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Salib A, Jayatilleke N, Seneviratne JA, Mayoh C, De Preter K, Speleman F, Cheung BB, Carter DR, Marshall GM. MYCN and SNRPD3 cooperate to maintain a balance of alternative splicing events that drives neuroblastoma progression. Oncogene 2024; 43:363-377. [PMID: 38049564 PMCID: PMC10824661 DOI: 10.1038/s41388-023-02897-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 11/05/2023] [Accepted: 11/14/2023] [Indexed: 12/06/2023]
Abstract
Many of the pro-tumorigenic functions of the oncogene MYCN are attributed to its regulation of global gene expression programs. Alternative splicing is another important regulator of gene expression and has been implicated in neuroblastoma development, however, the molecular mechanisms remain unknown. We found that MYCN up-regulated the expression of the core spliceosomal protein, SNRPD3, in models of neuroblastoma initiation and progression. High mRNA expression of SNRPD3 in human neuroblastoma tissues was a strong, independent prognostic factor for poor patient outcome. Repression of SNRPD3 expression correlated with loss of colony formation in vitro and reduced tumorigenicity in vivo. The effect of SNRPD3 on cell viability was in part dependent on MYCN as an oncogenic co-factor. RNA-sequencing revealed a global increase in the number of genes being differentially spliced when MYCN was overexpressed. Surprisingly, depletion of SNRPD3 in the presence of overexpressed MYCN further increased differential splicing, particularly of cell cycle regulators, such as BIRC5 and CDK10. MYCN directly bound SNRPD3, and the protein arginine methyltransferase, PRMT5, consequently increasing SNRPD3 methylation. Indeed, the PRMT5 inhibitor, JNJ-64619178, reduced cell viability and SNRPD3 methylation in neuroblastoma cells with high SNRPD3 and MYCN expression. Our findings demonstrate a functional relationship between MYCN and SNRPD3, which maintains the fidelity of MYCN-driven alternative splicing in the narrow range required for neuroblastoma cell growth. SNRPD3 methylation and its protein-protein interface with MYCN represent novel therapeutic targets. Hypothetical model for SNRPD3 as a co-factor for MYCN oncogenesis. SNRPD3 and MYCN participate in a regulatory loop to balance splicing fidelity in neuroblastoma cells. First MYCN transactivates SNRPD3 to lead to high-level expression. Second, SNRPD3 and MYCN form a protein complex involving PRMT5. Third, this leads to balanced alterative splicing (AS) activitiy that is favorable to neuroblastoma. Together this forms as a therapeutic vulnerability where SNRPD3 perturbation or PRMT5 inhibitors are selectively toxic to neuroblastoma by conditionally disturbing splicing activity.
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Affiliation(s)
- Alice Salib
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Nisitha Jayatilleke
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Janith A Seneviratne
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Chelsea Mayoh
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Katleen De Preter
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics (CMGG), Ghent University, Medical Research Building (MRB1), Ghent, Belgium
| | - Belamy B Cheung
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia
- School of Women's and Children's Health, UNSW Sydney, Kensington, NSW, 2052, Australia
| | - Daniel R Carter
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.
- School of Biomedical Engineering, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
| | - Glenn M Marshall
- Children's Cancer Institute, Lowy Cancer Research Centre, UNSW Sydney, Kensington, NSW, 2052, Australia.
- Kids Cancer Centre, Sydney Children's Hospital, Randwick, NSW, 2031, Australia.
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Jablonowski CM, Gil HJ, Pinto EM, Pichavaram P, Fleming AM, Clay MR, Hu D, Morton CL, Pruett-Miller SM, Hansen BS, Chen X, Jones KMD, Liu Y, Ma X, Yang J, Davidoff AM, Zambetti GP, Murphy AJ. TERT Expression in Wilms Tumor Is Regulated by Promoter Mutation or Hypermethylation, WT1, and N-MYC. Cancers (Basel) 2022; 14:cancers14071655. [PMID: 35406427 PMCID: PMC8996936 DOI: 10.3390/cancers14071655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/08/2022] [Accepted: 03/23/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The telomerase enzyme adds repetitive genetic sequences to the ends of chromosomes called telomeres to prevent cellular senescence. Gain of telomerase function is one of the hallmarks of human cancer. The telomerase protein is coded by the gene TERT and increased TERT RNA levels have been associated with disease relapse in Wilms tumor, the most common kidney cancer of childhood. This study aimed to determine the mechanisms of increased TERT expression in Wilms tumor. This study found mutations in the TERT promoter, increased methylation of the TERT promoter, and genomic copy number amplifications of TERT as potential mechanisms of TERT activation. Conversely, this study found that inactivating WT1 mutation was associated with low TERT RNA levels and telomerase activity. N-MYC overexpression in Wilms tumor cells resulted in increased TERT promoter activity and TERT transcription. TERT transcription is associated with molecular and histologic subgroups in Wilms tumor and telomere-targeted therapies warrant future investigation. Abstract Increased TERT mRNA is associated with disease relapse in favorable histology Wilms tumor (WT). This study sought to understand the mechanism of increased TERT expression by determining the association between TERT and WT1 and N-MYC, two proteins important in Wilms tumor pathogenesis that have been shown to regulate TERT expression. Three out of 45 (6.7%) WTs and the corresponding patient-derived xenografts harbored canonical gain-of-function mutations in the TERT promoter. This study identified near ubiquitous hypermethylation of the TERT promoter region in WT compared to normal kidney. WTs with biallelic inactivating mutations in WT1 (7/45, 15.6%) were found to have lower TERT expression by RNA-seq and qRT-PCR and lower telomerase activity determined by the telomerase repeat amplification protocol. Anaplastic histology and increased percentage of blastema were positively correlated with higher TERT expression and telomerase activity. In vitro shRNA knockdown of WT1 resulted in decreased expression of TERT, reduced colony formation, and decreased proliferation of WiT49, an anaplastic WT cell line with wild-type WT1. CRISPR-Cas9-mediated knockout of WT1 resulted in decreased expression of telomere-related gene pathways. However, an inducible Wt1-knockout mouse model showed no relationship between Wt1 knockout and Tert expression in normal murine nephrogenesis, suggesting that WT1 and TERT are coupled in transformed cells but not in normal kidney tissues. N-MYC overexpression resulted in increased TERT promoter activity and TERT transcription. Thus, multiple mechanisms of TERT activation are involved in WT and are associated with anaplastic histology and increased blastema. This study is novel because it identifies potential mechanisms of TERT activation in Wilms tumor that could be of therapeutic interests.
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Affiliation(s)
- Carolyn M. Jablonowski
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Hyea Jin Gil
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Emilia M. Pinto
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (E.M.P.); (G.P.Z.)
| | - Prahalathan Pichavaram
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Andrew M. Fleming
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Michael R. Clay
- Department of Pathology, University of Colorado Anschutz, Aurora, CO 80045, USA;
| | - Dongli Hu
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Christopher L. Morton
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Shondra M. Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.M.P.-M.); (B.S.H.)
| | - Baranda S. Hansen
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (S.M.P.-M.); (B.S.H.)
| | - Xiang Chen
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (X.C.); (K.M.D.J.); (Y.L.); (X.M.)
| | - Karissa M. Dieseldorff Jones
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (X.C.); (K.M.D.J.); (Y.L.); (X.M.)
| | - Yanling Liu
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (X.C.); (K.M.D.J.); (Y.L.); (X.M.)
| | - Xiaotu Ma
- Department of Computational Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (X.C.); (K.M.D.J.); (Y.L.); (X.M.)
| | - Jun Yang
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
| | - Andrew M. Davidoff
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
- Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA
| | - Gerard P. Zambetti
- Department of Pathology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA; (E.M.P.); (G.P.Z.)
| | - Andrew J. Murphy
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Mail Stop 133, Memphis, TN 38105, USA; (C.M.J.); (H.J.G.); (P.P.); (A.M.F.); (D.H.); (C.L.M.); (J.Y.); (A.M.D.)
- Division of Pediatric Surgery, Department of Surgery, University of Tennessee Health Science Center, Memphis, TN 38105, USA
- Correspondence:
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Buglyó G, Magyar Z, Romicsné Görbe É, Bánusz R, Csóka M, Micsik T, Mezei M, Yani JAS, Varga P, Sápi Z, Nagy B. miRNA Profiling of Hungarian Regressive Wilms' Tumor Formalin-Fixed Paraffin-Embedded (FFPE) Samples by Quantitative Real-Time Polymerase Chain Reaction (RT-PCR). Med Sci Monit 2021; 27:e932731. [PMID: 34608109 PMCID: PMC8501895 DOI: 10.12659/msm.932731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Wilms' tumor is a common renal malignancy of early childhood with a generally favorable prognosis depending upon histological subtype. It is becoming increasingly clear that differences in miRNA (microRNA) expression signature represent important clues helping us predict a tumor's response to chemotherapy. In our study, we aimed to reveal miRNAs deregulated in regressive Wilms' tumors from FFPE (formalin-fixed, paraffin-embedded) samples, also showing whether such samples are reliable miRNA sources in Wilms' tumor. MATERIAL AND METHODS Samples from 8 Hungarian patients (3 males, 5 females, aged 1 to 7 years) were analyzed by qRT-PCR (quantitative real-time PCR). A PCR array was used in a pilot experiment, and selected miRNAs (miR-128-3p, miR-184, miR-194-5p, miR-203a) were studied in the rest of the samples using individual primers. RESULTS miR-194-5p was underexpressed in all tumor samples. miR-184 and miR-203a were underexpressed in 7 cases, the exception being a case with a high ratio of necrotic blastemal tissue. Results obtained with miR-128-3p are difficult to interpret due to varying directions of expression changes. CONCLUSIONS We conclude that a downregulation of miR-184, miR-194-5p, and miR-203a expression is observed in both regressive and blastemal tumors, but larger-scale studies are needed to confirm whether the degree of their underexpression correlates with the number of blastemal elements in a sample. In most of our FFPE samples aged up to 9 years, RNA extraction provided miRNA with quantity and quality sufficient for qRT-PCR-based analysis, emphasizing the relevance of pathological archives as miRNA sources in future studies.
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Affiliation(s)
- Gergely Buglyó
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Zsófia Magyar
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Éva Romicsné Görbe
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Rita Bánusz
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Monika Csóka
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Tamás Micsik
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Márta Mezei
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Jaxi Ayman Shawky Yani
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Péter Varga
- Department of Obstetrics and Gynaecology, Baross Street Division, Semmelweis University, Budapest, Hungary
| | - Zoltán Sápi
- 1st Department of Pathology and Experimental Cancer Research, Semmelweis University, Budapest, Hungary
| | - Bálint Nagy
- Department of Human Genetics, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
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