全外显子组测序筛查食管鳞状细胞癌放疗抵抗相关基因研究  

Identification of critical radioresistance genes in esophageal squamous cell carcinoma by whole exome sequencing

作　　者：陈志明[1] 陈俊杰[2] 李李 丁倩 韩钰楠 赵洪瑜[1] Chen Zhiming;Chen Junjie;Li Li;Ding Qian;Han Yunan;Zhao Hongyu(Department of Radiotherapy&Oncology,Affiliated Hospital of Nantong University,Nantong 226001,China;Clinical Medical Center of Affiliated Hospital of Nantong University,Nantong 226001,China)

机构地区：[1]南通大学附属医院肿瘤放疗科,南通226001 [2]南通大学附属医院临床医学研究中心,南通226001

出　　处：《国际肿瘤学杂志》2023年第10期592-599,共8页Journal of International Oncology

基　　金：南通市基础科学研究项目(JC2020071)。

摘　　要：目的比较食管鳞状细胞癌(ESCC)术后放疗后不同预后患者的基因谱差异, 筛选与放疗抵抗相关的遗传变异。方法选择2015年1月至2019年12月在南通大学附属医院接受根治性手术及术后辅助放疗的32例ESCC患者为研究对象, 根据1年内是否出现照射野内复发分为复发组(放疗抵抗组, n=16)和稳定组(放疗敏感组, n=16)。分别提取患者的基因组DNA, 利用全外显子组测序(WES)技术进行高通量测序。应用Trimmomatic、BWA、Picard生物信息学分析软件处理数据, 通过GATK对比获得比对文件, 然后利用Vardict软件从测序数据中筛选出两组的各类遗传变异。采用Kaplan-Meier法估算患者无瘤生存期(DFS)、总生存期(OS)。Cox比例风险回归模型分析影响ESCC患者DFS和OS的独立危险因素。结果经样本数据质量控制, 本研究最终纳入26例患者进行后续分析, 复发组和稳定组各13例。全组非沉默肿瘤突变负荷中位数为0.95个/Mb, 突变碱基替换类型均以C>T的转换为主, 其次为C>G的颠换;发生频率最高的遗传变异依次是单核苷酸多态性(SNP)(75.1%)、缺失突变(13.7%)、插入突变(10.5%);复发组中肿瘤特有突变数目较稳定组稍高(中位突变数分别为36、34), 且两组突变频率前十的基因谱明显不同。复发组中检测到392个特有突变基因, 前5个分别为:MUC19、NPIPA5、EPPK1、FLG和FOXG1。稳定组检测到192个特有突变基因, 前5个分别为TCHH、WNK1、AIM1L、COL6A5和DPCR1。复发组中位DFS和中位OS分别为15.0个月(95%CI为10.1个月~未达到)和26.2个月(95%CI为19.8个月~未达到), 稳定组患者均未出现复发或转移。单因素分析发现, GRIK2(χ^(2)=6.81, P=0.009)、MUC4(χ^(2)=4.25, P=0.039)、MUC5B(χ^(2)=4.03, P=0.045)、PRRG1(χ^(2)=5.15, P=0.023)基因突变、3p缺失(χ^(2)=4.16, P=0.041)和14q缺失(χ^(2)=7.09, P=0.008)与DFS相关;FLG(χ^(2)=6.41, P=0.011)、NPIPA5(χ^(2)=4.57, P=0.033)、PKD1L2(χ^(2)=6.41, P=0.011)、FOXGObjective To compare the genetic spectrums of esophageal squamous cell carcinoma(ESCC)patients with different prognosis after postoperative radiotherapy and to screen the genetic variants associated with radiotherapy resistance.Methods A total of 32 ESCC patients who received radical surgery and postoperative adjuvant radiotherapy in Affiliated Hospital of Nantong University from January 2015 to December 2019 were selected as the study objects.According to whether there was any recurrence in the radiation field within 1 year,they were divided into a recurrence group(radiotherapy resistance group,n=16)and a stable group(radiotherapy sensitive group,n=16).Genomic DNA was extracted from patients and highthroughput sequencing was performed using whole exome sequencing(WES)technology.Biological information analysis software Trimmomatic,BWA and Picard were used to process the data and the alignment files were obtained by GATK comparison,then Vardict software was used to screen out various genetic variants from the sequencing data.The disease free survival(DFS)and overall survival(OS)were estimated by Kaplan-Meier method.Cox proportional hazard regression model was used to analyze the independent risk factors of DFS and OS of ESCC patients.Results After quality control of the sample data,26 patients were finally included in this study for follow-up analysis,13 in each of the recurrence and stable groups.The median tumor mutation burden of non-silent tumors in the whole group was 0.95 mutations/Mb.The substitution types of mutant bases were mainly C>T conversion,followed by C>G transmutation.The genetic variants with the highest frequency were single nucleotide polymorphism(SNP)(75.1%),deletion mutation(13.7%)and insertion mutation(10.5%).The number of tumor-specific mutations in the recurrence group was slightly higher than that in the stable group(median mutation number was 36 and 34,respectively),and the top ten gene profiles of mutation frequency were significantly different between the two groups.In the recurrence g

关 键 词：食道鳞癌 全外显子组测序 遗传变异 放疗抵抗 

分 类 号：R735.1[医药卫生—肿瘤]