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Binder S, Zipfel I, Friedrich M, Riedel D, Ende S, Kämpf C, Wiedemann K, Buschmann T, Puppel SH, Reiche K, Stadler PF, Horn F. Master and servant: LINC00152 - a STAT3-induced long noncoding RNA regulates STAT3 in a positive feedback in human multiple myeloma. BMC Med Genomics 2020; 13:22. [PMID: 32041604 PMCID: PMC7011539 DOI: 10.1186/s12920-020-0692-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 01/31/2020] [Indexed: 12/16/2022] Open
Abstract
Background The survival of INA-6 human multiple myeloma cells is strictly dependent upon the Interleukin-6-activated transcription factor STAT3. Although transcriptional analyses have revealed many genes regulated by STAT3, to date no protein-coding STAT3 target gene is known to mediate survival in INA-6 cells. Therefore, the aim here was to identify and analyze non-protein-coding STAT3 target genes. In addition to the oncogenic microRNA-21, we previously described five long noncoding RNAs (lncRNAs) induced by STAT3, named STAiRs. Here, we focus on STAT3-induced RNA 18 (STAiR18), an mRNA-like, long ncRNA that is duplicated in the human lineage. One STAiR18 locus is annotated as the already well described LINC00152/CYTOR, however, the other harbors the MIR4435-2HG gene and is, up to now, barely described. Methods CAPTURE-RNA-sequencing was used to analyze STAiR18 transcript architecture. To identify the STAiR18 and STAT3 phenotype, siRNA-based knockdowns were performed and microarrays were applied to identify their target genes. RNA-binding partners of STAiR18 were determined by Chromatin-Isolation-by-RNA-Purification (ChIRP) and subsequent sequencing. STAT3 expression in dependence of STAiR18 was investigated by immunoblots, chromatin- and RNA-immunoprecipitations. Results As identified by CAPTURE-RNA sequencing, a complex splice pattern originates from both STAiR18 loci, generating different transcripts. Knockdown of the most abundant STAiR18 isoforms dramatically decreased INA-6 cell vitality, suggesting a functional role in myeloma cells. Additionally, STAiR18 and STAT3 knockdowns yielded overlapping changes of transcription patterns in INA-6 cells, suggesting a close functional interplay between the two factors. Moreover, Chromatin isolation by RNA purification (ChIRP), followed by genome-wide RNA sequencing showed that STAiR18 associates specifically with the STAT3 primary transcript. Furthermore, the knockdown of STAiR18 reduced STAT3 levels on both the RNA and protein levels, suggesting a positive feedback between both molecules. Furthermore, STAiR18 knockdown changes the histone methylation status of the STAT3 locus, which explains the positive feedback and indicates that STAiR18 is an epigenetic modulator. Conclusion Hence, STAiR18 is an important regulator of myeloma cell survival and is strongly associated with the oncogenic function of STAT3. The close functional interplay between STAT3 and STAiR18 suggests a novel principle of regulatory interactions between long ncRNAs and signaling pathways.
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Affiliation(s)
- Stefanie Binder
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany. .,Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany.
| | - Ivonne Zipfel
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Maik Friedrich
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Diana Riedel
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany
| | - Stefanie Ende
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Christoph Kämpf
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Karolin Wiedemann
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Tilo Buschmann
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Sven-Holger Puppel
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Kristin Reiche
- Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
| | - Peter F Stadler
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.,German Centre for Integrative Biodiversity Research - iDiv, Halle-Jena-Leipzig, Germany.,Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany.,Department of Theoretical Chemistry, University of Vienna, Wien, Austria.,Center for RNA in Technology and Health, University of Copenhagen, København, Denmark.,Santa Fe Institute, Santa Fe, USA
| | - Friedemann Horn
- Institute of Clinical Immunology, Faculty of Medicine, University of Leipzig, Leipzig, Germany.,Fraunhofer Institute for Cell Therapy and Immunology, Department of Diagnostics, Leipzig, Germany
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Xu J, Guo J, Jiang Y, Liu Y, Liao K, Fu Z, Xiong Z. Improved characterization of the relationship between long intergenic non-coding RNA Linc00152 and the occurrence and development of malignancies. Cancer Med 2019; 8:4722-4731. [PMID: 31270960 PMCID: PMC6712457 DOI: 10.1002/cam4.2245] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2019] [Revised: 04/28/2019] [Accepted: 04/30/2019] [Indexed: 12/15/2022] Open
Abstract
Linc00152, located on chromosome 2p11.2, is a long intergenic non-coding RNA molecule with 828 nucleotides that is highly expressed in many types of human tumor tissues, especially in malignant tumors of the digestive system. Linc00152 promotes the occurrence and development of tumors by increasing tumor cell proliferation, invasion, metastasis, and apoptosis. Additionally, linc00152 contributes to the carcinogenesis of several cancers, including gastric cancer, liver cancer, hepatocellular carcinoma, gallbladder cancer, clear cell renal cell carcinoma, and colorectal cancer, by disturbing various signaling pathways (eg PI3K/AKT, mTOR, IL-1, and NOTCH 1 signaling pathways). High linc00152 expression levels are associated with chemoresistance as well as poor prognosis and shorter survival. Continual advances made in the relevant research have indicated that linc00152 may be useful as a new tumor molecular biomarker, applicable for tumor diagnosis, targeted therapy, and prognosis assessment. This review summarizes the progress in the research into the relationship between linc00152 and the occurrence and development of malignancies based on molecular functions, regulatory mechanisms, and clinical applications.
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Affiliation(s)
- Jiasheng Xu
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jingjing Guo
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yangkai Jiang
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yujun Liu
- Queen Mary College of Nanchang University, Nanchang, China
| | - Kaili Liao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhonghua Fu
- Department of Burns, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Zhenfang Xiong
- Department of Pathology, The First Affiliated Hospital of Nanchang University, Nanchang, China
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