Scientific Publications and Presentations

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

March 21, 2024

Ma, Tsai, Farghli, ..., Broom, Barrow & Sethupathy
Journal article published in Plos Genetics

While the role of the DNAJB1-PRKACA (DP) fusion protein in fibrolamellar carcinoma (FLC) was discovered a decade ago, it has been difficult to directly inhibit the function of this fusion protein. In this study, the investigators set out to identify downstream targets of the oncogene that could be exploited for new therapies. The investigators report downstream consequences of the DP fusion protein, changes in the levels of a long noncoding RNA (lncRNA) called LINC00473. LncRNA are RNA molecules that are not translated into proteins, but are responsible for regulating the expression of other proteins (i.e. if a protein is made or how much of the protein is made). Recent studies have shown that some lncRNAs are increased in tumors and can lead to the dysregulation of cell cycle and metabolism, the uncontrolled growth of cells, resistance to programmed cell death (a process known as apoptosis and a built-in safeguard mechanism to dispose of abnormal cells) and metastasis.

A wide array of next-generation sequencing analyses (specifically a technique known as RNA-seq) of FLC patient tissue samples, patient-derived xenografts and FLC cell lines showed elevated levels of LINC00473 as compared to normal cells. Previous reports have shown increased levels of LINC00473 in certain cancer types, including non-small cell lung tumors. In other cancers, such as colorectal cancer, the expression of LINC00473 was silenced (i.e. the gene was not converted into RNA, an essential step in gene expression). These findings indicate that abnormal levels (increased or decreased) of this agent can influence cell growth and metabolism.

To determine the functional role of LINC00473 in FLC, the team created engineered FLC cell lines which had increased or decreased levels of LINC00473.  Reduction in the levels of LINC00473 led to the decreased growth of cells and increased levels correlated with increased growth.  Further analysis of these cell lines showed that when LINC levels were high, other FLC-associated genes were also expressed at high levels. This combination of gain- and loss-of-function approaches identify LINC00473 as a critical regulator of changes that eventually lead to uncontrolled FLC growth.

Interestingly, the investigators found that of the genes that were overexpressed in response to high levels of LINC00473, the majority were involved in energy metabolism and blocking apoptosis (the programmed cell death pathway). Using a technique to analyze cell metabolism, the team observed that FLC cells use glucose and oxygen at a faster rate to increase energy production by modifying the function of mitochondria, the powerhouses of cells and the main sites of energy generation. Implantation of FLC-like cell lines overexpressing LINC00473 into mice led to rapid formation and growth of observable and measurable tumors.

This is the first published evidence of a lincRNA being involved in the development of FLC. Given the role of LINC00473 in FLC tumor growth, and its strong association with DP levels in FLC cells, it could be used as a biomarker for DP activity in cell-based drug screening efforts. It could also emerge as a potential therapeutic target for FLC.

The full publication can be accessed here.

Note: This study was partially funded by a grant from FCF. Tissue samples from the FCF biobank were also used in the analysis.