泪腺良性淋巴上皮病变与黏膜相关淋巴组织型淋巴瘤差异基因表达

Differentially expressed genes between benign lymphoepithelial lesions of lacrimal gland and mucosa-associated lymphoid tissue lymphoma

目的利用全外显子测序技术(WES)对比检测泪腺良性淋巴上皮病变(LGBLEL)和黏膜相关淋巴组织(MALT)淋巴瘤的基因序列,筛选差异表达基因并进行分析。方法采用横断面研究方法,连续纳入2015年1月至2017年11月就诊于首都医科大学附属北京同仁医院的5例LGBLEL患者和5例泪腺MALT淋巴瘤患者,收集患者外周血标本和临床资料。提取外周血DNA,利用WES进行基因测序,应用BWA软件进行差异基因筛选,应用HaplotypeCaller软件进行基因组变异筛查,用ANNOVAR软件对变异结果进行注释,用Varscan软件筛查单核苷酸变异和小插入/缺失基因,用ExomeCNV软件鉴定外显子拷贝数变异。通过蛋白互作网络分析以及功能模块网络构建,筛选出最大团中心值最高的突变枢纽基因。结果平均每个样本检出16.63 Gb数据。单核苷酸变异结果显示各样本常见的突变类型为同义突变和错义突变,LGBLEL组和MALT淋巴瘤组同义突变、错义突变的基因个数比较差异均无统计学意义(均P>0.05),LGBLEL组终止密码子缺失的基因个数多于MALT淋巴瘤组,差异有统计学意义(P<0.05)。小插入/缺失基因结果显示常见的突变类型是移码突变、非移码突变的插入突变和缺失突变,LGBLEL组与MALT淋巴瘤组的插入/缺失基因个数比较差异均无统计学意义(均P>0.05)。LGBLEL组和MALT淋巴瘤组发生外显子拷贝数变异的个数均较少,对最终结果无明显影响。对蛋白互作网络分析和功能模块网络的结果进行综合分析,最终共得到6个差异表达的关键基因,即IGFN1、TCP10、SLC45A4、BTBD7、PHGR1和PIEZ02基因。结论IGFN1、TCP10、SLC45A4、BTBD7、PHGR1及PIEZ02基因是LGBLEL和MALT的差异表达关键基因,可能与LGBLEL发展为MALT淋巴瘤的机制有关。

Objective To screen and analyze the differentially expressed genes between lacrimal gland benign lymphoepithelial lesions(LGBLEL)and mucosa-associated lymphoid tissue(MALT)lymphoma.Methods A cross-sectional study was performed.Ten consecutive patients were included in Beijing Tongren Hospital Affiliated to Capital Medical University from January 2015 to November 2017,including five patients with LGBLEL and five patients with MALT lymphoma.Clinical data and peripheral blood sample were collected from each patient.DNA was extracted from peripheral blood.The whole-exome sequencing(WES)was employed for gene sequencing.The BWA software was used for the screen of differentially expressed gene;GATK software was used to detect genomic variation;ANNOVAR software was used to annotate and predict the effects of the variation;Varscan software was used to analyze single nucleotide polymorphisms(SNPs)and insertion-deletions(InDels),and ExomeCNV software was used to identify copy number variations(CNVs).The mutated hub gene with the maximal clique centrality was screened out by the analysis of protein interaction network and construction of functional module network.This study was approved by an Ethics Committee of Beijing Tongren Hospital Affiliated to Capital Medical University.Written informed consent was obtained from each patient prior to any medical examination.Results There was 16.63 Gb sequencing data per sample on average.Synonymous mutation and missense mutation were the most common SNPs mutation types in the LGBLEL group and MALT lymphoma group,and no significant difference was found in gene mumber of synonymous mutation and missense mutation between the two groups.The number of terminating codon missing mutation genes in the LGBLEL group was more than that in the MALT lymphoma group(P<0.05).The most common InDels types were frameshift mutation,non-frameshift insertion and non-frameshift deletion,and there was no significant difference in gene number of InDels between the LGBLEL group and MALT lymphoma group.The number of exon CNVs was few in both two groups and showed no significant influence in final result.Six differentially expressed hub genes were found,including IGFN1,TCP10,SLC45A4,BTBD7,PHGR1 and PIEZ02.Conclusions IGFN1,TCP10,SLC45A4,BTBD7,PHGR1 and PIEZ02 genes may participate in the development of LGBLEL into MALT lymphoma.