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Wang Y, Xiao F, Zhao Y, Mao CX, Yu LL, Wang LY, Xiao Q, Liu R, Li X, McLeod HL, Hu BW, Huang YL, Lv QL, Xie XX, Huang WH, Zhang W, Guo CX, Li JG, Yin JY. A two-stage genome-wide association study to identify novel genetic loci associated with acute radiotherapy toxicity in nasopharyngeal carcinoma. Mol Cancer 2022; 21:169. [PMID: 35999636 PMCID: PMC9400233 DOI: 10.1186/s12943-022-01631-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 07/25/2022] [Indexed: 11/29/2022] Open
Abstract
Background Genetic variants associated with acute side effects of radiotherapy in nasopharyngeal carcinoma (NPC) remain largely unknown. Methods We performed a two-stage genome-wide association analysis including a total of 1084 patients, where 319 individuals in the discovery stage were genotyped for 688,783 SNPs using whole genome-wide screening microarray. Significant variants were then validated in an independent cohort of 765 patients using the MassARRAY system. Gene mapping, linkage disequilibrium, genome-wide association analysis, and polygenic risk score were conducted or calculated using FUMA, LDBlockShow, PLINK, and PRSice software programs, respectively. Results Five SNPs (rs6711678, rs4848597, rs4848598, rs2091255, and rs584547) showed statistical significance after validation. Radiotherapy toxicity was more serious in mutant minor allele carriers of all five SNPs. Stratified analysis further indicated that rs6711678, rs4848597, rs4848598, and rs2091255 correlated with skin toxicity in patients of EBV positive, late stage (III and IV), receiving both concurrent chemoradiotherapy and induction/adjuvant chemotherapy, and with OR values ranging from 1.92 to 2.66. For rs584547, high occurrence of dysphagia was found in A allele carriers in both the discovery (P = 1.27 × 10− 6, OR = 1.55) and validation (P = 0.002, OR = 4.20) cohorts. Furthermore, prediction models integrating both genetic and clinical factors for skin reaction and dysphagia were established. The area under curve (AUC) value of receiver operating characteristic (ROC) curves were 0.657 (skin reaction) and 0.788 (dysphagia). Conclusions Rs6711678, rs4848597, rs4848598, and rs2091255 on chromosome 2q14.2 and rs584547 were found to be novel risk loci for skin toxicity and dysphagia in NPC patients receiving radiotherapy. Trial registration Chinese Clinical Trial Register (registration number: ChiCTR-OPC-14005257 and CTXY-140007-2). Supplementary Information The online version contains supplementary material available at 10.1186/s12943-022-01631-8.
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Affiliation(s)
- Yang Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Fan Xiao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Yi Zhao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China.,Department of General Practice, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, Guangdong, P.R. China
| | - Chen-Xue Mao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Lu-Lu Yu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Lei-Yun Wang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Qi Xiao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Rong Liu
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Xi Li
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Howard L McLeod
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China.,Geriatric Oncology Consortium, Tampa, FL, 33612, USA.,USF Taneja College of Pharmacy, Tampa, FL, 33612, USA
| | - Bi-Wen Hu
- Center of Clinical Pharmacology, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, P. R. China
| | - Yu-Ling Huang
- Department of Radiation Oncology, Jiangxi Cancer Hospital of Nanchang University, Nanchang, 330029, P.R. China.,National Health Commission (NHC) Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma (Jiangxi Cancer Hospital of Nanchang University), Nanchang, 330029, P.R. China
| | - Qiao-Li Lv
- Department of Radiation Oncology, Jiangxi Cancer Hospital of Nanchang University, Nanchang, 330029, P.R. China.,National Health Commission (NHC) Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma (Jiangxi Cancer Hospital of Nanchang University), Nanchang, 330029, P.R. China
| | - Xiao-Xue Xie
- Departent of Radiotherapy, Hunan Provincial Tumor Hospital and Affiliated Tumor Hospital of Xiangya Medical School, Central South University, Changsha, 410013, P.R. China
| | - Wei-Hua Huang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Wei Zhang
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China.,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China
| | - Cheng-Xian Guo
- Center of Clinical Pharmacology, the Third Xiangya Hospital, Central South University, Changsha, 410013, Hunan, P. R. China.
| | - Jin-Gao Li
- Department of Radiation Oncology, Jiangxi Cancer Hospital of Nanchang University, Nanchang, 330029, P.R. China. .,National Health Commission (NHC) Key Laboratory of Personalized Diagnosis and Treatment of Nasopharyngeal Carcinoma (Jiangxi Cancer Hospital of Nanchang University), Nanchang, 330029, P.R. China.
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha, 410078, P. R. China. .,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha, 410078, P. R. China. .,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, 110 Xiangya Road, Changsha, 410078, P. R. China. .,National Clinical Research Center for Geriatric Disorders, 87 Xiangya Road, Changsha, 410008, Hunan, P.R. China. .,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha, 410078, P. R. China.
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Guo AX, Xiao F, Shao WH, Zhan Y, Zhang L, Xiong J, Gao Y, Yin JY. Sequential Whole Exome Sequencing Reveals Somatic Mutations Associated with Platinum Response in NSCLC. Onco Targets Ther 2020; 13:6485-6496. [PMID: 32753889 PMCID: PMC7342605 DOI: 10.2147/ott.s254747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/28/2020] [Indexed: 12/28/2022] Open
Abstract
Purpose Resistance is one of the main limitations of successful platinum treatment in non-small-cell lung cancer (NSCLC) patients. In this study, we aimed to identify somatic mutations associated with platinum response. Patients and Methods A total of 57 patients who received platinum-based chemotherapy only and 13 patients who received neoadjuvant chemotherapy (NAC) were enrolled. Somatic mutations were obtained from targeted and whole exome sequencing (WES). Results Somatic mutations in a total of 225 genes were observed. Nonsynonymous variants in EGFR, TTN, TP53 and KRAS, and copy number variations (SCNVs) in chromosome 8q24.3 and 22q11.21 were identified to be associated with platinum response. Based on these mutations, the mutational signature associated with the failure of DNA double-strand break and calcium signaling pathways were identified to be associated with platinum response. Besides, we observed a decrease in tumor mutational burden after chemotherapy. We also evaluated the mutation spectrum consistency between cell-free DNA (cfDNA) and tissue DNA. Somatic mutations detected in cfDNA were consistent with that in tDNA, which indicated that plasma might be used for somatic mutation detection. Conclusion These results support that somatic mutations can affect platinum drug response and provide potential clinical biomarkers for NSCLC treatment.
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Affiliation(s)
- Ao-Xiang Guo
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China
| | - Fan Xiao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China
| | - Wei-Hua Shao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China
| | - Yan Zhan
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China
| | - Le Zhang
- Department of Neurology, Xiangya Hospital, Central South University, Changsha, Hunan, People's Republic of China
| | - Jing Xiong
- Department of Gynaecology and Obstetrics, The Second Xiangya Hospital, Central South University, Changsha 410011, People's Republic of China
| | - Yang Gao
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, People's Republic of China.,Department of Thoracic Surgery, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Hunan Engineering Research Center for Pulmonary Nodules Precise Diagnosis & Treatment, Changsha 410078, People's Republic of China
| | - Ji-Ye Yin
- Department of Clinical Pharmacology, Xiangya Hospital, Central South University, Changsha 410078, People's Republic of China.,Institute of Clinical Pharmacology, Central South University, Hunan Key Laboratory of Pharmacogenetics, Changsha 410078, People's Republic of China.,Engineering Research Center of Applied Technology of Pharmacogenomics, Ministry of Education, Changsha 410078, People's Republic of China.,National Clinical Research Center for Geriatric Disorders, Changsha 410008, Hunan, People's Republic of China.,Hunan Key Laboratory of Precise Diagnosis and Treatment of Gastrointestinal Tumor, Changsha 410078, People's Republic of China
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