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Evaluating Real World Mutational Differences Between Hispanics and Asians in NSCLC at a Large Academic Institution in Los Angeles. Clin Lung Cancer 2022; 23:e443-e452. [PMID: 35902325 DOI: 10.1016/j.cllc.2022.06.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 06/03/2022] [Accepted: 06/16/2022] [Indexed: 01/27/2023]
Abstract
INTRODUCTION Hispanics living in the United States have higher rates of Epidermal Growth Factor Receptor (EGFR) mutations compared with Non-Hispanic Whites. While this higher incidence is like Asian patients living in the United States, the outcomes for Hispanic patients differ. We looked to compare the variances in mutational profiles between Hispanics and Asians in Los Angeles. PATIENTS AND METHODS Three hundred ninety three non-small cell lung cancer (NSCLC) patients treated at Los Angeles County + University of Southern California (LAC + USC) Medical Center and Norris Comprehensive Cancer Center who received comprehensive genomic profiling (CGP) were evaluated from July 2017 to August 2020. CGP was done using tissue biopsies (n = 211) from Caris Life Sciences and liquid biopsies (n = 231) from Guardant Health. Multivariate logistic regression evaluated the role of race between Hispanics and Asians. RESULTS In the Hispanic cohort (n = 90), 50.0% were male, median age of diagnosis was 62, 54.5% were non-smokers, and 85.5% had adenocarcinoma. In Asians (n = 142), 47.5% were male, median age of diagnosis was 65, 59.6% were non-smokers, and 83.8% had adenocarcinoma. Hispanic patients had greater prevalence of Kirsten rat sarcoma virus (KRAS) mutations (odds ratio [OR] 4.42, 95% confidence interval [95% CI]: 1.63-12.83) and lesser prevalence of EGFR mutations (OR 0.31, 95% CI: 0.16-0.59). There were a greater proportion of Hispanic smokers with KRAS mutations (14/41; 34.1%) than Asian smokers (4/58; 6.9%). CONCLUSION We saw a greater percentage of Hispanics with KRAS mutations despite similar smoking percentages along with a greater percentage of Asians with EGFR mutations. This study shows that ethnic and racial backgrounds of the patient can influence the effects of potentially carcinogenic exposures leading to variances of mutation frequency of NSCLC among different ethnicities.
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Lin G, Zhang K, Han Y, Peng R, Li J. Preparation of multiplexed control materials for cancer mutation analysis by genome editing in GM12878 cells. J Clin Lab Anal 2021; 36:e24139. [PMID: 34811797 PMCID: PMC8761438 DOI: 10.1002/jcla.24139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/06/2022] Open
Abstract
Background Quality control materials are necessary for assay development, test validation, and proficiency testing in cancer mutation analysis. Most of the existing controls for somatic mutations only harbor a single variant and are derived from unstable cell lines. This study aimed to establish a method to create stable multianalyte controls in a defined background by genome editing in GM12878 cells, which also can be applied for the reference of next‐generation sequencing. Methods GM12878 cells were electroporated with a donor plasmid containing a mutant DNA sequence and a Cas9/sgRNA expressing vector. The genome‐edited GM12878 cell was validated with Sanger sequencing, amplification refractory mutation system (ARMS), and next‐generation sequencing (NGS). Results We have successfully generated a mutant GM12878 cell line harboring the defined variants including single‐nucleotide variants (SNVs), small insertions and deletions (indels), and structural variants (SVs). The introduction of intended mutations in GM12878 cell line was confirmed by both ARMS and sequencing methods. Conclusions We developed a method for the preparation of the multiplexed controls for reference mutations in cancer gene by genome editing in GM12878 cells. This methodology can be used to generate other stable cancer reference materials with an unlimited supply.
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Affiliation(s)
- Guigao Lin
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Kuo Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Yanxi Han
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Rongxue Peng
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China.,Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
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Li Q, Zhou D, Pan J, Liu Z, Chen J. An ultrasensitive and simple fluorescence biosensor for detection of the Kras wild type by using the three-way DNA junction-driven catalyzed hairpin assembly strategy. Analyst 2019; 144:3088-3093. [DOI: 10.1039/c9an00195f] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A label-free platform for simple detection of the Kras gene was proposed by using the three-way DNA junction-driven catalyzed hairpin assembly strategy.
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Affiliation(s)
- Qiong Li
- College of Bioscience and Biotechnology
- Hunan Agricultural University
- Changsha 410128
- China
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
| | - Danhua Zhou
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental and Science &Technology
- Guangzhou 510650
- China
| | - Jiafeng Pan
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental and Science &Technology
- Guangzhou 510650
- China
| | - Zhi Liu
- College of Bioscience and Biotechnology
- Hunan Agricultural University
- Changsha 410128
- China
| | - Junhua Chen
- Guangdong Key Laboratory of Integrated Agro-environmental Pollution Control and Management
- Guangdong Institute of Eco-Environmental and Science &Technology
- Guangzhou 510650
- China
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Liu J, Zeng W, Huang C, Wang J, Xu L, Ma D. Upregulation of c-mesenchymal epithelial transition expression and RAS mutations are associated with late lung metastasis and poor prognosis in colorectal carcinoma. Exp Ther Med 2018; 15:4229-4242. [PMID: 29725370 PMCID: PMC5920233 DOI: 10.3892/etm.2018.5966] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/26/2018] [Indexed: 12/17/2022] Open
Abstract
The present study aimed to investigate whether c-mesenchymal epithelial transition factor (C-MET) overexpression combined with RAS (including KRAS, NRAS and HRAS) or BRAF mutations were associated with late distant metastases and the prognosis of patients with colorectal cancer (CRC). A total of 374 patients with stage III CRC were classified into 4 groups based on RAS/BRAF and C-MET status for comprehensive analysis. Mutations in RAS/BRAF were determined using Sanger sequencing and C-MET expression was examined using immunohistochemistry. The associations between RAS/BRAF mutations in combination with C-MET overexpression and clinicopathological variables including survival were evaluated. In addition, their predictive value for late distant metastases were statistically analyzed via logistic regression and receiver operating characteristic analysis. Among 374 patients, mutations in KRAS, NRAS, HRAS, BRAF and C-MET overexpression were observed in 43.9, 2.4, 0.3, 5.9 and 71.9% of cases, respectively. Considering RAS/BRAF mutations and C-MET overexpression, vascular invasion (P=0.001), high carcino-embryonic antigen level (P=0.031) and late distant metastases (P<0.001) were more likely to occur in patients of group 4. Furthermore, survival analyses revealed RAS/BRAF mutations may have a more powerful impact on survival than C-MET overexpression, although they were both predictive factors for adverse prognosis. Further logistic regression suggested that RAS/BRAF mutations and C-MET overexpression may predict late distant metastases. In conclusion, RAS/BRAF mutations and C-MET overexpression may serve as predictive indicators for metastatic behavior and poor prognosis of CRC.
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Affiliation(s)
- Jianhua Liu
- Department of Oncology, Cancer Center, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510180, P.R. China
| | - Weiqiang Zeng
- Department of Pharmacy, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510000, P.R. China
| | - Chengzhi Huang
- Department of Gastrointestinal Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510000, P.R. China
| | - Junjiang Wang
- Department of Gastrointestinal Surgery, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510000, P.R. China
| | - Lishu Xu
- Department of Gastroenterology, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510000, P.R. China
| | - Dong Ma
- Department of Oncology, Cancer Center, Guangdong General Hospital, Guangdong Academy of Medical Sciences, Guangzhou, Guangdong 510180, P.R. China
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Zhang Y, Wang L, Luo F, Qiu B, Guo L, Weng Z, Lin Z, Chen G. An electrochemiluminescence biosensor for Kras mutations based on locked nucleic acid functionalized DNA walkers and hyperbranched rolling circle amplification. Chem Commun (Camb) 2018; 53:2910-2913. [PMID: 28154878 DOI: 10.1039/c7cc00009j] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Herein, an electrochemiluminescence (ECL) biosensor for ultrasensitive and specific detection of Kras mutant genes has been developed on the basis of the high discrimination capability of locked nucleic acid (LNA) and dual signal amplification techniques including DNA walkers and hyperbranched rolling circle amplification (HRCA).
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Affiliation(s)
- Ying Zhang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Lixu Wang
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Fang Luo
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Bin Qiu
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Longhua Guo
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Zuquan Weng
- College of Biological Science and Technology, Fuzhou University, Fuzhou, Fujian 350116, China.
| | - Zhenyu Lin
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Guonan Chen
- Ministry of Education Key Laboratory of Analysis and Detection for Food Safety, Fujian Provincial Key Laboratory of Analysis and Detection for Food Safety, Fuzhou University, Fuzhou, Fujian 350116, China
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Quan X, Gao H, Wang Z, Li J, Zhao W, Liang W, Yu Q, Guo D, Hao Z, Liu J. Epidermal growth factor receptor somatic mutation analysis in 354 Chinese patients with non-small cell lung cancer. Oncol Lett 2018; 15:2131-2138. [PMID: 29434916 PMCID: PMC5776883 DOI: 10.3892/ol.2017.7622] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 10/26/2017] [Indexed: 12/20/2022] Open
Abstract
Lung cancer is one of the most common types of cancer worldwide, with the highest mortality rate of all types of cancer. In the present study, epidermal growth factor receptor (EGFR) mutations of 354 primary patients with non-small cell lung cancer (NSCLC) of Chinese ethnicity were detected following formalin-fixed and paraffin-embedded specimen DNA extraction, polymerase chain reaction amplification, and sanger sequencing. The total rate of occurrence of EGFR somatic mutation in these 354 patients was 48.02%. Of these detected EGFR mutations, 27.40% were located in exon 19 and 25.99% in exon 21. The most frequent mutation in exon 19 was E746-A750del (8.47%), and in exon 21, L858R (10.17%). EGFR mutation rates were significantly associated with sex [female vs. male: 60.13 vs. 38.81%; adjusted odds ratio (OR), 1.93, 95% confidence interval (CI), 1.07–3.51, P=0.029], age (<60 vs. ≥60; 58.62 vs. 40.67%; adjusted OR, 1.87; 95% CI, 1.20–2.92; P=0.006) and histology [adenocarcinoma (ADC) vs. non-ADC; 52.76 vs. 26.56%; adjusted OR, 2.35; 95% CI, 1.28–4.50; P=0.007]. The frequency of E746_A750del, Q787Q and L858R mutations were significantly different in ADC patients compared with squamous cell carcinoma patients (P<0.001). Furthermore, a novel EGFR mutation, M793K, was detected in 7 NSCLC patients with possible gefitinib resistance. The present study analyzed the EGFR exon 18–21 mutation occurrence profile for Chinese patients with NSCLC and identified significant associations between different EGFR mutations with demographic and histological factors. These results may offer clinical benefits and potential novel treatments.
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Affiliation(s)
| | - Hongjun Gao
- Department of Lung Cancer, Affiliated Hospital of Academy of Military Medical Sciences, Beijing 100071, P.R. China
| | - Zhikuan Wang
- Department of Medical Oncology, General Hospital of The Chinese People's Liberation Army, Beijing 100853, P.R. China
| | - Jie Li
- Department of Thoracic Surgery, General Hospital of The Chinese People's Liberation Army, Beijing 100853, P.R. China
| | - Wentao Zhao
- Vishuo MedTech Ltd., Beijing 100070, P.R. China
| | - Wei Liang
- Vishuo MedTech Ltd., Beijing 100070, P.R. China
| | - Qiang Yu
- Vishuo MedTech Ltd., Beijing 100070, P.R. China
| | | | | | - Jingxin Liu
- Department of Medical Engineering, China-Japan Union Hospital of Jilin University, Changchun, Jilin 130033, P.R. China
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Predictive and Prognostic Implications of Mutation Profiling and Microsatellite Instability Status in Patients with Metastatic Colorectal Carcinoma. Gastroenterol Res Pract 2018; 2018:4585802. [PMID: 29643917 PMCID: PMC5831938 DOI: 10.1155/2018/4585802] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 11/05/2017] [Accepted: 11/22/2017] [Indexed: 01/05/2023] Open
Abstract
To investigate whether mutation profiling and microsatellite instability (MSI) status were associated with clinicopathological features and the prognosis in metastatic colorectal cancer (mCRC), mutations in RAS (including KRAS, NRAS, and HRAS) and BRAF were determined by Sanger sequencing. Tumor mismatch repair proteins and MSI status were examined using immunohistochemistry and polymerase chain reaction, respectively. The clinical value of these abnormalities was statistically analyzed, and prognostic value of different treatment regimens was also evaluated. Among 461 mCRC patients, mutations in RAS, BRAF, and MSI-high (MSI-H) status were observed in 45.3% (209/461), 5.6% (26/461), and 6.5% (30/461) of cases, respectively. Brain metastasis and high carcinoembryonic antigen level were highly correlated with KRAS mutation (P = 0.011 and P < 0.001), and tumors from females or located in the right colon tended to harbor BRAF mutation (P = 0.039 and P = 0.001). RAS/BRAF mutations may predict brain and/or lung metastases. Although neither clinical nor prognostic importance of MSI status was identified in our study, KRAS and BRAF mutations were demonstrated to be independent prognostic factors for overall survival and progression-free survival. Besides, in wild-type group, patients treated with chemotherapy plus targeted therapy exhibited the most favorable prognosis. Therefore, RAS/BRAF mutations may serve as indicators for prognosis and treatment options in mCRC.
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Wang LY, Cui JJ, Guo AX, Yin JY. Clinical efficacy and safety of afatinib in the treatment of non-small-cell lung cancer in Chinese patients. Onco Targets Ther 2018; 11:529-538. [PMID: 29416353 PMCID: PMC5790073 DOI: 10.2147/ott.s136579] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Compared with various malignant tumors, lung cancer has high incidence and the highest mortality worldwide. Non-small-cell lung cancer (NSCLC), the most common kind of lung cancer, is still a great threat to the world, including China. Surgery, platinum-based chemotherapy, and radiotherapy are still the primary treatments for NSCLC patients in the clinic, whereas immunotherapy and targeted therapy are gradually playing more important roles. A next-generation tyrosine kinase inhibitor (TKI), afatinib, was developed as a targeted reagent for epidermal growth factor receptor (EGFR). This targeted drug was effective in a series of trials. The US Food and Drug Administration then approved afatinib as a new first-line treatment for EGFR L858R and exon 19 deletion mutant patients in 2013. This review focused on current clinical studies of afatinib. Although this TKI was not widely available in China until recently, we aim to provide a reference for its future use in China.
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Affiliation(s)
- Lei-Yun Wang
- Department of Clinical Pharmacology, XiangYa Hospital, Central South University, Changsha.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
| | - Jia-Jia Cui
- Department of Clinical Pharmacology, XiangYa Hospital, Central South University, Changsha.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
| | - Ao-Xiang Guo
- Department of Clinical Pharmacology, XiangYa Hospital, Central South University, Changsha.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, XiangYa Hospital, Central South University, Changsha.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, China
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Liu SY, Chen W, Chughtai EA, Qiao Z, Jiang JT, Li SM, Zhang W, Zhang J. PIK3CA gene mutations in Northwest Chinese esophageal squamous cell carcinoma. World J Gastroenterol 2017; 23:2585-2591. [PMID: 28465643 PMCID: PMC5394522 DOI: 10.3748/wjg.v23.i14.2585] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 02/19/2017] [Accepted: 03/02/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To evaluate PIK3CA gene mutational status in Northwest Chinese esophageal squamous cell carcinoma (ESCC) patients, and examine the associations of PIK3CA gene mutations with clinicopathological characteristics and clinical outcome.
METHODS A total of 210 patients with ESCC who underwent curative resection were enrolled in this study. Pyrosequencing was applied to investigate mutations in exons 9 and 20 of PIK3CA gene in 210 Northwest Chinese ESCCs. The associations of PIK3CA gene mutations with clinicopathological characteristics and clinical outcome were examined.
RESULTS PIK3CA gene mutations in exon 9 were detected in 48 cases (22.9%) of a non-biased database of 210 curatively resected Northwest Chinese ESCCs. PIK3CA gene mutations were not associated with sex, tobacco use, alcohol use, tumor location, stage, or local recurrence. When compared with wild-type PIK3CA gene cases, patients with PIK3CA gene mutations in exons 9 experienced significantly better disease-free survival and overall survival rates.
CONCLUSION The results of this study suggest that PIK3CA gene mutations could act as a prognostic biomarker in Northwest Chinese ESCC patients.
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Racial Differences in Esophageal Squamous Cell Carcinoma: Incidence and Molecular Features. BIOMED RESEARCH INTERNATIONAL 2017; 2017:1204082. [PMID: 28393072 PMCID: PMC5368356 DOI: 10.1155/2017/1204082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Revised: 02/28/2017] [Accepted: 03/02/2017] [Indexed: 12/11/2022]
Abstract
The incidence and histological type of esophageal cancer are highly variable depending on geographic location and race/ethnicity. Here we want to determine if racial difference exists in the molecular features of esophageal cancer. We firstly confirmed that the incidence rate of esophagus adenocarcinoma (EA) was higher in Whites than in Asians and Blacks, while the incidence of esophageal squamous cell carcinoma (ESCC) was highest in Asians. Then we compared the genome-wide somatic mutations, methylation, and gene expression to identify differential genes by race. The mutation frequencies of some genes in the same pathway showed opposite difference between Asian and White patients, but their functional effects to the pathway may be consistent. The global patterns of methylation and expression were similar, which reflected the common characteristics of ESCC tumors from different populations. A small number of genes had significant differences between Asians and Whites. More interesting, the racial differences of COL11A1 were consistent across multiple molecular levels, with higher mutation frequency, higher methylation, and lower expression in White patients. This indicated that COL11A1 might play important roles in ESCC, especially in White population. Additional studies are needed to further explore their functions in esophageal cancer.
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