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Wu Q, Liao R, Miao C, Hasnat M, Li L, Sun L, Wang X, Yuan Z, Jiang Z, Zhang L, Yu Q. Oncofetal SNRPE promotes HCC tumorigenesis by regulating the FGFR4 expression through alternative splicing. Br J Cancer 2024; 131:77-89. [PMID: 38796598 PMCID: PMC11231362 DOI: 10.1038/s41416-024-02689-5] [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: 12/25/2023] [Revised: 04/06/2024] [Accepted: 04/10/2024] [Indexed: 05/28/2024] Open
Abstract
BACKGROUND Due to insufficient knowledge about key molecular events, Hepatocellular carcinoma (HCC) lacks effective treatment targets. Spliceosome-related genes were significantly altered in HCC. Oncofetal proteins are ideal tumor therapeutic targets. Screening of differentially expressed Spliceosome-related oncofetal protein in embryonic liver development and HCC helps discover effective therapeutic targets for HCC. METHODS Differentially expressed spliceosome genes were analysis in fetal liver and HCC through bioinformatics analysis. Small nuclear ribonucleoprotein polypeptide E (SNRPE) expression was detected in fetal liver, adult liver and HCC tissues. The role of SNRPE in HCC was performed multiple assays in vitro and in vivo. SNRPE-regulated alternative splicing was recognized by RNA-Seq and confirmed by multiple assays. RESULTS We herein identified SNRPE as a crucial oncofetal splicing factor, significantly associated with the adverse prognosis of HCC. SOX2 was identified as the activator for SNRPE reactivation. Efficient knockdown of SNRPE resulted in the complete cessation of HCC tumorigenesis and progression. Mechanistically, SNRPE knockdown reduced FGFR4 mRNA expression by triggering nonsense-mediated RNA decay. A partial inhibition of SNRPE-induced malignant progression of HCC cells was observed upon FGFR4 knockdown. CONCLUSIONS Our findings highlight SNRPE as a novel oncofetal splicing factor and shed light on the intricate relationship between oncofetal splicing factors, splicing events, and carcinogenesis. Consequently, SNRPE emerges as a potential therapeutic target for HCC treatment. Model of oncofetal SNRPE promotes HCC tumorigenesis by regulating the AS of FGFR4 pre-mRNA.
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MESH Headings
- Animals
- Humans
- Mice
- Alternative Splicing
- Carcinogenesis/genetics
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Cell Line, Tumor
- Gene Expression Regulation, Neoplastic
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Mice, Nude
- Prognosis
- Receptor, Fibroblast Growth Factor, Type 4/genetics
- Receptor, Fibroblast Growth Factor, Type 4/metabolism
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Affiliation(s)
- Qipeng Wu
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Ruyan Liao
- Guangzhou Customs District Technology Center, Guangzhou, China
| | - Chunmeng Miao
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Muhammad Hasnat
- Institute of Pharmaceutical Sciences, University of Veterinary and Animal Sciences, Outfall Road, Lahore, Pakistan
| | - Le Li
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Lixin Sun
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Xinru Wang
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China
| | - Ziqiao Yuan
- Key Laboratory of Advanced Drug Preparation Technologies, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhenzhou Jiang
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China.
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing, China.
| | - Luyong Zhang
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China.
- The Center for Drug Research and Development, Guangdong Pharmaceutical University, Guangzhou, China.
| | - Qinwei Yu
- New Drug Screening Center, State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of Druggability of Biopharmaceuticals, China Pharmaceutical University, Nanjing, China.
- Key Laboratory of Drug Quality Control and Pharmacovigilance, Ministry of Education, China Pharmaceutical University, Nanjing, China.
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2
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Sun L, Liu Y, Guo X, Cui T, Wu C, Tao J, Cheng C, Chu Q, Ji C, Li X, Guo H, Liang S, Zhou H, Zhou S, Ma K, Zhang N, Wang J, Liu Y, Liu L. Acetylation-dependent regulation of core spliceosome modulates hepatocellular carcinoma cassette exons and sensitivity to PARP inhibitors. Nat Commun 2024; 15:5209. [PMID: 38890388 PMCID: PMC11189467 DOI: 10.1038/s41467-024-49573-7] [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: 06/29/2023] [Accepted: 06/09/2024] [Indexed: 06/20/2024] Open
Abstract
Despite the importance of spliceosome core components in cellular processes, their roles in cancer development, including hepatocellular carcinoma (HCC), remain poorly understood. In this study, we uncover a critical role for SmD2, a core component of the spliceosome machinery, in modulating DNA damage in HCC through its impact on BRCA1/FANC cassette exons and expression. Our findings reveal that SmD2 depletion sensitizes HCC cells to PARP inhibitors, expanding the potential therapeutic targets. We also demonstrate that SmD2 acetylation by p300 leads to its degradation, while HDAC2-mediated deacetylation stabilizes SmD2. Importantly, we show that the combination of Romidepsin and Olaparib exhibits significant therapeutic potential in multiple HCC models, highlighting the promise of targeting SmD2 acetylation and HDAC2 inhibition alongside PARP inhibitors for HCC treatment.
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Affiliation(s)
- Linmao Sun
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China
| | - Yufeng Liu
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China
| | - Xinyu Guo
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Tianming Cui
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China
| | - Chenghui Wu
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Jie Tao
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Cheng Cheng
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Qi Chu
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Changyong Ji
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Xianying Li
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Hongrui Guo
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China
| | - Shuhang Liang
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Huanran Zhou
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Department of Endocrinology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, China
| | - Shuo Zhou
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Kun Ma
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China
| | - Ning Zhang
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China
| | - Jiabei Wang
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China.
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China.
| | - Yao Liu
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China.
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China.
| | - Lianxin Liu
- Department of Hepatobiliary Surgery, Centre for Leading Medicine and Advanced Technologies of IHM, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, 230001, Anhui, China.
- Anhui Provincial Key Laboratory of Hepatopancreatobiliary Surgery, Hefei, 230001, Anhui, China.
- Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Hefei, 230001, Anhui, China.
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3
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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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4
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Song Y, Wang ZY, Luo J, Han WC, Wang XY, Yin C, Zhao WN, Hu SW, Zhang Q, Li YQ, Cao JL. CWC22-Mediated Alternative Splicing of Spp1 Regulates Nociception in Inflammatory Pain. Neuroscience 2023; 535:50-62. [PMID: 37838283 DOI: 10.1016/j.neuroscience.2023.10.006] [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: 06/06/2023] [Revised: 10/05/2023] [Accepted: 10/09/2023] [Indexed: 10/16/2023]
Abstract
Increasing evidence suggests that alternative splicing plays a critical role in pain, but its underlying mechanism remains elusive. Herein, we employed complete Freund's adjuvant (CFA) to induce inflammatory pain in mice. A combination of genomics research techniques, lentivirus-based genetic manipulations, behavioral tests, and molecular biological technologies confirmed that splicing factor Cwc22 mRNA and CWC22 protein were elevated in the spinal dorsal horn at 3 days after CFA injection. Knockdown of spinal CWC22 by lentivirus transfection (lenti-shCwc22) reversed CFA-induced thermal hyperalgesia and mechanical allodynia, whereas upregulation of spinal CWC22 (lenti-Cwc22) in naïve mice precipitated pain. Comprehensive transcriptome and genome analysis identified the secreted phosphoprotein 1 (Spp1) as a potential gene of CWC22-mediated alternative splicing, however, only Spp1 splicing variant 4 (Spp1 V4) was involved in thermal and mechanical nociceptive regulation. In conclusion, our findings demonstrate that spinal CWC22 regulates Spp1 V4 to participate in CFA-induced inflammatory pain. Blocking CWC22 or CWC22-mediated alternative splicing may provide a novel therapeutic target for the treatment of persistent inflammatory pain.
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Affiliation(s)
- Yu Song
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Department of Anesthesiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province 221002, China
| | - Zhi-Yong Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Department of Anesthesiology, The Affiliated Cancer Hospital of Nanjing Medical University, Nanjing, Jiangsu Province 210008, China
| | - Jun Luo
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Department of Critical Care Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu Province 221002, China
| | - Wen-Can Han
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China
| | - Xiao-Yi Wang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Department of Anesthesiology, Gulou Hospital Affiliated to Medical College of Nanjing University, Nanjing, Jiangsu Province 210008, China
| | - Cui Yin
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China
| | - Wei-Nan Zhao
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China
| | - Su-Wan Hu
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China
| | - Qi Zhang
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China
| | - Yan-Qiang Li
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China.
| | - Jun-Li Cao
- Jiangsu Province Key Laboratory of Anesthesiology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China; Jiangsu Province Key Laboratory of Anesthesia and Analgesia Application Technology, Xuzhou Medical University, Xuzhou, Jiangsu Province 221004, China.
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Montero-Hidalgo AJ, Pérez-Gómez JM, Martínez-Fuentes AJ, Gómez-Gómez E, Gahete MD, Jiménez-Vacas JM, Luque RM. Alternative splicing in bladder cancer: potential strategies for cancer diagnosis, prognosis, and treatment. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1760. [PMID: 36063028 DOI: 10.1002/wrna.1760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 05/13/2023]
Abstract
Bladder cancer is the most common malignancy of the urinary tract worldwide. The therapeutic options to tackle this disease comprise surgery, intravesical or systemic chemotherapy, and immunotherapy. Unfortunately, a wide number of patients ultimately become resistant to these treatments and develop aggressive metastatic disease, presenting a poor prognosis. Therefore, the identification of novel therapeutic approaches to tackle this devastating pathology is urgently needed. However, a significant limitation is that the progression and drug response of bladder cancer is strongly associated with its intrinsic molecular heterogeneity. In this sense, RNA splicing is recently gaining importance as a critical hallmark of cancer since can have a significant clinical value. In fact, a profound dysregulation of the splicing process has been reported in bladder cancer, especially in the expression of certain key splicing variants and circular RNAs with a potential clinical value as diagnostic/prognostic biomarkers or therapeutic targets in this pathology. Indeed, some authors have already evidenced a profound antitumor effect by targeting some splicing factors (e.g., PTBP1), mRNA splicing variants (e.g., PKM2, HYAL4-v1), and circular RNAs (e.g., circITCH, circMYLK), which illustrates new possibilities to significantly improve the management of this pathology. This review represents the first detailed overview of the splicing process and its alterations in bladder cancer, and highlights opportunities for the development of novel diagnostic/prognostic biomarkers and their clinical potential for the treatment of this devastating cancer type. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Antonio J Montero-Hidalgo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Jesús M Pérez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Antonio J Martínez-Fuentes
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Enrique Gómez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- Urology Service, HURS/IMIBIC, Cordoba, 14004, Spain
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
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6
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Yang Y, Huang T, Fan Y, Lu H, Shao J, Wang Y, Shen A. Significance of Spliceosome-Related Genes in the Prediction of Prognosis and Treatment Strategies for Lung Adenocarcinoma. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1753563. [PMID: 36389112 PMCID: PMC9652092 DOI: 10.1155/2022/1753563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 10/18/2022] [Indexed: 08/25/2023]
Abstract
BACKGROUND The leading cause of cancer-related fatalities globally is lung cancer; lung adenocarcinoma (LUAD) is the most common histological type in it. The spliceosome plays an important role in a majority of malignancies. However, it is yet unclear how spliceosome-related genes affect patients with LUAD in terms of treatment course and prognosis. METHODS Spliceosome-related genes were assessed from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database to obtain clinical information and gene expression in patients with LUAD. A spliceosome-related gene signature and prognostic model were constructed by using the least absolute shrinkage and selection operator (LASSO), time-dependent receiver operating characteristic (ROC), and nomogram. Immune infiltrate levels, mutation analysis, and pathway enrichment were predicted potential mechanisms of the signature by using single-sample gene set enrichment analysis (ssGSEA), Gene Set Cancer Analysis (GSCA) database, Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) database. Then, a protein-protein interaction (PPI) network and transcription factor- (TF-) hub gene and drug mining network were also established by Cytoscape software. RESULTS Firstly, we constructed a prognostic model for 11 spliceosome signature genes. Based on the prognostic risk score, we stratified patients with LUAD into high- and low-risk groups. The high- and low-risk groups were closely related to the OS, tumor immune infiltration level, immune checkpoint molecules, and tumor mutation burden (TMB) of LUAD patients. Based on PPI networks, we also predict relevant TF genes that may regulate signature prognostic genes. Finally, drugs including oxaliplatin, arsenic trioxide, cisplatin, and sunitinib were excavated for the treatment of the 11 spliceosome signature genes in LUAD patients. CONCLUSION In conclusion, this study is the first to explore the importance of spliceosome-related genes in the prognosis and treatment of LUAD. Through our study, we have innovatively provided potential prognosis genes and new therapeutic drug targets for the treatment of LUAD patients.
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Affiliation(s)
- Ying Yang
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Tianyi Huang
- Department of Pharmacy, Nantong University Xinling College, Nantong, China
| | - Yihui Fan
- Department of Thoracic Surgery, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Haimin Lu
- Department of Thoracic Surgery, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Jingjing Shao
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Yilang Wang
- Department of Oncology, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
| | - Aiguo Shen
- Cancer Research Center Nantong, Nantong Tumor Hospital, The Affiliated Tumor Hospital of Nantong University, Nantong University, Nantong, China
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Rao TD, Xu M, Eng S, Yang G, Manson R, Rosales N, Kumar R, Veillard IE, Zhou Q, Iasonos A, Ouerfelli O, Djaballah H, Spriggs DR, Yeku OO. Dual Fluorescence Isogenic Synthetic Lethal Kinase Screen and High-Content Secondary Screening for MUC16/CA125 Selective Agents. Mol Cancer Ther 2022; 21:775-785. [PMID: 35413118 DOI: 10.1158/1535-7163.mct-21-0572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 01/21/2022] [Accepted: 02/17/2022] [Indexed: 11/16/2022]
Abstract
Significant strides have been made in the development of precision therapeutics for cancer. Aberrantly expressed glycoproteins represent a potential avenue for therapeutic development. The MUC16/CA125 glycoprotein serves as a biomarker of disease and a driver of malignant transformation in epithelial ovarian cancer. Previously, we demonstrated a proof-of-principle approach to selectively targeting MUC16+ cells. In this report, we performed a synthetic lethal kinase screen using a human kinome RNAi library and identified key pathways preferentially targetable in MUC16+ cells using isogenic dual florescence ovarian cancer cell lines. Utilizing a separate approach, we performed high-content small-molecule screening of 6 different libraries of 356,982 compounds for MUC16/CA125 selective agents and identified lead candidates that showed preferential cytotoxicity in MUC16+ cells. Compounds with differential activity were selected and tested in various other ovarian cell lines or isogenic pairs to identify lead compounds for Structural Activity Relationship (SAR) selection. Lead siRNA and small molecule inhibitor candidates preferentially inhibited invasion of MUC16+ cells in vitro and in vivo and we show that this is due to decreased activation of MAP kinase, and non-receptor tyrosine kinases. Taken together, we present a comprehensive screening approach to the development of a novel class of MUC16-selective targeted therapeutics and identify candidates suitable for further clinical development.
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Affiliation(s)
- Thapi Dharma Rao
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Mengyao Xu
- Massachusetts General Hospital, Boston, United States
| | - Stephanie Eng
- Memorial Sloan Kettering Cancer Center, United States
| | - Guangli Yang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Robin Manson
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Nestor Rosales
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Raj Kumar
- Massachusetts General Hospital, Boston, Massachusetts, United States
| | | | - Qin Zhou
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Alexia Iasonos
- Memorial Sloan Kettering Cancer Center, New York, United States
| | | | | | | | - Oladapo O Yeku
- Massachusetts General Hospital, Boston, MA, United States
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Double-Stranded RNA Structural Elements Holding the Key to Translational Regulation in Cancer: The Case of Editing in RNA-Binding Motif Protein 8A. Cells 2021; 10:cells10123543. [PMID: 34944051 PMCID: PMC8699885 DOI: 10.3390/cells10123543] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 12/08/2021] [Accepted: 12/13/2021] [Indexed: 12/30/2022] Open
Abstract
Mesothelioma is an aggressive cancer associated with asbestos exposure. RNA-binding motif protein 8a (RBM8A) mRNA editing increases in mouse tissues upon asbestos exposure. The aim of this study was to further characterize the role of RBM8A in mesothelioma and the consequences of its mRNA editing. RBM8A protein expression was higher in mesothelioma compared to mesothelial cells. Silencing RBM8A changed splicing patterns in mesothelial and mesothelioma cells but drastically reduced viability only in mesothelioma cells. In the tissues of asbestos-exposed mice, editing of Rbm8a mRNA was associated with increased protein immunoreactivity, with no change in mRNA levels. Increased adenosine deaminase acting on dsRNA (ADAR)-dependent editing of Alu elements in the RBM8A 3′UTR was observed in mesothelioma cells compared to mesothelial cells. Editing stabilized protein expression. The unedited RBM8A 3′UTR had a stronger interaction with Musashi (MSI) compared to the edited form. The silencing of MSI2 in mesothelioma or overexpression of Adar2 in mesothelial cells resulted in increased RBM8A protein levels. Therefore, ADAR-dependent editing contributes to maintaining elevated RBM8A protein levels in mesothelioma by counteracting MSI2-driven downregulation. A wider implication of this mechanism for the translational control of protein expression is suggested by the editing of similarly structured Alu elements in several other transcripts.
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Li Y, Kardell MB, Wang F, Wang L, Zhu S, Bessho T, Peng A. The Sm core components of small nuclear ribonucleoproteins promote homologous recombination repair. DNA Repair (Amst) 2021; 108:103244. [PMID: 34768043 DOI: 10.1016/j.dnarep.2021.103244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 10/01/2021] [Accepted: 10/29/2021] [Indexed: 11/17/2022]
Abstract
DNA Double strand breaks (DSBs) are highly hazardous to the cell, and are repaired predominantly via non-homologous end joining (NHEJ) and homologous recombination (HR). Using DSB-mimicking DNA templates, our proteomic studies identified a group of Sm core proteins of small nuclear ribonucleoproteins (snRNPs) as potential DSB-associated proteins. We further confirmed that these Sm proteins were recruited to laser-induced DNA damage sites, and co-localized with established DNA damage repair factors. Depletion of Sm-D3 or Sm-B induced accumulation of γ-H2AX, and impaired the repair efficiency of HR, but not NHEJ. Furthermore, disruption of Sm-D3 reduced the protein level of HR factors, especially RAD51 and CHK1, but caused no change in the expression of repair factors involved in NHEJ. Mechanistically, Sm-D3 proteins bound RAD51, suppressed the ubiquitination of RAD51, and mediated the stabilization of RAD51; Sm-D3 depletion particularly impacted the level of RAD51 and CHK1 on damaged chromatin. As such, our studies characterized a role of Sm proteins in HR repair, via a new mechanism that is distinct from their conventional functions in RNA processing and gene regulation, but consistent with their direct recruitment to DNA damage sites and association with repair factors.
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Affiliation(s)
- Yanqiu Li
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Mary Bridget Kardell
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Feifei Wang
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Ling Wang
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Songli Zhu
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA
| | - Tadayoshi Bessho
- The Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Aimin Peng
- Department of Oral Biology, University of Nebraska Medical Center, Lincoln, NE, USA.
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Biology of the mRNA Splicing Machinery and Its Dysregulation in Cancer Providing Therapeutic Opportunities. Int J Mol Sci 2021; 22:ijms22105110. [PMID: 34065983 PMCID: PMC8150589 DOI: 10.3390/ijms22105110] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 05/07/2021] [Accepted: 05/07/2021] [Indexed: 12/13/2022] Open
Abstract
Dysregulation of messenger RNA (mRNA) processing—in particular mRNA splicing—is a hallmark of cancer. Compared to normal cells, cancer cells frequently present aberrant mRNA splicing, which promotes cancer progression and treatment resistance. This hallmark provides opportunities for developing new targeted cancer treatments. Splicing of precursor mRNA into mature mRNA is executed by a dynamic complex of proteins and small RNAs called the spliceosome. Spliceosomes are part of the supraspliceosome, a macromolecular structure where all co-transcriptional mRNA processing activities in the cell nucleus are coordinated. Here we review the biology of the mRNA splicing machinery in the context of other mRNA processing activities in the supraspliceosome and present current knowledge of its dysregulation in lung cancer. In addition, we review investigations to discover therapeutic targets in the spliceosome and give an overview of inhibitors and modulators of the mRNA splicing process identified so far. Together, this provides insight into the value of targeting the spliceosome as a possible new treatment for lung cancer.
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Cai L, Wu H, Zhou K. Improved cancer biomarkers identification using network-constrained infinite latent feature selection. PLoS One 2021; 16:e0246668. [PMID: 33571282 PMCID: PMC7877636 DOI: 10.1371/journal.pone.0246668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Accepted: 01/24/2021] [Indexed: 12/21/2022] Open
Abstract
Identifying biomarkers that are associated with different types of cancer is an important goal in the field of bioinformatics. Different researcher groups have analyzed the expression profiles of many genes and found some certain genetic patterns that can promote the improvement of targeted therapies, but the significance of some genes is still ambiguous. More reliable and effective biomarkers identification methods are then needed to detect candidate cancer-related genes. In this paper, we proposed a novel method that combines the infinite latent feature selection (ILFS) method with the functional interaction (FIs) network to rank the biomarkers. We applied the proposed method to the expression data of five cancer types. The experiments indicated that our network-constrained ILFS (NCILFS) provides an improved prediction of the diagnosis of the samples and locates many more known oncogenes than the original ILFS and some other existing methods. We also performed functional enrichment analysis by inspecting the over-represented gene ontology (GO) biological process (BP) terms and applying the gene set enrichment analysis (GSEA) method on selected biomarkers for each feature selection method. The enrichments analysis reports show that our network-constraint ILFS can produce more biologically significant gene sets than other methods. The results suggest that network-constrained ILFS can identify cancer-related genes with a higher discriminative power and biological significance.
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Affiliation(s)
- Lihua Cai
- Wuhan National Laboratory for Optoelectronics, School of Computer Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
- School of Mathematics and Computer Science, Guangdong Ocean University, Zhanjiang, Guangdong, China
| | - Honglong Wu
- Wuhan National Laboratory for Optoelectronics, School of Computer Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
- Shenzhen Genomics Institute, BGI-Shenzhen, Shenzhen, China
| | - Ke Zhou
- Wuhan National Laboratory for Optoelectronics, School of Computer Science & Technology, Huazhong University of Science & Technology, Wuhan, Hubei, China
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Chu KJ, Ma YS, Jiang XH, Wu TM, Wu ZJ, Li ZZ, Wang JH, Gao QX, Yi B, Shi Y, Wang HM, Gu LP, Zhang SQ, Wang GR, Liu JB, Fu D, Jiang XQ. Whole-Transcriptome Sequencing Identifies Key Differentially Expressed mRNAs, miRNAs, lncRNAs, and circRNAs Associated with CHOL. MOLECULAR THERAPY. NUCLEIC ACIDS 2020; 21:592-603. [PMID: 32721879 PMCID: PMC7390861 DOI: 10.1016/j.omtn.2020.06.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 06/19/2020] [Accepted: 06/23/2020] [Indexed: 12/11/2022]
Abstract
To systematically evaluate the whole-transcriptome sequencing data of cholangiocarcinoma (CHOL) to gain more insights into the transcriptomic landscape and molecular mechanism of this cancer, we performed whole-transcriptome sequencing based on the tumorous (C) and their corresponding non-tumorous adjacent to the tumors (CP) from eight CHOL patients. Subsequently, differential expression analysis was performed on the C and CP groups, followed by functional interaction prediction analysis to investigate gene-regulatory circuits in CHOL. In addition, The Cancer Genome Atlas (TCGA) for CHOL data was used to validate the results. In total, 2,895 differentially expressed messenger RNAs (dif-mRNAs), 56 differentially expressed microRNAs (dif-miRNAs), 151 differentially expressed long non-coding RNAs (dif-lncRNAs), and 110 differentially expressed circular RNAs (dif-circRNAs) were found in CHOL samples compared with controls. Enrichment analysis on those differentially expressed genes (DEGs) related to miRNA, lncRNA, and circRNA also identified the function of spliceosome. The downregulated hsa-miR-144-3p were significantly enriched in the competing endogenous RNA (ceRNA) complex network, which also included 7 upregulated and 13 downregulated circRNAs, 7 upregulated lncRNAs, and 90 upregulated and 40 downregulated mRNAs. Moreover, most of the DEGs and a few of the miRNAs (such as hsa-miR-144-3p) were successfully validated by TCGA data. The genes involved in RNA splicing and protein degradation processes and miR-144-3p may play fundamental roles in the pathogenesis of CHOL.
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Affiliation(s)
- Kai-Jian Chu
- Department of Biliary Tract Surgery I, Third Affiliated Hospital of Second Military Medical University, Shanghai 200438, China
| | - Yu-Shui Ma
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China; Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Xiao-Hui Jiang
- General Surgery, Nantong Tumor Hospital, Nantong 226631, China
| | - Ting-Miao Wu
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China
| | - Zhi-Jun Wu
- Department of Oncology, Nantong Second People's Hospital, Nantong 226002, China
| | - Zhi-Zhen Li
- Department of Biliary Tract Surgery I, Third Affiliated Hospital of Second Military Medical University, Shanghai 200438, China
| | - Jing-Han Wang
- Department of Biliary Tract Surgery I, Third Affiliated Hospital of Second Military Medical University, Shanghai 200438, China
| | - Qing-Xiang Gao
- Department of Biliary Tract Surgery I, Third Affiliated Hospital of Second Military Medical University, Shanghai 200438, China
| | - Bin Yi
- Department of Biliary Tract Surgery I, Third Affiliated Hospital of Second Military Medical University, Shanghai 200438, China
| | - Yi Shi
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Hui-Min Wang
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Li-Peng Gu
- Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China
| | - Su-Qing Zhang
- Department of Hepatobiliary Surgery, Nantong Tumor Hospital, Nantong 226631, China
| | - Gao-Ren Wang
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China
| | - Ji-Bin Liu
- Cancer Institute, Nantong Tumor Hospital, Nantong 226631, China.
| | - Da Fu
- Department of Radiology, The Fourth Affiliated Hospital of Anhui Medical University, Hefei 230012, China; Central Laboratory for Medical Research, Shanghai Tenth People's Hospital, Tongji University School of Medicine, Shanghai 200072, China.
| | - Xiao-Qing Jiang
- Department of Biliary Tract Surgery I, Third Affiliated Hospital of Second Military Medical University, Shanghai 200438, China.
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Silencing Core Spliceosome Sm Gene Expression Induces a Cytotoxic Splicing Switch in the Proteasome Subunit Beta 3 mRNA in Non-Small Cell Lung Cancer Cells. Int J Mol Sci 2020; 21:ijms21124192. [PMID: 32545483 PMCID: PMC7349683 DOI: 10.3390/ijms21124192] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Revised: 06/08/2020] [Accepted: 06/09/2020] [Indexed: 12/15/2022] Open
Abstract
The core spliceosomal Sm proteins were recently proposed as cancer-selective lethal targets in non-small cell lung cancer (NSCLC). In contrast, the loss of the commonly mutated cancer target SF3B1 appeared to be toxic to non-malignant cells as well. In the current study, the transcriptomes of A549 NSCLC cells, in which SF3B1 or SNRPD3 was silenced, were compared using RNA sequencing. The skipping of exon 4 of the proteasomal subunit beta type-3 (PSMB3) mRNA, resulting in a shorter PSMB3-S variant, occurred only after silencing SNRPD3. This observation was extended to the other six Sm genes. Remarkably, the alternative splicing of PSMB3 mRNA upon Sm gene silencing was not observed in non-malignant IMR-90 lung fibroblasts. Furthermore, PSMB3 was found to be overexpressed in NSCLC clinical samples and PSMB3 expression correlated with Sm gene expression. Moreover, a high PSMB3 expression corresponds to worse survival in patients with lung adenocarcinomas. Finally, silencing the canonical full-length PSMB3-L, but not the shorter PSMB3-S variant, was cytotoxic and was accompanied by a decrease in proteasomal activity. Together, silencing Sm genes, but not SF3B1, causes a cytotoxic alternative splicing switch in the PSMB3 mRNA in NSCLC cells only.
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Eymin B. Targeting the spliceosome machinery: A new therapeutic axis in cancer? Biochem Pharmacol 2020; 189:114039. [PMID: 32417188 DOI: 10.1016/j.bcp.2020.114039] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 05/12/2020] [Indexed: 02/06/2023]
Abstract
Pre-mRNA splicing is the removal of introns and ligation of exons to form mature mRNAs, and it provides a critical mechanism by which eukaryotic cells can regulate their gene expression. Strikingly, more than 90% of protein-encoding transcripts are alternatively spliced, through exon inclusion/skipping, differential use of 5' or 3' alternative splice sites, intron retention or selection of an alternative promoter, thereby drastically increasing protein diversity. Splicing is altered in various pathological conditions, including cancers. In the last decade, high-throughput transcriptomic analyses have identified thousands of splice variants in cancers, which can distinguish between tumoral and normal tissues as well as identify tumor types, subtypes and clinical stages. These abnormal or aberrantly expressed splice variants, found in all cancer hallmarks, can result from mutations in splice sites, deregulated expression or even somatic mutations of components of the spliceosome machinery. Therefore, and based on these recent observations, a new anti-cancer strategy of targeting the spliceosome machinery with small molecules has emerged; however, the potential for these therapies is still a matter of great debate. Notably, more preclinical studies are needed to clarify which splicing patterns are mainly affected by these compounds, which cancer patients could be the most eligible for these treatments and whether using these spliceosome inhibitors alone or in combination with chemotherapies or targeted therapies would provide better therapeutic benefits. In this commentary, I will discuss all of these aspects.
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Affiliation(s)
- Beatrice Eymin
- INSERM U1209, CNRS UMR5309, Institute For Advanced Biosciences, 38000 Grenoble, France; Université Grenoble Alpes, 38000 Grenoble, France.
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