DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma

Fibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogene DNAJB1-PRKACA (DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based and in vivo models of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease. Overall design: RNA-seq of FLC LINC00473-overexpression (LeGO-473ox) FLC monoclone cell and empty vector (LeGO-Ctl) control FLC monoclone cell samples. Also, RNA-seq of FLC patient samples for Primary & NML tumor samples. UPDATE: [Mar-25-2025] The title of Sample GSM7402776 was updated to 'FLC NML tumor RNA-seq sample #6'.

纤维板层型肝癌（fibrolamellar carcinoma, FLC）是一类罕见肝癌，其发病具有显著的年龄偏好性，尤其好发于青少年与年轻成人。目前尚无公认的标准治疗方案，亟需开发新型治疗手段。多数患者携带有DNAJB1-PRKACA融合致癌基因（DP融合），但目前尚未开发出针对性临床抑制剂，因此鉴定FLC发病机制的下游介导因子至关重要。
本研究中，我们鉴定出长链非编码RNA（long non-coding RNA, lncRNA）LINC00473是FLC肿瘤中上调最为显著的基因之一，并证实其在FLC肿瘤上皮细胞中可被RNA干扰（RNA interference, RNAi）介导的DP融合抑制作用显著下调。通过功能缺失与功能获得性实验，我们证实LINC00473可抑制细胞凋亡、上调FLC标志物基因的表达，并在细胞模型与体内疾病模型中促进FLC增殖。从分子机制来看，LINC00473在促进糖酵解进程并改变线粒体活性方面发挥重要作用：具体而言，LINC00473的敲低会提升备用呼吸能力——这是反映线粒体健康状态的重要指标。综上，我们提出LINC00473可作为这一致命疾病的潜在治疗靶点。
实验整体设计：对过表达LINC00473的FLC单克隆细胞（LeGO-473ox）及空载对照单克隆细胞（LeGO-Ctl）开展RNA测序（RNA-seq）；同时对FLC患者的原发肿瘤与正常匹配（NML）肿瘤样本进行RNA测序。
更新说明：[2025年3月25日] 样本GSM7402776的标题已更新为“FLC NML肿瘤RNA测序样本#6”。