Uncovering the functionally essential variations related to tumorigenesis and tumor progression from cancer genomics data is still challenging due to the genetic diversity among patients, and extensive inter- and intra-tumoral heterogeneity at different levels of gene expression regulation, including but not limited to the genomic, epigenomic, and transcriptional levels. To minimize the impact of germline genetic heterogeneities, in this study, we establish multiple primary cultures from the primary and recurrent tumors of a single patient with hepatocellular carcinoma (HCC). Multi-omics sequencing was performed for these cultures that encompass the diversity of tumor cells from the same patient. Variations in the genome sequence, epigenetic modification, and gene expression are used to infer the phylogenetic relationships of these cell cultures. We find the discrepancy among the relationships revealed by single nucleotide variations (SNVs) and transcriptional/epigenomic profiles from the cell cultures. We fail to find overlap between sample-specific mutated genes and differentially expressed genes (DEGs), suggesting that most of the heterogeneous SNVs among tumor stages or lineages of the patient are functionally insignificant. Moreover, copy number alterations (CNAs) and DNA methylation variation within gene bodies, rather than promoters, are significantly correlated with gene expression variability among these cell cultures. Pathway analysis of CNA/DNA methylation-related genes indicates that a single cell clone from the recurrent tumor exhibits distinct cellular characteristics and tumorigenicity, and such an observation is further confirmed by cellular experiments both in vitro and in vivo. Our systematic analysis reveals that CNAs and epigenomic changes, rather than SNVs, are more likely to contribute to the phenotypic diversity among subpopulations in the tumor. These findings suggest that new therapeutic strategies targeting gene dosage and epigenetic modification should be considered in personalized cancer medicine. This culture model may be applied to the further identification of plausible determinants of cancer metastasis and relapse.

中文翻译：

---

主细胞培养模型的多组学分析揭示了肿瘤内表型多样性的遗传和表观遗传基础。

由于患者之间的遗传多样性以及在不同水平的基因表达调节水平（包括但不限于基因组）上的广泛的肿瘤内和肿瘤内异质性，从癌症基因组学数据中发现与肿瘤发生和肿瘤进展相关的功能性基本变异仍然具有挑战性。 ，表观基因组和转录水平。为了最大程度地减少种系遗传异质性的影响，在这项研究中，我们从一名肝细胞癌（HCC）患者的原发和复发肿瘤中建立了多种原代培养。对这些培养物进行多组学测序，包括来自同一患者的肿瘤细胞的多样性。基因组序列的变化，表观遗传修饰和基因表达可用于推断这些细胞培养的系统发育关系。我们发现由细胞培养物中的单核苷酸变异（SNV）和转录/表观基因组图谱揭示的关系之间存在差异。我们未能发现样品特异性突变基因与差异表达基因（DEG）之间存在重叠，这表明患者的肿瘤分期或谱系中的大多数异质SNV在功能上均无关紧要。此外，基因体中而不是启动子上的拷贝数改变（CNA）和DNA甲基化变异与这些细胞培养物中的基因表达变异显着相关。CNA / DNA甲基化相关基因的通路分析表明，来自复发性肿瘤的单个细胞克隆具有明显的细胞特征和致瘤性，并且通过体内外的细胞实验进一步证实了这种观察。我们的系统分析表明，CNA和表观基因组变化而不是SNV，更可能有助于肿瘤亚群之间的表型多样性。这些发现表明，在个性化癌症医学中应考虑针对基因剂量和表观遗传修饰的新治疗策略。该培养模型可用于进一步鉴定癌症转移和复发的可能决定因素。这些发现表明，在个性化癌症医学中应考虑针对基因剂量和表观遗传修饰的新治疗策略。该培养模型可用于进一步鉴定癌症转移和复发的可能决定因素。这些发现表明，在个性化癌症医学中应考虑针对基因剂量和表观遗传修饰的新治疗策略。该培养模型可用于进一步鉴定癌症转移和复发的可能决定因素。