Abstract 1557: Defining the regulatory effects of candidate oncogenic non-coding RNA LINC00473 in fibrolamellar carcinoma

Abstract Fibrolamellar carcinoma (FLC) is a rare form of liver cancer that disproportionately affects adolescents, usually presents at advanced stages with no known risk factors or serum biomarkers, and exhibits high intrinsic drug resistance. The signature genetic event of FLC was identified in 2014 as a ~400kb heterozygous deletion resulting in the DNAJB1-PRKACA (or DP) fusion oncogene. The DP fusion occurs in over 80% of FLC patients and is sufficient for tumorigenesis in mice. Targeting DP pharmacologically has proved challenging; therefore, we performed multiple genome-scale studies to identify and target candidate downstream effectors that drive FLC development and progression. LINC00473, a primate-specific long non-coding RNA (lncRNA), emerged as a top candidate oncogene. Multiple models reveal strong induction of LINC00473 in FLC, including: (1) primary tumor relative to normal liver; (2) FLC patient-derived xenograft tumors (PDX); and (3) a newly developed FLC cell line derived from the PDX. Importantly, LINC00473 is upregulated in response to the fusion oncogene in HEK293 cells that express DP via CRISPR/Cas9-mediated deletion, and is dramatically downregulated in FLC cells upon DP knockdown by three independent siRNAs (collaboration with Alnylam Pharmaceuticals, Inc). Stable in vitro suppression of LINC00473 using two distinct short hairpin RNAs results in RNA depletion and significant reduction of cell proliferation. Concordantly, the stable overexpression of LINC00473 in FLC cells leads to a robust increase in gene expression and elevated cell proliferation. These data suggest that LINC00473 is a key regulator of FLC cell growth and survival. Next, to investigate the regulatory effects of LINC00473, we first determined that the lncRNA is enriched in the nucleus of FLC cells using subcellular fractionation followed by qRT-PCR, suggesting a role in transcriptional regulation. To investigate if LINC00473 acts downstream of the DP fusion to regulate gene expression programs mediating FLC phenotypes, we performed RNA-seq on FLC cells that harbor stable LINC00473 knockdown or overexpression. These data enabled us to define the altered gene expression profiles that result from LINC00473 dysregulation. Overall, this study elucidates the functional role of LINC00473 in the progression of FLC and helps advance the field by providing important biological insights into this disease. Citation Format: Rosanna K. Ma, Matt Kanke, Khashayar Vakili, Praveen Sethupathy. Defining the regulatory effects of candidate oncogenic non-coding RNA LINC00473 in fibrolamellar carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1557.