Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma. Epigenetic and transcriptomic characterization reveals progression markers and essential pathways in clear cell renal cell carcinoma

Identifying tumor-cell-specific markers and elucidating their epigenetic regulation and spatial heterogeneity provides mechanistic insights into cancer etiology. Here, we have performed snRNA-seq and snATAC-seq in 34 and 28 human clear cell renal cell carcinoma (ccRCC) specimens, respectively, with matched bulk proteogenomics data. By identifying 20 tumor-specific markers through a multi-omics tiered approach, we reveal an association between higher ceruloplasmin (CP) expression and reduced survival. CP knockdown, combined with spatial transcriptomics, suggests a role for CP in regulating hyalinized stroma and tumor-stroma interactions in ccRCC. Intratumoral heterogeneity analysis portrays tumor cell-intrinsic inflammation and epithelial-mesenchymal transition (EMT) as two distinguishing features of tumor subpopulations. Finally, BAP1 mutations are associated with widespread reduction of chromatin accessibility, while PBRM1 mutations generally increase accessibility, with the former affecting five times more accessible peaks than the latter. These integrated analyses reveal the cellular architecture of ccRCC, providing insights into key markers and pathways in ccRCC tumorigenesis. Overall design: We performed snRNA-seq on 34 samples (25 patients) and matched snATAC-seq on 28 of these samples (24 patients) from the Clinical Proteomic Tumor Analysis Consortium (CPTAC) ccRCC collection. ***RAW data will be deposited at dbGAP***

鉴定肿瘤细胞特异性标志物并阐明其表观遗传调控机制与空间异质性，可为癌症病因学提供机制层面的深入见解。本研究分别对34例和28例人类透明细胞肾细胞癌（clear cell renal cell carcinoma, ccRCC）样本开展单细胞核RNA测序（snRNA-seq）与单细胞核转座酶可及性测序（snATAC-seq），并配套获取了批量蛋白质基因组学（proteogenomics）数据。通过多组学分层策略鉴定出20种肿瘤特异性标志物后，本研究发现铜蓝蛋白（ceruloplasmin, CP）的高表达与患者不良生存预后存在显著关联。对CP进行基因敲低并结合空间转录组学（spatial transcriptomics）分析，提示CP在透明细胞肾细胞癌中参与调控透明样基质形成与肿瘤-基质相互作用。瘤内异质性分析显示，肿瘤细胞固有的炎症反应与上皮间质转化（epithelial-mesenchymal transition, EMT）是肿瘤亚群的两大标志性特征。最后，BAP1突变与染色质可及性的广泛降低相关，而PBRM1突变通常会提升染色质可及性；前者影响的可及性峰区数量是后者的五倍。这些整合组学分析揭示了透明细胞肾细胞癌的细胞架构，为阐明该肿瘤发生过程中的关键标志物与信号通路提供了新的见解。研究设计：本研究从临床蛋白质组肿瘤分析联盟（Clinical Proteomic Tumor Analysis Consortium, CPTAC）的透明细胞肾细胞癌数据集中共纳入34例样本（来自25名患者）开展单细胞核RNA测序，并对其中28例样本（来自24名患者）配套开展单细胞核转座酶可及性测序。***原始数据将提交至dbGAP数据库***