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More DA, Singh N, Mishra R, Muralidharan HP, Gopinath KS, Gopal C, Kumar A. Intronic miR-6741-3p targets the oncogene SRSF3: Implications for oral squamous cell carcinoma pathogenesis. PLoS One 2024; 19:e0296565. [PMID: 38781195 PMCID: PMC11115324 DOI: 10.1371/journal.pone.0296565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 04/23/2024] [Indexed: 05/25/2024] Open
Abstract
Epigenetic silencing through methylation is one of the major mechanisms for downregulation of tumor suppressor miRNAs in various malignancies. The aim of this study was to identify novel tumor suppressor miRNAs which are silenced by DNA hypermethylation and investigate the role of at least one of these in oral squamous cell carcinoma (OSCC) pathogenesis. We treated cells from an OSCC cell line SCC131 with 5-Azacytidine, a DNA methyltransferase inhibitor, to reactivate tumor suppressor miRNA genes silenced/downregulated due to DNA methylation. At 5-day post-treatment, total RNA was isolated from the 5-Azacytidine and vehicle control-treated cells. The expression of 2,459 mature miRNAs was analysed between 5-Azacytidine and control-treated OSCC cells by the microRNA microarray analysis. Of the 50 miRNAs which were found to be upregulated following 5-Azacytidine treatment, we decided to work with miR-6741-3p in details for further analysis, as it showed a mean fold expression of >4.0. The results of qRT-PCR, Western blotting, and dual-luciferase reporter assay indicated that miR-6741-3p directly targets the oncogene SRSF3 at the translational level only. The tumor-suppressive role of miR-6741-3p was established by various in vitro assays and in vivo study in NU/J athymic nude mice. Our results revealed that miR-6741-3p plays a tumor-suppressive role in OSCC pathogenesis, in part, by directly regulating SRSF3. Based on our observations, we propose that miR-6741-3p may serve as a potential biological target in tumor diagnostics, prognostic evaluation, and treatment of OSCC and perhaps other malignancies.
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Affiliation(s)
- Dhanashree Anil More
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Nivedita Singh
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | - Radha Mishra
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
| | | | | | - Champaka Gopal
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bengaluru, India
| | - Arun Kumar
- Department of Developmental Biology and Genetics, Indian Institute of Science, Bengaluru, India
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2
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Sun M, Tong Y, Yuan W, Wang Y, Pu Y, Huang W, Lv B, Xu C, Jiang W, Luo R, Fang R, Tang S, Ren L, Wang J, Feng J, Sun C, Shen K, He F, Hou Y, Ding C. Proteomic Characterization Identifies Clinically Relevant Subgroups of Gastrointestinal Stromal Tumors. Gastroenterology 2024; 166:450-465.e33. [PMID: 37995868 DOI: 10.1053/j.gastro.2023.11.284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 11/06/2023] [Accepted: 11/14/2023] [Indexed: 11/25/2023]
Abstract
BACKGROUND & AIMS Gastrointestinal stromal tumor (GIST) is the most common mesenchymal tumor of the gastrointestinal tract, and it has high metastatic and recurrence rates. We aimed to characterize the proteomic features of GIST to understand biological processes and treatment vulnerabilities. METHODS Quantitative proteomics and phosphoproteomics analyses were performed on 193 patients with GIST to reveal the biological characteristics of GIST. Data-driven hypotheses were tested by performing functional experiments using both GIST cell lines and xenograft mouse models. RESULTS Proteomic analysis revealed differences in the molecular features of GISTs from different locations or with different histological grades. MAPK7 was identified and functionally proved to be associated with tumor cell proliferation in GIST. Integrative analysis revealed that increased SQSTM1 expression inhibited the patient response to imatinib mesylate. Proteomics subtyping identified 4 clusters of tumors with different clinical and molecular attributes. Functional experiments confirmed the role of SRSF3 in promoting tumor cell proliferation and leading to poor prognosis. CONCLUSIONS Our study provides a valuable data resource and highlights potential therapeutic approaches for GIST.
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Affiliation(s)
- Mingjun Sun
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yexin Tong
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Yuan
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yunzhi Wang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Yan Pu
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wen Huang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Boqiong Lv
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Chen Xu
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Wei Jiang
- State Key Laboratory of Cell Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Rongkui Luo
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Rundong Fang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Shaoshuai Tang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Lei Ren
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jiachen Wang
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Jinwen Feng
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China
| | - Cheng Sun
- Department of Hepatobiliary Surgery, Anhui Provincial Clinical Research Center for Hepatobiliary Diseases, Anhui Province Key Laboratory of Hepatopancreatobiliary Surgery, The First Affiliated Hospital of University of Science and Technology of China (USTC), Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Chinese Academy of Sciences (CAS) Key Laboratory of Innate Immunity and Chronic Disease, School of Basic Medical Sciences, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, China; Institute of Immunology, University of Science and Technology of China, Hefei, China
| | - Kuntang Shen
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Fuchu He
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China; State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences, Beijing, China; Research Unit of Proteomics Driven Cancer Precision Medicine. Chinese Academy of Medical Sciences, Beijing, China.
| | - Yingyong Hou
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
| | - Chen Ding
- Institutes of Biomedical Sciences, State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Human Phenome Institute, Department of Pathology, Department of General Surgery, Zhongshan Hospital, Fudan University, Shanghai, China.
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3
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Arnold B, Riegger RJ, Okuda EK, Slišković I, Keller M, Bakisoglu C, McNicoll F, Zarnack K, Müller-McNicoll M. hGRAD: A versatile "one-fits-all" system to acutely deplete RNA binding proteins from condensates. J Cell Biol 2024; 223:e202304030. [PMID: 38108808 PMCID: PMC10726014 DOI: 10.1083/jcb.202304030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 09/18/2023] [Accepted: 11/21/2023] [Indexed: 12/19/2023] Open
Abstract
Nuclear RNA binding proteins (RBPs) are difficult to study because they often belong to large protein families and form extensive networks of auto- and crossregulation. They are highly abundant and many localize to condensates with a slow turnover, requiring long depletion times or knockouts that cannot distinguish between direct and indirect or compensatory effects. Here, we developed a system that is optimized for the rapid degradation of nuclear RBPs, called hGRAD. It comes as a "one-fits-all" plasmid, and integration into any cell line with endogenously GFP-tagged proteins allows for an inducible, rapid, and complete knockdown. We show that the nuclear RBPs SRSF3, SRSF5, SRRM2, and NONO are completely cleared from nuclear speckles and paraspeckles within 2 h. hGRAD works in various cell types, is more efficient than previous methods, and does not require the expression of exogenous ubiquitin ligases. Combining SRSF5 hGRAD degradation with Nascent-seq uncovered transient transcript changes, compensatory mechanisms, and an effect of SRSF5 on transcript stability.
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Affiliation(s)
- Benjamin Arnold
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ricarda J. Riegger
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ellen Kazumi Okuda
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- International Max Planck Research School for Cellular Biophysics, Frankfurt am Main, Germany
| | - Irena Slišković
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Mario Keller
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Cem Bakisoglu
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - François McNicoll
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Kathi Zarnack
- Institute of Molecular Biosciences, Goethe University Frankfurt, Frankfurt am Main, Germany
- Buchmann Institute for Molecular Life Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
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Wang G, Ren J, Zeng X, Chen X, Liang A, Wang X, Xu J. Serine and Arginine-Rich Splicing Factor 3 Promotes the Activation of Quiescent Mouse Neural Stem Cells. Stem Cells Dev 2024; 33:79-88. [PMID: 38115601 DOI: 10.1089/scd.2023.0172] [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] [Indexed: 12/21/2023] Open
Abstract
The quiescence and activation of adult stem cells are regulated by many kinds of molecular mechanisms, and RNA alternative splicing participates in regulating many cellular processes. However, the relationship between stem cell quiescence and activation regulation and gene alternative splicing has yet to be studied. In this study, we aimed to elucidate the regulation of stem cell quiescence and activation by RNA alternative splicing. The upregulated genes in activated mouse neural stem cells (NSCs), muscle stem cells, and hematopoietic stem cells were collected for Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis. The genes from three tissue stem cells underwent Venn analysis. The mouse NSCs were used for quiescence and reactivation induction. The immunostaining of cell-specific markers was performed to identify cell properties. The reverse transcription-polymerase chain reaction and western blotting were used to detect the gene expression and protein expression, respectively. We found that the upregulated genes in activated stem cells from three tissues were all enriched in RNA splicing-related biological processes; the upregulated RNA splicing-related genes in activated stem cells displayed tissue differences; mouse NSCs were successfully induced into quiescence and reactivation in vitro without losing differentiation potential; serine and arginine-rich splicing factor 3 (Srsf3) was highly expressed in the activated mouse NSCs, and the overexpression of SRSF3 protein promoted the activation of quiescent mouse NSCs and increased the neural cell production. Our data indicate that the alternative splicing change may underline the transition of quiescence and activation of stem cells. The manipulation of the splicing factor may benefit tissue repair by promoting the activation of quiescent stem cells.
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Affiliation(s)
- Guangming Wang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- Postdoctoral Station of Clinical Medicine, Shanghai Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Jie Ren
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
- East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xinhao Zeng
- Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Xu Chen
- Shanghai Eighth People's Hospital, Jiangsu University, Shanghai, China
| | - Aibin Liang
- Department of Hematology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xianli Wang
- School of Public Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jun Xu
- East Hospital, Tongji University School of Medicine, Shanghai, China
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5
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Chen J, Rao B, Huang Z, Xie C, Yu Y, Yang B, Wu D, Wang D, Qiu F, Zhou Y, Deng Y, Lu J. Circular RNA hsa_circ_0050386 suppresses non-small cell lung cancer progression via regulating the SRSF3/FN1 axis. J Transl Med 2024; 22:47. [PMID: 38216996 PMCID: PMC10785521 DOI: 10.1186/s12967-023-04812-1] [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: 09/26/2023] [Accepted: 12/17/2023] [Indexed: 01/14/2024] Open
Abstract
BACKGROUND Lung cancer is the most prevalent cancer worldwide, with non-small cell lung cancer (NSCLC) accounting for 85% of all cases. Circular RNAs(circRNA) play crucial roles in regulating the progression of lung cancer. Despite the identification of a large number of circRNAs, their expression patterns, functions, and mechanisms of action in NSCLC development remain unclear.This study aims to investigate the transcriptional expressions, functions, and potential mechanisms of circRNA hsa_circ_0050386 in NSCLC. METHODS Quantitative real-time polymerase chain reaction (qRT-PCR) was utilized for the analysis of hsa_circ_0050386 expression. Cell proliferation was detected using the IncuCyte Live Cell Analysis System and clone formation assays. Migration and invasion of NSCLC cells were evaluated through Transwell assays. Flow cytometry was performed to assay cell cycle and apoptosis. Western blot was used to investigate protein expression. Protein binding analysis was conducted by employing pull-down assays, RNA immunoprecipitation (RIP), and mass spectrometry. The role of hsa_circ_0050386 in vivo was evaluated through the use of a xenograft model. RESULTS The study discovered that hsa_circ_0050386 displayed lower expression levels in NSCLC tissues when compared to adjacent normal tissues. Patients exhibiting lower levels of hsa_circ_0050386 expression exhibited an inverse correlation with the Clinical Stage, T-stage, and M-stage of NSCLC. Functionally, hsa_circ_0050386 suppressed the proliferation and invasion of NSCLC cells both in vitro and in vivo. A comprehensive examination exposed the interaction between hsa_circ_0050386 and RNA binding protein Serine and arginine-rich splicing factor 3 (SRSF3), resulting in the down-regulation of Fibronectin 1 (FN1) expression, which inhibits the progression of NSCLC. CONCLUSIONS Our study shows that hsa_circ_0050386 suppresses the malignant biological behavior of NSCLC cells by down-regulating the expression of FN1, and may serve as a potential biomarker and therapeutic target for NSCLC treatment.
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Affiliation(s)
- Jinbin Chen
- The State Key Lab of Respiratory Disease, The School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
- Guangzhou Key Laboratory for Clinical Rapid Diagnosis and Early Warning of Infectious Diseases, KingMed School of Laboratory Medicine, Guangzhou Medical University, Guangzhou, 510180, China
| | - Boqi Rao
- The State Key Lab of Respiratory Disease, The School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Zeqin Huang
- The State Key Lab of Respiratory Disease, The School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Chen Xie
- The State Key Lab of Respiratory Disease, The School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yonghui Yu
- The State Key Lab of Respiratory Disease, The School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Binyao Yang
- Department of Central Laboratory, The 5th Affiliated Hospital of Guangzhou Medical University, Guangzhou, 510700, China
| | - Di Wu
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Dedong Wang
- Guangzhou Center for Disease Control and Prevention, Guangzhou, 510440, China
| | - Fuman Qiu
- The State Key Lab of Respiratory Disease, The School of Public Health, Guangzhou Medical University, Guangzhou, 511436, China
| | - Yifeng Zhou
- Department of Genetics, Medical College of Soochow University, Suzhou, 215123, China
| | - Yibin Deng
- Centre for Medical Laboratory Science, the Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshaner Rd., Youjiang District, Baise, 533000, China.
| | - Jiachun Lu
- The State Key Lab of Respiratory Disease, The First Affiliated Hospital, The School of Public Health, Guangzhou Medical University, Xinzao Town, Panyu District, Guangzhou, 511436, China.
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6
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Li D, Yu W, Lai M. Targeting serine- and arginine-rich splicing factors to rectify aberrant alternative splicing. Drug Discov Today 2023; 28:103691. [PMID: 37385370 DOI: 10.1016/j.drudis.2023.103691] [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: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Serine- and arginine-rich splicing factors are pivotal modulators of constitutive splicing and alternative splicing that bind to the cis-acting elements in precursor mRNAs and facilitate the recruitment and assembly of the spliceosome. Meanwhile, SR proteins shuttle between the nucleus and cytoplasm with a broad implication in multiple RNA-metabolizing events. Recent studies have demonstrated the positive correlation of overexpression and/or hyperactivation of SR proteins and development of the tumorous phenotype, indicating the therapeutic potentials of targeting SR proteins. In this review, we highlight key findings concerning the physiological and pathological roles of SR proteins. We have also investigated small molecules and oligonucleotides that effectively modulate the functions of SR proteins, which could benefit future studies of SR proteins.
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Affiliation(s)
- Dianyang Li
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China.
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
| | - Maode Lai
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Science (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China.
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7
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Wu W, Hu A, Xu H, Su J. LincRNA-EPS Alleviates Inflammation in TMJ Osteoarthritis by Binding to SRSF3. J Dent Res 2023; 102:1141-1151. [PMID: 37464762 DOI: 10.1177/00220345231180464] [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] [Indexed: 07/20/2023] Open
Abstract
Temporomandibular joint osteoarthritis (TMJOA) is a common inflammatory disease that can cause pain, cartilage degradation, and subchondral bone loss. However, the key regulatory factors and new targets for the treatment of TMJOA have yet to be determined. Long noncoding RNAs (lncRNAs) have shown remarkable potential in regulating tissue homeostasis and disease development. The long intergenic RNA-erythroid prosurvival (lincRNA-EPS) is reported to be an effective inhibitor of inflammation, but its role in TMJOA is unexplored. Here, we found that lincRNA-EPS is downregulated and negatively correlated with inflammatory factors in the condyles of TMJOA mice. LincRNA-EPS knockout aggravated inflammation and tissue destruction after TMJOA modeling. The in vitro studies confirmed that loss of lincRNA-EPS facilitated inflammatory factor expression in condylar chondrocytes, while recovered expression of lincRNA-EPS showed anti-inflammatory effects. Mechanistically, RNA sequencing revealed that the inflammatory response pathway nuclear factor-kappa B (NF-κB) was mostly affected by lincRNA-EPS deficiency. Moreover, lincRNA-EPS was proved to effectively bind to serine/arginine-rich splicing factor 3 (SRSF3) and inhibit its function in pyruvate kinase isoform M2 (PKM2) formation, thus restraining the PKM2/NF-κB pathway and the expression of inflammatory factors. In addition, local injection of the lincRNA-EPS overexpression lentivirus significantly alleviated inflammation, cartilage degradation, and subchondral bone loss in TMJOA mice. Overall, lincRNA-EPS regulated the inflammatory process of condylar chondrocytes by binding to SRSF3 and showed translational application potential in the treatment of TMJOA.
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Affiliation(s)
- W Wu
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - A Hu
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - H Xu
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - J Su
- Department of Prosthodontics, Stomatological Hospital and Dental School of Tongji University, Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
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8
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Campbell AE, Dyle MC, Albanese R, Matheny T, Sudheendran K, Cortázar MA, Forman T, Fu R, Gillen AE, Caruthers MH, Floor SN, Calviello L, Jagannathan S. Compromised nonsense-mediated RNA decay results in truncated RNA-binding protein production upon DUX4 expression. Cell Rep 2023; 42:112642. [PMID: 37314931 PMCID: PMC10592454 DOI: 10.1016/j.celrep.2023.112642] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 03/31/2023] [Accepted: 05/29/2023] [Indexed: 06/16/2023] Open
Abstract
Nonsense-mediated RNA decay (NMD) degrades transcripts carrying premature termination codons. NMD is thought to prevent the synthesis of toxic truncated proteins. However, whether loss of NMD results in widespread production of truncated proteins is unclear. A human genetic disease, facioscapulohumeral muscular dystrophy (FSHD), features acute inhibition of NMD upon expression of the disease-causing transcription factor, DUX4. Using a cell-based model of FSHD, we show production of truncated proteins from physiological NMD targets and find that RNA-binding proteins are enriched for aberrant truncations. The NMD isoform of one RNA-binding protein, SRSF3, is translated to produce a stable truncated protein, which is detected in FSHD patient-derived myotubes. Ectopic expression of truncated SRSF3 confers toxicity, and its downregulation is cytoprotective. Our results delineate the genome-scale impact of NMD loss. This widespread production of potentially deleterious truncated proteins has implications for FSHD biology as well as other genetic diseases where NMD is therapeutically modulated.
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Affiliation(s)
- Amy E Campbell
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael C Dyle
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Roberto Albanese
- Functional Genomics Research Centre, Human Technopole, 20157 Milan, Italy; Computational Biology Research Centre, Human Technopole, 20157 Milan, Italy
| | - Tyler Matheny
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Kavitha Sudheendran
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Michael A Cortázar
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Thomas Forman
- Department of Craniofacial Biology, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; Medical Scientist Training Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Rui Fu
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Austin E Gillen
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Marvin H Caruthers
- Department of Biochemistry, University of Colorado Boulder, Boulder, CO 80309, USA
| | - Stephen N Floor
- Department of Cell and Tissue Biology, University of California, San Francisco, San Francisco, CA 94143, USA; Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Lorenzo Calviello
- Functional Genomics Research Centre, Human Technopole, 20157 Milan, Italy; Computational Biology Research Centre, Human Technopole, 20157 Milan, Italy
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA; RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA.
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9
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Lai X, Li R, Wang P, Li M, Xiao C, Cao Q, Li X, Zhao W. Cumulative effects of weakly repressive regulatory regions in the 3' UTR maintain PD-1 expression homeostasis in mammals. Commun Biol 2023; 6:537. [PMID: 37202440 DOI: 10.1038/s42003-023-04922-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/08/2023] [Indexed: 05/20/2023] Open
Abstract
PD-1 has become a common target for cancer treatment. However, the molecular regulation of PD-1 expression homeostasis remains unclear. Here we report the PD-1 3' UTR can dramatically repress gene expression via promoting mRNA decay. Deletion of the PD-1 3' UTR inhibits T cell activity and promotes T-ALL cell proliferation. Interestingly, the robust repression is attributable to cumulative effects of many weak regulatory regions, which we show together are better able to maintain PD-1 expression homeostasis. We further identify several RNA binding proteins (RBPs) that modulate PD-1 expression via the 3' UTR, including IGF2BP2, RBM38, SRSF7, and SRSF4. Moreover, despite rapid evolution, PD-1 3' UTRs are functionally conserved and strongly repress gene expression through many common RBP binding sites. These findings reveal a previously unrecognized mechanism of maintaining PD-1 expression homeostasis and might represent a general model for how small regulatory effects play big roles in regulation of gene expression and biology.
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Affiliation(s)
- Xiaoqian Lai
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Rong Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Panpan Wang
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Meng Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Chenxi Xiao
- Undergraduate Program in Medicine, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Qiang Cao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China
| | - Xin Li
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.
| | - Wenxue Zhao
- Molecular Cancer Research Center, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, 518107, China.
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10
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Nishanth MJ, Jha S. Genome-wide landscape of RNA-binding protein (RBP) networks as potential molecular regulators of psychiatric co-morbidities: a computational analysis. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2023. [DOI: 10.1186/s43042-022-00382-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Background
Psychiatric disorders are a major burden on global health. These illnesses manifest as co-morbid conditions, further complicating the treatment. There is a limited understanding of the molecular and regulatory basis of psychiatric co-morbidities. The existing research in this regard has largely focused on epigenetic modulators, non-coding RNAs, and transcription factors. RNA-binding proteins (RBPs) functioning as multi-protein complexes are now known to be predominant controllers of multiple gene regulatory processes. However, their involvement in gene expression dysregulation in psychiatric co-morbidities is yet to be understood.
Results
Ten RBPs (QKI, ELAVL2, EIF2S1, SRSF3, IGF2BP2, EIF4B, SNRNP70, FMR1, DAZAP1, and MBNL1) were identified to be associated with psychiatric disorders such as schizophrenia, major depression, and bipolar disorders. Analysis of transcriptomic changes in response to individual depletion of these RBPs showed the potential influence of a large number of RBPs driving differential gene expression, suggesting functional cross-talk giving rise to multi-protein networks. Subsequent transcriptome analysis of post-mortem human brain samples from diseased and control individuals also suggested the involvement of ~ 100 RBPs influencing gene expression changes. These RBPs were found to regulate various processes including transcript splicing, mRNA transport, localization, stability, and translation. They were also found to form an extensive interactive network. Further, hnRNP, SRSF, and PCBP family RBPs, Matrin3, U2AF2, KHDRBS1, PTBP1, and also PABPN1 were found to be the hub proteins of the RBP network.
Conclusions
Extensive RBP networks involving a few hub proteins could result in transcriptome-wide dysregulation of post-transcriptional modifications, potentially driving multiple psychiatric disorders. Understanding the functional involvement of RBP networks in psychiatric disorders would provide insights into the molecular basis of psychiatric co-morbidities.
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11
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Saha Detroja T, Detroja R, Mukherjee S, Samson AO. Identifying Hub Genes Associated with Neoadjuvant Chemotherapy Resistance in Breast Cancer and Potential Drug Repurposing for the Development of Precision Medicine. Int J Mol Sci 2022; 23:ijms232012628. [PMID: 36293493 PMCID: PMC9603969 DOI: 10.3390/ijms232012628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 10/12/2022] [Accepted: 10/18/2022] [Indexed: 11/25/2022] Open
Abstract
Breast cancer is the second leading cause of morbidity and mortality in women worldwide. Despite advancements in the clinical application of neoadjuvant chemotherapy (NAC), drug resistance remains a major concern hindering treatment efficacy. Thus, identifying the key genes involved in driving NAC resistance and targeting them with known potential FDA-approved drugs could be applied to advance the precision medicine strategy. With this aim, we performed an integrative bioinformatics study to identify the key genes associated with NAC resistance in breast cancer and then performed the drug repurposing to identify the potential drugs which could use in combination with NAC to overcome drug resistance. In this study, we used publicly available RNA-seq datasets from the samples of breast cancer patients sensitive and resistant to chemotherapy and identified a total of 1446 differentially expressed genes in NAC-resistant breast cancer patients. Next, we performed gene co-expression network analysis to identify significantly co-expressed gene modules, followed by MCC (Multiple Correlation Clustering) clustering algorithms and identified 33 key hub genes associated with NAC resistance. mRNA–miRNA network analysis highlighted the potential impact of these hub genes in altering the regulatory network in NAC-resistance breast cancer cells. Further, several hub genes were found to be significantly involved in the poor overall survival of breast cancer patients. Finally, we identified FDA-approved drugs which could be useful for potential drug repurposing against those hub genes. Altogether, our findings provide new insight into the molecular mechanisms of NAC resistance and pave the way for drug repurposing techniques and personalized treatment to overcome NAC resistance in breast cancer.
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Affiliation(s)
| | - Rajesh Detroja
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G 2C4, Canada
| | - Sumit Mukherjee
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
- Correspondence: (S.M.); (A.O.S.)
| | - Abraham O. Samson
- The Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel
- Correspondence: (S.M.); (A.O.S.)
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12
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Chen H, Lv L, Liang R, Guo W, Liao Z, Chen Y, Zhu K, Huang R, Zhao H, Pu Q, Yuan Z, Zeng Z, Zheng X, Feng S, Qi X, Cai D. miR-486 improves fibrotic activity in myocardial infarction by targeting SRSF3/p21-Mediated cardiac myofibroblast senescence. J Cell Mol Med 2022; 26:5135-5149. [PMID: 36117396 PMCID: PMC9575141 DOI: 10.1111/jcmm.17539] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 12/03/2022] Open
Abstract
The regulation of fibrotic activities is key to improving pathological remodelling post‐myocardial infarction (MI). Currently, in the clinic, safe and curative therapies for cardiac fibrosis and improvement of the pathological fibrotic environment, scar formation and pathological remodelling post‐MI are lacking. Previous studies have shown that miR‐486 is involved in the regulation of fibrosis. However, it is still unclear how miR‐486 functions in post‐MI regeneration. Here, we first demonstrated that miR‐486 targeting SRSF3/p21 mediates the senescence of cardiac myofibroblasts to improve their fibrotic activity, which benefits the regeneration of MI by limiting scar size and post‐MI remodelling. miR‐486‐targeted silencing has high potential as a novel target to improve fibrotic activity, cardiac fibrosis and pathological remodelling.
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Affiliation(s)
- Hongyi Chen
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Luocheng Lv
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Ruoxu Liang
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Weimin Guo
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Zhaofu Liao
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Yilin Chen
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Kuikui Zhu
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Ruijin Huang
- Institute of Anatomy, Department of Neuroanatomy, Medical Faculty, University of Bonn, Germany
| | - Hui Zhao
- Stem Cell and Regeneration TRP, School of Biomedical Sciences, Chinese University of Hong Kong, Hong Kong
| | - Qin Pu
- Institute of Anatomy, Department of Neuroanatomy, Medical Faculty, University of Bonn, Germany
| | - Ziqiang Yuan
- Cancer Institute of New Jersey, Department of Medical Oncology, Robert Wood Johnson of Medical School, USA
| | - Zhaohua Zeng
- Division of Cardiology, Department of Internal Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| | - Xin Zheng
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Shanshan Feng
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Xufeng Qi
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
| | - Dongqing Cai
- Key Laboratory of Regenerative Medicine, Ministry of Education, Jinan University, Guangzhou, China.,Joint Laboratory for Regenerative Medicine, Chinese University of Hong Kong-Jinan University, Guangzhou, China.,International Base of Collaboration for Science and Technology (JNU), Ministry of Science and Technology, Guangzhou, China.,Department of Developmental and Regenerative Biology, Jinan University, Guangzhou, China
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13
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Saglam BS, Kanli A, Yanar S, Kasap M, Akpinar G. Investigation of the effect of meclofenamic acid on the proteome of LNCaP cells reveals changes in alternative polyadenylation and splicing machinery. MEDICAL ONCOLOGY (NORTHWOOD, LONDON, ENGLAND) 2022; 39:190. [PMID: 36071279 DOI: 10.1007/s12032-022-01795-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/09/2022] [Indexed: 12/24/2022]
Abstract
Prostate cancer is the most common type of cancer among men, and there is still no definitively effective drug treatment. Thus, the search for novel drug agents that may be used for the effective treatment continues. Meclofenamic acid (MA), a non-steroidal anti-inflammatory drug, with anti-tumor effects in various types of cancers was used to investigate its effects on LNCaP cells, a prostate cancer cell line, at the proteome level. The cells were treated with 80 µM MA for 24 h and a comparative proteomic analysis was performed with their untreated control cells. Proteins were extracted from the cells and then were subjected to two-dimensional gel electrophoresis. Protein spots displaying changes in their regulation ratios for more than two-fold were excised from the gels and identified with MALDI-TOF/TOF mass spectrometry. Bioinformatics analysis of the differentially regulated proteins that we identified showed that they were all associated with and took part in related pathways. Glycolytic pathway, cytoskeletal formation, transport activity, protein metabolism, and most notably an mRNA processing pathway were affected by the MA treatment. In addition to presenting a detailed information for what is happening inside the cells upon MA treatment, the proteins affected by MA treatment hold the potential to be novel targets for prostate cancer treatment provided that further in vivo experiments are carried out.
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Affiliation(s)
- Busra Sahinoz Saglam
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
| | - Aylin Kanli
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey.
| | - Sevinc Yanar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
- Department of Histology and Embryology, Faculty of Medicine, Sakarya University, Serdivan, Sakarya, Turkey
| | - Murat Kasap
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
| | - Gurler Akpinar
- Department of Medical Biology, Faculty of Medicine, Kocaeli University, İzmit, Kocaeli, Turkey
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14
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Lu X, Zhong J, Liu L, Zhang W, Zhao S, Chen L, Wei Y, Zhang H, Wu J, Chen W, Ge F. The function and regulatory mechanism of RNA-binding proteins in breast cancer and their future clinical treatment prospects. Front Oncol 2022; 12:929037. [PMID: 36052258 PMCID: PMC9424610 DOI: 10.3389/fonc.2022.929037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/25/2022] [Indexed: 11/19/2022] Open
Abstract
Breast cancer is the most common female malignancy, but the mechanisms regulating gene expression leading to its development are complex. In recent years, as epigenetic research has intensified, RNA-binding proteins (RBPs) have been identified as a class of posttranscriptional regulators that can participate in regulating gene expression through the regulation of RNA stabilization and degradation, intracellular localization, alternative splicing and alternative polyadenylation, and translational control. RBPs play an important role in the development of normal mammary glands and breast cancer. Functional inactivation or abnormal expression of RBPs may be closely associated with breast cancer development. In this review, we focus on the function and regulatory mechanisms of RBPs in breast cancer, as well as the advantages and challenges of RBPs as potential diagnostic and therapeutic targets in breast cancer, and discuss the potential of RBPs in clinical treatment.
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Affiliation(s)
- Xingjia Lu
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Jian Zhong
- Department of Reproductive Medicine, Affiliated Jinling Hospital, Nanjing Medical University, Nanjing, China
- Department of Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing, China
| | - Linlin Liu
- School of Forensic Medicine, Kunming Medical University, Kunming, China
| | - Wenzhu Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Shengdi Zhao
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Liang Chen
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
| | - Yuxian Wei
- Department of Endocrine Breast Surgery, First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Hong Zhang
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Jingxuan Wu
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- Kunming Medical University, No. 1 School of Clinical Medicine, Kunming, China
| | - Wenlin Chen
- Third Department of Breast Surgery, The Third Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Wenlin Chen, ; Fei Ge,
| | - Fei Ge
- Department of Breast Surgery, First Affiliated Hospital of Kunming Medical University, Kunming, China
- *Correspondence: Wenlin Chen, ; Fei Ge,
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15
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A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [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: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
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16
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He Y, Huang Y, Wang S, Zhang L, Gao H, Zhao Y, E G. Hereditary Basis of Coat Color and Excellent Feed Conversion Rate of Red Angus Cattle by Next-Generation Sequencing Data. Animals (Basel) 2022; 12:1509. [PMID: 35739846 PMCID: PMC9219544 DOI: 10.3390/ani12121509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 05/24/2022] [Accepted: 06/07/2022] [Indexed: 12/03/2022] Open
Abstract
Angus cattle have made remarkable contributions to the livestock industry worldwide as a commercial meat-type breed. Some evidence supported that Angus cattle with different coat colors have different feed-to-meat ratios, and the genetic basis of their coat color is inconclusive. Here, genome-wide association study was performed to investigate the genetic divergence of black and red Angus cattle with 63 public genome sequencing data. General linear model analysis was used to identify genomic regions with potential candidate variant/genes that contribute to coat color and feed conversion rate. Results showed that six single nucleotide polymorphisms (SNPs) and two insertion−deletions, which were annotated in five genes (ZCCHC14, ANKRD11, FANCA, MC1R, and LOC532875 [AFG3-like protein 1]), considerably diverged between black and red Angus cattle. The strongest associated loci, namely, missense mutation CHIR18_14705671 (c.296T > C) and frameshift mutation CHIR18_12999497 (c.310G>-), were located in MC1R. Three consecutive strongly associated SNPs were also identified and located in FANCA, which is widely involved in the Fanconi anemia pathway. Several SNPs of highly associated SNPs was notably enriched in ZCCHC14 and ANKRD11, which are related to myofiber growth and muscle development. This study provides a basis for the use of potential genetic markers to be used in future breeding programs to improve cattle selection in terms of coat color and meat phenotype. This study is also helpful to understand the hereditary basis of different coat colors and meat phenotypes. However, the putative candidate genes or markers identified in this study require further investigation to confirm their phenotypic causality and potential effective genetic relationships.
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Affiliation(s)
- Yongmeng He
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China; (Y.H.); (Y.H.); (S.W.); (Y.Z.)
| | - Yongfu Huang
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China; (Y.H.); (Y.H.); (S.W.); (Y.Z.)
| | - Shizhi Wang
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China; (Y.H.); (Y.H.); (S.W.); (Y.Z.)
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (L.Z.); (H.G.)
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (L.Z.); (H.G.)
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China; (Y.H.); (Y.H.); (S.W.); (Y.Z.)
| | - Guangxin E
- College of Animal Science and Technology, Southwest University, Chongqing 400716, China; (Y.H.); (Y.H.); (S.W.); (Y.Z.)
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17
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Wang ZW, Pan JJ, Hu JF, Zhang JQ, Huang L, Huang Y, Liao CY, Yang C, Chen ZW, Wang YD, Shen BY, Tian YF, Chen S. SRSF3-mediated regulation of N6-methyladenosine modification-related lncRNA ANRIL splicing promotes resistance of pancreatic cancer to gemcitabine. Cell Rep 2022; 39:110813. [PMID: 35545048 DOI: 10.1016/j.celrep.2022.110813] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 03/21/2022] [Accepted: 04/21/2022] [Indexed: 02/06/2023] Open
Abstract
Serine/arginine-rich splicing factor 3 (SRSF3) regulates mRNA alternative splicing of more than 90% of protein-coding genes, providing an essential source for biological versatility. This study finds that SRSF3 expression is associated with drug resistance and poor prognosis in pancreatic cancer. We also find that SRSF3 regulates ANRIL splicing and m6A modification of ANRIL in pancreatic cancer cells. More importantly, we demonstrate that m6A methylation on lncRNA ANRIL is essential for the splicing. Moreover, our results show that SRSF3 promotes gemcitabine resistance by regulating ANRIL's splicing and ANRIL-208 (one of the ANRIL spliceosomes) can enhance DNA homologous recombination repair (HR) capacity by forming a complex with Ring1b and EZH2. In conclusion, this study establishes a link between SRSF3, m6A modification, lncRNA splicing, and DNA HR in pancreatic cancer and demonstrates that abnormal alternative splicing and m6A modification are closely related to chemotherapy resistance in pancreatic cancer.
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Affiliation(s)
- Zu-Wei Wang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China
| | - Jing-Jing Pan
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China
| | - Jian-Fei Hu
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China
| | - Jia-Qiang Zhang
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Long Huang
- Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Yi Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China; Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Cheng-Yu Liao
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China
| | - Can Yang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China
| | - Zhi-Wen Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China
| | - Yao-Dong Wang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China; Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fuzhou 350001, China
| | - Bai-Yong Shen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Yi-Feng Tian
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China; Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fuzhou 350001, China.
| | - Shi Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, Fuzhou 350001, China; Department of Hepatopancreatobiliary Surgery, Fujian Provincial Hospital, Fuzhou 350001, China.
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18
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Luo J, Gao K, Chen M, Tian B. LINC01210 promotes malignant phenotypes of colorectal cancer through epigenetically upregulating SRSF3. Pathol Res Pract 2022; 234:153905. [PMID: 35462226 DOI: 10.1016/j.prp.2022.153905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 04/07/2022] [Accepted: 04/15/2022] [Indexed: 12/24/2022]
Abstract
Long non-coding RNAs (lncRNAs) have been linked to tumorigenesis. However, the role of LINC01210 in colorectal cancer (CRC) remains unclear. Relative levels of LINC01210 in CRC tissues and adjacent tissues were determined. Proliferative, migratory, and invasive abilities were examined in HCT116 cells and LoVo cells after silencing or overexpressing LINC01210. The interaction between LINC01210 and SRSF3 was explored by ChIP-PCR. Upregulated LINC01210 was associated with metastasis and advanced stage of CRC. Silencing LINC01210 attenuated proliferative, migratory, and invasive abilities in LoVo cells, while overexpressing LINC01210 promoted proliferative, migratory, and invasive abilities in HCT116 cells. Mechanism study revealed that LINC01210 increased the expression of SRSF3 by recruiting mixed lineage leukaemia protein-1, which upregulated the trimethylation of H3K4 me3 on SRSF3 promoter. Silencing SRSF3 reversed the effects of LINC01210 on CRC cells. In conclusions, LINC01210 accelerated proliferation and invasion in CRC cells through epigenetically upregulating SRSF3, and may be a potential therapeutic target for CRC treatment.
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Affiliation(s)
- Jia Luo
- Department of Pharmacy, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha 410008, Hunan Province, China
| | - Kai Gao
- Department of Gastrointestinal Surgery, Xiangya Third Hospital of Central South University, Changsha, Hunan Province, China
| | - Miao Chen
- Department of Gastrointestinal Surgery, Xiangya Third Hospital of Central South University, Changsha, Hunan Province, China
| | - Buning Tian
- Department of Gastrointestinal Surgery, Xiangya Third Hospital of Central South University, Changsha, Hunan Province, China.
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Li Z, Huang H, Wu X, Yu T, Xiao F, Zhou H, Shang A, Yang Y. SRSF3 Expression Serves as a Potential Biomarker for Prognostic and Immune Response in Pan-Cancer. Front Oncol 2022; 12:808530. [PMID: 35494088 PMCID: PMC9047863 DOI: 10.3389/fonc.2022.808530] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 03/15/2022] [Indexed: 11/13/2022] Open
Abstract
Serine-rich splicing factor3 (SRSF3) plays an essential role in cell proliferation and inducing and maintaining of cancers as a proto-oncogene. However, the mechanisms of SRSF3 in pan-cancers are still unknown. In our study, a visualized prognostic landscape of SRSF3 in pan-cancer was investigated and the relationship between SRSF3 expression and immune infiltration was also investigated. The expression pattern and prognostic worth of SRSF3 among pan-cancers were explored through different databases, namely, the TCGA and Kaplan–Meier Plotter. Moreover, the survival analysis including Kaplan-Meier method for evaluating between groups was conducted. Further analyses including the correlation between expression SRSF expression and immune infiltration including tumor mutation burden (TMB), microsatellite instability (MSI) was investigated using Spearman test. In ACC, KIRP and UCEC cancer, upregulated expression of SRSF3 was associated with worse disease-free interval (DFI), representing a mechanism in promoting progression of tumor. Our results showed that SRSF3 expression was positively correlated immune cell infiltration, TMB, MSI in certain cancer types, indicating SRSF3 expression to potential value of therapy response. Additionally, we explored the functional characteristics of SRSF in vitro through western blot detecting the expression level of the apoptosis-related proteins in SW480 and 786-O cells. SRSF3 expression was upregulated in pan-cancer tissue compared with normal tissue, which confirmed by immunohistochemistry and its expression indicated poor overall survival and death-specific survival. Therefore, SRSF3 was found to be a possible biomarker for prognostic and therapeutic assessment through bioinformatic analysis. SRSF3 is expressed in various cancers and its high expression correlated to poor survival and disease progression. In summary, SRSF3 expression can be considered as a prognostic biomarker in pan-cancer and therapeutic evaluation.
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Affiliation(s)
- Zihua Li
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Orthopedics, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Hui Huang
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Xinbo Wu
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- Department of Orthopedics, Shanghai Tenth People’s Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Tao Yu
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Fajiao Xiao
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Haichao Zhou
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
| | - Anquan Shang
- Department of Laboratory Medicine, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Anquan Shang, ; Yunfeng Yang,
| | - Yunfeng Yang
- Department of Orthopedics, Shanghai Tongji Hospital, School of Medicine, Tongji University, Shanghai, China
- *Correspondence: Anquan Shang, ; Yunfeng Yang,
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SRSF3 facilitates replication of influenza A virus via binding and promoting the transport of viral mRNA. Vet Microbiol 2022; 266:109343. [DOI: 10.1016/j.vetmic.2022.109343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 01/11/2022] [Accepted: 01/16/2022] [Indexed: 12/17/2022]
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Exploring the multifunctionality of SR proteins. Biochem Soc Trans 2021; 50:187-198. [PMID: 34940860 PMCID: PMC9022966 DOI: 10.1042/bst20210325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 12/01/2021] [Accepted: 12/02/2021] [Indexed: 12/31/2022]
Abstract
Members of the arginine–serine-rich protein family (SR proteins) are multifunctional RNA-binding proteins that have emerged as key determinants for mRNP formation, identity and fate. They bind to pre-mRNAs early during transcription in the nucleus and accompany bound transcripts until they are translated or degraded in the cytoplasm. SR proteins are mostly known for their essential roles in constitutive splicing and as regulators of alternative splicing. However, many additional activities of individual SR proteins, beyond splicing, have been reported in recent years. We will summarize the different functions of SR proteins and discuss how multifunctionality can be achieved. We will also highlight the difficulties of studying highly versatile SR proteins and propose approaches to disentangle their activities, which is transferrable to other multifunctional RBPs.
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Identification of SRSF3 target mRNAs using inducible TRIBE. Biochem Biophys Res Commun 2021; 578:21-27. [PMID: 34534741 DOI: 10.1016/j.bbrc.2021.09.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/06/2021] [Accepted: 09/08/2021] [Indexed: 11/22/2022]
Abstract
Serine and arginine-rich splicing factor 3 (SRSF3), the smallest member of the Ser/Arg-rich (SR) RNA-binding protein family, regulates multiple aspects of post-transcriptional gene expression program. Although SRSF3 is essential for early embryo development, reprogramming, and pluripotency maintenance, the RNA targets and specificity of RNA recognition of SRSF3 are not well understood in human pluripotent stem cells. In this study, we used inducible TRIBE (targets of RNA binding sites by editing) to identify RNA targets and binding motifs of SRSF3 in human embryonic stem cells (hESCs). We identified 3888 confident binding sites of SRSF3, corresponding to 1222 gene targets. Our results showed that nearly half of the binding sites were distributed in exons, reflecting the alternative splicing function of SRSF3. Motif analysis demonstrated that two of the SRSF3 recognition sequences were the same as the motifs identified in mouse embryonic stem cells, suggesting the recognition sequences of SRSF3 may be conserved in mammals. Overall, our analyses revealed the RNA targets of SRSF3 and uncovered its RNA recognition specificity, providing a valuable resource for understanding the function of SRSF3 in human embryonic stem cells.
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Chen S, Yang C, Wang ZW, Hu JF, Pan JJ, Liao CY, Zhang JQ, Chen JZ, Huang Y, Huang L, Zhan Q, Tian YF, Shen BY, Wang YD. CLK1/SRSF5 pathway induces aberrant exon skipping of METTL14 and Cyclin L2 and promotes growth and metastasis of pancreatic cancer. J Hematol Oncol 2021; 14:60. [PMID: 33849617 PMCID: PMC8045197 DOI: 10.1186/s13045-021-01072-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/29/2021] [Indexed: 12/11/2022] Open
Abstract
Background Both aberrant alternative splicing and m6A methylation play complicated roles in the development of pancreatic cancer (PC), while the relationship between these two RNA modifications remains unclear. Methods RNA sequencing (RNA-seq) was performed using 15 pairs of pancreatic ductal adenocarcinoma (PDAC) tissues and corresponding normal tissues, and Cdc2-like kinases 1 (CLK1) was identified as a significantly upregulated alternative splicing related gene. Real-time quantitative PCR (qPCR) and western blotting were applied to determine the CLK1 levels. The prognostic value of CLK1 was elucidated by Immunohistochemistry (IHC) analyses in two independent PDAC cohorts. The functional characterizations and mechanistic insights of CLK1 in PDAC growth and metastasis were evaluated with PDAC cell lines and nude mice. SR-like splicing factors5250-Ser (SRSF5250-Ser) was identified as an important target phosphorylation site by phosphorylation mass spectrometry. Through transcriptome sequencing, Methyltransferase-like 14exon10 (METTL14exon10) and Cyclin L2exon6.3 skipping were identified as key alternative splicing events regulated by the CLK1-SRSF5 axis. RIP assays, RNA-pulldown and CLIP-qPCR were performed to confirm molecular interactions and the precise binding sites. The roles of the shift of METTL14exon 10 and Cyclin L2exon6.3 skipping were surveyed. Results CLK1 expression was significantly increased in PDAC tissues at both the mRNA and protein levels. High CLK1 expression was associated with poor prognosis. Elevated CLK1 expression promoted growth and metastasis of PC cells in vitro and in vivo. Mechanistically, CLK1 enhanced phosphorylation on SRSF5250-Ser, which inhibited METTL14exon10 skipping while promoted Cyclin L2exon6.3 skipping. In addition, aberrant METTL14exon 10 skipping enhanced the N6-methyladenosine modification level and metastasis, while aberrant Cyclin L2exon6.3 promoted proliferation of PDAC cells. Conclusions The CLK1/SRSF5 pathway induces aberrant exon skipping of METTL14 and Cyclin L2, which promotes growth and metastasis and regulates m6A methylation of PDAC cells. This study suggests the potential prognostic value and therapeutic targeting of this pathway in PDAC patients. Supplementary Information The online version contains supplementary material available at 10.1186/s13045-021-01072-8.
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Affiliation(s)
- Shi Chen
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China. .,Department of Hepatobiliary Pancreatic Surgery, Fujian Provincial Hospital, Fuzhou, 350001, People's Republic of China.
| | - Can Yang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Zu-Wei Wang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Jian-Fei Hu
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Jing-Jing Pan
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Cheng-Yu Liao
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China
| | - Jia-Qiang Zhang
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No.197 Ruijin Second Road, Shanghai, 200025, People's Republic of China
| | - Jiang-Zhi Chen
- Department of Hepatobiliary Surgery, Union Hospital, Fujian Medical University, Fuzhou, 350001, People's Republic of China
| | - Yi Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China.,Center for Experimental Research in Clinical Medicine, Fujian Provincial Hospital, Fuzhou, 350001, People's Republic of China
| | - Long Huang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China.,Department of Hepatobiliary Pancreatic Surgery, Fujian Provincial Hospital, Fuzhou, 350001, People's Republic of China
| | - Qian Zhan
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No.197 Ruijin Second Road, Shanghai, 200025, People's Republic of China
| | - Yi-Feng Tian
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China.,Department of Hepatobiliary Pancreatic Surgery, Fujian Provincial Hospital, Fuzhou, 350001, People's Republic of China
| | - Bai-Yong Shen
- Department of General Surgery, Pancreatic Disease Center, Research Institute of Pancreatic Diseases, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, No.197 Ruijin Second Road, Shanghai, 200025, People's Republic of China.
| | - Yao-Dong Wang
- Shengli Clinical Medical College of Fujian Medical University, Fujian Medical University, No. 134, East Street, Fuzhou, 350001, Fujian Province, People's Republic of China. .,Department of Hepatobiliary Pancreatic Surgery, Fujian Provincial Hospital, Fuzhou, 350001, People's Republic of China.
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