Schachtschneider Kyle M, Redlon Luke N, Lokken Ryan Peter, Huang Yu-Hui, Guzman Grace, Schook Lawrence B, Gaba Ron C
Department of Radiology, University of Illinois at Chicago, Chicago, Illinois, United States of America.
Department of Biochemistry and Molecular Genetics, University of Illinois at Chicago, Chicago, Illinois, United States of America.
PLoS One. 2025 May 27;20(5):e0324145. doi: 10.1371/journal.pone.0324145. eCollection 2025.
Combined hepatocellular carcinoma-cholangiocarcinoma (HCC-CCA) is a rare liver tumor comprising histologic features of both HCC and CCA. Due to its heterogeneous nature, treatment of combined HCC-CCA is a significant clinical challenge and prognosis remains poor. Therefore, further understanding of the tumor biology underlying the individual subtypes of this mixed tumor is required to improve treatment stratification and optimize treatment strategies. This study sought to identify altered epigenetic regulation and gene expression patterns in the individual components of combined HCC-CCA. Formalin fixed paraffin embedded (FFPE) tumor specimens from 9 patients diagnosed with combined HCC-CCA were utilized in this study. Hematoxylin and eosin (H&E) staining was performed for each sample, and regions representative of the individual HCC and CCA components were delineated. Adjacent unstained slides were cut and dissected to separate HCC and CCA components. DNA and RNA extraction was performed for each sample for DNA methylation (n = 7 HCC and 7 CCA) and gene expression (n = 7 HCC and 8 CCA) profiling via reduced representation bisulfite sequencing (RRBS) and RNA-seq, respectively. Samples did not cluster by tumor type when comparing genome-wide DNA methylation or gene expression patterns. Of the 5 patients with DNA methylation data available for both subtypes, 4 clustered by patient as opposed to cancer subtype, suggesting similar epigenetic regulatory patterns arising from development in the same microenvironment and genetic background. Differential analysis resulted in the identification of 57 differentially expressed genes (DEGs) and 808 differentially methylated regions (DMRs) between the HCC and CCA subtypes. Genes associated with DMRs were associated with Wnt signaling, voltage-gated channels, metal binding, and cellular regulation. Finally, increased expression of several genes previously implicated in tumor aggressiveness, prognosis, and treatment responses were identified. These results highlight the potential importance of accounting for underlying HCC and CCA tumor biology when determining the optimal course of treatment for this deadly disease.
肝细胞癌-胆管癌（HCC-CCA）是一种罕见的肝脏肿瘤，兼具肝细胞癌（HCC）和胆管癌（CCA）的组织学特征。由于其异质性，HCC-CCA的治疗是一项重大的临床挑战，预后仍然很差。因此，需要进一步了解这种混合肿瘤各个亚型背后的肿瘤生物学，以改善治疗分层并优化治疗策略。本研究旨在确定HCC-CCA各个组分中表观遗传调控和基因表达模式的改变。本研究使用了来自9例诊断为HCC-CCA患者的福尔马林固定石蜡包埋（FFPE）肿瘤标本。对每个样本进行苏木精和伊红（H&E）染色，并划定代表各个HCC和CCA组分的区域。切割并解剖相邻的未染色玻片以分离HCC和CCA组分。分别通过简化代表性亚硫酸氢盐测序（RRBS）和RNA测序对每个样本进行DNA甲基化（n = 7例HCC和7例CCA）和基因表达（n = 7例HCC和8例CCA）分析，以进行DNA提取和RNA提取。在比较全基因组DNA甲基化或基因表达模式时，样本未按肿瘤类型聚类。在5例可获得两种亚型DNA甲基化数据的患者中，有4例按患者聚类，而非癌症亚型，这表明在相同的微环境和遗传背景下发育产生了相似的表观遗传调控模式。差异分析导致在HCC和CCA亚型之间鉴定出57个差异表达基因（DEG）和808个差异甲基化区域（DMR）。与DMR相关的基因与Wnt信号传导、电压门控通道、金属结合和细胞调节有关。最后，鉴定出先前与肿瘤侵袭性、预后和治疗反应相关的几个基因的表达增加。这些结果突出了在确定这种致命疾病的最佳治疗方案时考虑潜在的HCC和CCA肿瘤生物学的潜在重要性。
