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Bojko J, Kollareddy M, Szemes M, Bellamy J, Poon E, Moukachar A, Legge D, Vincent EE, Jones N, Malik S, Greenhough A, Paterson A, Park JH, Gallacher K, Chesler L, Malik K. Spliceosomal vulnerability of MYCN-amplified neuroblastoma is contingent on PRMT5-mediated regulation of epitranscriptomic and metabolomic pathways. Cancer Lett 2024:217263. [PMID: 39313128 DOI: 10.1016/j.canlet.2024.217263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 09/12/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024]
Abstract
Approximately 50% of poor prognosis neuroblastomas arise due to MYCN over-expression. We previously demonstrated that MYCN and PRMT5 proteins interact and PRMT5 knockdown led to apoptosis of MYCN amplified (MNA) neuroblastoma. Here we evaluate the highly selective first-in-class PRMT5 inhibitor GSK3203591 and its in vivo analogue GSK3326593 as targeted therapeutics for MNA neuroblastoma. Cell-line analyses show MYCN-dependent growth inhibition and apoptosis, with approximately 200-fold greater sensitivity of MNA neuroblastoma lines. RNA sequencing of three MNA neuroblastoma lines treated with GSK3203591 reveal deregulated MYCN transcriptional programmes and altered mRNA splicing, converging on key regulatory pathways such as DNA damage response, epitranscriptomics and cellular metabolism. Stable isotope labelling experiments in the same cell lines demonstrate that glutamine metabolism is impeded following GSK3203591 treatment, linking with disruption of the MLX/Mondo nutrient sensors via intron retention of MLX mRNA. Interestingly, glutaminase (GLS) protein decreases after GSK3203591 treatment despite unchanged transcript levels. We demonstrate that the RNA methyltransferase METTL3 and cognate reader YTHDF3 proteins are lowered following their mRNAs undergoing GSK3203591-induced splicing alterations, indicating epitranscriptomic regulation of GLS; accordingly, we observe decreases of GLS mRNA m6A methylation following GSK3203591 treatment, and decreased GLS protein following YTHDF3 knockdown. In vivo efficacy of GSK3326593 is confirmed by increased survival of Th-MYCN mice, with drug treatment triggering splicing events and protein decreases consistent with in vitro data. Together our study demonstrates the PRMT5-dependent spliceosomal vulnerability of MNA neuroblastoma and identifies the epitranscriptome and glutamine metabolism as critical determinants of this sensitivity.
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Affiliation(s)
- Jodie Bojko
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Madhu Kollareddy
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Marianna Szemes
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Jacob Bellamy
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Evon Poon
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Ahmad Moukachar
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Danny Legge
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Emma E Vincent
- Translational Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
| | - Nicholas Jones
- Institute of Life Science, Swansea University Medical School, Swansea University, Swansea SA2 8PP, UK
| | - Sally Malik
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Alex Greenhough
- College of Health, Science and Society, University of the West of England, Bristol, BS16 1QY, UK
| | - Alex Paterson
- Insilico Consulting ltd, Wapping Wharf, Bristol, England, United Kingdom
| | - Ji Hyun Park
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Kelli Gallacher
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK
| | - Louis Chesler
- Division of Clinical Studies, The Institute of Cancer Research, London, UK
| | - Karim Malik
- Cancer Epigenetics Laboratory, School of Cellular and Molecular Medicine, University of Bristol, Bristol, UK.
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Raghav Y, Dilliott AA, Petrozziello T, Kim SE, Berry JD, Cudkowicz ME, Vakili K, Fraenkel E, Farhan SMK, Sadri-Vakili G. Identification of gene fusions associated with amyotrophic lateral sclerosis. Muscle Nerve 2024; 69:477-489. [PMID: 38305586 DOI: 10.1002/mus.28043] [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: 05/04/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/03/2024]
Abstract
INTRODUCTION/AIMS Genetics is an important risk factor for amyotrophic lateral sclerosis (ALS), a neurodegenerative disease affecting motor neurons. Recent findings demonstrate that in addition to specific genetic mutations, structural variants caused by genetic instability can also play a causative role in ALS. Genomic instability can lead to deletions, duplications, insertions, inversions, and translocations in the genome, and these changes can sometimes lead to fusion of distinct genes into a single transcript. Gene fusion events have been studied extensively in cancer; however, they have not been thoroughly investigated in ALS. The aim of this study was to determine whether gene fusions are present in ALS. METHODS Gene fusions were identified using STAR Fusion v1.10.0 software in bulk RNA-Seq data from human postmortem samples from publicly available data sets from Target ALS and the New York Genome Center ALS Consortium. RESULTS We report the presence of gene fusion events in several brain regions as well as in spinal cord samples in ALS. Although most gene fusions were intra-chromosomal events between neighboring genes and present in both ALS and control samples, there was a significantly greater number of unique gene fusions in ALS compared to controls. Lastly, we identified specific gene fusions with a significant burden in ALS, that were absent from both control samples and known cancer gene fusion databases. DISCUSSION Collectively, our findings reveal an enrichment of gene fusions in ALS and suggest that these events may be an additional genetic cause linked to ALS pathogenesis.
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Affiliation(s)
- Yogindra Raghav
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Allison A Dilliott
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
| | - Tiziana Petrozziello
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Spencer E Kim
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - James D Berry
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Merit E Cudkowicz
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
| | - Khashayar Vakili
- Department of Surgery, Boston Children's Hospital, Boston, Massachusetts, USA
| | - Ernest Fraenkel
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sali M K Farhan
- Department of Neurology and Neurosurgery, McGill University, Montreal, Quebec, Canada
- Department of Genetics, McGill University, Montreal, Quebec, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montreal, Quebec, Canada
| | - Ghazaleh Sadri-Vakili
- Sean M. Healey &AMG Center for ALS at Mass General, Massachusetts General Hospital, Boston, Massachusetts, USA
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3
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Singh S, Fang J, Jin H, Van de Velde LA, Wu Q, Cortes A, Morton CL, Woolard MA, Quarni W, Steele JA, Connelly JP, He L, Thorne R, Turner G, Confer T, Johnson M, Caufield WV, Freeman BB, Lockey T, Pruett-Miller SM, Wang R, Davidoff AM, Thomas PG, Yang J. RBM39 degrader invigorates natural killer cells to eradicate neuroblastoma despite cancer cell plasticity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.21.586157. [PMID: 38585889 PMCID: PMC10996557 DOI: 10.1101/2024.03.21.586157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
The cellular plasticity of neuroblastoma is defined by a mixture of two major cell states, adrenergic (ADRN) and mesenchymal (MES), which may contribute to therapy resistance. However, how neuroblastoma cells switch cellular states during therapy remains largely unknown and how to eradicate neuroblastoma regardless of their cell states is a clinical challenge. To better understand the lineage switch of neuroblastoma in chemoresistance, we comprehensively defined the transcriptomic and epigenetic map of ADRN and MES types of neuroblastomas using human and murine models treated with indisulam, a selective RBM39 degrader. We showed that cancer cells not only undergo a bidirectional switch between ADRN and MES states, but also acquire additional cellular states, reminiscent of the developmental pliancy of neural crest cells. The lineage alterations are coupled with epigenetic reprogramming and dependency switch of lineage-specific transcription factors, epigenetic modifiers and targetable kinases. Through targeting RNA splicing, indisulam induces an inflammatory tumor microenvironment and enhances anticancer activity of natural killer cells. The combination of indisulam with anti-GD2 immunotherapy results in a durable, complete response in high-risk transgenic neuroblastoma models, providing an innovative, rational therapeutic approach to eradicate tumor cells regardless of their potential to switch cell states.
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4
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Jablonowski CM, Quarni W, Singh S, Tan H, Bostanthirige DH, Jin H, Fang J, Chang TC, Finkelstein D, Cho JH, Hu D, Pagala V, Sakurada SM, Pruett-Miller SM, Wang R, Murphy A, Freeman K, Peng J, Davidoff AM, Wu G, Yang J. Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing associated with therapeutic response to splicing inhibitor. eLife 2024; 12:RP90993. [PMID: 38488852 PMCID: PMC10942784 DOI: 10.7554/elife.90993] [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] [Indexed: 03/17/2024] Open
Abstract
Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that jumonji domain containing 6, arginine demethylase, and lysine hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven human neuroblastoma. JMJD6 cooperates with MYC in cellular transformation of murine neural crest cells by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a 'molecular glue' that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.
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Affiliation(s)
| | - Waise Quarni
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Shivendra Singh
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Haiyan Tan
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | | | - Hongjian Jin
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Jie Fang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Ti-Cheng Chang
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - David Finkelstein
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Ji-Hoon Cho
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | - Dongli Hu
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Vishwajeeth Pagala
- Center for Proteomics and Metabolomics, St Jude Children's Research HospitalMemphisUnited States
| | - Sadie Miki Sakurada
- Department of Cell and Molecular Biology, St Jude Children's Research HospitalMemphisUnited States
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St Jude Children's Research HospitalMemphisUnited States
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s HospitalColumbusUnited States
| | - Andrew Murphy
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
| | - Kevin Freeman
- Genetics, Genomics & Informatics, The University of Tennessee Health Science Center (UTHSC)MemphisUnited States
| | - Junmin Peng
- Department of Structural Biology, St Jude Children’s Research HospitalMemphisUnited States
| | - Andrew M Davidoff
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
| | - Gang Wu
- Center for Applied Bioinformatics, St Jude Children’s Research HospitalMemphisUnited States
| | - Jun Yang
- Department of Surgery, St Jude Children’s Research HospitalMemphisUnited States
- St Jude Graduate School of Biomedical Sciences, St Jude Children’s Research HospitalMemphisUnited States
- Department of Pathology and Laboratory Medicine, College of Medicine, The University of Tennessee Health Science CenterMemphisUnited States
- College of Graduate Health Sciences, University of Tennessee Health Science CenterMemphisUnited States
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5
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Jablonowski C, Quarni W, Singh S, Tan H, Bostanthirige DH, Jin H, Fang J, Chang TC, Finkelstein D, Cho JH, Hu D, Pagala V, Sakurada SM, Pruett-Miller SM, Wang R, Murphy A, Freeman K, Peng J, Davidoff AM, Wu G, Yang J. Metabolic reprogramming of cancer cells by JMJD6-mediated pre-mRNA splicing is associated with therapeutic response to splicing inhibitor. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546606. [PMID: 37425900 PMCID: PMC10327027 DOI: 10.1101/2023.06.26.546606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Dysregulated pre-mRNA splicing and metabolism are two hallmarks of MYC-driven cancers. Pharmacological inhibition of both processes has been extensively investigated as potential therapeutic avenues in preclinical and clinical studies. However, how pre-mRNA splicing and metabolism are orchestrated in response to oncogenic stress and therapies is poorly understood. Here, we demonstrate that Jumonji Domain Containing 6, Arginine Demethylase and Lysine Hydroxylase, JMJD6, acts as a hub connecting splicing and metabolism in MYC-driven neuroblastoma. JMJD6 cooperates with MYC in cellular transformation by physically interacting with RNA binding proteins involved in pre-mRNA splicing and protein homeostasis. Notably, JMJD6 controls the alternative splicing of two isoforms of glutaminase (GLS), namely kidney-type glutaminase (KGA) and glutaminase C (GAC), which are rate-limiting enzymes of glutaminolysis in the central carbon metabolism in neuroblastoma. Further, we show that JMJD6 is correlated with the anti-cancer activity of indisulam, a "molecular glue" that degrades splicing factor RBM39, which complexes with JMJD6. The indisulam-mediated cancer cell killing is at least partly dependent on the glutamine-related metabolic pathway mediated by JMJD6. Our findings reveal a cancer-promoting metabolic program is associated with alternative pre-mRNA splicing through JMJD6, providing a rationale to target JMJD6 as a therapeutic avenue for treating MYC-driven cancers.
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6
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Li S, Qi Y, Yu J, Hao Y, Xu L, Ding X, Zhang M, Geng J. Aurora kinase A regulates cancer-associated RNA aberrant splicing in breast cancer. Heliyon 2023; 9:e17386. [PMID: 37415951 PMCID: PMC10320321 DOI: 10.1016/j.heliyon.2023.e17386] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 06/03/2023] [Accepted: 06/15/2023] [Indexed: 07/08/2023] Open
Abstract
The contribution of oncogenes to tumor-associated RNA splicing and the relevant molecular mechanisms therein require further elaboration. Here, we show that oncogenic Aurora kinase A (AURKA) promotes breast cancer-related RNA aberrant splicing in a context-dependent manner. AURKA regulated pan-breast cancer-associated RNA splicing events including GOLGA4, RBM4 and UBQLN1. Aberrant splicing of GOLGA4 and RBM4 was closely related to breast cancer development. Mechanistically, AURKA interacted with the splicing factor YBX1 and promoted AURKA-YBX1 complex-mediated GOLGA4 exon inclusion. AURKA binding to the splicing factor hnRNPK promoted AURKA-hnRNPK complex-mediated RBM4 exon skipping. Analysis of clinical data identified an association between the AURKA-YBX1/hnRNPK complex and poor prognosis in breast cancer. Blocking AURKA nuclear translocation with small molecule drugs partially reversed the oncogenic splicing of RBM4 and GOLGA4 in breast cancer cells. In summary, oncogenic AURKA executes its function on modulating breast cancer-related RNA splicing, and nuclear AURKA is distinguished as a hopeful target in the case of treating breast cancer.
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Affiliation(s)
- Sisi Li
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Jiachuan Yu
- Department of Anesthesiology, The First Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Yuchao Hao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, China
| | - Lingzhi Xu
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Xudong Ding
- Department of Pathology, The Second Affiliated Hospital of Dalian Medical University, Dalian, China
| | - Minghui Zhang
- Department of Oncology, Chifeng City Hospital, Chifeng, China
| | - Jingshu Geng
- Department of Pathology, Harbin Medical University Cancer Hospital, Harbin, China
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Gangras P, Gelfanova V, Williams GD, Handelman SK, Smith RM, Debets MF. Investigating SH-SY5Y Neuroblastoma Cell Surfaceome as a Model for Neuronal-Targeted Novel Therapeutic Modalities. Int J Mol Sci 2022; 23:ijms232315062. [PMID: 36499391 PMCID: PMC9739866 DOI: 10.3390/ijms232315062] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/23/2022] [Accepted: 11/26/2022] [Indexed: 12/05/2022] Open
Abstract
The SH-SY5Y neuroblastoma cells are a widely used in vitro model approximating neurons for testing the target engagement of therapeutics designed for neurodegenerative diseases and pain disorders. However, their potential as a model for receptor-mediated delivery and uptake of novel modalities, such as antibody-drug conjugates, remains understudied. Investigation of the SH-SY5Y cell surfaceome will aid in greater in vitro to in vivo correlation of delivery and uptake, thereby accelerating drug discovery. So far, the majority of studies have focused on total cell proteomics from undifferentiated and differentiated SH-SY5Y cells. While some studies have investigated the expression of specific proteins in neuroblastoma tissue, a global approach for comparison of neuroblastoma cell surfaceome to the brain and dorsal root ganglion (DRG) neurons remains uninvestigated. Furthermore, an isoform-specific evaluation of cell surface proteins expressed on neuroblastoma cells remains unexplored. In this study, we define a bioinformatic workflow for the identification of high-confidence surface proteins expressed on brain and DRG neurons using tissue proteomic and transcriptomic data. We then delineate the SH-SY5Y cell surfaceome by surface proteomics and show that it significantly overlaps with the human brain and DRG neuronal surface proteome. We find that, for 32% of common surface proteins, SH-SY5Y-specific major isoforms are alternatively spliced, maintaining their protein-coding ability, and are predicted to localize to the cell surface. Validation of these isoforms using surface proteomics confirms a SH-SY5Y-specific alternative NRCAM (neuron-glia related cell adhesion molecule) isoform, which is absent in typical brain neurons, but present in neuroblastomas, making it a receptor of interest for neuroblastoma-specific therapeutics.
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8
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Ma K, Zhang P, Xia Y, Dong L, Li Y, Liu L, Liu Y, Wang Y. A signature based on five immune-related genes to predict the survival and immune characteristics of neuroblastoma. BMC Med Genomics 2022; 15:242. [PMID: 36419120 PMCID: PMC9685875 DOI: 10.1186/s12920-022-01400-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2022] [Accepted: 11/18/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND MYCN amplification (MNA) has been proved to be related to poor prognosis in neuroblastoma (NBL), but the MYCN-related immune signatures and genes remain unclear. METHODS Enrichment analysis was used to identify the significant enrichment pathways of differentially expressed immune-related genes (DEIRGs). Weight gene coexpression network analysis (WGCNA) was applied to reveal the correlation between these DEIRGs and MYCN status. Univariate and multivariate Cox analyses were used to construct risk model. The relevant fractions of immune cells were evaluated by CIBERSORT and single-sample gene set enrichment analysis (ssGSEA). RESULTS Five genes, including CHGA, PTGER1, SHC3, PLXNC1, and TRIM55 were enrolled into the risk model. Kaplan-Meier survival analysis and receiver operating characteristic (ROC) curve showed that our model performed well in predicting the outcomes of NBL (3-years AUC = 0.720, 5-year AUC = 0.775, 10-years AUC = 0.782), which has been validated in the GSE49711 dataset and the E-MTAB-8248 dataset. By comparing with the tumor immune dysfunction and exclusion (TIDE) and tumor inflammation signature (TIS), we further proved that our model is reliable. Univariate and multivariate Cox regression analyses indicated that the risk score, age, and MYCN can serve as independent prognostic factors in the E-MATB-8248. Functional enrichment analysis showed the DEIRGs were enriched in leukocyte adhesion-related signaling pathways. Gene set enrichment analysis (GSEA) revealed the significantly enriched pathways of the five MYCN-related DEIRGs. The risk score was negatively correlated with the immune checkpoint CD274 (PD-L1) but no significant difference with the TMB. We also confirmed the prognostic value of our model in predicting immunotherapeutics. CONCLUSION We constructed and verified a signature based on DEIRG that related to MNA and predicted the survival of NBL based on relevant immune signatures. These findings could provide help for predicting prognosis and developing immunotherapy in NBL.
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Affiliation(s)
- KeXin Ma
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
| | - PeiPei Zhang
- Department of Neonatology, Children’s Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Yu Xia
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
| | - Lin Dong
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
| | - Ying Li
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
| | - Liu Liu
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
| | - YaJuan Liu
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
| | - YouJun Wang
- Department of Pediatrics, The Fifth Affiliated Hospital of Zhengzhou University, No. 3 Kangfuqian Street, Zhengzhou, China
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Ye Z, Bing A, Zhao S, Yi S, Zhan X. Comprehensive analysis of spliceosome genes and their mutants across 27 cancer types in 9070 patients: clinically relevant outcomes in the context of 3P medicine. EPMA J 2022; 13:335-350. [DOI: 10.1007/s13167-022-00279-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Accepted: 04/25/2022] [Indexed: 12/19/2022]
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10
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Pitolli C, Marini A, Sette C, Pagliarini V. Non-Canonical Splicing and Its Implications in Brain Physiology and Cancer. Int J Mol Sci 2022; 23:ijms23052811. [PMID: 35269953 PMCID: PMC8911335 DOI: 10.3390/ijms23052811] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/02/2022] [Indexed: 02/01/2023] Open
Abstract
The advance of experimental and computational techniques has allowed us to highlight the existence of numerous different mechanisms of RNA maturation, which have been so far unknown. Besides canonical splicing, consisting of the removal of introns from pre-mRNA molecules, non-canonical splicing events may occur to further increase the regulatory and coding potential of the human genome. Among these, splicing of microexons, recursive splicing and biogenesis of circular and chimeric RNAs through back-splicing and trans-splicing processes, respectively, all contribute to expanding the repertoire of RNA transcripts with newly acquired regulatory functions. Interestingly, these non-canonical splicing events seem to occur more frequently in the central nervous system, affecting neuronal development and differentiation programs with important implications on brain physiology. Coherently, dysregulation of non-canonical RNA processing events is associated with brain disorders, including brain tumours. Herein, we summarize the current knowledge on molecular and regulatory mechanisms underlying canonical and non-canonical splicing events with particular emphasis on cis-acting elements and trans-acting factors that all together orchestrate splicing catalysis reactions and decisions. Lastly, we review the impact of non-canonical splicing on brain physiology and pathology and how unconventional splicing mechanisms may be targeted or exploited for novel therapeutic strategies in cancer.
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Affiliation(s)
- Consuelo Pitolli
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Alberto Marini
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
| | - Vittoria Pagliarini
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168 Rome, Italy; (C.P.); (C.S.)
- GSTEP-Organoids Research Core Facility, IRCCS Fondazione Policlinico Universitario Agostino Gemelli, 00168 Rome, Italy;
- Correspondence:
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11
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Singh S, Quarni W, Goralski M, Wan S, Jin H, Van de Velde LA, Fang J, Wu Q, Abu-Zaid A, Wang T, Singh R, Craft D, Fan Y, Confer T, Johnson M, Akers WJ, Wang R, Murray PJ, Thomas PG, Nijhawan D, Davidoff AM, Yang J. Targeting the spliceosome through RBM39 degradation results in exceptional responses in high-risk neuroblastoma models. SCIENCE ADVANCES 2021; 7:eabj5405. [PMID: 34788094 PMCID: PMC8598007 DOI: 10.1126/sciadv.abj5405] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 09/27/2021] [Indexed: 06/13/2023]
Abstract
Aberrant alternative pre-mRNA splicing plays a critical role in MYC-driven cancers and therefore may represent a therapeutic vulnerability. Here, we show that neuroblastoma, a MYC-driven cancer characterized by splicing dysregulation and spliceosomal dependency, requires the splicing factor RBM39 for survival. Indisulam, a “molecular glue” that selectively recruits RBM39 to the CRL4-DCAF15 E3 ubiquitin ligase for proteasomal degradation, is highly efficacious against neuroblastoma, leading to significant responses in multiple high-risk disease models, without overt toxicity. Genetic depletion or indisulam-mediated degradation of RBM39 induces significant genome-wide splicing anomalies and cell death. Mechanistically, the dependency on RBM39 and high-level expression of DCAF15 determine the exquisite sensitivity of neuroblastoma to indisulam. Our data indicate that targeting the dysregulated spliceosome by precisely inhibiting RBM39, a vulnerability in neuroblastoma, is a valid therapeutic strategy.
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Affiliation(s)
- Shivendra Singh
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Waise Quarni
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Maria Goralski
- Department of Internal Medicine, Program in Molecular Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. K3.124, Dallas, TX 75390, USA
| | - Shibiao Wan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Hongjian Jin
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Lee-Ann Van de Velde
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jie Fang
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Qiong Wu
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ahmed Abu-Zaid
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Tingting Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s Hospital, 700 Children’s Drive, Columbus, OH 43205, USA
| | - Ravi Singh
- Division of Radiation Biophysics, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - David Craft
- Division of Radiation Biophysics, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Yiping Fan
- Center for Applied Bioinformatics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Thomas Confer
- Center for In Vivo Imaging and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Melissa Johnson
- Center for In Vivo Imaging and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Walter J. Akers
- Center for In Vivo Imaging and Therapeutics, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Ruoning Wang
- Center for Childhood Cancer and Blood Disease, Abigail Wexner Research Institute, Nationwide Children’s Hospital, 700 Children’s Drive, Columbus, OH 43205, USA
| | - Peter J. Murray
- Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Paul G. Thomas
- Department of Immunology, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Deepak Nijhawan
- Department of Internal Medicine, Program in Molecular Medicine, University of Texas Southwestern Medical Center, 5323 Harry Hines Blvd. K3.124, Dallas, TX 75390, USA
| | - Andrew M. Davidoff
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Jun Yang
- Department of Surgery, St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
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12
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Guo H, Wang S, Xie A, Sun W, Wei C, Xian S, Yin H, Li M, Sun H, Li H, Meng T, Zhang J, Huang Z. Ral GEF with the PH Domain and SH3 Binding Motif 1 Regulated by Splicing Factor Junction Plakoglobin and Pyrimidine Metabolism Are Prognostic in Uterine Carcinosarcoma. DISEASE MARKERS 2021; 2021:1484227. [PMID: 34745385 PMCID: PMC8568522 DOI: 10.1155/2021/1484227] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 09/14/2021] [Indexed: 01/14/2023]
Abstract
Uterine carcinosarcoma (UCS) is a highly invasive malignant tumor that originated from the uterine epithelium. Many studies suggested that the abnormal changes of alternative splicing (AS) of pre-mRNA are related to the occurrence and metastasis of the tumor. This study investigates the mechanism of alternative splicing events (ASEs) in the tumorigenesis and metastasis of UCS. RNA-seq of UCS samples and alternative splicing event (ASE) data of UCS samples were downloaded from The Cancer Genome Atlas (TCGA) and TCGASpliceSeq databases, several times. Firstly, we performed the Cox regression analysis to identify the overall survival-related alternative splicing events (OSRASEs). Secondly, a multivariate model was applied to approach the prognostic values of the risk score. Afterwards, a coexpressed network between splicing factors (SFs) and OSRASEs was constructed. In order to explore the relationship between the potential prognostic signaling pathways and OSRASEs, we fabricated a network between these pathways and OSRASEs. Finally, validations from multidimension platforms were used to explain the results unambiguously. 1,040 OSRASEs were identified by Cox regression. Then, 6 OSRASEs were incorporated in a multivariable model by Lasso regression. The area under the curve (AUC) of the receiver operator characteristic (ROC) curve was 0.957. The risk score rendered from the multivariate model was corroborated to be an independent prognostic factor (P < 0.001). In the network of SFs and ASEs, junction plakoglobin (JUP) noteworthily regulated RALGPS1-87608-AT (P < 0.001, R = 0.455). Additionally, RALGPS1-87608-AT (P = 0.006) showed a prominent relationship with distant metastasis. KEGG pathways related to prognosis of UCS were selected by gene set variation analysis (GSVA). The pyrimidine metabolism (P < 0.001, R = -0.470) was the key pathway coexpressed with RALGPS1. We considered that aberrant JUP significantly regulated RALGPS1-87608-AT and the pyrimidine metabolism pathway might play a significant part in the metastasis and prognosis of UCS.
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Affiliation(s)
- Hongjun Guo
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
| | - Siqiao Wang
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China
- Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China
| | - Aiqing Xie
- School of Ocean and Earth Science, Tongji University, 1239 Siping Road, Shanghai 200092, China
| | - Wenhuizi Sun
- Department of Gynaecology, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China
| | - Chenlu Wei
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
| | - Shuyuan Xian
- Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China
| | - Huabin Yin
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai, China
| | - Mingxiao Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
| | - Hanlin Sun
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
| | - Hong Li
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
| | - Tong Meng
- Department of Orthopedics, Shanghai General Hospital, School of Medicine, Shanghai Jiaotong University, 100 Haining Road, Shanghai, China
- Tongji University Cancer Center, Shanghai Tenth People's Hospital, Tongji University School of Medicine, 301 Yanchang Road, Shanghai 200072, China
| | - Jie Zhang
- Division of Spine, Department of Orthopedics, Tongji Hospital Affiliated to Tongji University School of Medicine, 389 Xincun Road, Shanghai, China
- Tongji University School of Medicine, 1239 Siping Road, Shanghai 200092, China
| | - Zongqiang Huang
- Department of Obstetrics and Gynecology, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
- Department of Orthopedics, The First Affiliated Hospital of Zhengzhou University, 1 East Jianshe Road, Zhengzhou, China
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