■肝细胞癌(HCC),代表80%以上的原发性肝癌病例,缺乏令人满意的病因和诊断方法。本研究旨在通过使用单细胞RNA测序(scRNA-seq)和RNA测序(RNA-seq)数据构建诊断模型,阐明程序性细胞死亡相关基因(CDRGs)在HCC中的作用。
■六类CDRG,包括细胞凋亡,坏死,自噬,焦亡,铁性凋亡,和角化,被收集。来自血液来源外泌体的RNA-seq数据来自exoRBase数据库,来自TCGA数据库的癌组织的RNA-seq数据,和来自GEO数据库的scRNA-seq数据。随后,我们将来自exoRBase和TCGA数据库的HCC队列的差异表达基因(DEGs)与CDRGs相交,以及从单细胞数据集获得的DEG。然后使用临床指标和机器学习方法筛选候选生物标志物基因,从而构建了肝癌的七基因诊断模型。此外,来自Mendeley数据门户的HCC的scRNA-seq和空间转录组测序(stRNA-seq)数据用于研究这七个关键基因的潜在机制及其与免疫检查点阻断(ICB)治疗的关联。最后,我们通过定量聚合酶链反应(qPCR)和免疫组织化学实验验证了关键分子在组织和血液来源的外泌体中的表达。
■集体,我们共获得50个样本和104,288个单细胞。经过细致的筛选,我们建立了肝癌的七基因诊断模型,在exoRBaseHCC队列(训练集:AUC=1;测试集:AUC=0.847)和TCGAHCC队列(训练集:AUC=1;测试集:AUC=0.976)中均显示出高诊断效能。随后的分析显示,HCC簇3表现出更高的干性指数,可以作为肝癌细胞分化轨迹的起点,还显示与微环境中其他细胞类型的更丰富的相互作用。值得注意的是,关键基因TRIB3和NQO1在HCC细胞中表达水平升高。实验验证进一步证实了它们在癌症患者的肿瘤组织和血液来源的外泌体中的表达升高。此外,stRNA分析不仅证实了这些发现,而且提示TRIB3和NQO1高表达的患者可能对ICB治疗有更有利的反应.
■七基因诊断模型在肝癌筛查中表现出显著的准确性,TRIB3正在成为肝癌的有希望的诊断工具和治疗靶点。
UNASSIGNED: Hepatocellular carcinoma (HCC), representing more than 80% of primary liver cancer cases, lacks satisfactory etiology and diagnostic methods. This study aimed to elucidate the role of programmed cell death-associated genes (CDRGs) in HCC by constructing a diagnostic model using single-cell RNA sequencing (scRNA-seq) and RNA sequencing (RNA-seq) data.
UNASSIGNED: Six categories of CDRGs, including apoptosis, necroptosis, autophagy, pyroptosis, ferroptosis, and cuproptosis, were collected. RNA-seq data from blood-derived exosomes were sourced from the exoRBase database, RNA-seq data from cancer tissues from the TCGA database, and scRNA-seq data from the GEO database. Subsequently, we intersected the differentially expressed genes (DEGs) of the HCC cohort from exoRBase and TCGA databases with CDRGs, as well as DEGs obtained from single-cell datasets. Candidate biomarker genes were then screened using clinical indicators and a machine learning approach, resulting in the construction of a seven-gene diagnostic model for HCC. Additionally, scRNA-seq and spatial transcriptome sequencing (stRNA-seq) data of HCC from the Mendeley data portal were used to investigate the underlying mechanisms of these seven key genes and their association with immune checkpoint blockade (ICB) therapy. Finally, we validated the expression of key molecules in tissues and blood-derived exosomes through quantitative Polymerase Chain Reaction (qPCR) and immunohistochemistry experiments.
UNASSIGNED: Collectively, we obtained a total of 50 samples and 104,288 single cells. Following the meticulous screening, we established a seven-gene diagnostic model for HCC, demonstrating high diagnostic efficacy in both the exoRBase HCC cohort (training set: AUC = 1; testing set: AUC = 0.847) and TCGA HCC cohort (training set: AUC = 1; testing set: AUC = 0.976). Subsequent analysis revealed that HCC cluster 3 exhibited a higher stemness index and could serve as the starting point for the differentiation trajectory of HCC cells, also displaying more abundant interactions with other cell types in the microenvironment. Notably, key genes TRIB3 and NQO1 displayed elevated expression levels in HCC cells. Experimental validation further confirmed their elevated expression in both tumor tissues and blood-derived exosomes of cancer patients. Additionally, stRNA analysis not only substantiated these findings but also suggested that patients with high TRIB3 and NQO1 expression might respond more favorably to ICB therapy.
UNASSIGNED: The seven-gene diagnostic model demonstrated remarkable accuracy in HCC screening, with TRIB3 emerging as a promising diagnostic tool and therapeutic target for HCC.