diameter disease. The loss of 19q (P = 0.005) and gains of l3q (P = 0.045), 18p (P = 0.018) were significantly correlated with pathologic grade. The gain of 7p (P = 0.009) and deletion of 19q (P = 0.018) were seen more frequently in patients with Grade III-IV tumors. Chromosome amplifications in ESCC at 1q (P = 0.008), 7p (P = 0.008), 8q (P = 0.018) and deletions at 3p (P = 0.021), 11q (P = 0.002), 17p (P = 0.012) were related to lymph node metastasis; the gains of 1q (P = 0.026) and 6q (P = 0.017) and the loss of 11q (P = 0.001) were significant in different isoforms of HPV infection. We identified some chromosomes in which the genes were related to the tumorgenesis of ESCC, which may be a theme for future investigation.
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Affiliation(s)
- Xiao-Bin Cui
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Yan-Xia Tian
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Cai-Pu Chun
- Department of Pathology, Nongyishi HospitalAkesu, China
| | - Hao Peng
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Chun-Xia Liu
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Lan Yang
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Jian-Ming Hu
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Hua-Hua Xin
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Xi Chen
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Ning Wang
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Yu-Tao Wei
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Lai-Bo Yin
- Department of Thoracic and Cardiovascular Surgery, The First Affiliated Hospital, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Yun-Zhao Chen
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
| | - Feng Li
- Key Laboratory for Xinjiang Endemic and Ethnic Diseases, Department of Pathology, School of Medicine, Shihezi UniversityShihezi, Xinjiang, China
- Department of Pathology, Medical Research Center, Beijing Chaoyang Hospital, Capital Medical UniversityBeijing, China
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14
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Lin DC, Wang MR, Koeffler HP. Genomic and Epigenomic Aberrations in Esophageal Squamous Cell Carcinoma and Implications for Patients. Gastroenterology 2018; 154:374-389. [PMID: 28757263 PMCID: PMC5951382 DOI: 10.1053/j.gastro.2017.06.066] [Citation(s) in RCA: 172] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Revised: 06/05/2017] [Accepted: 06/07/2017] [Indexed: 12/28/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is a common malignancy without effective therapy. The exomes of more than 600 ESCCs have been sequenced in the past 4 years, and numerous key aberrations have been identified. Recently, researchers reported both inter- and intratumor heterogeneity. Although these are interesting observations, their clinical implications are unclear due to the limited number of samples profiled. Epigenomic alterations, such as changes in DNA methylation, histone acetylation, and RNA editing, also have been observed in ESCCs. However, it is not clear what proportion of ESCC cells carry these epigenomic aberrations or how they contribute to tumor development. We review the genomic and epigenomic characteristics of ESCCs, with a focus on emerging themes. We discuss their clinical implications and future research directions.
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Affiliation(s)
- De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore; National University Cancer Institute, National University Hospital Singapore, Singapore
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15
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RNA editing of SLC22A3 drives early tumor invasion and metastasis in familial esophageal cancer. Proc Natl Acad Sci U S A 2017; 114:E4631-E4640. [PMID: 28533408 DOI: 10.1073/pnas.1703178114] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Like many complex human diseases, esophageal squamous cell carcinoma (ESCC) is known to cluster in families. Familial ESCC cases often show early onset and worse prognosis than the sporadic cases. However, the molecular genetic basis underlying the development of familial ESCC is mostly unknown. We reported that SLC22A3 is significantly down-regulated in nontumor esophageal tissues from patients with familial ESCC compared with tissues from patients with sporadic ESCCs. A-to-I RNA editing of the SLC22A3 gene results in its reduced expression in the nontumor esophageal tissues of familial ESCCs and is significantly correlated with lymph node metastasis. The RNA-editing enzyme ADAR2, a familial ESCC susceptibility gene identified by our post hoc genome-wide association study, is positively correlated with the editing level of SLC22A3 Moreover, functional studies showed that SLC22A3 is a metastasis suppressor in ESCC, and deregulation of SLC22A3 facilitates cell invasion and filopodia formation by reducing its direct association with α-actinin-4 (ACTN4), leading to the increased actin-binding activity of ACTN4 in normal esophageal cells. Collectively, we now show that A-to-I RNA editing of SLC22A3 contributes to the early development and progression of familial esophageal cancer in high-risk individuals.
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16
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Shibamoto M, Hirata H, Eguchi H, Sawada G, Sakai N, Kajiyama Y, Mimori K. The loss of CASP4 expression is associated with poor prognosis in esophageal squamous cell carcinoma. Oncol Lett 2017; 13:1761-1766. [PMID: 28454321 DOI: 10.3892/ol.2017.5646] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 08/12/2016] [Indexed: 12/19/2022] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) has high biological malignant potential among the various digestive tract cancers and is associated with a poor prognosis. To identify novel genes involved in tumor progression, the present study analyzed the genetic and transcriptional alterations in two clinical cohorts, totaling 157 cases of ESCC (78 cases from the discovery set and 79 cases from the validation set). From the discovery set, gene expression and copy number profiles were analyzed using expression arrays and array-comparative genomic hybridization, respectively. Notably, a copy number loss of caspase-4 (CASP4) was observed in 82% of ESCC cases and CASP4 expression levels were significantly associated with copy number levels. Gene set enrichment analysis demonstrated that the upregulation of CASP4 expression levels was associated with the signaling pathways involved in apoptosis, inflammatory responses and immune responses. The present study demonstrated that CASP4 expression levels were significantly associated with the expression levels of the endoplasmic reticulum (ER) stress marker glucose-regulated protein 78, indicating that CASP4 has a role in cell death induced by ER stress in ESCC. In the survival analysis the CASP4 low expression group exhibited a poor prognosis, compared with the CASP4 high expression group in the discovery set (P=0.003); this observation was reproduced in the validation set (P=0.037). Therefore, the results of the current study suggest that CASP4 may function as a tumor-suppressor gene and may have applications as a biomarker for the prediction of the prognosis in ESCC.
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Affiliation(s)
- Misako Shibamoto
- Department of Esophageal and Gastroenterological Surgery, Juntendo University School of Medicine, Tokyo 113-8431, Japan
| | - Hidenari Hirata
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita 874-0838, Japan.,Department of Radiology, Kyushu University Beppu Hospital, Beppu, Oita 874-0838, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita 874-0838, Japan
| | - Genta Sawada
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita 874-0838, Japan
| | - Noritaka Sakai
- Department of Esophageal and Gastroenterological Surgery, Juntendo University School of Medicine, Tokyo 113-8431, Japan
| | - Yoshiaki Kajiyama
- Department of Esophageal and Gastroenterological Surgery, Juntendo University School of Medicine, Tokyo 113-8431, Japan
| | - Koshi Mimori
- Department of Surgery, Kyushu University Beppu Hospital, Beppu, Oita 874-0838, Japan
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17
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Polymorphisms of the Stem Cell Marker Gene CD133 and the Risk of Lung Cancer in Chinese Population. Lung 2016; 194:393-400. [PMID: 27130457 DOI: 10.1007/s00408-016-9876-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Accepted: 04/04/2016] [Indexed: 01/06/2023]
Abstract
OBJECTIVE To explore the association of functional single-nucleotide polymorphisms (SNPs) of CD133 with the risk of lung cancer. METHODS We conducted a hospital-based, case-control study of 1017 lung cancer patients and 1035 cancer-free controls frequency-matched by age and sex. Four functional CD133 SNPs (rs2240688 A > C, rs10022537 T > A, rs7686732 C > G, and rs3130 C > T) were selected and genotyped. Unconditional univariate and multivariate logistic regression analyses were carried out to evaluate the associations of genotypes of CD133 SNPs with lung cancer risk. RESULTS Compared with rs2240688 AA genotype, the variant AC/CC genotypes were associated with a statistically increased risk of lung cancer under a recessive model (adjusted odds ratio 1.19; 95 % confidence interval 1.01-1.42). The risk remained in patients with other histology types, but not with adenocarcinoma and squamous cell cancers. CONCLUSIONS These findings suggest that SNP rs2240688 A > C of CD133 may be a potential biomarker for genetic susceptibility to lung cancer, but require further research with larger populations.
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18
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Sun J, Zhu M, Shen W, Wang C, Dai J, Xu L, Jin G, Hu Z, Ma H, Shen H. A potentially functional polymorphism in ABCG2 predicts clinical outcome of non-small cell lung cancer in a Chinese population. THE PHARMACOGENOMICS JOURNAL 2016; 17:280-285. [PMID: 26951883 DOI: 10.1038/tpj.2016.2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 10/06/2015] [Accepted: 11/26/2015] [Indexed: 12/29/2022]
Abstract
ABCG2, CD133 and CD117 are pivotal markers of cancer stem cell, which are involved in carcinogenesis and cancer progression. The expression of these genes has been reported to be associated with the development and progression of many cancers, including non-small cell lung cancer (NSCLC). We selected and genotyped 9 potentially functional single-nucleotide polymorphisms in the 3 genes in a clinical cohort of 1001 NSCLC patients in a Chinese population. We found that variant genotypes of ABCG2 rs3114020 were associated with a significantly increased risk of death for NSCLC (additive model: adjusted hazard ratio=1.25, 95% confidence intervals=1.10-1.42, P<0.001). Further stepwise regression analysis suggested that rs3114020 was an independent risk factor for the prognosis of NSCLC. Besides, histology interacted with the genetic effect of rs3114020 in relation to NSCLC survival in the interaction analysis. Our findings show that ABCG2 rs3114020 might be one of the candidate biomarkers for NSCLC survival in this Chinese population, especially among patients with adenocarcinoma.
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Affiliation(s)
- J Sun
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - M Zhu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - W Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - C Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - J Dai
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - L Xu
- Jiangsu Key Laboratory of Molecular and Translational Cancer Research, Collaborative Innovation Center For Cancer Personalized Medicine, Nanjing Medical University Affiliated Cancer Hospital, Nanjing, China
| | - G Jin
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Z Hu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - H Ma
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - H Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center of Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.,Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, China
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19
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Hu N, Kadota M, Liu H, Abnet CC, Su H, Wu H, Freedman ND, Yang HH, Wang C, Yan C, Wang L, Gere S, Hutchinson A, Song G, Wang Y, Ding T, Qiao YL, Koshiol J, Dawsey SM, Giffen C, Goldstein AM, Taylor PR, Lee MP. Genomic Landscape of Somatic Alterations in Esophageal Squamous Cell Carcinoma and Gastric Cancer. Cancer Res 2016; 76:1714-23. [PMID: 26857264 DOI: 10.1158/0008-5472.can-15-0338] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Accepted: 12/08/2015] [Indexed: 01/01/2023]
Abstract
Gastric cancer and esophageal cancer are the second and sixth leading causes of cancer-related death worldwide. Multiple genomic alterations underlying gastric cancer and esophageal squamous cell carcinoma (ESCC) have been identified, but the full spectrum of genomic structural variations and mutations have yet to be uncovered. Here, we report the results of whole-genome sequencing of 30 samples comprising tumor and blood from 15 patients, four of whom presented with ESCC, seven with gastric cardia adenocarcinoma (GCA), and four with gastric noncardia adenocarcinoma. Analyses revealed that an A>C mutation was common in GCA, and in addition to the preferential nucleotide sequence of A located 5 prime to the mutation as noted in previous studies, we found enrichment of T in the 5 prime base. The A>C mutations in GCA suggested that oxidation of guanine may be a potential mechanism underlying cancer mutagenesis. Furthermore, we identified genes with mutations in gastric cancer and ESCC, including well-known cancer genes, TP53, JAK3, BRCA2, FGF2, FBXW7, MSH3, PTCH, NF1, ERBB2, and CHEK2, and potentially novel cancer-associated genes, KISS1R, AMH, MNX1, WNK2, and PRKRIR Finally, we identified recurrent chromosome alterations in at least 30% of tumors in genes, including MACROD2, FHIT, and PARK2 that were often intragenic deletions. These structural alterations were validated using the The Cancer Genome Atlas dataset. Our studies provide new insights into understanding the genomic landscape, genome instability, and mutation profile underlying gastric cancer and ESCC development. Cancer Res; 76(7); 1714-23. ©2016 AACR.
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Affiliation(s)
- Nan Hu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Mitsutaka Kadota
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Huaitian Liu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Christian C Abnet
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Hua Su
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Hailong Wu
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Howard H Yang
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Chaoyu Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Chunhua Yan
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Lemin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sheryl Gere
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Amy Hutchinson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland. Cancer Genomics Research Laboratory, Leidos, Gaithersburg, Maryland
| | - Guohong Song
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yuan Wang
- Shanxi Cancer Hospital, Taiyuan, Shanxi, PR China
| | - Ti Ding
- Shanxi Cancer Hospital, Taiyuan, Shanxi, PR China
| | - You-Lin Qiao
- Cancer Institute, Chinese Academy of Medical Sciences, Beijing, PR China
| | - Jill Koshiol
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sanford M Dawsey
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Carol Giffen
- Information Management Services, Inc., Silver Spring, Maryland
| | - Alisa M Goldstein
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland
| | - Philip R Taylor
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, Bethesda, Maryland.
| | - Maxwell P Lee
- Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland.
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20
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Wen J, Liu QW, Luo KJ, Ling YH, Xie XY, Yang H, Hu Y, Fu JH. MIIP expression predicts outcomes of surgically resected esophageal squamous cell carcinomas. Tumour Biol 2016; 37:10141-8. [PMID: 26825982 DOI: 10.1007/s13277-015-4633-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 12/10/2015] [Indexed: 12/13/2022] Open
Abstract
The migration and invasion inhibitory protein (MIIP) was shown to function as a tumor suppressor gene in gliomas by inhibiting tumor cell growth, migration, and invasion. However, its role and clinical significance in esophageal squamous cell carcinoma (ESCC) have not been elucidated. We investigated the correlation of MIIP expression and clinical outcome in a group of surgically resected ESCCs. Tissue microarrays constructed of 253 surgically resected ESCC primary tumors and paired paracancerous normal esophageal epithelia were used for MIIP evaluation by immunohistochemistry. The clinical and prognostic significance of MIIP expression was analyzed statistically. The expression of MIIP expression in cancer tissues was increased significantly in comparison with the paired paracancerous normal epithelia (P < 0.001). And, MIIP expression was associated with ESCC cells' differentiation (P < 0.001). By Kaplan-Meier analysis, patients with low MIIP expression exhibited significantly improved overall survival (OS, P = 0.039) and a tendency of improved disease-free survival (DFS, P = 0.086) than those with high MIIP expression. In addition, MIIP expression could distinguish OS or DFS of patients with tumors in stage T3-4 (P = 0.020, 0.028), N0 (P = 0.008, 0.032), and stage II (P = 0.004, 0.019), as well as at lower thoracic esophagus (P = 0.024, 0.090). Multivariate analysis showed that MIIP expression was an independent prognostic factor in ESCC OS and DFS. In conclusion, MIIP expressed higher in ESCCs than in paracancerous normal esophageal epithelia and was a positive, independent prognostic factor in resected ESCCs.
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Affiliation(s)
- Jing Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Qian-Wen Liu
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Kong-Jia Luo
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Yi-Hong Ling
- Department of Pathology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Xiu-Ying Xie
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Hong Yang
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China
| | - Yi Hu
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China.
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China.
| | - Jian-Hua Fu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China.
- Guangdong Esophageal Cancer Institute, 651 Dongfeng East Road, Guangzhou, 510060, China.
- Department of Thoracic Oncology, Sun Yat-Sen University Cancer Center, 651 Dongfeng East Road, Guangzhou, 510060, China.
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21
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Cheng C, Cui H, Zhang L, Jia Z, Song B, Wang F, Li Y, Liu J, Kong P, Shi R, Bi Y, Yang B, Wang J, Zhao Z, Zhang Y, Hu X, Yang J, He C, Zhao Z, Wang J, Xi Y, Xu E, Li G, Guo S, Chen Y, Yang X, Chen X, Liang J, Guo J, Cheng X, Wang C, Zhan Q, Cui Y. Genomic analyses reveal FAM84B and the NOTCH pathway are associated with the progression of esophageal squamous cell carcinoma. Gigascience 2016; 5:1. [PMID: 26759717 PMCID: PMC4709967 DOI: 10.1186/s13742-015-0107-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 12/23/2015] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Esophageal squamous cell carcinoma (ESCC) is the sixth most lethal cancer worldwide and the fourth most lethal cancer in China. Genomic characterization of tumors, particularly those of different stages, is likely to reveal additional oncogenic mechanisms. Although copy number alterations and somatic point mutations associated with the development of ESCC have been identified by array-based technologies and genome-wide studies, the genomic characterization of ESCCs from different stages of the disease has not been explored. Here, we have performed either whole-genome sequencing or whole-exome sequencing on 51 stage I and 53 stage III ESCC patients to characterize the genomic alterations that occur during the various clinical stages of ESCC, and further validated these changes in 36 atypical hyperplasia samples. RESULTS Recurrent somatic amplifications at 8q were found to be enriched in stage I tumors and the deletions of 4p-q and 5q were particularly identified in stage III tumors. In particular, the FAM84B gene was amplified and overexpressed in preclinical and ESCC tumors. Knockdown of FAM84B in ESCC cell lines significantly reduced in vitro cell growth, migration and invasion. Although the cancer-associated genes TP53, PIK3CA, CDKN2A and their pathways showed no significant difference between stage I and stage III tumors, we identified and validated a prevalence of mutations in NOTCH1 and in the NOTCH pathway that indicate that they are involved in the preclinical and early stages of ESCC. CONCLUSIONS Our results suggest that FAM84B and the NOTCH pathway are involved in the progression of ESCC and may be potential diagnostic targets for ESCC susceptibility.
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Affiliation(s)
- Caixia Cheng
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Pathology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Heyang Cui
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Ling Zhang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Zhiwu Jia
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Bin Song
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Oncology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Fang Wang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Yaoping Li
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Jing Liu
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Pengzhou Kong
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Ruyi Shi
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Yanghui Bi
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Bin Yang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Juan Wang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Zhenxiang Zhao
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Yanyan Zhang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Xiaoling Hu
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Jie Yang
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Chanting He
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Zhiping Zhao
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Jinfen Wang
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Yanfeng Xi
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Enwei Xu
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Guodong Li
- />Department of Pathology, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Shiping Guo
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Yunqing Chen
- />Department of Tumor Surgery, Shanxi Cancer Hospital, Taiyuan, Shanxi 030001 China
| | - Xiaofeng Yang
- />Department of Urology Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Xing Chen
- />Department of Endoscopy, Shanxi Provincial People’s Hospital, Taiyuan, Shanxi 030001 China
| | - Jianfang Liang
- />Department of Pathology, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Jiansheng Guo
- />Department of General Surgery, First Hospital of Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Xiaolong Cheng
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
| | - Chuangui Wang
- />Institute of Translational Medicine, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 201620 China
| | - Qimin Zhan
- />Cancer Institute and Cancer Hospital, State Key Laboratory of Molecular Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021 China
| | - Yongping Cui
- />Translational Medicine Research Center, Shanxi Medical University, Taiyuan, Shanxi 030001 China
- />Key Laboratory of Cellular Physiology, Ministry of Education, Shanxi Medical University, Taiyuan, Shanxi 030001 China
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22
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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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23
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Sawada G, Niida A, Hirata H, Komatsu H, Uchi R, Shimamura T, Takahashi Y, Kurashige J, Matsumura T, Ueo H, Takano Y, Ueda M, Sakimura S, Shinden Y, Eguchi H, Sudo T, Sugimachi K, Yamasaki M, Tanaka F, Tachimori Y, Kajiyama Y, Natsugoe S, Fujita H, Tanaka Y, Calin G, Miyano S, Doki Y, Mori M, Mimori K. An Integrative Analysis to Identify Driver Genes in Esophageal Squamous Cell Carcinoma. PLoS One 2015; 10:e0139808. [PMID: 26465158 PMCID: PMC4605796 DOI: 10.1371/journal.pone.0139808] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2014] [Accepted: 09/17/2015] [Indexed: 11/18/2022] Open
Abstract
Background Few driver genes have been well established in esophageal squamous cell carcinoma (ESCC). Identification of the genomic aberrations that contribute to changes in gene expression profiles can be used to predict driver genes. Methods We searched for driver genes in ESCC by integrative analysis of gene expression microarray profiles and copy number data. To narrow down candidate genes, we performed survival analysis on expression data and tested the genetic vulnerability of each genes using public RNAi screening data. We confirmed the results by performing RNAi experiments and evaluating the clinical relevance of candidate genes in an independent ESCC cohort. Results We found 10 significantly recurrent copy number alterations accompanying gene expression changes, including loci 11q13.2, 7p11.2, 3q26.33, and 17q12, which harbored CCND1, EGFR, SOX2, and ERBB2, respectively. Analysis of survival data and RNAi screening data suggested that GRB7, located on 17q12, was a driver gene in ESCC. In ESCC cell lines harboring 17q12 amplification, knockdown of GRB7 reduced the proliferation, migration, and invasion capacities of cells. Moreover, siRNA targeting GRB7 had a synergistic inhibitory effect when combined with trastuzumab, an anti-ERBB2 antibody. Survival analysis of the independent cohort also showed that high GRB7 expression was associated with poor prognosis in ESCC. Conclusion Our integrative analysis provided important insights into ESCC pathogenesis. We identified GRB7 as a novel ESCC driver gene and potential new therapeutic target.
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Affiliation(s)
- Genta Sawada
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Atsushi Niida
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Hidenari Hirata
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Hisateru Komatsu
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Ryutaro Uchi
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Teppei Shimamura
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yusuke Takahashi
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Junji Kurashige
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Tae Matsumura
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Hiroki Ueo
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Yuki Takano
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Masami Ueda
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Shotaro Sakimura
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Yoshiaki Shinden
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Hidetoshi Eguchi
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Tomoya Sudo
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Keishi Sugimachi
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Makoto Yamasaki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Fumiaki Tanaka
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
| | - Yuji Tachimori
- Department of Surgery, National Cancer Center Hospital, Tokyo, Japan
| | - Yoshiaki Kajiyama
- Department of Esophageal and Gastroenterological Surgery, Juntendo University School of Medicine, Tokyo, Japan
| | - Shoji Natsugoe
- Department of Surgical Oncology and Digestive Surgery, Kagoshima University School of Medicine, Kagoshima, Japan
| | - Hiromasa Fujita
- Department of Surgery, Kurume University School of Medicine, Kurume, Japan
| | - Yoichi Tanaka
- Division of Gastroenterological Surgery, Saitama Cancer Center, Saitama, Japan
| | - George Calin
- Department of Experimental Therapeutics and The Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, Texas, United States of America
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan
| | - Yuichiro Doki
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Masaki Mori
- Department of Gastroenterological Surgery, Graduate School of Medicine, Osaka University, 2-2 Yamadaoka, Suita 565-0871, Japan
| | - Koshi Mimori
- Department of Surgery, Beppu Hospital, Kyushu University, 4546, Tsurumihara, Beppu 874-0838, Japan
- * E-mail:
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24
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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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25
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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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Liao X, Chen Y, Liu D, Li F, Li X, Jia W. High Expression of LAMP3 Is a Novel Biomarker of Poor Prognosis in Patients with Esophageal Squamous Cell Carcinoma. Int J Mol Sci 2015; 16:17655-67. [PMID: 26263981 PMCID: PMC4581213 DOI: 10.3390/ijms160817655] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Revised: 07/15/2015] [Accepted: 07/27/2015] [Indexed: 01/12/2023] Open
Abstract
Lysosomal-associated membrane protein 3 (LAMP3), identified as a molecular marker of mature dendritic cells, is one of the LAMP family members. Its expression was induced by hypoxia, and was associated with hypoxia mediated metastasis in breast and cervical cancers. However, epithelial expression of LAMP3 and its prognostic value in esophageal squamous cell carcinoma (ESCC) is still unknown. In the current study, mRNA expression of LAMP3 in 157 ESCC tissues and 50 adjacent normal tissues was detected by quantitative real-time PCR (qRT-PCR). LAMP3 protein expression in 46 paired cancerous and normal tissues was detected by immunohistochemistry (IHC). Then, DNA copy number was examined to observe its potential correlation with mRNA expression. The results showed that both mRNA and protein expression level of LAMP3 was significantly higher in cancerous tissues compared with normal controls (p < 0.001). LAMP3 DNA copy number was amplified in 70% of ESCC tissues and positive correlated with mRNA expression (p = 0.037). Furthermore, patients with higher LAMP3 expression had worse overall survival (HR = 1.90, 95% CI = 1.17-3.09, p = 0.010) and disease-free survival (HR = 1.80, 95% CI = 1.18-2.74, p = 0.006). In conclusion, our results suggest that epithelial LAMP3 expression is an independent prognostic biomarker for ESCC.
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Affiliation(s)
- Xiaoyu Liao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Yuanbin Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Deqing Liu
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Fangfang Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Xizhao Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
| | - Weihua Jia
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat-Sen University Cancer Center, Guangzhou, China.
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Meng QB, Kang WM, Yu JC, Liu YQ, Ma ZQ, Zhou L, Cui QC, Zhou WX. Overexpression of eukaryotic translation initiation factor 5A2 (EIF5A2) correlates with cell aggressiveness and poor survival in gastric cancer. PLoS One 2015; 10:e0119229. [PMID: 25793713 PMCID: PMC4368542 DOI: 10.1371/journal.pone.0119229] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 01/29/2015] [Indexed: 12/17/2022] Open
Abstract
Eukaryotic translation initiation factor 5A2 (EIF5A2) plays an important role in tumor progression and prognosis evaluation. However, little information is available about its potential role in gastric cancer. This study aimed to investigate the function of EIF5A2 in tumor progression and its potential mechanisms. EIF5A2 expression was measured in human gastric cancer cell lines, the immortalized gastric mucosal epithelial cell line (GES-1) and human gastric cancer tissues and knocked down by RNA interference or upregulated by EIF5A2 plasmid transfection. Cell proliferation, migration and invasion were assessed in vitro. The downstream targets of EIF5A2 were examined by western blotting. EIF5A2 and its potential target metastasis-associated protein 1 (MTA1) expression were examined in 160 pairs of human gastric cancer and adjacent non-tumor specimens using immunohistochemistry (IHC) staining, and its correlation with clinicopathological features and survival was investigated. Knockdown of EIF5A2 or MTA1 caused an apparent suppression of HGC27 cell proliferation, migration and invasion. After knockdown of EIF5A2 in HGC27 cells, E-cadherin levels were upregulated and vimentin, cyclin D1, cyclin D3, C-MYC and MTA1 levels were downregulated. Upregulation of EIF5A2 in MKN45 cells resulted in the converse. IHC results showed a positive correlation between EIF5A2 and MTA1 expression in gastric cancers (P<0.001). Both EIF5A2 and MTA1 overexpression were correlated with pT stage (P=0.018 and P=0.042), pN stage (P=0.037 and P=0.020) and lymphovascular invasion (P=0.016 and P=0.044). EIF5A2 or MTA1 overexpression was significantly associated with poor overall survival and disease-free survival (All P<0.05). Multivariate analyses identified EIF5A2 as an independent predictor for both overall survival (P=0.012) and disease-free survival (P=0.008) in gastric cancer patients. Our findings indicate that EIF5A2 upregulation plays an important oncogenic role in gastric cancer. EIF5A2 may represent a new predictor for poor survival and is a potential therapeutic target for gastric cancer.
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Affiliation(s)
- Qing-Bin Meng
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
- Department of Gastrointestinal Surgery, the First Hospital of Wu Han City, Wuhan city, Hubei Provence, China
| | - Wei-Ming Kang
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Jian-Chun Yu
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Yu-Qin Liu
- Cell Center, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences, Wuhan city, Beijing, China
| | - Zhi-Qiang Ma
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Li Zhou
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Quan-Cai Cui
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, China
| | - Wei-Xun Zhou
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, Beijing, 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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29
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Ning Z, Zhu H, Li F, Liu Q, Liu G, Tan T, Zhang B, Chen S, Li G, Huang D, Meltzer SJ, Zhang H. Tumor suppression by miR-31 in esophageal carcinoma is p21-dependent. Genes Cancer 2014; 5:436-44. [PMID: 25568668 PMCID: PMC4279440 DOI: 10.18632/genesandcancer.38] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Accepted: 10/08/2014] [Indexed: 02/05/2023] Open
Abstract
microRNA regulation network is important for the cancer genetic heterogeneity. Relative to the increasing numbers of microRNA's targets identified, upstream regulatory mechanisms that control functional microRNAs are less well-documented. Here, we investigated the function of miR-31, a pleiotropically-acting microRNA, in esophageal squamous cell cancer (ESCC). We demonstrated that miR-31 only exerted tumor-suppressive effects in TE-7 ESCC cells, but not in TE-1 ESCC cells, although both of these cell lines harbor inactive p53. Interestingly, TE-1 cells highly expressed p21, while p21 levels were virtually undetectable in TE-7 cells, suggesting a p21-dependent mechanism of miR-31-mediated tumor suppression. Accordingly, knockdown of p21 in TE-1 cells reversed the tumor suppressive actions of miR-31. In patient ESCC specimens, real-time RT-PCR analysis revealed that expression of E2F2 and STK40, two known miR-31 target oncogenes, was negatively correlated with the expression of miR-31 in a p21-dependent manner, supporting the conclusion that miR-31 only downregulates its target oncogenes when p21 levels are low. Collectively, these data suggest a novel mechanism through which the tumor-suppressive effect of miR-31 is p21-dependent. In addition, we speculate that delivery of miR-31 could provide therapeutic benefit in the personalized management of a subgroup of ESCC patients with p21-deficient tumors.
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Affiliation(s)
- Zhifeng Ning
- Laboratory for Translational Oncology basic medicine college, Hubei University of Science and Technology, Xianning, Hubei province, China
- Department of Biotherapy and Gastrointestinal Medical Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Hua Zhu
- Department of Surgery, Davis Heart and Lung Research Institute, the Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Feifei Li
- Department of Biotherapy and Gastrointestinal Medical Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Qing Liu
- Department of Biotherapy and Gastrointestinal Medical Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Gefei Liu
- Department of Cell Biology, Shantou University Medical College, Shantou, Guangdong, China
| | - Tao Tan
- Department of Surgery, Davis Heart and Lung Research Institute, the Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Bo Zhang
- Department of Surgery, Davis Heart and Lung Research Institute, the Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Shaobin Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Guanwu Li
- Department of Biochemistry, Shantou University Medical College, Shantou, Guangdong, China
| | - Dongyang Huang
- Department of Cell Biology, Shantou University Medical College, Shantou, Guangdong, China
| | - Stephen J. Meltzer
- Division of Gastroenterology, Department of Medicine, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Hao Zhang
- Department of Biotherapy and Gastrointestinal Medical Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Tumor Tissue Bank, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
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30
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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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Lin DC, Hao JJ, Nagata Y, Xu L, Shang L, Meng X, Sato Y, Okuno Y, Varela AM, Ding LW, Garg M, Liu LZ, Yang H, Yin D, Shi ZZ, Jiang YY, Gu WY, Gong T, Zhang Y, Xu X, Kalid O, Shacham S, Ogawa S, Wang MR, Koeffler HP. Genomic and molecular characterization of esophageal squamous cell carcinoma. Nat Genet 2014; 46:467-73. [PMID: 24686850 PMCID: PMC4070589 DOI: 10.1038/ng.2935] [Citation(s) in RCA: 468] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2013] [Accepted: 03/05/2014] [Indexed: 02/06/2023]
Abstract
Esophageal squamous cell carcinoma (ESCC) is prevalent worldwide and particularly common in certain regions of Asia. Here we report the whole-exome or targeted deep sequencing of 139 paired ESCC cases, and analysis of somatic copy number variations (SCNV) of over 180 ESCCs. We identified previously uncharacterized mutated genes such as FAT1, FAT2, ZNF750 and KMT2D, in addition to those already known (TP53, PIK3CA and NOTCH1). Further SCNV evaluation, immunohistochemistry and biological analysis suggested their functional relevance in ESCC. Notably, RTK-MAPK-PI3K pathways, cell cycle and epigenetic regulation are frequently dysregulated by multiple molecular mechanisms in this cancer. Our approaches also uncovered many druggable candidates, and XPO1 was further explored as a therapeutic target because it showed both gene mutation and protein overexpression. Our integrated study unmasks a number of novel genetic lesions in ESCC and provides an important molecular foundation for understanding esophageal tumors and developing therapeutic targets.
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Affiliation(s)
- De-Chen Lin
- Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, USA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Jia-Jie Hao
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yasunobu Nagata
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Liang Xu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Li Shang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xuan Meng
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yusuke Sato
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yusuke Okuno
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ana Maria Varela
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Manoj Garg
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Li-Zhen Liu
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Dong Yin
- Medical Research Center, Sun Yat-Sen Memorial Hospital, Guangzhou, China
| | - Zhi-Zhou Shi
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yan-Yi Jiang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Wen-Yue Gu
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ting Gong
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Yu Zhang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Xin Xu
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - Ori Kalid
- Karyopharm Therapeutics, Natick, MA, USA
| | | | - Seishi Ogawa
- Cancer Genomics Project, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
| | - H. Phillip Koeffler
- Cedars-Sinai Medical Center, Division of Hematology/Oncology, UCLA School of Medicine, Los Angeles, USA
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
- National University Cancer Institute, National University Hospital Singapore, Singapore
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32
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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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33
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Cervigne NK, Machado J, Goswami RS, Sadikovic B, Bradley G, Perez-Ordonez B, Galloni NN, Gilbert R, Gullane P, Irish JC, Jurisica I, Reis PP, Kamel-Reid S. Recurrent genomic alterations in sequential progressive leukoplakia and oral cancer: drivers of oral tumorigenesis? Hum Mol Genet 2014; 23:2618-28. [PMID: 24403051 PMCID: PMC3990162 DOI: 10.1093/hmg/ddt657] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A significant proportion (up to 62%) of oral squamous cell carcinomas (OSCCs) may arise from oral potential malignant lesions (OPMLs), such as leukoplakia. Patient outcomes may thus be improved through detection of lesions at a risk for malignant transformation, by identifying and categorizing genetic changes in sequential, progressive OPMLs. We conducted array comparative genomic hybridization analysis of 25 sequential, progressive OPMLs and same-site OSCCs from five patients. Recurrent DNA copy number gains were identified on 1p in 20/25 cases (80%) with minimal, high-level amplification regions on 1p35 and 1p36. Other regions of gains were frequently observed: 11q13.4 (68%), 9q34.13 (64%), 21q22.3 (60%), 6p21 and 6q25 (56%) and 10q24, 19q13.2, 22q12, 5q31.2, 7p13, 10q24 and 14q22 (48%). DNA losses were observed in >20% of samples and mainly detected on 5q31.2 (35%), 16p13.2 (30%), 9q33.1 and 9q33.29 (25%) and 17q11.2, 3p26.2, 18q21.1, 4q34.1 and 8p23.2 (20%). Such copy number alterations (CNAs) were mapped in all grades of dysplasia that progressed, and their corresponding OSCCs, in 70% of patients, indicating that these CNAs may be associated with disease progression. Amplified genes mapping within recurrent CNAs (KHDRBS1, PARP1, RAB1A, HBEGF, PAIP2, BTBD7) were selected for validation, by quantitative real-time PCR, in an independent set of 32 progressive leukoplakia, 32 OSSCs and 21 non-progressive leukoplakia samples. Amplification of BTBD7, KHDRBS1, PARP1 and RAB1A was exclusively detected in progressive leukoplakia and corresponding OSCC. BTBD7, KHDRBS1, PARP1 and RAB1A may be associated with OSCC progression. Protein–protein interaction networks were created to identify possible pathways associated with OSCC progression.
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Affiliation(s)
- Nilva K Cervigne
- Division of Applied Molecular Oncology, Ontario Cancer Institute
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Cheng M, Yang L, Yang R, Yang X, Deng J, Yu B, Huang D, Zhang S, Wang H, Qiu F, Zhou Y, Lu J. A microRNA-135a/b binding polymorphism in CD133 confers decreased risk and favorable prognosis of lung cancer in Chinese by reducing CD133 expression. Carcinogenesis 2013; 34:2292-2299. [DOI: 10.1093/carcin/bgt181] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023] Open
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Shi ZZ, Shang L, Jiang YY, Hao JJ, Zhang Y, Zhang TT, Lin DC, Liu SG, Wang BS, Gong T, Zhan QM, Wang MR. Consistent and differential genetic aberrations between esophageal dysplasia and squamous cell carcinoma detected by array comparative genomic hybridization. Clin Cancer Res 2013; 19:5867-78. [PMID: 24009147 DOI: 10.1158/1078-0432.ccr-12-3753] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Our aim was to identify frequent genomic aberrations in both esophageal squamous cell carcinoma (ESCC) and esophageal dysplasia and to discover important copy number-driving genes and microRNAs (miRNA) in ESCC. EXPERIMENTAL DESIGN We conducted array-based comparative genomic hybridization (array CGH) on 59 ESCC resection samples and 16 dysplasia biopsy samples. Expression of genes at 11q13.3 was analyzed by real-time PCR (RT-PCR) and immunohistochemistry (IHC). Integrated analysis was conducted to identify genes or miRNAs with copy number-expression correlations. RESULTS Array CGH identified 11 amplifications and eight homozygous deletions in ESCC. Integrated analysis of array CGH data with matched gene expression microarray data showed that 90 overexpressed genes and 24 underexpressed genes were consistent with DNA copy number changes, including 12 copy number-driving miRNAs. In esophageal dysplasia, six gains, four losses, 12 amplifications, and four homozygous deletions were detected. Amplifications of 7p11.2 and 11q13.2-11q13.3 (CCND1) and homozygous deletion at 9p21.3 (CDKN2A) were consistent genomic changes in both dysplasia and carcinoma. ANO1 at 11q13.3 was overexpressed at the mRNA and protein levels in tumors, and higher mRNA expression was correlated with the copy number increase. In particular, ANO1 expression was elevated in moderate dysplasia compared with normal esophageal epithelium. IHC revealed that ANO1 overexpression was positively correlated with lymph node metastasis and advanced clinical stage. Knockdown of ANO1 significantly inhibited the proliferation of KYSE30 and KYSE510 cells. CONCLUSION Copy number aberrations in both esophageal dysplasia and ESCC may be useful as potential biomarkers for early detection. In addition, ANO1 may be a candidate target gene in esophageal tumorigenesis.
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Affiliation(s)
- Zhi-Zhou Shi
- Authors' Affiliation: State Key Laboratory of Molecular Oncology, Cancer Institute and Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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Investigation of tumor suppressing function of CACNA2D3 in esophageal squamous cell carcinoma. PLoS One 2013; 8:e60027. [PMID: 23560067 PMCID: PMC3616168 DOI: 10.1371/journal.pone.0060027] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Accepted: 02/22/2013] [Indexed: 12/21/2022] Open
Abstract
Background Deletion of 3p is one of the most frequent genetic alterations in esophageal squamous cell carcinoma (ESCC), suggesting the existence of one or more tumor suppressor genes (TSGs) within these regions. In this study, one TSG, CACNA2D3 at 3p21.1, was characterized. Methods Expression of CACNA2D3 in ESCCs was tested by quantitative real-time PCR and tissue microarray. The mechanism of CACNA2D3 downregulation was investigated by methylation-specific polymerase chain reaction (MS-PCR). The tumor suppressive function of CACNA2D3 was characterized by both in vitro and in vivo tumorigenic assays, cell migration and invasion assays. Results CACNA2D3 was frequently downregulated in ESCCs (24/48, 50%), which was significantly associated with promoter methylation and allele loss (P<0.05). Tissue microarray result showed that downregulation of CACNA2D3 was detected in (127/224, 56.7%) ESCCs, which was significantly associated with lymph node metastasis (P = 0.01), TNM staging (P = 0.003) and poor outcome of ESCC patients (P<0.05). Functional studies demonstrated that CACNA2D3 could inhibit tumorigenicity, cell motility and induce apoptosis. Mechanism study found that CACNA2D3 could arrest cell cycle at G1/S checkpoint by increasing expressions of p21 and p53 and decreasing expression of CDK2. In addition, CACNA2D3 could upregulate intracellular free cytosolic Ca2+ and subsequently induce apoptosis. Conclusion CACNA2D3 is a novel TSG responsible to the 3p21 deletion event and plays a critical suppressing role in the development and progression of ESCC.
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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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Byrne JA, Chen Y, Martin La Rotta N, Peters GB. Challenges in identifying candidate amplification targets in human cancers: chromosome 8q21 as a case study. Genes Cancer 2012; 3:87-101. [PMID: 23050042 DOI: 10.1177/1947601912456287] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2012] [Accepted: 07/08/2012] [Indexed: 12/13/2022] Open
Abstract
Detailed genomic characterization of cancer specimens is required to identify all genes whose dysregulation contributes to tumorigenesis and/or tumor progression. These include amplification target genes, whose oncogenic functions derive from their overexpression in response to increased gene copy number, and which increasingly serve as therapeutic targets and predictive markers. We propose that identifying novel amplification target genes is becoming more challenging, and may require the comparative analysis of multiple studies mapping gene copy number changes and/or defining associations between gene copy number and expression. We therefore reviewed the array comparative genomic hybridization and single nucleotide polymorphism profiling literature to identify copy number increases that were restricted to chromosome 8q21 in human cancers, which were reported most frequently in breast cancer. We determined the minimal regions of overlap between gained regions and then examined which chromosome 8q21 genes were most frequently overexpressed, or otherwise supported, in individual studies. As these combined approaches supported the previously proposed amplification targets TCEB1, TPD52, and WWP1, the comparison of multiple genomic studies may therefore effectively predict candidate gene amplification targets, and prioritize these for further study.
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Affiliation(s)
- Jennifer A Byrne
- Molecular Oncology Laboratory, Children's Cancer Research Unit, Kids Research Institute, The Children's Hospital at Westmead, Westmead, Australia ; The University of Sydney Discipline of Paediatrics and Child Health, The Children's Hospital at Westmead, Westmead, Australia
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Hao JJ, Shi ZZ, Zhao ZX, Zhang Y, Gong T, Li CX, Zhan T, Cai Y, Dong JT, Fu SB, Zhan QM, Wang MR. Characterization of genetic rearrangements in esophageal squamous carcinoma cell lines by a combination of M-FISH and array-CGH: further confirmation of some split genomic regions in primary tumors. BMC Cancer 2012; 12:367. [PMID: 22920630 PMCID: PMC3561653 DOI: 10.1186/1471-2407-12-367] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Accepted: 08/17/2012] [Indexed: 01/29/2023] Open
Abstract
Background Chromosomal and genomic aberrations are common features of human cancers. However, chromosomal numerical and structural aberrations, breakpoints and disrupted genes have yet to be identified in esophageal squamous cell carcinoma (ESCC). Methods Using multiplex-fluorescence in situ hybridization (M-FISH) and oligo array-based comparative hybridization (array-CGH), we identified aberrations and breakpoints in six ESCC cell lines. Furthermore, we detected recurrent breakpoints in primary tumors by dual-color FISH. Results M-FISH and array-CGH results revealed complex numerical and structural aberrations. Frequent gains occurred at 3q26.33-qter, 5p14.1-p11, 7pter-p12.3, 8q24.13-q24.21, 9q31.1-qter, 11p13-p11, 11q11-q13.4, 17q23.3-qter, 18pter-p11, 19 and 20q13.32-qter. Losses were frequent at 18q21.1-qter. Breakpoints that clustered within 1 or 2 Mb were identified, including 9p21.3, 11q13.3-q13.4, 15q25.3 and 3q28. By dual-color FISH, we observed that several recurrent breakpoint regions in cell lines were also present in ESCC tumors. In particular, breakpoints clustered at 11q13.3-q13.4 were identified in 43.3% (58/134) of ESCC tumors. Both 11q13.3-q13.4 splitting and amplification were significantly correlated with lymph node metastasis (LNM) (P = 0.004 and 0.022) and advanced stages (P = 0.004 and 0.039). Multivariate logistic regression analysis revealed that only 11q13.3-q13.4 splitting was an independent predictor for LNM (P = 0.026). Conclusions The combination of M-FISH and array-CGH helps produce more accurate karyotypes. Our data provide significant, detailed information for appropriate uses of these ESCC cell lines for cytogenetic and molecular biological studies. The aberrations and breakpoints detected in both the cell lines and primary tumors will contribute to identify affected genes involved in the development and progression 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 Science, 17 Panjiayuan Nanli, Chaoyang District, Beijing, 100021, China
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Sun SJ, Feng L, Zhao GQ, Dong ZM. HAX-1 promotes the chemoresistance, invasion, and tumorigenicity of esophageal squamous carcinoma cells. Dig Dis Sci 2012; 57:1838-46. [PMID: 22451114 DOI: 10.1007/s10620-012-2108-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/26/2011] [Accepted: 02/21/2012] [Indexed: 01/07/2023]
Abstract
BACKGROUND HAX-1 is an anti-apoptotic factor and regulates the expression of DNA pol β. Interestingly, DNA polymerase pol β is overexpressed in esophageal squamous cell carcinoma (ESCC). However, the functional role of HAX-1 in ESCC remains unclear. AIMS To investigate the role of HAX-1 in chemoresistance, invasion, and tumorigenicity of ESCC. METHODS Lentivirus-mediated overexpression or knockdown of HAX-1 was employed to establish ESCC EC9706 cell lines that expressed HAX-1 at different levels. The biological behaviors of these engineered cells were characterized in vitro and in vivo using a xenograft nude mice model. In addition, HAX-1 and pol β expression in the tumor tissues was detected by RT-PCR and immunohistochemistry. RESULTS HAX-1 overexpression promoted cell proliferation and resistance against cisplatin, increased cell invasion and suppressed apoptosis along with increased pol β expression. Conversely, HAX-1 knockdown inhibited the malignant phenotypes of EC9706 cells. The xenograft nude mice model demonstrated that HAX-1 overexpression or depletion led to increased or decreased tumor growth in vivo, respectively. Furthermore, a positive correlation of HAX-1 and pol β expression in the tumor tissues was observed. CONCLUSIONS HAX-1 promotes the proliferation, chemoresistance, invasion, and tumorigenicity of ESCC, and this is correlated with increased poly β expression. HAX-1 may represent a potential target to overcome the resistance and metastasis of ESCC.
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Affiliation(s)
- Sa-jia Sun
- Department of Pathophysiology, College of Basic Medical Sciences, Zhengzhou University, Zhengzhou, Henan, People's Republic of China.
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Bandla S, Pennathur A, Luketich JD, Beer DG, Lin L, Bass AJ, Godfrey TE, Litle VR. Comparative genomics of esophageal adenocarcinoma and squamous cell carcinoma. Ann Thorac Surg 2012; 93:1101-6. [PMID: 22450065 DOI: 10.1016/j.athoracsur.2012.01.064] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2011] [Revised: 01/18/2012] [Accepted: 01/20/2012] [Indexed: 12/20/2022]
Abstract
BACKGROUND Esophageal cancer consists of two major histologic types: esophageal squamous cell carcinoma (ESCC), predominant globally, and esophageal adenocarcinoma (EAC), which has a higher incidence in westernized countries. Five-year overall survival is 15%. Clinical trials frequently combine histologic types although they are different diseases with distinct origins. In the evolving era of personalized medicine and targeted therapies, we hypothesized that ESCC and EAC have genomic differences important for developing new therapeutic strategies for esophageal cancer. METHODS We explored DNA copy number abnormalities in 70 ESCCs with publicly available array data and 189 EACs from our group. All data was from single nucleotide polymorphism arrays. Analysis was performed using a segmentation algorithm. Log ratio thresholds for copy number gain and loss were set at ±0.2 (approximately 2.3 and 1.7 copies, respectively). RESULTS The ESCC and EAC genomes showed some copy number abnormalities with similar frequencies (eg, CDKN2A, EGFR, KRAS, MYC, CDK6, MET) but also many copy number abnormalities with different frequencies between histologic types, most of which were amplification events. Some of these regions harbor genes for which targeted therapies are currently available (VEGFA, ERBB2) or for which agents are in clinical trials (PIK3CA, FGFR1). Other regions contain putative oncogenes that may be targeted in the future. CONCLUSIONS Using single nucleotide polymorphism arrays we compared genomic abnormalities in a large cohort of EACs and ESCCs. We report here the similar and different frequencies of copy number abnormalities in ESCC and EAC. These results may allow development of histology-specific therapeutic agents for esophageal cancer.
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Affiliation(s)
- Santhoshi Bandla
- Department of Surgery, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642-8410, USA
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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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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: 26] [Impact Index Per Article: 2.2] [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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Li Y, Chen L, Nie CJ, Zeng TT, Liu H, Mao X, Qin Y, Zhu YH, Fu L, Guan XY. Downregulation of RBMS3 is associated with poor prognosis in esophageal squamous cell carcinoma. Cancer Res 2011; 71:6106-15. [PMID: 21844183 DOI: 10.1158/0008-5472.can-10-4291] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Deletions on chromosome 3p occur often in many solid tumors, including esophageal squamous cell carcinoma (ESCC), suggesting the existence at this location of one or more tumor suppressor genes (TSG). In this study, we characterized RBMS3 gene encoding an RNA-binding protein as a candidate TSG located at 3p24. Downregulation of RBMS3 mRNA and protein levels was documented in approximately 50% of the primary ESCCs examined. Clinical association studies determined that RBMS3 downregulation was associated with poor clinical outcomes. RBMS3 expression effectively suppressed the tumorigenicity of ESCC cells in vitro and in vivo, including by inhibition of cell growth rate, foci formation, soft agar colony formation, and tumor formation in nude mice. Molecular analyses revealed that RBMS3 downregulated c-Myc and CDK4, leading to subsequent inhibition of Rb phosphorylation. Together, our findings suggest a tumor suppression function for the human RBMS3 gene in ESCC, acting through c-Myc downregulation, with genetic loss of this gene in ESCC contributing to poor outcomes in this deadly disease.
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Affiliation(s)
- Yan Li
- State Key Laboratory of Oncology in Southern China, Cancer Center, Sun Yat-sen University, Guangzhou, China
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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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Shi ZZ, Liang JW, Zhan T, Wang BS, Lin DC, Liu SG, Hao JJ, Yang H, Zhang Y, Zhan QM, Zhang KT, Wang MR. Genomic alterations with impact on survival in esophageal squamous cell carcinoma identified by array comparative genomic hybridization. Genes Chromosomes Cancer 2011; 50:518-26. [PMID: 21484929 DOI: 10.1002/gcc.20875] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2010] [Accepted: 03/07/2011] [Indexed: 11/08/2022] Open
Abstract
Risk assessment of esophageal squamous cell carcinoma (ESCC) is currently based on clinicopathological parameters. To identify genomic markers that can predict overall survival in ESCC, we performed array comparative genomic hybridization (array CGH) on a screening set of 35 tumor samples from ESCC patients. Prognosis association of the genes selected on the basis of the array CGH results was further validated by real-time PCR in two independent sample sets (n = 151 and 84). Genomic analysis revealed seven high-level amplifications and two homozygous deletions. Gain of 11q13.2 and loss of 7q34 and 18q21.1-q23 were associated with poor outcome. Gain of 11q13.2 was an independent prognostic factor and was selected for further validation. In both validation sets of samples, copy number increase of CPT1A in 11q13.2 was correlated with short overall survival (P = 0.015, n = 151 and P = 0.044, n = 84). Multivariate analysis confirmed that CPT1A gain provided prognostic information in ESCC (HR, 1.643; 95% CI: 1.076-2.509; P = 0.022; HR, 2.488; 95% CI: 1.235-5.013; P = 0.011). Immunohistochemistry showed significant correlation between strong expression of CPT1A protein and poor outcome of ESCC patients (P = 0.018, n = 73). Our data suggest that gain of CPT1A may be a candidate prognostic factor.
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Affiliation(s)
- Zhi-Zhou Shi
- State Key Laboratory of Molecular Oncology, Cancer Institute Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, China
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Tuna M, Smid M, Zhu D, Martens JWM, Amos CI. Association between acquired uniparental disomy and homozygous mutations and HER2/ER/PR status in breast cancer. PLoS One 2010; 5:e15094. [PMID: 21152100 PMCID: PMC2994899 DOI: 10.1371/journal.pone.0015094] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2010] [Accepted: 10/21/2010] [Indexed: 01/01/2023] Open
Abstract
Background Genetic alterations in cellular signaling networks are a hallmark of cancer, however, effective methods to discover them are lacking. A novel form of abnormality called acquired uniparental disomy (aUPD) was recently found to pinpoint the region of mutated genes in various cancers, thereby identifying the region for next-generation sequencing. Methods/Principal Findings We retrieved large genomic data sets from the Gene Expression Omnibus database to perform genome-wide analysis of aUPD in breast tumor samples and cell lines using approaches that can reliably detect aUPD. aUPD was identified in 52.29% of the tumor samples. The most frequent aUPD regions were located at chromosomes 2q, 3p, 5q, 9p, 9q, 10q, 11q, 13q, 14q and 17q. We evaluated the data for any correlation between the most frequent aUPD regions and HER2/neu, ER, and PR status, and found a statistically significant correlation between the recurrent regions of aUPD and triple negative (TN) breast cancers. aUPD at chromosome 17q (VEZF1, WNT3), 3p (SUMF1, GRM7), 9p (MTAP, NFIB) and 11q (CASP1, CASP4, CASP5) are predictors for TN. The frequency of aUPD was found to be significantly higher in TN breast cancer cases compared to HER2/neu-positive and/or ER or PR-positive cases. Furthermore, using previously published mutation data, we found TP53 homozygously mutated in cell lines having aUPD in that locus. Conclusions/Significance We conclude that aUPD is a common and non-random molecular feature of breast cancer that is most prominent in triple negative cases. As aUPD regions are different among the main pathological subtypes, specific aUPD regions may aid the sub-classification of breast cancer. In addition, we provide statistical support using TP53 as an example that identifying aUPD regions can be an effective approach in finding aberrant genes. We thus conclude that a genome-wide scale analysis of aUPD regions for homozygous sequence alterations can provide valuable insights into breast tumorigenesis.
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Affiliation(s)
- Musaffe Tuna
- Department of Epidemiology, The University of Texas M. D. Anderson Cancer Center, Houston, Texas, United States of America.
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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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Shi H, Li N, Li S, Chen C, Wang W, Xu C, Zhang J, Jin H, Zhang H, Zhao H, Song W, Feng Q, Feng X, Shen X, Yao L, Zhao Q. Expression of NDRG2 in esophageal squamous cell carcinoma. Cancer Sci 2010; 101:1292-9. [PMID: 20331630 PMCID: PMC11158127 DOI: 10.1111/j.1349-7006.2010.01529.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
N-Myc downstream-regulated gene 2 (NDRG2), a new member of the N-Myc downstream-regulated gene family, has been found to be a differentially expressed gene involved in a variety of cancers. The present study aimed to investigate the expression of NDRG2 in esophageal squamous cell carcinoma (ESCC). Immunohistochemistry was performed in 154 samples from patients with ESCC to detect the expression level of NDRG2 and C-MYC. Results indicated that the expression level of NDRG2 in the cancer samples was significantly lower than that in normal tissues; the trend of C-MYC was the reverse. The Wilcoxon-Mann-Whitney test showed significant difference in the expression of NDRG2 in patients with different T stage, TNM stage, and differentiation degree of cancers (P = 0.036, 0.031, 0.001, respectively). Patients in stages I and II were followed up for 5 consecutive years and Kaplan-Meier survival analysis demonstrated that the survival time of ESCC patients with high expression of NDRG2 was longer than those with low expression during the 5-year follow-up period (P = 0.0018). Cox regression analysis indicated that low expression of NDRG2, cancer stage of pT1, and distant organ metastasis (pM1) were the independent poor prognostic factors of ESCC (P = 0.004, 0.019, 0.0013, respectively). Furthermore, up-regulation of NDRG2 was introduced to ESCC cell lines (EC9706 and EC109) by plasmid transfection. In vivo and in vitro studies indicated that overexpression of NDRG2 markedly reduced proliferation and promoted the apoptosis of EC9706 and EC109 cells. In summary, our results demonstrated that NDRG2 played an important role in the proliferation of ESCC cells and the expression of NDRG2 in ESCC was closely related with the prognosis.
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Affiliation(s)
- Hai Shi
- State Key Laboratory of Cancer Biology, Department of Gastrointestinal Surgery, Xijing Hospital, The Fourth Military Medical University, Xi'an, China
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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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