Journal article
The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis
Journal of molecular biology, v 438(6), 169653
23 Jan 2026
PMID: 41581654
Abstract
[Display omitted]
•FAM99A is a liver-enriched lncRNA downregulated across liver cancer subtypes.•FAM99A expression declines during primary hepatocyte dedifferentiation and HBV infection.•FAM99A-203 is the predominant isoform with altered splicing patterns in tumors.•FAM99A suppresses cellular protein synthesis rates and anchorage-independent growth.•FAM99A interacts with translation initiation factors and RNA helicases.
Primary liver cancer represents a significant global health burden, with limited therapeutic options for advanced disease. Long non-coding RNAs (lncRNAs) are increasingly found to play crucial roles in hepatic biology and disease progression. Here, we identify FAM99A as a highly liver-enriched lncRNA that is systematically downregulated across liver malignancies, with reduced expression correlating with poor clinical outcomes. FAM99A exhibits remarkable tissue specificity with minimal expression outside the liver, and its levels rapidly decline during primary hepatocyte dedifferentiation in culture. Through isoform analysis, we establish FAM99A-203 as the predominant transcript in normal liver tissue and observe altered isoform distribution in liver cancers. Functionally, FAM99A overexpression inhibits anchorage-independent growth in liver cancer cell lines. Transcriptomic analysis reveals that FAM99A negatively regulates translation-related pathways in both liver cancer cells and primary hepatocytes. This is corroborated by protein synthesis assays showing that FAM99A overexpression substantially reduces global translation rates. Targeted RNase H-mediated extraction coupled with mass spectrometry identifies multiple components of the translation machinery as direct FAM99A binding partners, including eukaryotic translation initiation factors and RNA helicases involved in ribosome biogenesis. Clinical data analysis demonstrates significant inverse correlations between FAM99A expression and ribosomal protein genes in liver cancer patients. Additionally, hepatitis B virus appears to downregulate FAM99A expression, potentially contributing to its oncogenic properties. Our findings establish FAM99A as a liver-enriched translational regulator that exerts tumor-suppressive effects by restraining protein synthesis rates, offering insights into hepatocarcinogenesis and the potential of FAM99A as both a biomarker and agent in new therapeutic avenues.
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Details
- Title
- The Liver-Enriched Long Non-Coding RNA FAM99A Suppresses Tumorigenesis through Negative Regulation of Protein Synthesis
- Creators
- Nima Sarfaraz - Graduate Program in Molecular and Cell Biology and Genetics, Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USARanjit Kaur - Graduate Program in Molecular and Cell Biology and Genetics, Graduate School of Biomedical Sciences and Professional Studies, College of Medicine, Drexel University, Philadelphia, Pennsylvania, USASky Harper - Drexel University, ChemistryLilly Oni - Drexel UniversitySrinivas Somarowthu - Drexel University, Biochemistry and Molecular BiologyMichael J. Bouchard - Drexel University, Biochemistry and Molecular Biology
- Publication Details
- Journal of molecular biology, v 438(6), 169653
- Publisher
- Elsevier Ltd
- Number of pages
- 28
- Grant note
- Pennsylvania Department of Health CURE Grant: 4100095603
This work was supported by the Pennsylvania Department of Health CURE Grant [SAP #4100095603].
- Resource Type
- Journal article
- Language
- English
- Academic Unit
- Biochemistry and Molecular Biology; Chemistry
- Web of Science ID
- WOS:001685662600001
- Scopus ID
- 2-s2.0-105029138486
- Other Identifier
- 991022155868804721