Single-Cell DNA Sequencing Reveals Punctuated and Gradual Clonal Evolution in Hepatocellular Carcinoma
Single-Cell DNA Sequencing Reveals Punctuated and Gradual Clonal Evolution in Hepatocellular Carcinoma
复制标题
单细胞 DNA 测序揭示肝细胞癌的间断和渐进克隆进化
DOI：
10.1053/j.gastro.2021.08.052
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发表时间：
2021-12-11
期刊：
影响因子：
29.4
通讯作者：
Zhang，Ning
中科院分区：
文献类型：
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作者：
Guo，Lin;Yi，Xianfu;Zhang，Ning
背景与目的基因组不稳定性引起的拷贝数改变（CNAs）是肿瘤内异质性的主要来源。CNAs如何在肝细胞癌（HCC）中演变仍然是未知的。MethodsWe进行了单细胞DNA测序（scDNA-seq）从10例HCC患者中分离的1275个细胞，从另外1例患者中分离的356个细胞的倍性分辨的scDNA-seq，以及从另外3例患者中分离的27，344个细胞的单细胞RNA测序。三个统计拟合模型进行了比较，以探讨CNA积累pattern.ResultsCells在肿瘤中分为以下3个亚群：整倍体，假整倍体，和非整倍体。我们的scDNA-seq分析显示，CNA积累遵循双相拷贝数进化模型，即间断阶段之后是渐进阶段。渐进期延长的患者表现出更高的瘤内异质性和更差的无病生存期。整合17例HCC患者的批量RNA测序、1196例肝肿瘤的已发表数据集和202例HCC肿瘤的免疫组化染色，我们发现CAD（一种参与嘧啶合成的基因）的高表达与快速肿瘤发生和生存率降低相关。我们的单细胞RNA测序数据和已发表的其他癌症类型的scDNA-seq数据集验证了双相拷贝数进化模型。此外，倍性分辨的scDNA-seq揭示了二倍体和多倍体-非整倍体细胞的共同克隆起源，表明多倍体肿瘤细胞是由二倍体肿瘤细胞的全基因组加倍产生的。结论我们的工作揭示了一种新的双相拷贝数进化模型，显示HCC的渐进期越长，病情越严重，确定CAD作为HCC早期复发的一个有希望的生物标志物，并支持多倍体HCC的二倍体起源。
Background & AimsCopy number alterations (CNAs), elicited by genome instability, are a major source of intratumor heterogeneity. How CNAs evolve in hepatocellular carcinoma (HCC) remains unknown.MethodsWe performed single-cell DNA sequencing (scDNA-seq) on 1275 cells isolated from 10 patients with HCC, ploidy-resolved scDNA-seq on 356 cells from 1 additional patient, and single-cell RNA sequencing on 27,344 cells from 3 additional patients. Three statistical fitting models were compared to investigate the CNA accumulation pattern.ResultsCells in the tumor were categorized into the following 3 subpopulations: euploid, pseudoeuploid, and aneuploid. Our scDNA-seq analysis revealed that CNA accumulation followed a dual-phase copy number evolution model, that is, a punctuated phase followed by a gradual phase. Patients who exhibited prolonged gradual phase showed higher intratumor heterogeneity and worse disease-free survival. Integrating bulk RNA sequencing of 17 patients with HCC, published datasets of 1196 liver tumors, and immunohistochemical staining of 202 HCC tumors, we found that high expression ofCAD, a gene involved in pyrimidine synthesis, was correlated with rapid tumorigenesis and reduced survival. The dual-phase copy number evolution model was validated by our single-cell RNA sequencing data and published scDNA-seq datasets of other cancer types. Furthermore, ploidy-resolved scDNA-seq revealed the common clonal origin of diploid- and polyploid-aneuploid cells, suggesting that polyploid tumor cells were generated by whole genome doubling of diploid tumor cells.ConclusionsOur work revealed a novel dual-phase copy number evolution model, showed HCC with longer gradual phase was more severe, identifiedCADas a promising biomarker for early recurrence of HCC, and supported the diploid origin of polyploid HCC.