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Singh K, Lin J, Zhong Y, Burčul A, Mohan P, Jiang M, Sun L, Yong-Gonzalez V, Viale A, Cross JR, Hendrickson RC, Rätsch G, Ouyang Z, Wendel HG. c-MYC regulates mRNA translation efficiency and start-site selection in lymphoma. J Exp Med 2019; 216:1509-1524. [PMID: 31142587 PMCID: PMC6605752 DOI: 10.1084/jem.20181726] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 02/22/2019] [Accepted: 04/19/2019] [Indexed: 12/24/2022] Open
Abstract
The oncogenic c-MYC (MYC) transcription factor has broad effects on gene expression and cell behavior. We show that MYC alters the efficiency and quality of mRNA translation into functional proteins. Specifically, MYC drives the translation of most protein components of the electron transport chain in lymphoma cells, and many of these effects are independent from proliferation. Specific interactions of MYC-sensitive RNA-binding proteins (e.g., SRSF1/RBM42) with 5'UTR sequence motifs mediate many of these changes. Moreover, we observe a striking shift in translation initiation site usage. For example, in low-MYC conditions, lymphoma cells initiate translation of the CD19 mRNA from a site in exon 5. This results in the truncation of all extracellular CD19 domains and facilitates escape from CD19-directed CAR-T cell therapy. Together, our findings reveal MYC effects on the translation of key metabolic enzymes and immune receptors in lymphoma cells.
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Affiliation(s)
- Kamini Singh
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jianan Lin
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Biomedical Engineering, University of Connecticut, Storrs, CT
| | - Yi Zhong
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Antonija Burčul
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Prathibha Mohan
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Man Jiang
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Liping Sun
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Vladimir Yong-Gonzalez
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Agnes Viale
- Integrated Genomics Operation, Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Justin R Cross
- Donald B. and Catherine C. Marron Cancer Metabolism Center, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ronald C Hendrickson
- Proteomics and Microchemistry, Memorial Sloan- Kettering Cancer Center, New York, NY
| | - Gunnar Rätsch
- Computational Biology Department, Memorial Sloan Kettering Cancer Center, New York, NY
- Biomedical Informatics, Department of Computer Science, Swiss Federal Institute of Technology, Zürich, Switzerland
| | - Zhengqing Ouyang
- The Jackson Laboratory for Genomic Medicine, Farmington, CT
- Department of Genetics and Genome Sciences and Institute for System Genomics, University of Connecticut Health Center, Farmington, CT
| | - Hans-Guido Wendel
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY
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152
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The d16HER2 Splice Variant: A Friend or Foe of HER2-Positive Cancers? Cancers (Basel) 2019; 11:cancers11070902. [PMID: 31261614 PMCID: PMC6678616 DOI: 10.3390/cancers11070902] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 06/24/2019] [Accepted: 06/25/2019] [Indexed: 12/18/2022] Open
Abstract
Human epidermal growth factor receptor 2 (ERBB2 or HER2) amplification/overexpression is associated with a particularly aggressive molecular subtype of breast cancer (BC), characterized by a poor prognosis, increased metastatic potential, and disease recurrence. As only approximately 50% of HER2-positive patients respond to HER2-targeted therapies, greater knowledge of the biology of HER2 and the mechanisms that underlie drug susceptibility is needed to improve cure rates. Evidence suggests that the coexistence of full-length, wild-type HER2 (wtHER2) and altered forms of HER2—such as carboxy-terminus-truncated fragments, activating mutations, and splice variants—significantly increases the heterogeneity of HER2-positive disease, affecting its biology, clinical course, and treatment response. In particular, expression of the d16HER2 splice variant in human HER2-positive BC has a crucial pathobiological function, wherein the absence of sixteen amino acids from the extracellular domain induces the formation of stable and constitutively active HER2 homodimers on the tumor cell surface. Notably, the d16HER2 variant significantly influences the initiation and aggressiveness of tumors, cancer stem cell properties, epithelial–mesenchymal transition (EMT), and the susceptibility of HER2-positive BC cells to trastuzumab compared with its wtHER2 counterpart, thus constituting a novel and potentially clinically useful biomarker. The aims of this review are to summarize the existing evidence regarding the pathobiological functions of the d16HER2 variant and discuss its current and future value with regard to risk assessment and treatment choices in HER2-positive disease.
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153
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Liu Y, Li Z, Xu Z, Jin X, Gong Y, Xia X, Yao Y, Xu Z, Zhou Y, Xu H, Li S, Peng Y, Wu X, Dai L. Proteomic Maps of Human Gastrointestinal Stromal Tumor Subgroups. Mol Cell Proteomics 2019; 18:923-935. [PMID: 30804049 PMCID: PMC6495251 DOI: 10.1074/mcp.ra119.001361] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 02/18/2019] [Indexed: 02/05/2023] Open
Abstract
Gastrointestinal stromal tumor (GIST) is a common sarcoma of gastrointestinal tract (GIT) with high metastatic and recurrence rates, but the proteomic features are still less understood. Here we performed systematic quantitative proteome profiling of GIST from 13 patients classified into very low/low, intermediate and high risk subgroups. An extended cohort of GIST (n = 131) was used for immunohistochemical validation of proteins of interest. In total, 9177 proteins were quantified, covering 55.9% of the GIT transcriptome from The Human Protein Altas. Out of the 9177 quantified proteins, 4930 proteins were observed in all 13 cases with 517 upregulated and 187 downregulated proteins in tumorous tissues independent of risk stage. Pathway analysis showed that the downregulated proteins were mostly enriched in metabolic pathway, whereas the upregulated proteins mainly belonged to spliceosome pathway. In addition, 131 proteins showed differentially expressed patterns among GIST subgroups with statistical significance. The 13 GIST cases were classified into 3 subgroups perfectly based on the expression of these proteins. The intensive comparison of molecular phenotypes and possible functions of quantified oncoproteins, tumor suppressors, phosphatases and kinases between GIST subgroups was carried out. Immunohistochemical analysis of the phosphatase PTPN1 (n = 117) revealed that the GIST patients with high PTPN1 expression had low chances of developing metastasis. Collectively, this work provides valuable information for understanding the inherent biology and evolution of GIST.
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Affiliation(s)
- Yu Liu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhigui Li
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhiqiang Xu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiuxiu Jin
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yanqiu Gong
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xuyang Xia
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yuqin Yao
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Zhaofen Xu
- §Department of Pathology, The Second People's Hospital of Neijiang City, Sichuan province, Neijiang 641000, China
| | - Yong Zhou
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Heng Xu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Shuangqing Li
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Yong Peng
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China
| | - Xiaoting Wu
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China;.
| | - Lunzhi Dai
- From the ‡Department of General Practice and Department of Gastrointestinal Surgery, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, Chengdu 610041, China;.
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154
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Iwai K, Yaguchi M, Nishimura K, Yamamoto Y, Tamura T, Nakata D, Dairiki R, Kawakita Y, Mizojiri R, Ito Y, Asano M, Maezaki H, Nakayama Y, Kaishima M, Hayashi K, Teratani M, Miyakawa S, Iwatani M, Miyamoto M, Klein MG, Lane W, Snell G, Tjhen R, He X, Pulukuri S, Nomura T. Anti-tumor efficacy of a novel CLK inhibitor via targeting RNA splicing and MYC-dependent vulnerability. EMBO Mol Med 2019; 10:emmm.201708289. [PMID: 29769258 PMCID: PMC5991599 DOI: 10.15252/emmm.201708289] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The modulation of pre-mRNA splicing is proposed as an attractive anti-neoplastic strategy, especially for the cancers that exhibit aberrant pre-mRNA splicing. Here, we discovered that T-025 functions as an orally available and potent inhibitor of Cdc2-like kinases (CLKs), evolutionally conserved kinases that facilitate exon recognition in the splicing machinery. Treatment with T-025 reduced CLK-dependent phosphorylation, resulting in the induction of skipped exons, cell death, and growth suppression in vitro and in vivo Further, through growth inhibitory characterization, we identified high CLK2 expression or MYC amplification as a sensitive-associated biomarker of T-025. Mechanistically, the level of CLK2 expression correlated with the magnitude of global skipped exons in response to T-025 treatment. MYC activation, which altered pre-mRNA splicing without the transcriptional regulation of CLKs, rendered cancer cells vulnerable to CLK inhibitors with synergistic cell death. Finally, we demonstrated in vivo anti-tumor efficacy of T-025 in an allograft model of spontaneous, MYC-driven breast cancer, at well-tolerated dosage. Collectively, our results suggest that the novel CLK inhibitor could have therapeutic benefits, especially for MYC-driven cancer patients.
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Affiliation(s)
- Kenichi Iwai
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Masahiro Yaguchi
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Kazuho Nishimura
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yukiko Yamamoto
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Toshiya Tamura
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Daisuke Nakata
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Ryo Dairiki
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yoichi Kawakita
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Ryo Mizojiri
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yoshiteru Ito
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Moriteru Asano
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Hironobu Maezaki
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Yusuke Nakayama
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Misato Kaishima
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Kozo Hayashi
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Mika Teratani
- Integrated Technology Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Shuichi Miyakawa
- Biomolecular Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Misa Iwatani
- Biomolecular Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Maki Miyamoto
- Drug Metabolism & Pharmacokinetics Research Laboratories, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
| | - Michael G Klein
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Wes Lane
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Gyorgy Snell
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Richard Tjhen
- Department of Structural Biology, Takeda California Inc., San Diego, CA, USA
| | - Xingyue He
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Sai Pulukuri
- Oncology Drug Discovery Unit, Takeda Pharmaceuticals International Co., Cambridge, MA, USA
| | - Toshiyuki Nomura
- Oncology Drug Discovery Unit, Takeda Pharmaceutical Company, Limited, Fujisawa, Japan
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155
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Pacini C, Koziol MJ. Bioinformatics challenges and perspectives when studying the effect of epigenetic modifications on alternative splicing. Philos Trans R Soc Lond B Biol Sci 2019; 373:rstb.2017.0073. [PMID: 29685977 PMCID: PMC5915717 DOI: 10.1098/rstb.2017.0073] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2017] [Indexed: 02/07/2023] Open
Abstract
It is widely known that epigenetic modifications are important in regulating transcription, but several have also been reported in alternative splicing. The regulation of pre-mRNA splicing is important to explain proteomic diversity and the misregulation of splicing has been implicated in many diseases. Here, we give a brief overview of the role of epigenetics in alternative splicing and disease. We then discuss the bioinformatics methods that can be used to model interactions between epigenetic marks and regulators of splicing. These models can be used to identify alternative splicing and epigenetic changes across different phenotypes. This article is part of a discussion meeting issue ‘Frontiers in epigenetic chemical biology’.
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Affiliation(s)
- Clare Pacini
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK.,Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
| | - Magdalena J Koziol
- Wellcome Trust Cancer Research UK Gurdon Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QN, UK .,Department of Zoology, University of Cambridge, Downing Street, Cambridge, CB2 3EJ, UK
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156
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Denichenko P, Mogilevsky M, Cléry A, Welte T, Biran J, Shimshon O, Barnabas GD, Danan-Gotthold M, Kumar S, Yavin E, Levanon EY, Allain FH, Geiger T, Levkowitz G, Karni R. Specific inhibition of splicing factor activity by decoy RNA oligonucleotides. Nat Commun 2019; 10:1590. [PMID: 30962446 PMCID: PMC6453957 DOI: 10.1038/s41467-019-09523-0] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/12/2019] [Indexed: 12/31/2022] Open
Abstract
Alternative splicing, a fundamental step in gene expression, is deregulated in many diseases. Splicing factors (SFs), which regulate this process, are up- or down regulated or mutated in several diseases including cancer. To date, there are no inhibitors that directly inhibit the activity of SFs. We designed decoy oligonucleotides, composed of several repeats of a RNA motif, which is recognized by a single SF. Here we show that decoy oligonucleotides targeting splicing factors RBFOX1/2, SRSF1 and PTBP1, can specifically bind to their respective SFs and inhibit their splicing and biological activities both in vitro and in vivo. These decoy oligonucleotides present an approach to specifically downregulate SF activity in conditions where SFs are either up-regulated or hyperactive. Alternative splicing, critical for gene expression, is deregulated in many diseases. Here the authors develop decoy oligonucleotides to specifically downregulate splicing factors activity.
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Affiliation(s)
- Polina Denichenko
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Maxim Mogilevsky
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Antoine Cléry
- Institute of Molecular Biology and Biophysics, ETH Zurich, Hönggerbergring 64, 8093, Zurich, Switzerland
| | - Thomas Welte
- Dynamic Biosensors, GmbH, Lochhamer Strasse 15, 82152, Martinsried/Planegg, Germany
| | - Jakob Biran
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Odelia Shimshon
- Department of Medicinal Chemistry, Institute for Drug Research, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Georgina D Barnabas
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Miri Danan-Gotthold
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Saran Kumar
- Department of Developmental Biology and Cancer Research, Institute for Medical Research Israel-Canada, Faculty of Medicine, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Eylon Yavin
- Department of Medicinal Chemistry, Institute for Drug Research, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel
| | - Erez Y Levanon
- Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat Gan, 52900, Israel
| | - Frédéric H Allain
- Institute of Molecular Biology and Biophysics, ETH Zurich, Hönggerbergring 64, 8093, Zurich, Switzerland
| | - Tamar Geiger
- Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Gil Levkowitz
- Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, 9112001, Israel.
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157
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Wang E, Lu SX, Pastore A, Chen X, Imig J, Chun-Wei Lee S, Hockemeyer K, Ghebrechristos YE, Yoshimi A, Inoue D, Ki M, Cho H, Bitner L, Kloetgen A, Lin KT, Uehara T, Owa T, Tibes R, Krainer AR, Abdel-Wahab O, Aifantis I. Targeting an RNA-Binding Protein Network in Acute Myeloid Leukemia. Cancer Cell 2019; 35:369-384.e7. [PMID: 30799057 PMCID: PMC6424627 DOI: 10.1016/j.ccell.2019.01.010] [Citation(s) in RCA: 197] [Impact Index Per Article: 39.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 11/26/2018] [Accepted: 01/18/2019] [Indexed: 02/07/2023]
Abstract
RNA-binding proteins (RBPs) are essential modulators of transcription and translation frequently dysregulated in cancer. We systematically interrogated RBP dependencies in human cancers using a comprehensive CRISPR/Cas9 domain-focused screen targeting RNA-binding domains of 490 classical RBPs. This uncovered a network of physically interacting RBPs upregulated in acute myeloid leukemia (AML) and crucial for maintaining RNA splicing and AML survival. Genetic or pharmacologic targeting of one key member of this network, RBM39, repressed cassette exon inclusion and promoted intron retention within mRNAs encoding HOXA9 targets as well as in other RBPs preferentially required in AML. The effects of RBM39 loss on splicing further resulted in preferential lethality of spliceosomal mutant AML, providing a strategy for treatment of AML bearing RBP splicing mutations.
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Affiliation(s)
- Eric Wang
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Sydney X Lu
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Alessandro Pastore
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Xufeng Chen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Jochen Imig
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Stanley Chun-Wei Lee
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Kathryn Hockemeyer
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Yohana E Ghebrechristos
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Akihide Yoshimi
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Daichi Inoue
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Michelle Ki
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Hana Cho
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Lillian Bitner
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Andreas Kloetgen
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Taisuke Uehara
- Tsukuba Research Laboratories, Eisai Company, Ltd, Tsukuba, Ibaraki 300-4352, Japan
| | - Takashi Owa
- Tsukuba Research Laboratories, Eisai Company, Ltd, Tsukuba, Ibaraki 300-4352, Japan
| | - Raoul Tibes
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program and Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
| | - Iannis Aifantis
- Department of Pathology and Laura & Isaac Perlmutter Cancer Center, NYU School of Medicine, New York, NY 10016, USA.
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158
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Coltri PP, Dos Santos MGP, da Silva GHG. Splicing and cancer: Challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-RNA 2019; 10:e1527. [PMID: 30773852 DOI: 10.1002/wrna.1527] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/14/2018] [Accepted: 01/17/2019] [Indexed: 12/11/2022]
Abstract
Cancer arises from alterations in several metabolic processes affecting proliferation, growth, replication and death of cells. A fundamental challenge in the study of cancer biology is to uncover molecular mechanisms that lead to malignant cellular transformation. Recent genomic analyses revealed that many molecular alterations observed in cancers come from modifications in the splicing process, including mutations in pre-mRNA regulatory sequences, mutations in spliceosome components, and altered ratio of specific splicing regulators. While alterations in splice site preferences might generate alternative isoforms enabling different biological functions, these might also be responsible for nonfunctional isoforms that can eventually cause dysregulation in cellular processes. Molecular characteristics of regulatory sequences and proteins might also be important prognostic tools revealing a cancer-specific splicing pattern and linking splicing control to cancer development. The connection between cancer biology and splicing regulation is of primary importance to understand the mechanisms leading to disease and also to improve development of therapeutic approaches. Splicing modulation is being explored in new anti-cancer therapies and further investigation of targeted splicing factors is critical for the success of these strategies. This article is categorized under: RNA Processing > Splicing Mechanisms RNA-Based Catalysis > RNA Catalysis in Splicing and Translation RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Patricia P Coltri
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Maria G P Dos Santos
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Guilherme H G da Silva
- Department of Cell and Developmental Biology, Institute for Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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159
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Lee KH, Ku JH. Targeting splicing factors as molecular non-muscle invasive bladder cancer predictors. Transl Androl Urol 2019; 7:S715-S717. [PMID: 30687604 PMCID: PMC6323290 DOI: 10.21037/tau.2018.10.09] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Affiliation(s)
- Kyoung-Hwa Lee
- Department of Urology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Ja Hyeon Ku
- Department of Urology, Seoul National University Hospital, Seoul, Republic of Korea
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160
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Li Y, Yu S, Wang X, Ye X, He B, Quan M, Gao Y. SRPK1 facilitates tumor cell growth via modulating the small nucleolar RNA expression in gastric cancer. J Cell Physiol 2019; 234:13582-13591. [PMID: 30633341 DOI: 10.1002/jcp.28036] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Accepted: 11/30/2018] [Indexed: 01/11/2023]
Abstract
Serine-arginine protein kinase 1 (SRPK1) is the main regulator in alternative splicing by phosphorylating splicing factors rich in serine/arginine repeats. Its overexpression has been found in multiple cancer types and contributes to cancer development. Here we report the role of SRPK1 and underlying mechanism in gastric cancer (GC) cell growth. We found that SRPK1 was frequently upregulated in GC samples compared with their adjacent corresponding normal tissues by immunohistochemistry and western blot analysis. Knockdown of SRPK1 in GC cells suppressed cell growth in cell viability assays, colony formation assays and nude mice xenograft model, whereas overexpression of SRPK1 promotes opposite phenotypes in these assays. By a complementary DNA microarray analysis, we found that SRPK1 knockdown had significant inhibitory effects on a majority of small nucleolar RNAs expression. Among them, snoRA42, snoRA74A, and snoRD10 were selected for further functional experiments. Cell growth curves on a plate and in soft agar indicated that the three snoRNAs play potential oncogenic function in GC. In addition, SRPK1 could co-immunoprecipitated with NCL, a nucleolar phosphoprotein involved in the synthesis and maturation of ribosomes. These results suggested that SRPK1 contributes to GC development by a new possible mechanism involving snoRNAs mediated signaling.
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Affiliation(s)
- Yandong Li
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Shijun Yu
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiao Wang
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xiaojuan Ye
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China.,Department of Hematology & Oncology, the People's Hospital of Beilun District, Beilun Branch Hospital of the First Affiliated Hospital of Medical School of Zhejiang University, Ningbo, China
| | - Bin He
- Research Center for Translational Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ming Quan
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Yong Gao
- Department of Oncology, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, China
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161
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Latorre E, Ostler EL, Faragher RGA, Harries LW. FOXO1 and ETV6 genes may represent novel regulators of splicing factor expression in cellular senescence. FASEB J 2019; 33:1086-1097. [PMID: 30088951 DOI: 10.1096/fj.201801154r] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
Cellular plasticity is a key facet of cellular homeostasis requiring correct temporal and spatial patterns of alternative splicing. Splicing factors, which orchestrate this process, demonstrate age-related dysregulation of expression; they are emerging as potential influences on aging and longevity. The upstream drivers of these alterations are still unclear but may involve aberrant cellular signaling. We compared the phosphorylation status of proteins in multiple signaling pathways in early and late passage human primary fibroblasts. We then assessed the impact of chemical inhibition or targeted knockdown of direct downstream targets of the ERK and AKT pathways on splicing factor expression, cellular senescence, and proliferation kinetics in senescent primary human fibroblasts. Components of the ERK and AKT signaling pathways demonstrated altered activation during cellular aging. Inhibition of AKT and ERK pathways led to up-regulation of splicing factor expression, reduction in senescent cell load, and partial reversal of multiple cellular senescence phenotypes in a dose-dependent manner. Furthermore, targeted knockdown of the genes encoding the downstream targets FOXO1 or ETV6 was sufficient to mimic these observations. Our results suggest that age-associated dysregulation of splicing factor expression and cellular senescence may derive in part from altered activity of ERK and AKT signaling and may act in part through the ETV6 and FOXO1 transcription factors. Targeting the activity of downstream effectors of ERK and AKT may therefore represent promising targets for future therapeutic intervention.-Latorre, E., Ostler, E. L., Faragher, R. G. A., Harries, L. W. FOXO1 and ETV6 genes may represent novel regulators of splicing factor expression in cellular senescence.
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Affiliation(s)
- Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon, United Kingdom; and
| | - Elizabeth L Ostler
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Richard G A Faragher
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Brighton, United Kingdom
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Devon, United Kingdom; and
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162
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Asadzadeh-Aghdaei H, Zadeh-Esmaeel MM, Esmaeili S, Rezaei Tavirani M, Rezaei Tavirani S, Mansouri V, Montazer F. Effects of high fat medium conditions on cellular gene expression profile: a network analysis approach. GASTROENTEROLOGY AND HEPATOLOGY FROM BED TO BENCH 2019; 12:S130-S135. [PMID: 32099613 PMCID: PMC7011064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
AIM This study aimed to evaluate high fat medium (HFM) effect on the gene expression profile of human Sk-hep1 cells and to determine critical differential proteins. BACKGROUND There is a correlation between high fat diet (HFD), obesity, and non-alcoholic fatty liver disease. Despite wide range of investigations, understanding molecular mechanism of HFD effect on onset and progression of NAFLD warrants further examination. In this study, network analysis is applied to obtain a clear perspective about HFD effects and NAFLD. METHODS Gene expression profiles of human Sk-hep1 cells treated with HFM versus controls were extracted from GEO. Data were analyzed by GEO2R where the significant and characterized DEGs were included in the PPI network. The top 10 nodes of query DEGs based on four centrality parameters were selected to determine central nodes. The common hub nodes with at least other one central group were identified as central nodes. Action map was provided for the introduced central nodes. RESULTS Heterogeneous nuclear ribonucleoprotein family including A1, A2/B1, D, R, and D-like, and five proteins (PRPF40A, SRSF1, PCF11, LSM8, and HSP90AA1) were introduced as differential proteins. CONCLUSION mRNA processing and several biological terms including hypoxia and oxidative stress, apoptosis, regulation of cell morphology and cytoskeletal organization, and differentiation of micro tubes were introduced as dysregulated terms under HFM condition.
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Affiliation(s)
- Hamid Asadzadeh-Aghdaei
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad-Mehdi Zadeh-Esmaeel
- Laser Application in Medical Sciences Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Somayeh Esmaeili
- Traditional Medicine and Materia Medica Research Center, Department of Traditional Pharmacy, School of Traditional Medicine,, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mostafa Rezaei Tavirani
- Proteomics Research Center, Faculty of Paramedical Sciences, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Sina Rezaei Tavirani
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Vahid Mansouri
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Fatemeh Montazer
- Firoozabadi Clinical Research Development Unit, Iran University of Medical Sciences, Tehran, Iran
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163
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Tyson-Capper A, Gautrey H. Regulation of Mcl-1 alternative splicing by hnRNP F, H1 and K in breast cancer cells. RNA Biol 2018; 15:1448-1457. [PMID: 30468106 PMCID: PMC6333436 DOI: 10.1080/15476286.2018.1551692] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 10/10/2018] [Accepted: 11/02/2018] [Indexed: 01/27/2023] Open
Abstract
Myeloid cell leukemia-1 (Mcl -1) is one of the most frequently amplified genes in cancer, and its overexpression is associated with poor prognosis and drug resistance. As a member of the Bcl-2 family it is involved in the control of the mitochondrial (intrinsic) cell death pathway. Alternative splicing of the (Mcl-1) gene results in the expression of two functionally distinct proteins, the anti-apoptotic Mcl-1L (exon 2 included) and the pro-apoptotic Mcl-1S (exon 2 skipped). Our data shows that transfecting siRNAs that target hnRNP K and the hnRNP F/H family result in a switch in splicing towards the pro-apoptotic Mcl-1S. Specific binding sites for these and other Mcl-1 splicing factors were investigated and identified by RNA immunoprecipitation and through construction of a Mcl-1 minigene construct. Moreover, this study shows up to a 30 fold change in the levels of Mcl-1S can be achieved through double and triple knockdowns of the most significant RNA binding proteins involved in Mcl-1 splicing, as well as activation of the mitochondrial cell death pathway. Targeting the splicing process of Mcl-1 along with other apoptotic regulators provides an exciting new therapeutic target in cancer cells, and may provide a way to overcome therapy resistance.
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Affiliation(s)
- Alison Tyson-Capper
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Hannah Gautrey
- Institute of Cellular Medicine, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
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164
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Sheng J, Zhao Q, Zhao J, Zhang W, Sun Y, Qin P, Lv Y, Bai L, Yang Q, Chen L, Qi Y, Zhang G, Zhang L, Gu C, Deng X, Liu H, Meng S, Gu H, Liu Q, Coulson JM, Li X, Sun B, Wang Y. SRSF1 modulates PTPMT1 alternative splicing to regulate lung cancer cell radioresistance. EBioMedicine 2018; 38:113-126. [PMID: 30429088 PMCID: PMC6306353 DOI: 10.1016/j.ebiom.2018.11.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 10/31/2018] [Accepted: 11/02/2018] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Radioresistance is the major cause of cancer treatment failure. Additionally, splicing dysregulation plays critical roles in tumorigenesis. However, the involvement of alternative splicing in resistance of cancer cells to radiotherapy remains elusive. We sought to investigate the key role of the splicing factor SRSF1 in the radioresistance in lung cancer. METHODS Lung cancer cell lines, xenograft mice models, and RNA-seq were employed to study the detailed mechanisms of SRSF1 in lung cancer radioresistance. Clinical tumor tissues and TCGA dataset were utilized to determine the expression levels of distinct SRSF1-regulated splicing isoforms. KM-plotter was applied to analyze the survival of cancer patients with various levels of SRSF1-regulated splicing isoforms. FINDINGS Splicing factors were screened to identify their roles in radioresistance, and SRSF1 was found to be involved in radioresistance in cancer cells. The level of SRSF1 is elevated in irradiation treated lung cancer cells, whereas knockdown of SRSF1 sensitizes cancer cells to irradiation. Mechanistically, SRSF1 modulates various cancer-related splicing events, particularly the splicing of PTPMT1, a PTEN-like mitochondrial phosphatase. Reduced SRSF1 favors the production of short isoforms of PTPMT1 upon irradiation, which in turn promotes phosphorylation of AMPK, thereby inducing DNA double-strand break to sensitize cancer cells to irradiation. Additionally, the level of the short isoform of PTPMT1 is decreased in cancer samples, which is correlated to cancer patients' survival. CONCLUSIONS Our study provides mechanistic analyses of aberrant splicing in radioresistance in lung cancer cells, and establishes SRSF1 as a potential therapeutic target for sensitization of patients to radiotherapy.
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Affiliation(s)
- Junxiu Sheng
- Department of Radiation Oncology, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Qingzhi Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China.
| | - Yu Sun
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Pan Qin
- Faculty of electronic information and electrical engineering, Dalian university of Technology, Dalian 116001, China
| | - Yuesheng Lv
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Lu Bai
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Quan Yang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Lei Chen
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Yangfan Qi
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Ge Zhang
- Department of Immunology, Dalian Medical University, Dalian 116044, China
| | - Lin Zhang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Chundong Gu
- Department of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Xiaoqin Deng
- Department of Radiation Oncology, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China
| | - Han Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Songshu Meng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Hong Gu
- Faculty of electronic information and electrical engineering, Dalian university of Technology, Dalian 116001, China
| | - Quentin Liu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Judy M Coulson
- Cellular & Molecular Physiology Department, University of Liverpool, UKL69 3BX, UK
| | - Xiaoling Li
- Signal Transduction Laboratory, NIEHS, RTP, NC 27709, USA
| | - Bing Sun
- Department of Thoracic Surgery, First Affiliated Hospital, Dalian Medical University, Dalian 116044, China.
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China.
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165
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Martínez-Terroba E, Ezponda T, Bértolo C, Sainz C, Remírez A, Agorreta J, Garmendia I, Behrens C, Pio R, Wistuba II, Montuenga LM, Pajares MJ. The oncogenic RNA-binding protein SRSF1 regulates LIG1 in non-small cell lung cancer. J Transl Med 2018; 98:1562-1574. [PMID: 30181552 DOI: 10.1038/s41374-018-0128-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/16/2018] [Accepted: 08/03/2018] [Indexed: 01/22/2023] Open
Abstract
In recent years, the relevance of RNA metabolism has been increasingly recognized in a variety of diseases. Modifications in the levels of RNA-binding proteins elicit changes in the expression of cancer-related genes. Here we evaluate whether SRSF1 regulates the expression of DNA repair genes, and whether this regulation has a relevant role in lung carcinogenesis. An in silico analysis was performed to evaluate the association between the expression of SRSF1 and DNA repair genes. In vitro functional analyses were conducted in SRSF1 or DNA ligase 1 (LIG1)-downregulated non-small cell lung cancer (NSCLC) cell lines. In addition, the prognostic value of LIG1 was evaluated in NSCLC patients by immunohistochemistry. We found a significant correlation between the DNA repair gene LIG1 and SRSF1 in NSCLC cell lines. Moreover, SRSF1 binds to LIG1 mRNA and regulates its expression by increasing its mRNA stability and enhancing its translation in an mTOR-dependent manner. Furthermore, siRNA-mediated LIG1 inhibition reduced proliferation and increased apoptosis of NSCLC cells. Finally, the expression of LIG1 was an independent prognostic factor for NSCLC, as confirmed in a series of 210 patients. These results show that LIG1 is regulated by the oncoprotein SRSF1 and plays a relevant role in lung cancer cell proliferation and progression. LIG1 is associated with poor prognosis in non-small lung cancer patients.
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Affiliation(s)
- Elena Martínez-Terroba
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Teresa Ezponda
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Cristina Bértolo
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Cristina Sainz
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Ana Remírez
- Program in Solid Tumors, CIMA, Pamplona, Spain
| | - Jackeline Agorreta
- Program in Solid Tumors, CIMA, Pamplona, Spain. .,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Navarra's Health Research Institute (IDISNA), Pamplona, Spain.
| | - Irati Garmendia
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain
| | - Carmen Behrens
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Ruben Pio
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra's Health Research Institute (IDISNA), Pamplona, Spain.,Department of Biochemistry and Genetics, School of Science, University of Navarra, Pamplona, Spain
| | - Ignacio I Wistuba
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.,Department of Translational Molecular Pathology, The University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Luis M Montuenga
- Program in Solid Tumors, CIMA, Pamplona, Spain. .,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain. .,Navarra's Health Research Institute (IDISNA), Pamplona, Spain.
| | - María J Pajares
- Program in Solid Tumors, CIMA, Pamplona, Spain.,Department of Pathology, Anatomy and Physiology, School of Medicine, University of Navarra, Pamplona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Navarra's Health Research Institute (IDISNA), Pamplona, Spain
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166
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Escobar-Hoyos L, Knorr K, Abdel-Wahab O. Aberrant RNA Splicing in Cancer. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2018; 3:167-185. [PMID: 32864546 DOI: 10.1146/annurev-cancerbio-030617-050407] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
RNA splicing, the enzymatic process of removing segments of premature RNA to produce mature RNA, is a key mediator of proteome diversity and regulator of gene expression. Increased systematic sequencing of the genome and transcriptome of cancers has identified a variety of means by which RNA splicing is altered in cancer relative to normal cells. These findings, in combination with the discovery of recurrent change-of-function mutations in splicing factors in a variety of cancers, suggest that alterations in splicing are drivers of tumorigenesis. Greater characterization of altered splicing in cancer parallels increasing efforts to pharmacologically perturb splicing and early-phase clinical development of small molecules that disrupt splicing in patients with cancer. Here we review recent studies of global changes in splicing in cancer, splicing regulation of mitogenic pathways critical in cancer transformation, and efforts to therapeutically target splicing in cancer.
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Affiliation(s)
- Luisa Escobar-Hoyos
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,David M. Rubenstein Center for Pancreatic Cancer Research, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Department of Pathology, Stony Brook University, Stony Brook, NY 11794, USA
| | | | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.,Weill Cornell Medical College, New York, NY 10065, USA.,Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
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167
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Xu L, Zhang H, Mei M, Du C, Huang X, Li J, Wang Y, Bao S, Zheng H. Phosphorylation of serine/arginine-rich splicing factor 1 at tyrosine 19 promotes cell proliferation in pediatric acute lymphoblastic leukemia. Cancer Sci 2018; 109:3805-3815. [PMID: 30320932 PMCID: PMC6272096 DOI: 10.1111/cas.13834] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 09/21/2018] [Accepted: 10/04/2018] [Indexed: 12/21/2022] Open
Abstract
Serine/arginine‐rich splicing factor 1 (SRSF1) has been linked to various human cancers including pediatric acute lymphoblastic leukemia (ALL). Our previous study has shown that SRSF1 potentially contributes to leukemogenesis; however, its underlying mechanism remains unclear. In this study, leukemic cells were isolated from pediatric ALL bone marrow samples, followed by immunoprecipitation assays and mass spectrometry analysis specific to SRSF1. Subcellular localization of the SRSF1 protein and its mutants were analyzed by immunofluorescence staining. Cell growth, colony formation, cell apoptosis, and the cell cycle were investigated using stable leukemic cell lines generated with lentivirus‐mediated overexpressed WT or mutant plasmids. Cytotoxicity of the Tie2 kinase inhibitor was also evaluated. Our results showed the phosphorylation of SRSF1 at tyrosine 19 (Tyr‐19) was identified in newly diagnosed ALL samples, but not in complete remission or normal control samples. Compared to the SRSF1 WT cells, the missense mutants of the Tyr‐19 phosphorylation affected the subcellular localization of SRSF1. In addition, the Tyr‐19 phosphorylation of SRSF1 also led to increased cell proliferation and enhanced colony‐forming properties by promoting the cell cycle. Remarkably, we further identified the kinase Tie2 as a potential therapeutic target in leukemia cells. In conclusion, we identify for the first time that the phosphorylation state of SRSF1 is linked to different phases in pediatric ALL. The Tyr‐19 phosphorylation of SRSF1 disrupts its subcellular localization and promotes proliferation in leukemia cells by driving cell‐cycle progression. Inhibitors targeting Tie2 kinase that could catalyze Tyr‐19 phosphorylation of SRSF1 offer a promising therapeutic target for treatment of pediatric ALL.
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Affiliation(s)
- Liting Xu
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Han Zhang
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Mei Mei
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Chaohao Du
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Xiahe Huang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Jing Li
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yingchun Wang
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Shilai Bao
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
| | - Huyong Zheng
- Beijing Key Laboratory of Pediatric Hematology Oncology, National Key Discipline of Pediatrics, Ministry of Education, Key Laboratory of Major Diseases in Children, Ministry of Education, Hematology Oncology Center, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
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168
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Molavi G, Samadi N, Hosseingholi EZ. The roles of moonlight ribosomal proteins in the development of human cancers. J Cell Physiol 2018; 234:8327-8341. [PMID: 30417503 DOI: 10.1002/jcp.27722] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Accepted: 09/23/2018] [Indexed: 12/13/2022]
Abstract
"Moonlighting protein" is a term used to define a single protein with multiple functions and different activities that are not derived from gene fusions, multiple RNA splicing, or the proteolytic activity of promiscuous enzymes. Different proteinous constituents of ribosomes have been shown to have important moonlighting extra-ribosomal functions. In this review, we introduce the impact of key moonlight ribosomal proteins and dependent signal transduction in the initiation and progression of various cancers. As a future perspective, the potential role of these moonlight ribosomal proteins in the diagnosis, prognosis, and development of novel strategies to improve the efficacy of therapies for human cancers has been suggested.
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Affiliation(s)
- Ghader Molavi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
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169
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El Marabti E, Younis I. The Cancer Spliceome: Reprograming of Alternative Splicing in Cancer. Front Mol Biosci 2018; 5:80. [PMID: 30246013 PMCID: PMC6137424 DOI: 10.3389/fmolb.2018.00080] [Citation(s) in RCA: 152] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Accepted: 08/09/2018] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing allows for the expression of multiple RNA and protein isoforms from one gene, making it a major contributor to transcriptome and proteome diversification in eukaryotes. Advances in next generation sequencing technologies and genome-wide analyses have recently underscored the fact that the vast majority of multi-exon genes under normal physiology engage in alternative splicing in tissue-specific and developmental-specific manner. On the other hand, cancer cells exhibit remarkable transcriptome alterations partly by adopting cancer-specific splicing isoforms. These isoforms and their encoded proteins are not insignificant byproducts of the abnormal physiology of cancer cells, but either drivers of cancer progression or small but significant contributors to specific cancer hallmarks. Thus, it is paramount that the pathways that regulate alternative splicing in cancer, including the splicing factors that bind to pre-mRNAs and modulate spliceosome recruitment. In this review, we present a few distinct cases of alternative splicing in cancer, with an emphasis on their regulation as well as their contribution to cancer cell phenotype. Several categories of splicing aberrations are highlighted, including alterations in cancer-related genes that directly affect their pre-mRNA splicing, mutations in genes encoding splicing factors or core spliceosomal subunits, and the seemingly mutation-free disruptions in the balance of the expression of RNA-binding proteins, including components of both the major (U2-dependent) and minor (U12-dependent) spliceosomes. Given that the latter two classes cause global alterations in splicing that affect a wide range of genes, it remains a challenge to identify the ones that contribute to cancer progression. These challenges necessitate a systematic approach to decipher these aberrations and their impact on cancer. Ultimately, a sufficient understanding of splicing deregulation in cancer is predicted to pave the way for novel and innovative RNA-based therapies.
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Affiliation(s)
- Ettaib El Marabti
- Biological Sciences Program, Carnegie Mellon University in Qatar, Doha, Qatar
| | - Ihab Younis
- Biological Sciences Program, Carnegie Mellon University in Qatar, Doha, Qatar
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170
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Abstract
Breast cancer is known to be a heterogeneous disease driven by a large repertoire of molecular abnormalities, which contribute to its diverse clinical behaviour. Despite the success of targeted therapy approaches for breast cancer patient management, there is still a lack of the molecular understanding of aggressive forms of the disease and clinical management of these patients remains difficult. The advent of high-throughput sequencing technologies has paved the way for a more complete understanding of the molecular make-up of the breast cancer genome. As such, it is becoming apparent that disruption of canonical splicing within breast cancer governs its clinical progression. In this review, we discuss the role of dysregulation of spliceosomal component genes and associated factors in the progression of breast cancer, their role in therapy resistance and the use of quantitative isoform expression as potential prognostic and predictive biomarkers with a particular focus on oestrogen receptor-positive breast cancer.
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Affiliation(s)
- Abigail Read
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research CentreThe Institute of Cancer Research, London, UK
- Division of Molecular PathologyThe Institute of Cancer Research, London, UK
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171
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Yang S, Jia R, Bian Z. SRSF5 functions as a novel oncogenic splicing factor and is upregulated by oncogene SRSF3 in oral squamous cell carcinoma. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2018; 1865:1161-1172. [DOI: 10.1016/j.bbamcr.2018.05.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 05/25/2018] [Accepted: 05/26/2018] [Indexed: 10/25/2022]
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172
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Gao Y, Vasic R, Halene S. Role of alternative splicing in hematopoietic stem cells during development. Stem Cell Investig 2018; 5:26. [PMID: 30221171 DOI: 10.21037/sci.2018.08.02] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 08/13/2018] [Indexed: 12/20/2022]
Affiliation(s)
- Yimeng Gao
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Radovan Vasic
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06511, USA
| | - Stephanie Halene
- Section of Hematology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06511, USA
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173
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Disruption by SaCas9 Endonuclease of HERV-K env, a Retroviral Gene with Oncogenic and Neuropathogenic Potential, Inhibits Molecules Involved in Cancer and Amyotrophic Lateral Sclerosis. Viruses 2018; 10:v10080412. [PMID: 30087231 PMCID: PMC6115762 DOI: 10.3390/v10080412] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Revised: 08/03/2018] [Accepted: 08/04/2018] [Indexed: 12/14/2022] Open
Abstract
The human endogenous retrovirus (HERV)-K, human mouse mammary tumor virus like-2 (HML-2) subgroup of HERVs is activated in several tumors and has been related to prostate cancer progression and motor neuron diseases. The cellular splicing factor 2/alternative splicing factor (SF2/ASF) is a positive regulator of gene expression, coded by a potent proto-oncogene, amplified, and abnormally expressed in tumors. TAR DNA-binding protein-43 (TDP-43) is a DNA/RNA-binding protein, negative regulator of alternative splicing, known for causing neurodegeneration, and with complex roles in oncogenesis. We used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology, with the Cas9 system from Staphylococcus aureus (SaCas9), to disrupt the HERV-K(HML-2)env gene, and evaluated the effects on cultured cells. The tool was tested on human prostate cancer LNCaP cells, whose HERV-Kenv transcription profile is known. It caused HERV-K(HML-2)env disruption (the first reported of a HERV gene), as evaluated by DNA sequencing, and inhibition of env transcripts and proteins. The HERV-K(HML-2)env disruption was found to interfere with important regulators of cell expression and proliferation, involved in manaling, RNA-binding, and alternative splicing, such as epidermal growth factor receptor (EGF-R), nuclear factor kappa-light-chain-enhancer of activated B cells (NF-κB), SF2/ASF, and TDP-43. These novel findings suggest that HERV-K is not an innocent bystander, they reinforce its links to oncogenesis and motor neuron diseases, and they open potential innovative therapeutic options.
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174
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Bielli P, Panzeri V, Lattanzio R, Mutascio S, Pieraccioli M, Volpe E, Pagliarulo V, Piantelli M, Giannantoni A, Di Stasi SM, Sette C. The Splicing Factor PTBP1 Promotes Expression of Oncogenic Splice Variants and Predicts Poor Prognosis in Patients with Non-muscle-Invasive Bladder Cancer. Clin Cancer Res 2018; 24:5422-5432. [PMID: 30012566 DOI: 10.1158/1078-0432.ccr-17-3850] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Revised: 05/02/2018] [Accepted: 07/10/2018] [Indexed: 11/16/2022]
Abstract
Purpose: Non-muscle-invasive bladder cancer (NMIBC) is a malignant disease characterized by high heterogeneity, which corresponds to dysregulated gene expression and alternative splicing (AS) profiles. Bioinformatics analyses of splicing factors potentially linked to bladder cancer progression identified the heterogeneous nuclear ribonucleoprotein I (i.e., PTBP1) as candidate. This study aimed at investigating whether PTBP1 expression associates with clinical outcome in patients with NMIBC.Experimental Design: A cohort of 152 patients presenting with primary NMIBC (pTa-pT1) was enrolled. Primary NMIBCs were assessed for PTBP1 expression by IHC, and the results were correlated with clinical data using Kaplan-Meier curves and Cox regression analyses. Cell proliferation and survival assays were performed to assess the function of PTBP1. Furthermore, the impact of PTBP1 on the AS pattern of specific bladder cancer-related genes was investigated in cancer cell lines and in patients' specimens.Results: Public datasets querying highlighted a positive correlation between PTBP1 expression and NMIBC progression, which was then confirmed by IHC analysis. High PTBP1 expression was associated with worse clinical outcome in terms of incidence of tumor relapse and survival in patients with NMIBC. Interestingly, downregulation of PTBP1 in bladder cancer cell lines affected prosurvival features. Accordingly, PTBP1 modulated AS of bladder cancer-related genes in cell lines and patient's specimens.Conclusions: PTBP1 expression correlates with disease progression, poor prognosis, and worse survival in patients with NMIBC. Downregulation of PTBP1 expression affects prosurvival features of bladder cancer cells and modulates AS of genes with relevance for bladder cancer, suggesting its role as an outcome-predictor in this disease. Clin Cancer Res; 24(21); 5422-32. ©2018 AACR.
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Affiliation(s)
- Pamela Bielli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Valentina Panzeri
- Fondazione Santa Lucia IRCCS, Rome, Italy.,Department of Science Medical/Chirurgic and Translational Medicine, University of Rome "Sapienza", Rome, Italy.,Institute of Human Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rossano Lattanzio
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy.,Center of Excellence on Aging and Translational Medicine (CeSi-Met), G. d'Annunzio University, Chieti, Italy
| | - Simona Mutascio
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
| | - Marco Pieraccioli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Rome, Italy.,Fondazione Santa Lucia IRCCS, Rome, Italy
| | | | - Vincenzo Pagliarulo
- Department of Emergency and Organ Transplantation, University Aldo Moro, Bari, Italy
| | - Mauro Piantelli
- Department of Medical, Oral & Biotechnological Sciences, G. d'Annunzio University, Chieti, Italy
| | - Antonella Giannantoni
- Department of Surgical and Biomedical Sciences, University of Perugia, Perugia, Italy
| | - Savino M Di Stasi
- Department of Experimental Medicine and Surgery, University of Rome Tor Vergata, Rome, Italy.
| | - Claudio Sette
- Fondazione Santa Lucia IRCCS, Rome, Italy. .,Institute of Human Anatomy and Cell Biology, Università Cattolica del Sacro Cuore, Rome, Italy
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175
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Urbanski L, Leclair N, Anczuków O. Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1476. [PMID: 29693319 PMCID: PMC6002934 DOI: 10.1002/wrna.1476] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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176
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Splicing factors as regulators of miRNA biogenesis – links to human disease. Semin Cell Dev Biol 2018; 79:113-122. [DOI: 10.1016/j.semcdb.2017.10.008] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 10/09/2017] [Accepted: 10/09/2017] [Indexed: 12/16/2022]
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177
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Blue RE, Curry EG, Engels NM, Lee EY, Giudice J. How alternative splicing affects membrane-trafficking dynamics. J Cell Sci 2018; 131:jcs216465. [PMID: 29769303 PMCID: PMC6031328 DOI: 10.1242/jcs.216465] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The cell biology field has outstanding working knowledge of the fundamentals of membrane-trafficking pathways, which are of critical importance in health and disease. Current challenges include understanding how trafficking pathways are fine-tuned for specialized tissue functions in vivo and during development. In parallel, the ENCODE project and numerous genetic studies have revealed that alternative splicing regulates gene expression in tissues and throughout development at a post-transcriptional level. This Review summarizes recent discoveries demonstrating that alternative splicing affects tissue specialization and membrane-trafficking proteins during development, and examines how this regulation is altered in human disease. We first discuss how alternative splicing of clathrin, SNAREs and BAR-domain proteins influences endocytosis, secretion and membrane dynamics, respectively. We then focus on the role of RNA-binding proteins in the regulation of splicing of membrane-trafficking proteins in health and disease. Overall, our aim is to comprehensively summarize how trafficking is molecularly influenced by alternative splicing and identify future directions centered on its physiological relevance.
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Affiliation(s)
- R Eric Blue
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ennessa G Curry
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Nichlas M Engels
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Eunice Y Lee
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jimena Giudice
- Department of Cell Biology & Physiology, School of Medicine, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- McAllister Heart Institute, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Curriculum in Genetics and Molecular Biology (GMB), The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
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178
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Chen YT, Chang IYF, Liu H, Ma CP, Kuo YP, Shih CT, Shih YH, Kang L, Tan BCM. Tumor-associated intronic editing of HNRPLL generates a novel splicing variant linked to cell proliferation. J Biol Chem 2018; 293:10158-10171. [PMID: 29769310 DOI: 10.1074/jbc.ra117.001197] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/29/2018] [Indexed: 01/02/2023] Open
Abstract
Processing of the eukaryotic transcriptome is a dynamic regulatory mechanism that confers genetic diversity, and splicing and adenosine to inosine (A-to-I) RNA editing are well-characterized examples of such processing. Growing evidence reveals the cross-talk between the splicing and RNA editing, but there is a paucity of substantial evidence for its mechanistic details and contribution in a physiological context. Here, our findings demonstrate that tumor-associated differential RNA editing, in conjunction with splicing machinery, regulates the expression of variants of HNRPLL, a gene encoding splicing factor. We discovered an HNRPLL transcript variant containing an additional exon 12A (E12A), which is a substrate of ADAR1 and ADAR2. Adenosine deaminases acting on RNA (ADAR) direct deaminase-dependent expression of the E12A transcript, and ADAR-mediated regulation of E12A is largely splicing-based, and does not affect the stability or nucleocytoplasmic distribution of the transcript. Furthermore, ADAR-mediated modification of exon 12A generates an enhancer for the oncogenic splicing factor SRSF1 and consequently promotes the frequency of alternative splicing. Gene expression profiling by RNA-seq revealed that E12A acts distinctly from HNRPLL and regulates a set of growth-related genes, such as cyclin CCND1 and growth factor receptor TGFBR1 Accordingly, silencing E12A expression leads to impaired clonogenic ability and enhanced sensitivity to doxorubicin, thus highlighting the significance of this alternative isoform in tumor cell survival. In summary, we present the interplay of RNA editing and splicing as a regulatory mechanism of gene expression and also its physiological relevance. These findings extend our understanding of transcriptional dynamics and provide a mechanistic explanation to the link of RNA editors to tumorigenesis.
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Affiliation(s)
- Yi-Tung Chen
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | | | - Hsuan Liu
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,Molecular Medicine Research Center.,Department of Biochemistry, College of Medicine, and.,the Division of Colon and Rectal Surgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
| | - Chung-Pei Ma
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Yu-Ping Kuo
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Chieh-Tien Shih
- From the Graduate Institute of Biomedical Sciences, College of Medicine.,the Department of Biomedical Sciences, College of Medicine
| | - Ying-Hsin Shih
- the Department of Biomedical Sciences, College of Medicine
| | - Lin Kang
- the Edward Via College of Osteopathic Medicine, Blacksburg, Virginia 24060, and
| | - Bertrand Chin-Ming Tan
- From the Graduate Institute of Biomedical Sciences, College of Medicine, .,the Department of Biomedical Sciences, College of Medicine.,Molecular Medicine Research Center.,the Department of Neurosurgery, Lin-Kou Medical Center, Chang Gung Memorial Hospital, Taoyuan 333, Taiwan
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179
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A SRSF1 self-binding mechanism restrains Mir505-3p from inhibiting proliferation of neural tumor cell lines. Anticancer Drugs 2018; 29:40-49. [PMID: 29120871 DOI: 10.1097/cad.0000000000000564] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Srsf1 has currently been demonstrated to be an oncogene that is precisely autoregulated for normal physiology. Although Mir505-3p has been reported as one of the regulatory miRNAs of Srsf1 in mouse embryonic fibroblast (MEF), the inhibitory effect of Mir505-3p on Srsf1 is poorly described in neural tumors. Whether SRSF1 autoregulation interferes with miRNA targeting on the Srsf1 transcript is unclear. In this work, we screened out one target site, out of three potential target sites on 3' UTR of Srsf1 transcript, that was required for Mir505-3p targeting. We showed that Mir505-3p was capable of inhibiting tumor proliferation driven by SRSF1 in two neural tumor cell lines, Neuro-2a (N2a) and U251, exclusively in serum-reduced condition. We observed that the protein level of SRSF1 was gradually promoted by increasing concentration of serum. We also found that overexpressed exogenous SRSF1 protein abolished this RNA interfering related targeting, suggesting that serum-rich condition restrains Mir505-3p from inhibiting Srsf1 transcript after inducing SRSF1 protein overexpression. Moreover, by applying bioinformatic analysis, the SRSF1 self-binding motif was found proximal to the Mir505-3p target site, which was required for a SRSF1 competitive self-binding interaction. The interaction of overexpressed exogenous SRSF1 protein and the SRSF1 self-binding motif was sufficient to restrain Mir505-3p from targeting the Srsf1 transcript. These results provide a better understanding of how tumorous microenvironment influences anticancer therapy in the neural system, suggesting potential strategic design for anticancer drugs.
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180
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Cui X, Zhang L, Meng J, Rao MK, Chen Y, Huang Y. MeTDiff: A Novel Differential RNA Methylation Analysis for MeRIP-Seq Data. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2018; 15:526-534. [PMID: 29610101 DOI: 10.1109/tcbb.2015.2403355] [Citation(s) in RCA: 66] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
N6-Methyladenosine (m6A) transcriptome methylation is an exciting new research area that just captures the attention of research community. We present in this paper, MeTDiff, a novel computational tool for predicting differential m6A methylation sites from Methylated RNA immunoprecipitation sequencing (MeRIP-Seq) data. Compared with the existing algorithm exomePeak, the advantages of MeTDiff are that it explicitly models the reads variation in data and also devices a more power likelihood ratio test for differential methylation site prediction. Comprehensive evaluation of MeTDiff's performance using both simulated and real datasets showed that MeTDiff is much more robust and achieved much higher sensitivity and specificity over exomePeak. The R package "MeTDiff" and additional details are available at: https://github.com/compgenomics/MeTDiff.
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181
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Li L, Feng J, Chen Y, Li S, Ou M, Sun W, Tang L. Estradiol shows anti-skin cancer activities through decreasing MDM2 expression. Oncotarget 2018; 8:8459-8474. [PMID: 28035066 PMCID: PMC5352414 DOI: 10.18632/oncotarget.14275] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Accepted: 11/30/2016] [Indexed: 12/19/2022] Open
Abstract
Estradiol plays important roles in many biological responses inducing tumor genesis and cancer treatment. However, the effects of estradiol on tumors were inconsistent among a lot of researches and the mechanism is not fully understood. Our previous study indicated that splicing factor hnRNPA1 could bind to the human homologue of mouse double minute (MDM2), an oncogene which has been observed to be over-expressed in numerous types of cancers. In this research, we investigated whether and how estradiol correlate to cancer cell behaviors through heterogeneous nuclear ribonucleoprotein (hnRNPA1) and MDM2. Results showed that 10×10-13Mestradiol elevated the expression of hnRNPA1 regardless ER expression in cells, and then down-regulated the expression of MDM2. At the same time, estradiol inhibited cell proliferation, migration and epithelial-mesenchymal transition progression of A375 and GLL19 cells. While, knocking down hnRNPA1 through the transfection of hnRNPA1 siRNA led to the increase of MDM2 at both protein level and gene level In vivo experiment, subcutaneous injection with estradiol every two days near the tumor at doses of 2.5mg/kg/d suppressed tumor growth and reduced MDM2 expression. In a word, via increasing hnRNPA1 level and then reducing the expression of MDM2, estradiol prevented carcinogenesis in melanomas. We confirmed therapeutic effect of estradiol, as well as a new way for estradiol to resist skin cancer.
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Affiliation(s)
- Li Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Jianguo Feng
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.,Department of Anesthesiology, The Affiliated Hospital of Southwest Medical University, Sichuan, China
| | - Ying Chen
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Shun Li
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Mengting Ou
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Weichao Sun
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
| | - Liling Tang
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China
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182
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Functional and prognostic significance of long non-coding RNA MALAT1 as a metastasis driver in ER negative lymph node negative breast cancer. Oncotarget 2018; 7:40418-40436. [PMID: 27250026 PMCID: PMC5130017 DOI: 10.18632/oncotarget.9622] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Accepted: 05/09/2016] [Indexed: 12/15/2022] Open
Abstract
MALAT1 (metastasis associated lung adenocarcinoma transcript1) is a conserved long non-coding RNA, known to regulate gene expression by modulating transcription and post-transcriptional pre-mRNA processing of a large number of genes. MALAT1 expression is deregulated in various tumors, including breast cancer. However, the significance of such abnormal expression is yet to be fully understood. In this study, we demonstrate that regulation of aggressive breast cancer cell traits by MALAT1 is not predicted solely based on an elevated expression level but is context specific. By performing loss- and gain-of-function studies, both under in vitro and in vivo conditions, we demonstrate that MALAT1 facilitates cell proliferation, tumor progression and metastasis of triple-negative breast cancer (TNBC) cells despite having a comparatively lower expression level than ER or HER2-positive breast cancer cells. Furthermore, MALAT1 regulates the expression of several cancer metastasis-related genes, but displays molecular subtype specific correlations with such genes. Assessment of the prognostic significance of MALAT1 in human breast cancer (n=1992) revealed elevated MALAT1 expression was associated with decreased disease-specific survival in ER negative, lymph node negative patients of the HER2 and TNBC molecular subtypes. Multivariable analysis confirmed MALAT1 to have independent prognostic significance in the TNBC lymph node negative patient subset (HR=2.64, 95%CI 1.35 − 5.16, p=0.005). We propose that the functional significance of MALAT1 as a metastasis driver and its potential use as a prognostic marker is most promising for those patients diagnosed with ER negative, lymph node negative breast cancer who might otherwise mistakenly be stratified to have low recurrence risk.
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183
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Sokół E, Kędzierska H, Czubaty A, Rybicka B, Rodzik K, Tański Z, Bogusławska J, Piekiełko-Witkowska A. microRNA-mediated regulation of splicing factors SRSF1, SRSF2 and hnRNP A1 in context of their alternatively spliced 3'UTRs. Exp Cell Res 2018; 363:208-217. [PMID: 29331391 DOI: 10.1016/j.yexcr.2018.01.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 12/29/2017] [Accepted: 01/08/2018] [Indexed: 12/30/2022]
Abstract
SRSF1, SRSF2 and hnRNP A1 are splicing factors that regulate the expression of oncogenes and tumor suppressors. SRSF1 and SRSF2 contribute to the carcinogenesis in the kidney. Despite their importance, the mechanisms regulating their expression in cancer are not entirely understood. Here, we investigated the microRNA-mediated regulation of SRSF1, SRSF2 and hnRNP A1 in renal cancer. The expression of microRNAs predicted to target SRSF1, SRSF2 and hnRNP A1 was disturbed in renal tumors compared with controls. Using qPCR, Western blot/ICC and luciferase reporter system assays we identified microRNAs that contribute to the regulation of expression of SRSF1 (miR-10b-5p, miR-203a-3p), SRSF2 (miR-183-5p, miR-200c-3p), and hnRNP A1 (miR-135a-5p, miR-149-5p). Silencing of SRSF1 and SRSF2 enhanced the expression of their targeting microRNAs. miR-183-5p and miR-200c-3p affected the expression of SRSF2-target genes, TNFRSF1B, TNFRSF9, CRADD and TP53. 3'UTR variants of SRSF1 and SRSF2 differed by the presence of miRNA-binding sites. In conclusion, we identified a group of microRNAs that contribute to the regulation of expression of SRSF1, SRSF2 and hnRNP A1. The microRNAs targeting SRSF1 and SRSF2 are involved in a regulatory feedback loop. microRNAs miR-183-5p and miR-200c-3p that target SRSF2, affect the expression of genes involved in apoptotic regulation.
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Affiliation(s)
- Elżbieta Sokół
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Alicja Czubaty
- Department of Molecular Biology, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096 Warsaw, Poland
| | - Beata Rybicka
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Katarzyna Rodzik
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Zbigniew Tański
- Masovian Specialist Hospital in Ostrołęka, Ostrołęka, Poland
| | - Joanna Bogusławska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland.
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, Marymoncka 99/103, 01-813 Warsaw, Poland.
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184
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Saha P, Datta K. Multi-functional, multicompartmental hyaluronan-binding protein 1 (HABP1/p32/gC1qR): implication in cancer progression and metastasis. Oncotarget 2018. [PMID: 29535843 PMCID: PMC5828189 DOI: 10.18632/oncotarget.24082] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Cancer is a complex, multi-factorial, multi-stage disease and a global threat to human health. Early detection of nature and stage of cancer is highly crucial for disease management. Recent studies have proved beyond any doubt about the involvement of the ubiquitous, myriad ligand binding, multi-functional human protein, hyaluronan-binding protein 1 (HABP1), which is identical to the splicing factor associated protein (p32) and the receptor of the globular head of the complement component (gC1qR) in tumorigenesis and cancer metastasis. Simultaneously three laboratories have discovered and named this protein separately as mentioned. Subsequently, different scientists have worked on the distinct functions in cellular processes ranging from immunological response, splicing mechanism, sperm-oocyte interactions, cell cycle regulation to cancer and have concentrated in their respective area of interest, referring it as either p32 or gC1qR or HABP1. HABP1 overexpression has been reported in almost all the tissue-specific forms of cancer and correlated with stage and poor prognosis in patients. In order to tackle this deadly disease and for therapeutic intervention, it is imperative to focus on all the regulatory aspects of this protein. Hence, this work is an attempt to combine an assortment of information on this protein to have an overview, which suggests its use as a diagnostic marker for cancer. The knowledge might assist in the designing of drugs for therapeutic intervention of HABP1/p32/gC1qR regulated specific ligand mediated pathways in cancer.
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Affiliation(s)
- Paramita Saha
- Biochemistry and Toxicology Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Kasturi Datta
- Biochemistry and Toxicology Laboratory, School of Environmental Sciences, Jawaharlal Nehru University, New Delhi 110067, India
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185
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Prendergast GC, Malachowski WP, DuHadaway JB, Muller AJ. Discovery of IDO1 Inhibitors: From Bench to Bedside. Cancer Res 2018; 77:6795-6811. [PMID: 29247038 DOI: 10.1158/0008-5472.can-17-2285] [Citation(s) in RCA: 403] [Impact Index Per Article: 67.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 09/23/2017] [Accepted: 11/01/2017] [Indexed: 01/11/2023]
Abstract
Small-molecule inhibitors of indoleamine 2,3-dioxygenase-1 (IDO1) are emerging at the vanguard of experimental agents in oncology. Here, pioneers of this new drug class provide a bench-to-bedside review on preclinical validation of IDO1 as a cancer therapeutic target and on the discovery and development of a set of mechanistically distinct compounds, indoximod, epacadostat, and navoximod, that were first to be evaluated as IDO inhibitors in clinical trials. As immunometabolic adjuvants to widen therapeutic windows, IDO inhibitors may leverage not only immuno-oncology modalities but also chemotherapy and radiotherapy as standards of care in the oncology clinic. Cancer Res; 77(24); 6795-811. ©2017 AACR.
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Affiliation(s)
| | | | - James B DuHadaway
- Lankenau Institute for Medical Research (LIMR), Wynnewood, Pennsylvania
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186
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Therapeutic Applications of Targeted Alternative Splicing to Cancer Treatment. Int J Mol Sci 2017; 19:ijms19010075. [PMID: 29283381 PMCID: PMC5796025 DOI: 10.3390/ijms19010075] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/16/2022] Open
Abstract
A growing body of studies has documented the pathological influence of impaired alternative splicing (AS) events on numerous diseases, including cancer. In addition, the generation of alternatively spliced isoforms is frequently noted to result in drug resistance in many cancer therapies. To gain comprehensive insights into the impacts of AS events on cancer biology and therapeutic developments, this paper highlights recent findings regarding the therapeutic routes of targeting alternative-spliced isoforms and splicing regulators to treatment strategies for distinct cancers.
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187
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Plesa M, Gagné V, Glisovic S, Younan M, Sharif-Askari B, Laverdière C, Alos N, Leclerc JM, Sallan SE, Neuberg D, Kutok JL, Silverman LB, Sinnett D, Krajinovic M. Influence of BCL2L11 polymorphism on osteonecrosis during treatment of childhood acute lymphoblastic leukemia. THE PHARMACOGENOMICS JOURNAL 2017; 19:33-41. [PMID: 29282361 DOI: 10.1038/s41397-017-0002-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Revised: 07/06/2017] [Accepted: 09/18/2017] [Indexed: 11/09/2022]
Abstract
Osteonecrosis (ON) is corticosteroid-related complication, reported in children with acute lymphoblastic leukemia (ALL). We have previously found that polymorphisms in BCL2L11 gene coding for pro-apoptotic Bim protein influence reduction of overall survival (OS) in a corticosteroid (CS) dose-dependent manner in childhood ALL patients. The same set of SNPs was here investigated for an association with CS-related ON assessed retrospectively in 304 children with ALL from Quebec (QcALL cohort) who received Dana-Farber Cancer Institute (DFCI) ALL treatment protocols. Two-year cumulative incidence of symptomatic ON was 10.6%. Two BCL2L11 polymorphisms, the 891T>G (rs2241843) in all QcALL patients and 29201C>T (rs724710) in high-risk group were significantly associated with ON, P = 0.009 and P = 0.003, respectively. The association remained significant in multivariate model (HR891TT = 2.4, 95% CI 1.2-4.8, P = 0.01 and HR29201CC = 5.7, 95% CI 1.6-20.9, P = 0.008). Both polymorphisms influenced viability of dexamethasone treated lymphoblastoid cell lines (P ≤ 0.03). The 891T>G influenced Bim gamma isoform levels (0.03) and its association with ON was also confirmed in replication DFCI cohort (N = 168, P = 0.03). QcALL children had a high incidence of ON during therapy, which was highly associated with BCL2L11 polymorphisms.
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Affiliation(s)
- Maria Plesa
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada.,Department of Pharmacology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Vincent Gagné
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada
| | - Sanja Glisovic
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada
| | - Melissa Younan
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada
| | - Bahram Sharif-Askari
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada
| | - Caroline Laverdière
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Nathalie Alos
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Jean-Marie Leclerc
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, MA, USA
| | - Donna Neuberg
- Department of Biostatistics & Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jeffery L Kutok
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, MA, USA
| | - Daniel Sinnett
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
| | - Maja Krajinovic
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, Canada. .,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada. .,Department of Pharmacology, Faculty of Medicine, University of Montreal, Montreal, QC, Canada.
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188
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Inflammatory Reprogramming with IDO1 Inhibitors: Turning Immunologically Unresponsive 'Cold' Tumors 'Hot'. Trends Cancer 2017; 4:38-58. [PMID: 29413421 DOI: 10.1016/j.trecan.2017.11.005] [Citation(s) in RCA: 113] [Impact Index Per Article: 16.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Revised: 11/07/2017] [Accepted: 11/14/2017] [Indexed: 01/24/2023]
Abstract
We discuss how small-molecule inhibitors of the tryptophan (Trp) catabolic enzyme indoleamine 2,3-dioxygenase (IDO) represent a vanguard of new immunometabolic adjuvants to safely enhance the efficacy of cancer immunotherapy, radiotherapy, or 'immunogenic' chemotherapy by leveraging responses to tumor neoantigens. IDO inhibitors re-program inflammatory processes to help clear tumors by blunting tumor neovascularization and restoring immunosurveillance. Studies of regulatory and effector pathways illuminate IDO as an inflammatory modifier. Recent work suggests that coordinate targeting of the Trp catabolic enzymes tryptophan 2,3-dioxygenase (TDO) and IDO2 may also safely broaden efficacy. Understanding IDO inhibitors as adjuvants to turn immunologically 'cold' tumors 'hot' can seed new concepts in how to improve the efficacy of cancer therapy while limiting collateral damage.
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189
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Jyotsana N, Heuser M. Exploiting differential RNA splicing patterns: a potential new group of therapeutic targets in cancer. Expert Opin Ther Targets 2017; 22:107-121. [PMID: 29235382 DOI: 10.1080/14728222.2018.1417390] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
INTRODUCTION Mutations in genes associated with splicing have been found in hematologic malignancies, but also in solid cancers. Aberrant cancer specific RNA splicing either results from mutations or misexpression of the spliceosome genes directly, or from mutations in splice sites of oncogenes or tumor suppressors. Areas covered: In this review, we present molecular targets of aberrant splicing in various malignancies, information on existing and emerging therapeutics against such targets, and strategies for future drug development. Expert opinion: Alternative splicing is an important mechanism that controls gene expression, and hence pharmacologic and genetic control of aberrant alternative RNA splicing has been proposed as a potential therapy in cancer. To identify and validate aberrant RNA splicing patterns as therapeutic targets we need to (1) characterize the most common genetic aberrations of the spliceosome and of splice sites, (2) understand the dysregulated downstream pathways and (3) exploit in-vivo disease models of aberrant splicing. Antisense oligonucleotides show promising activity, but will benefit from improved delivery tools. Inhibitors of mutated splicing factors require improved specificity, as alternative and aberrant splicing are often intertwined like two sides of the same coin. In summary, targeting aberrant splicing is an early but emerging field in cancer treatment.
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Affiliation(s)
- Nidhi Jyotsana
- a Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation , Hannover Medical School , Hannover , Germany
| | - Michael Heuser
- a Department of Hematology, Hemostasis, Oncology and Stem Cell Transplantation , Hannover Medical School , Hannover , Germany
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190
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Chen L, Luo C, Shen L, Liu Y, Wang Q, Zhang C, Guo R, Zhang Y, Xie Z, Wei N, Wu W, Han J, Feng Y. SRSF1 Prevents DNA Damage and Promotes Tumorigenesis through Regulation of DBF4B Pre-mRNA Splicing. Cell Rep 2017; 21:3406-3413. [DOI: 10.1016/j.celrep.2017.11.091] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 10/20/2017] [Accepted: 11/27/2017] [Indexed: 10/25/2022] Open
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191
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Agrawal AA, Yu L, Smith PG, Buonamici S. Targeting splicing abnormalities in cancer. Curr Opin Genet Dev 2017; 48:67-74. [PMID: 29136527 DOI: 10.1016/j.gde.2017.10.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/19/2017] [Accepted: 10/13/2017] [Indexed: 01/11/2023]
Abstract
Recently splicing has been recognized as a key pathway in cancer. Although aberrant splicing has been shown to be a consequence of mutations or the abnormal expression of splicing factors (trans-effect changes) or mutations in the splicing sequences (cis-effect mutations), the connections between aberrant splicing and cancer initiation or progression are still not well understood. Here we review the mutational landscape of splicing factors in cancer and associated splicing consequences, along with the most important examples of the therapeutic approaches targeting the spliceosome currently being investigated in oncology.
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Affiliation(s)
| | - Lihua Yu
- H3 Biomedicine, Inc., Cambridge, MA, USA
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192
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Galganski L, Urbanek MO, Krzyzosiak WJ. Nuclear speckles: molecular organization, biological function and role in disease. Nucleic Acids Res 2017; 45:10350-10368. [PMID: 28977640 PMCID: PMC5737799 DOI: 10.1093/nar/gkx759] [Citation(s) in RCA: 296] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 08/18/2017] [Indexed: 12/13/2022] Open
Abstract
The nucleoplasm is not homogenous; it consists of many types of nuclear bodies, also known as nuclear domains or nuclear subcompartments. These self-organizing structures gather machinery involved in various nuclear activities. Nuclear speckles (NSs) or splicing speckles, also called interchromatin granule clusters, were discovered as sites for splicing factor storage and modification. Further studies on transcription and mRNA maturation and export revealed a more general role for splicing speckles in RNA metabolism. Here, we discuss the functional implications of the localization of numerous proteins crucial for epigenetic regulation, chromatin organization, DNA repair and RNA modification to nuclear speckles. We highlight recent advances suggesting that NSs facilitate integrated regulation of gene expression. In addition, we consider the influence of abundant regulatory and signaling proteins, i.e. protein kinases and proteins involved in protein ubiquitination, phosphoinositide signaling and nucleoskeletal organization, on pre-mRNA synthesis and maturation. While many of these regulatory proteins act within NSs, direct evidence for mRNA metabolism events occurring in NSs is still lacking. NSs contribute to numerous human diseases, including cancers and viral infections. In addition, recent data have demonstrated close relationships between these structures and the development of neurological disorders.
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Affiliation(s)
- Lukasz Galganski
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Martyna O Urbanek
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
| | - Wlodzimierz J Krzyzosiak
- Department of Molecular Biomedicine, Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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193
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Latorre E, Birar VC, Sheerin AN, Jeynes JCC, Hooper A, Dawe HR, Melzer D, Cox LS, Faragher RGA, Ostler EL, Harries LW. Small molecule modulation of splicing factor expression is associated with rescue from cellular senescence. BMC Cell Biol 2017; 18:31. [PMID: 29041897 PMCID: PMC5645932 DOI: 10.1186/s12860-017-0147-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Altered expression of mRNA splicing factors occurs with ageing in vivo and is thought to be an ageing mechanism. The accumulation of senescent cells also occurs in vivo with advancing age and causes much degenerative age-related pathology. However, the relationship between these two processes is opaque. Accordingly we developed a novel panel of small molecules based on resveratrol, previously suggested to alter mRNA splicing, to determine whether altered splicing factor expression had potential to influence features of replicative senescence. Results Treatment with resveralogues was associated with altered splicing factor expression and rescue of multiple features of senescence. This rescue was independent of cell cycle traverse and also independent of SIRT1, SASP modulation or senolysis. Under growth permissive conditions, cells demonstrating restored splicing factor expression also demonstrated increased telomere length, re-entered cell cycle and resumed proliferation. These phenomena were also influenced by ERK antagonists and agonists. Conclusions This is the first demonstration that moderation of splicing factor levels is associated with reversal of cellular senescence in human primary fibroblasts. Small molecule modulators of such targets may therefore represent promising novel anti-degenerative therapies. Electronic supplementary material The online version of this article (10.1186/s12860-017-0147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Vishal C Birar
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - Angela N Sheerin
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - J Charles C Jeynes
- Centre for Biomedical Modelling and Analysis, University of Exeter, Exeter, Devon, EX2 5DW, UK
| | - Amy Hooper
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Helen R Dawe
- College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | - David Melzer
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Lynne S Cox
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Richard G A Faragher
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - Elizabeth L Ostler
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK.
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK.
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194
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Transcriptomic Characterization of the Human Cell Cycle in Individual Unsynchronized Cells. J Mol Biol 2017; 429:3909-3924. [PMID: 29045817 DOI: 10.1016/j.jmb.2017.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 10/05/2017] [Accepted: 10/07/2017] [Indexed: 12/14/2022]
Abstract
The highly fine-tuned dynamics of cell cycle gene expression have been intensely studied for several decades. However, some previous observations may be difficult to fully decouple from artifacts induced by traditional cell synchronization procedures. In addition, bulk cell measurements may have disguised intricate details. Here, we address this by sorting and transcriptomic sequencing of single cells progressing through the cell cycle without prior synchronization. Genes and pathways with known cell cycle roles are confirmed, associated regulatory sequence motifs are determined, and we also establish ties between other biological processes and the unsynchronized cell cycle. Importantly, we find the G1 phase to be surprisingly heterogeneous, with transcriptionally distinct early and late time points. We additionally note that mRNAs accumulate to reach maximum total levels at mitosis and find that stable transcripts show reduced cell-to-cell variability, consistent with the transcriptional burst model of gene expression. Our study provides the first detailed transcriptional profiling of an unsynchronized human cell cycle.
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195
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Song X, Zeng Z, Wei H, Wang Z. Alternative splicing in cancers: From aberrant regulation to new therapeutics. Semin Cell Dev Biol 2017; 75:13-22. [PMID: 28919308 DOI: 10.1016/j.semcdb.2017.09.018] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 09/09/2017] [Accepted: 09/11/2017] [Indexed: 12/18/2022]
Abstract
Alternative splicing is one of the most common mechanisms for gene regulation in humans, and plays a vital role to increase the complexity of functional proteins. In this article, we seek to provide a general review on the relationships between alternative splicing and tumorigenesis. We briefly introduce the basic rules for regulation of alternative splicing, and discuss recent advances on dynamic regulation of alternative splicing in cancers by highlighting the roles of a variety of RNA splicing factors in tumorigenesis. We further discuss several important questions regarding the splicing of long noncoding RNAs and back-splicing of circular RNAs in cancers. Finally, we discuss the current technologies that can be used to manipulate alternative splicing and serve as potential cancer treatment.
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Affiliation(s)
- Xiaowei Song
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China; Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China.
| | - Zhenyu Zeng
- Department of Cardiology, Changhai Hospital, 168 Changhai Road, Shanghai 200433, China
| | - Huanhuan Wei
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Zefeng Wang
- CAS Key Lab for Computational Biology, CAS Center for Excellence in Molecular Cell Science, CAS-MPG Partner Institute for Computational Biology, Shanghai Institute for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China.
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196
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Liu J, Bhadra M, Sinnakannu JR, Yue WL, Tan CW, Rigo F, Ong ST, Roca X. Overcoming imatinib resistance conferred by the BIM deletion polymorphism in chronic myeloid leukemia with splice-switching antisense oligonucleotides. Oncotarget 2017; 8:77567-77585. [PMID: 29100409 PMCID: PMC5652800 DOI: 10.18632/oncotarget.20658] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/25/2017] [Indexed: 11/25/2022] Open
Abstract
Many tyrosine kinase-driven cancers, including chronic myeloid leukemia (CML), are characterized by high response rates to specific tyrosine kinase inhibitors (TKIs) like imatinib. In East Asians, primary imatinib resistance is caused by a deletion polymorphism in Intron 2 of the BIM gene, whose product is required for TKI-induced apoptosis. The deletion biases BIM splicing from exon 4 to exon 3, generating splice isoforms lacking the exon 4-encoded pro-apoptotic BH3 domain, which impairs the ability of TKIs to induce apoptosis. We sought to identify splice-switching antisense oligonucleotides (ASOs) that block exon 3 but enhance exon 4 splicing, and thereby resensitize BIM deletion-containing cancers to imatinib. First, we mapped multiple cis-acting splicing elements around BIM exon 3 by minigene mutations, and found an exonic splicing enhancer acting via SRSF1. Second, by a systematic ASO walk, we isolated ASOs that corrected the aberrant BIM splicing. Eight of 67 ASOs increased exon 4 levels in BIM deletion-containing cells, and restored imatinib-induced apoptosis and TKI sensitivity. This proof-of-principle study proves that resistant CML cells by BIM deletion polymorphism can be resensitized to imatinib via splice-switching BIM ASOs. Future optimizations might yield a therapeutic ASO as precision-medicine adjuvant treatment for BIM-polymorphism-associated TKI-resistant CML and other cancers.
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Affiliation(s)
- Jun Liu
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Malini Bhadra
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Wan Lin Yue
- School of Biological Sciences, Nanyang Technological University, Singapore.,CN Yang Scholars Programme, Nanyang Technological University, Singapore
| | - Cheryl Weiqi Tan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Frank Rigo
- Ionis Pharmaceuticals, Carlsbad, California, USA
| | - S Tiong Ong
- Cancer and Stem Cell Biology Signature Research Programme, Duke-NUS Medical School, Singapore.,Department of Haematology, Singapore General Hospital, Singapore.,Department of Medical Oncology, National Cancer Centre Singapore, Singapore.,Department of Medicine, Duke University Medical Center, Durham, North Carolina, USA
| | - Xavier Roca
- School of Biological Sciences, Nanyang Technological University, Singapore
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197
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Sheng J, Zhao J, Xu Q, Wang L, Zhang W, Zhang Y. Bioinformatics analysis of SRSF1-controlled gene networks in colorectal cancer. Oncol Lett 2017; 14:5393-5399. [PMID: 29113173 PMCID: PMC5656040 DOI: 10.3892/ol.2017.6900] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/15/2017] [Indexed: 12/13/2022] Open
Abstract
Colorectal cancer is the third most common type of cancer and the fourth leading cause of cancer-associated mortality worldwide. Serine/arginine-rich splicing factor 1 (SRSF1) is a well-characterized oncogenic factor that promotes tumorigenesis by controlling a number of alternative splicing events. However, there is limited network analysis, from a global aspect, to study the effect of SRSF1 on colorectal cancer. In the present study, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of available gene regulation data from The Cancer Genome Atlas database revealed the enriched functions and signaling pathways of SRSF1. Subsequently, Oncomine analysis was performed, which demonstrated that SRSF1 was upregulated in a number of types of colon cancer. From overlapping the analysis of 2,678 SRSF1-related genes and 3,625 colorectal cancer genes in GeneCards, 468 genes were identified as SRSF1-related colorectal cancer genes. The GO results revealed that these overlapped genes were primarily enriched in metabolic processes, response to DNA damage, regulation of the cell cycle and a number of additional biological processes. KEGG pathway analysis revealed that SRSF1-related colorectal cancer genes were associated with the cell cycle, deregulated signaling pathways associated with cancer progression and colorectal cancer signaling pathways. In addition, the Search Tool for the Retrieval of Interacting Genes/Proteins database and Cytoscape analysis demonstrated that 468 SRSF1-related colorectal cancer genes exhibit potential interaction networks in which these genes were enriched in DNA metabolic processes, cell cycle regulation and regulation of apoptosis. The results of the present study suggested that SRSF1 exhibited an increased degree of interaction with key molecules, including NUF2 NDC80 kinetochore complex component, kinesin family member 2C, structural maintenance of chromosomes 3, ATM serine/threonine kinase, BRCA1 DNA repair associated, protein kinase DNA-activated catalytic polypeptide, heat shock protein 90 alpha family class A member 1, ras homolog family member A, and phosphatase and tensin homolog. Collectively, the bioinformatics analysis of the present study indicated that SRSF1 may have key functions in the progression and development of colorectal cancer.
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Affiliation(s)
- Junxiu Sheng
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China.,Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Jinyao Zhao
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Qiuhong Xu
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Linlin Wang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Wenjing Zhang
- Institute of Cancer Stem Cell, Cancer Center, Dalian Medical University, Dalian, Liaoning 116044, P.R. China
| | - Yang Zhang
- Department of Oncology, The Second Affiliated Hospital of Dalian Medical University, Dalian, Liaoning 116023, P.R. China
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198
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Sariyer R, De-Simone FI, Donadoni M, Hoek JB, Chang SL, Sariyer IK. Alcohol-Mediated Missplicing of Mcl-1 Pre-mRNA is Involved in Neurotoxicity. Alcohol Clin Exp Res 2017; 41:1715-1724. [PMID: 28800142 DOI: 10.1111/acer.13474] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 08/06/2017] [Indexed: 01/14/2023]
Abstract
BACKGROUND Heavy and chronic ethanol (EtOH) exposure can cause significant structural and functional damage to the adult brain. The most devastating consequence of EtOH exposure is the neurotoxicity associated with the depletion of neurons. Regulation of splice variants in the brain can modulate protein functions, which may ultimately affect behaviors associated with alcohol dependence and EtOH-mediated neurotoxicity. As alcohol consumption is associated with neurotoxicity, it is possible that altered splicing of survival and pro-survival factors during the development of alcoholism may contribute to the neurotoxicity. METHODS Primary human neurons and a neuroblastoma cell line were exposed to different concentrations of EtOH for various time periods. Cell viability and neuronal marker expression were analyzed by MTT assay and immunoblotting, respectively. Effect of EtOH exposure on splicing regulatory protein expression and alternative splicing of candidate genes was analyzed by a biochemical approach. Transcriptional activity of serine/arginine-rich splicing factor 1 (SRSF1) gene was determined by reporter gene analysis. RESULTS Our results suggest that EtOH exposure to neuronal cells at 25 mM and higher concentrations are detrimental. In addition, EtOH exposure caused a dramatic reduction in SRSF1 expression levels. Furthermore, EtOH exposure led to pre-mRNA missplicing of Mcl-1, a pro-survival member of the Bcl-2 family, by down-regulating the expression levels of SRSF1. Moreover, ectopic expression of both SRSF1 and Mcl-1L isoform was able to recover EtOH-mediated neurotoxicity. CONCLUSIONS Our results suggest that EtOH exposure can lead to pre-mRNA missplicing of Mcl-1 in neuronal cells. Our results indicate that EtOH exposure of neurons leads to a decrease in the ratio of Mcl-1L/Mcl-1S by favoring pro-apoptotic Mcl-1S splicing over anti-apoptotic Mcl-1L isoform suggesting that Mcl-1S may play a crucial role in neurotoxicity associated with alcohol consumption.
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Affiliation(s)
- Rahsan Sariyer
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Francesca I De-Simone
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Martina Donadoni
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania
| | - Jan B Hoek
- Department of Pathology, Anatomy and Cell Biology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Sulie L Chang
- Institute of NeuroImmune Pharmacology and Department of Biological Sciences, Seton Hall University, South Orange, New Jersey
| | - Ilker Kudret Sariyer
- Department of Neuroscience, Center for Neurovirology, Temple University School of Medicine, Philadelphia, Pennsylvania
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199
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Xie N, Chen M, Dai R, Zhang Y, Zhao H, Song Z, Zhang L, Li Z, Feng Y, Gao H, Wang L, Zhang T, Xiao RP, Wu J, Cao CM. SRSF1 promotes vascular smooth muscle cell proliferation through a Δ133p53/EGR1/KLF5 pathway. Nat Commun 2017; 8:16016. [PMID: 28799539 PMCID: PMC5561544 DOI: 10.1038/ncomms16016] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 05/19/2017] [Indexed: 02/07/2023] Open
Abstract
Though vascular smooth muscle cell (VSMC) proliferation underlies all cardiovascular hyperplastic disorders, our understanding of the molecular mechanisms responsible for this cellular process is still incomplete. Here we report that SRSF1 (serine/arginine-rich splicing factor 1), an essential splicing factor, promotes VSMC proliferation and injury-induced neointima formation. Vascular injury in vivo and proliferative stimuli in vitro stimulate SRSF1 expression. Mice lacking SRSF1 specifically in SMCs develop less intimal thickening after wire injury. Expression of SRSF1 in rat arteries enhances neointima formation. SRSF1 overexpression increases, while SRSF1 knockdown suppresses the proliferation and migration of cultured human aortic and coronary arterial SMCs. Mechanistically, SRSF1 favours the induction of a truncated p53 isoform, Δ133p53, which has an equal proliferative effect and in turn transcriptionally activates Krüppel-like factor 5 (KLF5) via the Δ133p53-EGR1 complex, resulting in an accelerated cell-cycle progression and increased VSMC proliferation. Our study provides a potential therapeutic target for vascular hyperplastic disease. The hyperproliferation of vascular smooth muscle cells underlies many vascular diseases. Here Xie et al. show that the splicing factor SRSF1 is an endogenous stimulator of human and mouse aortic smooth muscle cell proliferation via the Δ133p53/EGR1/KLF5 signalling axis, identifying potential therapeutic targets for vascular proliferative disorders.
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Affiliation(s)
- Ning Xie
- Capital Institute of Pediatrics, Beijing 100020, China.,Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Min Chen
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Rilei Dai
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Yan Zhang
- Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Hanqing Zhao
- National Institute of Biological Sciences, Beijing 102206, China
| | - Zhiming Song
- Department of Cardiology, Peking University, Third Hospital, Beijing 100191, China
| | - Lufeng Zhang
- Department of Cardiology, Peking University, Third Hospital, Beijing 100191, China
| | - Zhenyan Li
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Yuanqing Feng
- Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Hua Gao
- Center for Bioinformatics, Peking University, Beijing 100871, China
| | - Li Wang
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Ting Zhang
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Rui-Ping Xiao
- Institute of Molecular Medicine, Peking University, Beijing 100871, China
| | - Jianxin Wu
- Capital Institute of Pediatrics, Beijing 100020, China
| | - Chun-Mei Cao
- Capital Institute of Pediatrics, Beijing 100020, China.,Institute of Molecular Medicine, Peking University, Beijing 100871, China.,Research Center on Pediatric Development and Diseases, Chinese Academy of Medical Sciences, Beijing 100730, China
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200
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Chen C, Xue S, Zhang J, Chen W, Gong D, Zheng J, Ma J, Xue W, Chen Y, Zhai W, Zheng J. DNA-methylation-mediated repression of miR-766-3p promotes cell proliferation via targeting SF2 expression in renal cell carcinoma. Int J Cancer 2017; 141:1867-1878. [PMID: 28657135 DOI: 10.1002/ijc.30853] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Revised: 05/15/2017] [Accepted: 06/14/2017] [Indexed: 01/10/2023]
Abstract
Aberrant expression of microRNA (miRNA) emerges as an important role in a wide range of human malignances, and further identification as well as validation of the change of these endogenous non-protein-coding transcripts is warranted. Here, we identify a novel epigenetic regulation of miR-766-3p and investigate its biological function as well as clinical significance in renal cell carcinoma (RCC). Bisulfate analysis elucidates that the promoter of miR-766-3p is highly methylated in RCC tissues compared to non-tumorous tissues. Notably, the downregulation of miR-766-3p is obviously associated with clinical stage and worse prognosis in RCC patients. Upregulated miR-766-3p attenuates cell-cycle progression via targeting SF2 expression and additional SF2/P-AKT/P-ERK signaling pathway. Moreover, high level of SF2, as a novel oncoprotein in RCC, was significantly associated with poor survival in a large cohort of RCC specimens. Taken together, our study presents a road map for the prediction and validation of miR-766-3p/SF2 axis and thus imparts a therapeutic way for further RCC progression.
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Affiliation(s)
- Chen Chen
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, 200072, China
| | - Sheng Xue
- Department of Urology, Shanghai Tenth People's Hospital, Nanjing Medical University, Nanjing, China.,Department of Urology, The First Affliated Hospital of Bengbu Medical College Bengbu, Anhui, China
| | - Jin Zhang
- Department of Urology, Renji Hospital, School of Medicine in Shanghai Jiao Tong University, 160 Pujian Road, Pudong District, Shanghai, 200127, China
| | - Wei Chen
- Department of Urology, Renji Hospital, School of Medicine in Shanghai Jiao Tong University, 160 Pujian Road, Pudong District, Shanghai, 200127, China
| | - Dongkui Gong
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, 200072, China
| | - Jiayi Zheng
- Department of Pathology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, 200072, China
| | - Junjie Ma
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, 200072, China
| | - Wei Xue
- Department of Urology, Renji Hospital, School of Medicine in Shanghai Jiao Tong University, 160 Pujian Road, Pudong District, Shanghai, 200127, China
| | - Yonghui Chen
- Department of Urology, Renji Hospital, School of Medicine in Shanghai Jiao Tong University, 160 Pujian Road, Pudong District, Shanghai, 200127, China
| | - Wei Zhai
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, 200072, China.,Department of Urology, Renji Hospital, School of Medicine in Shanghai Jiao Tong University, 160 Pujian Road, Pudong District, Shanghai, 200127, China
| | - Junhua Zheng
- Department of Urology, Shanghai Tenth People's Hospital, School of Medicine in Tongji University, Shanghai, 200072, China.,Department of Urology, Shanghai First People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, China
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