| Background:Gastric cancer is common in China.The prognosis of early gastric cancer(EGC)and advanced gastric cancer is markedly different.Screening methods based on endoscopy were inadequate and needed to be supplemented.Studies on gastric cancer genome showed that the heterogeneity of gene mutations among different gastric cancer was large.Studies on EGC immune repertoire(IR)showed that the diversity of T cell receptor(TCR)repertoire increased with the progression of cancer.However,these studies didn't focus on the dynamics of EGC development.In the present study,by deep sequencing of multi-timepoint samples,the genomic and IR characteristics of EGC were analyzed to explore the mechanism of EGC development and to provide clues for early diagnosis of EGC.Methods:Patients who underwent endoscopic submucosal dissection(ESD)in 2018 and had previously taken gastric mucosa and blood samples at Peking Union Medical College Hospital were retrospectively collected.Finally,a total of 15 patients were included with 75 gastric mucosa samples and 29 blood samples.Whole exome sequencing(WES)and high-throughput IR sequencing were conducted to all samples.WES data were analyzed for genome atlas,mutational signatures,copy number variation(CNV),microsatellite instability(MSI),tumor mutational burden(TMB)and evolutionary tree.IR data were analyzed for diversity,clonality,Morisita-Horn similarity overlap index(MOI)and clone frequency.Main analysis software included Cutadapt,Pyclone,Mixer,Rstudio and SPSS.Main statistical methods included T-test,ANOVA,Kruskal-Wallis test,chi-square test and Fisher' s exact test.The significant level was set to two-tailed p<0.05.Results:This study described the genome atlas of EGC.Genes with high mutation frequency included TTN(66.7%),SYNE1(53.3%)and DSCAM(46.7%),CNV was generally present in all lesion samples.Some high-frequency mutations could distinguish between the lesion and reference samples,with an accuracy of 0.781.Along with the development from inflammation/intestinal metaplasia to low-grade intraepithelial neoplasia(LGIN)and then to EGC,TMB increased first but then decreased(0.72±0.75/Mb vs 3.77±2.01/Mb vs 1.28±1.22/Mb,p<0.001).The number of DNA damage repair(DDR)pathway mutations in lesion samples was significantly higher than that in reference samples(1.13±1.72 vs 0.18±0.67,p=0.001),and high TMB,MSI positive and multiple DDR pathway mutations were correlated.Dynamic analysis of genome data showed that the proportion of random mutations was high while the proportion of driver gene mutations was low in premalignant lesions.As cancer progressed,key driver gene mutations remained.The diversity of blood cells TCR repertoire was significantly higher than that of tissue samples in EGC.The diversity of lesion samples TCR repertoire was higher than that of the reference samples(p=0.041),while the clonality was lower(p=0.0015).High-frequency TCR clones in tissue samples lacked specificity,and the proportion of TCR clones against neoantigens was low.Conclusions:Before the emergence of EGC,a certain number of gene mutations had appeared in the lesion mucosa,which was related to the damage of DDR.At the same time,T cells accumulated in the gastric mucosa,eliminating clones with random mutations,causing a temporary decline in TMB.However,due to the low specificity of tumor-infiltrating T cells,clones with driver gene mutations remained and gradually developed into EGC.The genomic and IR characteristics during this process helped to identify EGC before pathological changes. |
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