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Lee B, Katsushima K, Pokhrel R, Yuan M, Stapleton S, Jallo G, Wechsler-Reya RJ, Eberhart CG, Ray A, Perera RJ. The long non-coding RNA SPRIGHTLY and its binding partner PTBP1 regulate exon 5 skipping of SMYD3 transcripts in group 4 medulloblastomas. Neurooncol Adv 2022; 4:vdac120. [PMID: 36267874 PMCID: PMC9569026 DOI: 10.1093/noajnl/vdac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Background Although some of the regulatory genes, signaling pathways, and gene regulatory networks altered in medulloblastomas (MB) are known, the roles of non-coding RNAs, particularly long non-coding RNAs (lncRNAs), are poorly described. Here we report that the lncRNA SPRIGHTLY (SPRY4-IT1) gene is upregulated in group 4 medulloblastoma (G4 MB). Methods SPRIGHTLY expression was assessed in MB subgroup patient-derived xenografts, cell lines, and patient samples. The effect of SPRIGHTLY hemizygous deletion on proliferation, invasion, apoptosis, and colony formation were assessed in vitro and on tumor growth in vivo. dChIRP pull-down assays were used to assess SPRIGHTLY-binding partners, confirmed by immunoprecipitation. SMYD3 ΔE5 transcripts were examined in cell lines and publicly available RNA-seq data. Pathway analysis was performed by phospho-kinase profiling and RNA-seq. Results CRISPR/Cas9 deletion of SPRIGHTLY reduced cell viability and invasion and increased apoptosis in G4 MB cell lines in vitro. SPRIGHTLY hemizygous-deleted G4 MB cells injected into mouse cerebellums produced smaller tumors than those derived from parental cells expressing both copies of SPRIGHTLY. SPRIGHTLY lncRNA bound to the intronic region of the SMYD3 pre-mRNA transcript. SPRIGHTLY also interacted with PTPB1 protein to regulate SMYD3 exon skipping to produce an aberrant protein. SPRIGHTLY-driven SMYD3 regulation enhanced the expression of EGFR pathway genes in G4 MB cell lines and activated cell coagulation/hemostasis-related gene expression, suggesting a novel oncogenic role in G4 MB. Conclusions These results demonstrate the importance of SPRIGHTLY lncRNA as a promoter of G4 MB and the role of the SPRIGHTLY-SMYD3-PTPB1 axis as an important oncogenic regulator in MB.
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Affiliation(s)
- Bongyong Lee
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Keisuke Katsushima
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Rudramani Pokhrel
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Menglang Yuan
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Stacie Stapleton
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - George Jallo
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
| | - Robert J Wechsler-Reya
- Sanford Burnham Prebys Medical Discovery Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Charles G Eberhart
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Department of Pathology, Johns Hopkins University School of Medicine, 720 Rutland Ave – Ross Bldg 558, Baltimore, MD 21205, USA
| | - Animesh Ray
- Riggs School of Applied Life Sciences, Keck Graduate Institute, Claremont CA, 91711, USA
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ranjan J Perera
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, School of Medicine, Johns Hopkins University, 1650 Orleans St., Baltimore, MD 21231, USA
- Johns Hopkins All Children’s Hospital, 600 5th St. South, St. Petersburg, FL 33701, USA
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