Profiling of hepatocellular carcinoma neoantigens reveals immune microenvironment and clonal evolution related patterns

Objective: Neoantigens derived from tumor-specific genomic alterations have demonstrated great potential for immunotherapeutic interventions in cancers. However, the comprehensive profile of hepatocellular carcinoma(HCC) neoantigens and their complex interplay with immune microenvironment and tumor evolution have not been fully addressed.Methods: Here we integrated whole exome sequencing data, transcriptome sequencing data and clinical information of 72 primary HCC patients to characterize the HCC neoantigen profile, and systematically explored its interactions with tumor clonal evolution, driver mutations and immune microenvironments.Results: We observed that higher somatic mutation/neoantigen load was associated with better clinical outcomes and HCC patients could be further divided into two subgroups with distinct prognosis based on their neoantigen expression patterns. HCC subgroup with neoantigen expression probability high(NEP-H) showed more aggressive pathologic features including increased incidence of tumor thrombus(P=0.038), higher recurrence rate(P=0.029),more inclined to lack tumor capsule(P=0.026) and with more microsatellite instability sites(P=0.006). In addition,NEP-H subgroup was also characterized by higher chance to be involved in tumor clonal evolution [odds ratio(OR)=46.7, P<0.001]. Gene set enrichment analysis revealed that upregulation of MYC and its targets could suppress immune responses, leading to elevated neoantigen expression proportion in tumor cells. Furthermore, we discovered an immune escape mechanism that tumors could become more inconspicuous by evolving subclones with less immunogenicity. We observed that smaller clonal mutation clusters with higher immunogenicity in tumor were more likely to involve in clonal evolution. Based on identified neoantigen profiles, we also discovered series of neoantigenic hotspot genes, which could serve as potential actionable targets in future.Conclusions: Our results revealed the landscape of HCC neoantigens and discovered two clinically relevant subgroups with distinct neoantigen expression patterns, suggesting the neoantigen expression should be fully considered in future immunotherapeutic interventions.

循环肿瘤DNA对中国肝癌诊断价值的Meta分析

目的系统评价循环肿瘤DNA(ctDNA)在中国人群原发性肝癌(肝癌)中的诊断价值。方法检索PubMed、Web of Science、Embase、中国知网、万方、维普数据库中从建库至2021年11月关于应用ctDNA诊断肝癌的文献。中英文检索词为循环肿瘤DNA、ctDNA、游离DNA、循环DNA、cfDNA、血浆DNA、血清DNA,以及肝癌、肝细胞癌、肝肿瘤、肝脏肿瘤、原发性肝癌等。对纳入文献进行数据提取和质量评估后,采用Review Manager 5.3和Stata 15.1统计软件计算合并敏感度、特异度,绘制森林图和综合受试者操作特征(sROC)曲线并计算曲线下面积(AUC)。通过Meta回归分析和亚组分析分析异质性来源。绘制Deek's漏斗图检验发表偏倚。结果共纳入符合标准的文献25篇,包括4063例肝癌患者和3509例对照。其中5项研究为检测ctDNA浓度的定量分析,14篇为检测ctDNA中的肿瘤特异性单基因甲基化的定性分析,6篇通过ctDNA的特征构建模型进行诊断。定量研究组的合并敏感度、特异度及AUC分别为0.68(0.58~0.77)、0.82(0.71~0.89)和0.81(0.77~0.84);定性研究组相应为0.55(0.47~0.62)、0.99(0.93~1.00)和0.80(0.77~0.83);模型构建组相应为0.81(0.72~0.87)、0.91(0.85~0.94)和0.93(0.90~0.95)。Deek's漏斗图检验显示,定量研究组(t=1.080,P>0.05)、定性研究组(t=0.690,P>0.05)和模型构建组(t=0.230,P>0.05)均不存在明显的发表偏倚。结论ctDNA在我国肝癌诊断中具有良好的应用价值,利用ctDNA构建模型的诊断性能优于定量分析和定性分析。