Function of non-coding RNAs in liver cancer
Pathology
Cell Biology
Final Report Abstract
Long non-coding RNAs (lncRNAs) have recently emerged as a relevant class of functional molecules in the cell and have been linked to many physiological and pathological processes. While many lncRNAs are deregulated in different diseases including cancer, their cellular functions and molecular mechanisms of action are often unknown. Here, we have studied the role of lncRNAs in the most common form of liver cancer, hepatocellular carcinoma (HCC). Using expression profiling and siRNA screening, we have identified a number of lncRNAs linked to HCC and analyzed their functions and mechanisms. The lncRNA CASC9 is overexpressed in HCC and its silencing reduces cell proliferation in vitro and tumor growth in vivo. CASC9 interacts with the protein HNRNPL to regulate common target genes via the AKT pathway. The lncRNA lincNMR is also overexpressed in cancer and its knockdown induces senescence, reduces cell proliferation and viability in vitro and in vivo. It interacts with and activates the transcription factor YBX1 leading to the expression of factors required for nucleotide metabolism and the production of dNTPs, which are required for cell cycle progression. However, our analyses also document that not all annotated lncRNAs indeed are non-coding. We have identified CASIMO1 as the first microprotein linked to cancer derived from a transcript formerly annotated as lncRNA. In addition to the identification of novel lncRNA players and their functions in cancer, we have also pursued methodological questions comparing RNAi- and CRISPR-based approaches for lncRNAs. We find that only 38% of all human lncRNAs can be targeted by CRISPRi safely without affecting another gene as off-target. This poses an important challenge to be controlled for in CRISPR-based approaches for non-coding (and coding) target genes, especially when analyzing complex genomic loci harboring multiple genes. In summary, this project has shed light onto the important role of multiple novel non-coding RNAs in the development of liver cancer down to their molecular mechanism - combined with studies into the feasibility of approaches to silence their expression.
Publications
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A cautionary tale of sense-antisense gene pairs: Independent regulation despite inverse correlation of expression. Nucleic Acids Research (2017) 45: 12496-12508
A Goyal, E Fiskin, T Gutschner, M Polycarpou-Schwarz, M Groß, J Neugebauer, M Gandhi, M Caudron-Herger, V Benes, S Diederichs
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Challenges of CRISPR / Cas9 applications for long non-coding RNA genes. Nucleic Acids Research (2017) 45: e12
A Goyal, K Myacheva, M Groß, M Klingenberg, B Duran-Arque, S Diederichs
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Non-coding RNA in hepatocellular carcinoma: Mechanisms, biomarkers and therapeutic targets. Journal of Hepatology (2017) 67: 603-618
M Klingenberg, A Matsuda, S Diederichs, T Patel
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RNA motifs and combinatorial prediction of interactions, stability and localization of noncoding RNAs. Nature Structural & Molecular Biology (2018) 25: 1070-1076
M Gandhi, M Caudron-Herger, S Diederichs
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The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation. Oncogene (2018) 37: 4750-4768
M Polycarpou-Schwarz, M Groß, P Mestdagh, J Schott, SE Grund, C Hildenbrand, J Rom, S Aulmann, HP Sinn, J Vandesompele, S Diederichs
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The lncRNA CASC9 and RNA binding protein HNRNPL form a complex and co-regulate genes linked to AKT signaling. Hepatology (2018) 68: 1817-1832
M Klingenberg, M Groß, A Goyal, M Polycarpou-Schwarz, T Miersch, AS Ernst, J Leupold, N Patil, U Warnken, H Allgayer, T Longerich, P Schirmacher, M Boutros, S Diederichs
