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

PLoS Genet. 2024 Mar 21;20(3):e1011216. doi: 10.1371/journal.pgen.1011216. eCollection 2024 Mar.

Abstract

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 noncoding 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 disease models. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, which indicates mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.

MeSH terms

  • Adolescent
  • Carcinoma, Hepatocellular* / genetics
  • Carcinoma, Hepatocellular* / pathology
  • Cyclic AMP-Dependent Protein Kinase Catalytic Subunits / genetics
  • HSP40 Heat-Shock Proteins / genetics
  • HSP40 Heat-Shock Proteins / metabolism
  • Humans
  • Liver Neoplasms* / metabolism
  • RNA, Long Noncoding* / genetics
  • RNA, Long Noncoding* / metabolism
  • Young Adult

Substances

  • Cyclic AMP-Dependent Protein Kinase Catalytic Subunits
  • DNAJB1 protein, human
  • HSP40 Heat-Shock Proteins
  • PRKACA protein, human
  • RNA, Long Noncoding
  • LINC00473 RNA, human

Supplementary concepts

  • Fibrolamellar hepatocellular carcinoma

Grants and funding

This work was supported by funding from the College of Veterinary Medicine Graduate Fellowship (awarded to RKM), Center for Vertebrate Genomics Scholar Award (awarded to RKM), Sandra Atlas Bass Endowment for Cancer Research (awarded to PS), and a Fibrolamellar Cancer Foundation Research Grant (awarded to PS). The authors confirm that the funders had no role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript.