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Malakar P, Shukla S, Mondal M, Kar RK, Siddiqui JA. The nexus of long noncoding RNAs, splicing factors, alternative splicing and their modulations. RNA Biol 2024; 21:1-20. [PMID: 38017665 PMCID: PMC10761143 DOI: 10.1080/15476286.2023.2286099] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/14/2023] [Indexed: 11/30/2023] Open
Abstract
The process of alternative splicing (AS) is widely deregulated in a variety of cancers. Splicing is dependent upon splicing factors. Recently, several long noncoding RNAs (lncRNAs) have been shown to regulate AS by directly/indirectly interacting with splicing factors. This review focuses on the regulation of AS by lncRNAs through their interaction with splicing factors. AS mis-regulation caused by either mutation in splicing factors or deregulated expression of splicing factors and lncRNAs has been shown to be involved in cancer development and progression, making aberrant splicing, splicing factors and lncRNA suitable targets for cancer therapy. This review also addresses some of the current approaches used to target AS, splicing factors and lncRNAs. Finally, we discuss research challenges, some of the unanswered questions in the field and provide recommendations to advance understanding of the nexus of lncRNAs, AS and splicing factors in cancer.
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Affiliation(s)
- Pushkar Malakar
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Sudhanshu Shukla
- Department of Biosciences and Bioengineering, Indian Institute of Technology Dharwad, Dharwad, Karnataka, India
| | - Meghna Mondal
- Department of Biomedical Science and Technology, School of Biological Sciences, Ramakrishna Mission Vivekananda Educational Research Institute (RKMVERI), Kolkata, India
| | - Rajesh Kumar Kar
- Department of Neurosurgery, School of Medicine, Yale University, New Haven, CT, USA
| | - Jawed Akhtar Siddiqui
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE, USA
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2
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He J, Qiu W, Li Y, Wei C, Bai Z, Jia J, Cai H. Advances in the Application of Apoptotic Proteins and Alternative Splicing in Tumor Therapy: A Narrative Review. IRANIAN JOURNAL OF PUBLIC HEALTH 2023; 52:1311-1319. [PMID: 37593500 PMCID: PMC10430389 DOI: 10.18502/ijph.v52i7.13233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2023] [Accepted: 04/18/2023] [Indexed: 08/19/2023]
Abstract
An apoptosis-resistant state determined by apoptotic protein expression is commonly seen in the initiation, progression, and treatment failure stages of human cancer, and anti-tumor drugs targeting apoptotic proteins have been increasingly developed over the past three decades. However, the frequently alternative splicing of apoptotic proteins diminished the ability of targeting drugs to bind to apoptotic proteins and, consequently, limit the drug efficacy. Currently, accumulating evidence has demonstrated that many alternative splicing events have been associated to apoptosis resistance in different cancers. Therefore, the intervention targeting alternative splicing for regulating tumor cell apoptosis is expected to become a new strategy and new direction of antitumor therapy. Here, we present well established alternative splicing events that occur in different apoptosis-related genes and their modification by several approaches with cancer therapeutic purposes.
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Affiliation(s)
- Jin He
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Weitao Qiu
- Gansu Provincial Maternity and Child-Care Hospital, Lanzhou 730050, China
| | - Yonghong Li
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Chaojun Wei
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Zhongtian Bai
- The Second Department of General Surgery, Lanzhou University First Hospital, Lanzhou 730000, China
| | - Jing Jia
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
| | - Hui Cai
- NHC Key Laboratory of Diagnosis and Therapy of Gastrointestinal Tumor, Gansu Provincial Hospital, Lanzhou 730000, China
- Key Laboratory of Molecular Diagnostics and Precision Medicine for Surgical Oncology in Gansu Province, Gansu Provincial Hospital, Lanzhou 730000, China
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3
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Jia R, Zheng ZM. Oncogenic SRSF3 in health and diseases. Int J Biol Sci 2023; 19:3057-3076. [PMID: 37416784 PMCID: PMC10321290 DOI: 10.7150/ijbs.83368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Serine/arginine rich splicing factor 3 (SRSF3) is an important multi-functional splicing factor, and has attracted increasing attentions in the past thirty years. The importance of SRSF3 is evidenced by its impressively conserved protein sequences in all animals and alternative exon 4 which represents an autoregulatory mechanism to maintain its proper cellular expression level. New functions of SRSF3 have been continuously discovered recently, especially its oncogenic function. SRSF3 plays essential roles in many cellular processes by regulating almost all aspects of RNA biogenesis and processing of many target genes, and thus, contributes to tumorigenesis when overexpressed or disregulated. This review updates and highlights the gene, mRNA, and protein structure of SRSF3, the regulatory mechanisms of SRSF3 expression, and the characteristics of SRSF3 targets and binding sequences that contribute to SRSF3's diverse molecular and cellular functions in tumorigenesis and human diseases.
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Affiliation(s)
- Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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4
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Nemeth Z, Hildebrandt E, Parsa N, Fleming AB, Wasson R, Pittman K, Bell X, Granger JP, Ryan MJ, Drummond HA. Epithelial sodium channels in macrophage migration and polarization: role of proinflammatory cytokines TNFα and IFNγ. Am J Physiol Regul Integr Comp Physiol 2022; 323:R763-R775. [PMID: 36189990 PMCID: PMC9639769 DOI: 10.1152/ajpregu.00207.2022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/13/2022] [Accepted: 09/26/2022] [Indexed: 11/22/2022]
Abstract
Migration of monocytes-macrophages plays an important role in phagocytosis of pathogens and cellular debris in a variety of pathophysiological conditions. Although epithelial Na+ channels (ENaCs) are required for normal migratory responses in other cell types, their role in macrophage migration signaling is unknown. To address this possibility, we determined whether ENaC message is present in several peripheral blood monocyte cell populations and tissue-resident macrophages in healthy humans using the Human Protein Atlas database (www.proteinatlas.org) and the mouse monocyte cell line RAW 264.7 using RT-PCR. We then determined that selective ENaC inhibition with amiloride inhibited chemotactic migration (∼50%), but not phagocytosis, of the mouse monocyte-macrophage cell line RAW 264.7. Furthermore, we generated a cell line stably expressing an NH2-terminal truncated αENaC to interrupt normal channel trafficking and found it suppressed migration. Prolonged exposure (48 h) of RAW 264.7 cells to proinflammatory cytokines interferon γ (IFNγ) and/or tumor necrosis factor α (TNFα) inhibited RAW 264.7 migration and abolished the amiloride (1 µM)-sensitive component of migration, a finding consistent with ENaC downregulation. To determine if proinflammatory cytokines regulate αENaC protein expression, cells were exposed to proinflammatory cytokines IFNγ (10 ng/mL, last 48 h) and TNFα (10 ng/mL, last 24 h). By Western blot analysis, we found whole cell αENaC protein is reduced ≥50%. Immunofluorescence demonstrated heterogeneous αENaC inhibition. Finally, we found that overnight exposure to amiloride stimulated morphological changes and increased polarization marker expression. Our findings suggest that ENaC may be a critical molecule in macrophage migration and polarization.
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Affiliation(s)
- Zoltan Nemeth
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Emily Hildebrandt
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Nicholas Parsa
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Adam B Fleming
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Robert Wasson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Katarina Pittman
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Xavier Bell
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Joey P Granger
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
| | - Michael J Ryan
- Department of Pharmacology, Physiology and Neuroscience, University of South Carolina School of Medicine, Columbia, South Carolina
| | - Heather A Drummond
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, Mississippi
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p53 Isoforms as Cancer Biomarkers and Therapeutic Targets. Cancers (Basel) 2022; 14:cancers14133145. [PMID: 35804915 PMCID: PMC9264937 DOI: 10.3390/cancers14133145] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The well-known tumor suppressor protein p53 plays important roles in tumor prevention through transcriptional regulation of its target genes. Reactivation of p53 activity has been a potent strategy for cancer treatment. Accumulating evidences indicate that p53 isoforms truncated/modified in the N- or C-terminus can modulate the p53 pathway in a p53-dependent or p53-independent manner. It is thus imperative to characterize the roles of the p53 isoforms in cancer development. This review illustrates how p53 isoforms participate in tumor development and/or suppression. It also summarizes the knowledge about the p53 isoforms as promising cancer biomarkers and therapeutic targets. Abstract This review aims to summarize the implications of the major isoforms of the tumor suppressor protein p53 in aggressive cancer development. The current knowledge of p53 isoforms, their involvement in cell-signaling pathways, and their interactions with other cellular proteins or factors suggests the existence of an intricate molecular network that regulates their oncogenic function. Moreover, existing literature about the involvement of the p53 isoforms in various cancers leads to the proposition of therapeutic solutions by altering the cellular levels of the p53 isoforms. This review thus summarizes how the major p53 isoforms Δ40p53α/β/γ, Δ133p53α/β/γ, and Δ160p53α/β/γ might have clinical relevance in the diagnosis and effective treatments of cancer.
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Sahin I, George A, Seyhan AA. Therapeutic Targeting of Alternative RNA Splicing in Gastrointestinal Malignancies and Other Cancers. Int J Mol Sci 2021; 22:11790. [PMID: 34769221 PMCID: PMC8583749 DOI: 10.3390/ijms222111790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/22/2022] Open
Abstract
Recent comprehensive genomic studies including single-cell RNA sequencing and characterization have revealed multiple processes by which protein-coding and noncoding RNA processing are dysregulated in many cancers. More specifically, the abnormal regulation of mRNA and precursor mRNA (pre-mRNA) processing, which includes the removal of introns by splicing, is frequently altered in tumors, producing multiple different isoforms and diversifying protein expression. These alterations in RNA processing result in numerous cancer-specific mRNAs and pathogenically spliced events that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumor suppressor genes. Abnormally spliced pre-mRNAs are also associated with resistance to cancer treatment, and certain cancers are highly sensitive to the pharmacological inhibition of splicing. The discovery of these alterations in RNA processing has not only provided new insights into cancer pathogenesis but identified novel therapeutic vulnerabilities and therapeutic opportunities in targeting these aberrations in various ways (e.g., small molecules, splice-switching oligonucleotides (SSOs), and protein therapies) to modulate alternative RNA splicing or other RNA processing and modification mechanisms. Some of these strategies are currently progressing toward clinical development or are already in clinical trials. Additionally, tumor-specific neoantigens produced from these pathogenically spliced events and other abnormal RNA processes provide a potentially extensive source of tumor-specific therapeutic antigens (TAs) for targeted cancer immunotherapy. Moreover, a better understanding of the molecular mechanisms associated with aberrant RNA processes and the biological impact they play might provide insights into cancer initiation, progression, and metastasis. Our goal is to highlight key alternative RNA splicing and processing mechanisms and their roles in cancer pathophysiology as well as emerging therapeutic alternative splicing targets in cancer, particularly in gastrointestinal (GI) malignancies.
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Affiliation(s)
- Ilyas Sahin
- Division of Hematology Oncology, Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL 32610, USA;
| | - Andrew George
- Department of Chemistry, Brown University, Providence, RI 02912, USA;
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
| | - Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI 02912, USA
- Cancer Center at Brown University, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
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7
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Dou Z, Zhao D, Chen X, Xu C, Jin X, Zhang X, Wang Y, Xie X, Li Q, Di C, Zhang H. Aberrant Bcl-x splicing in cancer: from molecular mechanism to therapeutic modulation. J Exp Clin Cancer Res 2021; 40:194. [PMID: 34118966 PMCID: PMC8196531 DOI: 10.1186/s13046-021-02001-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/30/2021] [Indexed: 12/13/2022] Open
Abstract
Bcl-x pre-mRNA splicing serves as a typical example to study the impact of alternative splicing in the modulation of cell death. Dysregulation of Bcl-x apoptotic isoforms caused by precarious equilibrium splicing is implicated in genesis and development of multiple human diseases, especially cancers. Exploring the mechanism of Bcl-x splicing and regulation has provided insight into the development of drugs that could contribute to sensitivity of cancer cells to death. On this basis, we review the multiple splicing patterns and structural characteristics of Bcl-x. Additionally, we outline the cis-regulatory elements, trans-acting factors as well as epigenetic modifications involved in the splicing regulation of Bcl-x. Furthermore, this review highlights aberrant splicing of Bcl-x involved in apoptosis evade, autophagy, metastasis, and therapy resistance of various cancer cells. Last, emphasis is given to the clinical role of targeting Bcl-x splicing correction in human cancer based on the splice-switching oligonucleotides, small molecular modulators and BH3 mimetics. Thus, it is highlighting significance of aberrant splicing isoforms of Bcl-x as targets for cancer therapy.
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Affiliation(s)
- Zhihui Dou
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Dapeng Zhao
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaohua Chen
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Caipeng Xu
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaodong Jin
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xuetian Zhang
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yupei Wang
- Medical Genetics Center of Gansu Maternal and Child Health Care Center, Lanzhou, 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qiang Li
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
| | - Cuixia Di
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China.
| | - Hong Zhang
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China.
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Natua S, Dhamdhere SG, Mutnuru SA, Shukla S. Interplay within tumor microenvironment orchestrates neoplastic RNA metabolism and transcriptome diversity. WILEY INTERDISCIPLINARY REVIEWS-RNA 2021; 13:e1676. [PMID: 34109748 DOI: 10.1002/wrna.1676] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 05/03/2021] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
The heterogeneous population of cancer cells within a tumor mass interacts intricately with the multifaceted aspects of the surrounding microenvironment. The reciprocal crosstalk between cancer cells and the tumor microenvironment (TME) shapes the cancer pathophysiome in a way that renders it uniquely suited for immune tolerance, angiogenesis, metastasis, and therapy resistance. This dynamic interaction involves a dramatic reconstruction of the transcriptomic landscape of tumors by altering the synthesis, modifications, stability, and processing of gene readouts. In this review, we categorically evaluate the influence of TME components, encompassing a myriad of resident and infiltrating cells, signaling molecules, extracellular vesicles, extracellular matrix, and blood vessels, in orchestrating the cancer-specific metabolism and diversity of both mRNA and noncoding RNA, including micro RNA, long noncoding RNA, circular RNA among others. We also highlight the transcriptomic adaptations in response to the physicochemical idiosyncrasies of TME, which include tumor hypoxia, extracellular acidosis, and osmotic stress. Finally, we provide a nuanced analysis of existing and prospective therapeutics targeting TME to ameliorate cancer-associated RNA metabolism, consequently thwarting the cancer progression. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA Turnover and Surveillance > Regulation of RNA Stability RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Shruti Ganesh Dhamdhere
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Srinivas Abhishek Mutnuru
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal Bypass Road, Bhauri, Bhopal, Madhya Pradesh, 462066, India
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Hotspot exons are common targets of splicing perturbations. Nat Commun 2021; 12:2756. [PMID: 33980843 PMCID: PMC8115636 DOI: 10.1038/s41467-021-22780-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 02/24/2021] [Indexed: 11/08/2022] Open
Abstract
High-throughput splicing assays have demonstrated that many exonic variants can disrupt splicing; however, splice-disrupting variants distribute non-uniformly across genes. We propose the existence of exons that are particularly susceptible to splice-disrupting variants, which we refer to as hotspot exons. Hotspot exons are also more susceptible to splicing perturbation through drug treatment and knock-down of RNA-binding proteins. We develop a classifier for exonic splice-disrupting variants and use it to infer hotspot exons. We estimate that 1400 exons in the human genome are hotspots. Using panels of splicing reporters, we demonstrate how the ability of an exon to tolerate a mutation is inversely proportional to the strength of its neighboring splice sites. Splicing-disrupting mutations are linked to diseases. By employing a machine learning approach, the authors show that certain exons, termed hotspot exons, are enriched for splicing-disruption variants and susceptible to splicing perturbations.
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10
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Inoue M, Enomoto M, Yoshimura M, Mizowaki T. Pharmacological inhibition of sodium-calcium exchange activates NADPH oxidase and induces infection-independent NETotic cell death. Redox Biol 2021; 43:101983. [PMID: 33933883 PMCID: PMC8105669 DOI: 10.1016/j.redox.2021.101983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 04/12/2021] [Accepted: 04/19/2021] [Indexed: 01/03/2023] Open
Abstract
In addition to its function of innate immunity against invading pathogens, neutrophil extracellular traps (NETs) promote thrombosis, autoimmune disease, and cancer metastasis; therefore, unnecessary exposure to the triggers of infection-independent NET generation should be avoided. We herein show that inhibition of forward-mode Na+/Ca2+ exchange by amiloride analogs, 5-(N-ethyl-N-isopropyl)amiloride (EIPA) and 5-(N-Methyl-N-isobutyl)amiloride (MIA), triggers NETotic cell death independently of infectious stimuli. Isolated human neutrophils treated with EIPA and MIA undergo NETotic cell death by an increase of intracellular Ca2+ following activation of NADPH oxidase and the resultant upregulation of intracellular ROS. EIPA- and MIA-mediated intracellular Ca2+ increase is attributed to the competitive binding of EIPA and MIA against Na+ to Na+/Ca2+ exchanger 1 (NCX1). These results demonstrate a new mechanism of infection-independent NET generation and implicate NCX1 as a physiologic regulator of intracellular calcium balance and NETotic cell death. Two of the amiloride analogs, EIPA and MIA, induce NETotic cell death without infectious stimuli. EIPA and MIA inhibit the forward-mode Na+/Ca2+ exchange and promote the intracellular Ca2+ overload. Intracellular Ca2+ overload by EIPA and MIA activates NADPH oxidase, elevates intracellular ROS level, and induces resultant NETotic cell death.
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Affiliation(s)
- Minoru Inoue
- Department of Radiation Oncology and Image-applied Therapy, Kyoto University Graduate School of Medicine, Kyoto, Japan.
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, Department of Medical Biophysics, University Health Network, University of Toronto, Toronto, Ontario, Canada
| | - Michio Yoshimura
- Department of Radiation Oncology and Image-applied Therapy, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Takashi Mizowaki
- Department of Radiation Oncology and Image-applied Therapy, Kyoto University Graduate School of Medicine, Kyoto, Japan
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11
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Natua S, Ashok C, Shukla S. Hypoxia-induced alternative splicing in human diseases: the pledge, the turn, and the prestige. Cell Mol Life Sci 2021; 78:2729-2747. [PMID: 33386889 PMCID: PMC11072330 DOI: 10.1007/s00018-020-03727-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/24/2020] [Accepted: 11/28/2020] [Indexed: 12/30/2022]
Abstract
Maintenance of oxygen homeostasis is an indispensable criterion for the existence of multicellular life-forms. Disruption of this homeostasis due to inadequate oxygenation of the respiring tissues leads to pathological hypoxia, which acts as a significant stressor in several pathophysiological conditions including cancer, cardiovascular defects, bacterial infections, and neurological disorders. Consequently, the hypoxic tissues develop necessary adaptations both at the tissue and cellular level. The cellular adaptations involve a dramatic alteration in gene expression, post-transcriptional and post-translational modification of gene products, bioenergetics, and metabolism. Among the key responses to oxygen-deprivation is the skewing of cellular alternative splicing program. Herein, we discuss the current concepts of oxygen tension-dependent alternative splicing relevant to various pathophysiological conditions. Following a brief description of cellular response to hypoxia and the pre-mRNA splicing mechanism, we outline the impressive number of hypoxia-elicited alternative splicing events associated with maladies like cancer, cardiovascular diseases, and neurological disorders. Furthermore, we discuss how manipulation of hypoxia-induced alternative splicing may pose promising strategies for novel translational diagnosis and therapeutic interventions.
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Affiliation(s)
- Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Cheemala Ashok
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, 462066, Madhya Pradesh, India.
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12
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Zhang Y, Qian J, Gu C, Yang Y. Alternative splicing and cancer: a systematic review. Signal Transduct Target Ther 2021; 6:78. [PMID: 33623018 PMCID: PMC7902610 DOI: 10.1038/s41392-021-00486-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 01/31/2023] Open
Abstract
The abnormal regulation of alternative splicing is usually accompanied by the occurrence and development of tumors, which would produce multiple different isoforms and diversify protein expression. The aim of the present study was to conduct a systematic review in order to describe the regulatory mechanisms of alternative splicing, as well as its functions in tumor cells, from proliferation and apoptosis to invasion and metastasis, and from angiogenesis to metabolism. The abnormal splicing events contributed to tumor progression as oncogenic drivers and/or bystander factors. The alterations in splicing factors detected in tumors and other mis-splicing events (i.e., long non-coding and circular RNAs) in tumorigenesis were also included. The findings of recent therapeutic approaches targeting splicing catalysis and splicing regulatory proteins to modulate pathogenically spliced events (including tumor-specific neo-antigens for cancer immunotherapy) were introduced. The emerging RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms were also discussed. However, further studies are still required to address the association between alternative splicing and cancer in more detail.
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Affiliation(s)
- Yuanjiao Zhang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunyan Gu
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ye Yang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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13
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Sanidas E, Velliou M, Papadopoulos D, Fotsali A, Iliopoulos D, Mantzourani M, Toutouzas K, Barbetseas J. Antihypertensive Drugs and Risk of Cancer: Between Scylla and Charybdis. Am J Hypertens 2020; 33:1049-1058. [PMID: 32529212 DOI: 10.1093/ajh/hpaa098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/21/2020] [Accepted: 06/09/2020] [Indexed: 12/14/2022] Open
Abstract
Antihypertensive drugs namely angiotensin-converting enzyme inhibitors, angiotensin II receptor blockers, calcium channel blockers, beta blockers, and diuretics are among the most clearly documented regimens worldwide with an overall cardioprotective benefit. Given that malignancy is the second leading cause of mortality, numerous observational studies aimed to investigate the carcinogenic potential of these agents with conflicting results. The purpose of this review was to summarize current data in an effort to explore rare side effects and new mechanisms linking antihypertensive drugs with the risk of developing cancer.
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Affiliation(s)
- Elias Sanidas
- Hypertension Excellence Centre—ESH, Department of Cardiology, LAIKO General Hospital, Athens, Greece
| | - Maria Velliou
- Hypertension Excellence Centre—ESH, Department of Cardiology, LAIKO General Hospital, Athens, Greece
| | - Dimitrios Papadopoulos
- Hypertension Excellence Centre—ESH, Department of Cardiology, LAIKO General Hospital, Athens, Greece
| | - Anastasia Fotsali
- Hypertension Excellence Centre—ESH, Department of Cardiology, LAIKO General Hospital, Athens, Greece
| | - Dimitrios Iliopoulos
- Laboratory of Experimental Surgery and Surgical Research “N.S. Christeas”, University of Athens, Medical School, Athens, Greece
| | - Marina Mantzourani
- 1st Department of Internal Medicine, LAIKO General Hospital, University of Athens, Medical School, Athens, Greece
| | - Konstantinos Toutouzas
- University of Athens, 1st Department of Cardiology, Hippokrateion Hospital, Athens, Greece
| | - John Barbetseas
- Hypertension Excellence Centre—ESH, Department of Cardiology, LAIKO General Hospital, Athens, Greece
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14
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Zhou Z, Gong Q, Lin Z, Wang Y, Li M, Wang L, Ding H, Li P. Emerging Roles of SRSF3 as a Therapeutic Target for Cancer. Front Oncol 2020; 10:577636. [PMID: 33072610 PMCID: PMC7544984 DOI: 10.3389/fonc.2020.577636] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/28/2020] [Indexed: 12/14/2022] Open
Abstract
Ser/Arg-rich (SR) proteins are RNA-binding proteins known as constitutive and alternative splicing (AS) regulators that regulate multiple aspects of the gene expression program. Ser/Arg-rich splicing factor 3 (SRSF3) is the smallest member of the SR protein family, and its level is controlled by multiple factors and involves complex mechanisms in eukaryote cells, whereas the aberrant expression of SRSF3 is associated with many human diseases, including cancer. Here, we review state-of-the-art research on SRSF3 in terms of its function, expression, and misregulation in human cancers. We emphasize the negative consequences of the overexpression of the SRSF3 oncogene in cancers, the pathways underlying SRSF3-mediated transformation, and implications of potential anticancer drugs by downregulation of SRSF3 expression for cancer therapy. Cumulative research on SRSF3 provides critical insight into its essential part in maintaining cellular processes, offering potential new targets for anti-cancer therapy.
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Affiliation(s)
- Zhixia Zhou
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Qi Gong
- Departments of Pediatrics, Second Clinical Medical College of Qingdao University, Qingdao, China
| | - Zhijuan Lin
- Key Laboratory for Immunology in Universities of Shandong Province, School of Clinical Medicine, Weifang Medical University, Weifang, China
| | - Yin Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Mengkun Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Lu Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Hongfei Ding
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
| | - Peifeng Li
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao, China
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15
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Farina AR, Cappabianca L, Sebastiano M, Zelli V, Guadagni S, Mackay AR. Hypoxia-induced alternative splicing: the 11th Hallmark of Cancer. J Exp Clin Cancer Res 2020; 39:110. [PMID: 32536347 PMCID: PMC7294618 DOI: 10.1186/s13046-020-01616-9] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022] Open
Abstract
Hypoxia-induced alternative splicing is a potent driving force in tumour pathogenesis and progression. In this review, we update currents concepts of hypoxia-induced alternative splicing and how it influences tumour biology. Following brief descriptions of tumour-associated hypoxia and the pre-mRNA splicing process, we review the many ways hypoxia regulates alternative splicing and how hypoxia-induced alternative splicing impacts each individual hallmark of cancer. Hypoxia-induced alternative splicing integrates chemical and cellular tumour microenvironments, underpins continuous adaptation of the tumour cellular microenvironment responsible for metastatic progression and plays clear roles in oncogene activation and autonomous tumour growth, tumor suppressor inactivation, tumour cell immortalization, angiogenesis, tumour cell evasion of programmed cell death and the anti-tumour immune response, a tumour-promoting inflammatory response, adaptive metabolic re-programming, epithelial to mesenchymal transition, invasion and genetic instability, all of which combine to promote metastatic disease. The impressive number of hypoxia-induced alternative spliced protein isoforms that characterize tumour progression, classifies hypoxia-induced alternative splicing as the 11th hallmark of cancer, and offers a fertile source of potential diagnostic/prognostic markers and therapeutic targets.
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Affiliation(s)
- Antonietta Rosella Farina
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Lucia Cappabianca
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Michela Sebastiano
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Veronica Zelli
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Stefano Guadagni
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
| | - Andrew Reay Mackay
- Department of Applied Clinical and Biotechnological Sciences, University of L’Aquila, 67100 L’Aquila, Italy
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16
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Rahman MA, Nasrin F, Bhattacharjee S, Nandi S. Hallmarks of Splicing Defects in Cancer: Clinical Applications in the Era of Personalized Medicine. Cancers (Basel) 2020; 12:cancers12061381. [PMID: 32481522 PMCID: PMC7352608 DOI: 10.3390/cancers12061381] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 05/25/2020] [Accepted: 05/25/2020] [Indexed: 12/14/2022] Open
Abstract
Alternative splicing promotes proteome diversity by using limited number of genes, a key control point of gene expression. Splicing is carried out by large macromolecular machineries, called spliceosome, composed of small RNAs and proteins. Alternative splicing is regulated by splicing regulatory cis-elements in RNA and trans-acting splicing factors that are often tightly regulated in a tissue-specific and developmental stage-specific manner. The biogenesis of ribonucleoprotein (RNP) complexes is strictly regulated to ensure that correct complements of RNA and proteins are coordinated in the right cell at the right time to support physiological functions. Any perturbations that impair formation of functional spliceosomes by disrupting the cis-elements, or by compromising RNA-binding or function of trans-factors can be deleterious to cells and result in pathological consequences. The recent discovery of oncogenic mutations in splicing factors, and growing evidence of the perturbed splicing in multiple types of cancer, underscores RNA processing defects as a critical driver of oncogenesis. These findings have resulted in a growing interest in targeting RNA splicing as a therapeutic approach for cancer treatment. This review summarizes our current understanding of splicing alterations in cancer, recent therapeutic efforts targeting splicing defects in cancer, and future potentials to develop novel cancer therapies.
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17
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Sun Y, Yan L, Guo J, Shao J, Jia R. Downregulation of SRSF3 by antisense oligonucleotides sensitizes oral squamous cell carcinoma and breast cancer cells to paclitaxel treatment. Cancer Chemother Pharmacol 2019; 84:1133-1143. [PMID: 31515668 DOI: 10.1007/s00280-019-03945-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2019] [Accepted: 08/28/2019] [Indexed: 12/30/2022]
Abstract
PURPOSE Paclitaxel (PTX) is widely used in the chemotherapy of many cancers, including breast cancer and oral squamous cell carcinoma (OSCC). However, many patients respond poorly to PTX treatment. The SRSF3 oncogene and several splicing factors play important roles in OSCC tumorigenesis. This study aimed to understand the function of splicing factors in PTX treatment and improve the therapeutic effects of PTX treatment. METHODS Splicing factors regulated by PTX treatment were screened in CAL 27 cell by reverse transcription polymerase chain reaction. The function of SRSF3 in PTX treatment was analyzed by gain-of-function or loss-of-function assay in OSCC cell lines CAL 27 and SCC-9 and breast cancer cell line MCF-7. Alternative splicing of SRSF3 exon 4 in cancer tissues or cells was analyzed by RT-PCR and online program TSVdb. SRSF3-specific antisense oligonucleotide (ASO) SR-3 was used to downregulate SRSF3 expression and enhance the effect of PTX treatment. RESULTS PTX treatment decreased SRSF3 expression, and SRSF3 overexpression rescued the growth inhibition caused by PTX in both OSCC and breast cancer cells. Moreover, we found that PTX treatment could repress SRSF3 exon 4 (containing an in-frame stop codon) exclusion and then decrease the SRSF3 protein expression. Increased exclusion of SRSF3 exon 4 is correlated with poor survival in OSCC and breast cancer patients. SR-3 downregulated SRSF3 protein expression and significantly increased the sensitivity of cancer cells to PTX treatment. CONCLUSIONS SRSF3 downregulation by ASO sensitizes cancer cells to PTX treatment.
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Affiliation(s)
- Yanan Sun
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, 430079, Wuhan, People's Republic of China
| | - Lingyan Yan
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, 430079, Wuhan, People's Republic of China
| | - Jihua Guo
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, 430079, Wuhan, People's Republic of China.
| | - Jun Shao
- Hubei Cancer Hospital, 116 Zhuodaoquan South Load, 430079, Wuhan, People's Republic of China.
| | - Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) and Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, 430079, Wuhan, People's Republic of China.
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18
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Rhine CL, Neil C, Glidden DT, Cygan KJ, Fredericks AM, Wang J, Walton NA, Fairbrother WG. Future directions for high-throughput splicing assays in precision medicine. Hum Mutat 2019; 40:1225-1234. [PMID: 31297895 DOI: 10.1002/humu.23866] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 07/02/2019] [Accepted: 07/06/2019] [Indexed: 11/12/2022]
Abstract
Classification of variants of unknown significance is a challenging technical problem in clinical genetics. As up to one-third of disease-causing mutations are thought to affect pre-mRNA splicing, it is important to accurately classify splicing mutations in patient sequencing data. Several consortia and healthcare systems have conducted large-scale patient sequencing studies, which discover novel variants faster than they can be classified. Here, we compare the advantages and limitations of several high-throughput splicing assays aimed at mitigating this bottleneck, and describe a data set of ~5,000 variants that we analyzed using our Massively Parallel Splicing Assay (MaPSy). The Critical Assessment of Genome Interpretation group (CAGI) organized a challenge, in which participants submitted machine learning models to predict the splicing effects of variants in this data set. We discuss the winning submission of the challenge (MMSplice) which outperformed existing software. Finally, we highlight methods to overcome the limitations of MaPSy and similar assays, such as tissue-specific splicing, the effect of surrounding sequence context, classifying intronic variants, synthesizing large exons, and amplifying complex libraries of minigene species. Further development of these assays will greatly benefit the field of clinical genetics, which lack high-throughput methods for variant interpretation.
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Affiliation(s)
- Christy L Rhine
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Christopher Neil
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - David T Glidden
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Kamil J Cygan
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.,Center for Computational Molecular Biology, Brown University, Providence, Rhode Island
| | - Alger M Fredericks
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Jing Wang
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island
| | - Nephi A Walton
- Genomic Medicine Institute, Geisinger, Danville, Pennsylvania
| | - William G Fairbrother
- Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island.,Center for Computational Molecular Biology, Brown University, Providence, Rhode Island.,Hassenfeld Child Health Innovation Institute of Brown University, Providence, Rhode Island
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19
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Lee C, Chang W, Chang Y, Yang J, Chang C, Hsu K, Chen Y, Liu T, Chen Y, Lin S, Wu Y, Chang J. Alternative splicing in human cancer cells is modulated by the amiloride derivative 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxide. Mol Oncol 2019; 13:1744-1762. [PMID: 31152681 PMCID: PMC6670021 DOI: 10.1002/1878-0261.12524] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Revised: 04/30/2019] [Accepted: 05/30/2019] [Indexed: 12/11/2022] Open
Abstract
Alternative splicing (AS) is a process that enables the generation of multiple protein isoforms with different biological properties from a single mRNA. Cancer cells often use the maneuverability conferred by AS to produce proteins that contribute to growth and survival. In our previous studies, we identified that amiloride modulates AS in cancer cells. However, the effective concentration of amiloride required to modulate AS is too high for use in cancer treatment. In this study, we used computational algorithms to screen potential amiloride derivatives for their ability to regulate AS in cancer cells. We found that 3,5-diamino-6-chloro-N-(N-(2,6-dichlorobenzoyl)carbamimidoyl)pyrazine-2-carboxamide (BS008) can regulate AS of apoptotic gene transcripts, including HIPK3, SMAC, and BCL-X, at a lower concentration than amiloride. This splicing regulation involved various splicing factors, and it was accompanied by a change in the phosphorylation state of serine/arginine-rich proteins (SR proteins). RNA sequencing was performed to reveal that AS of many other apoptotic gene transcripts, such as AATF, ATM, AIFM1, NFKB1, and API5, was also modulated by BS008. In vivo experiments further indicated that treatment of tumor-bearing mice with BS008 resulted in a marked decrease in tumor size. BS008 also had inhibitory effects in vitro, either alone or in a synergistic combination with the cytotoxic chemotherapeutic agents sorafenib and nilotinib. BS008 enabled sorafenib dose reduction without compromising antitumor activity. These findings suggest that BS008 may possess therapeutic potential for cancer treatment.
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Affiliation(s)
- Chien‐Chin Lee
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
| | - Wen‐Hsin Chang
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Primary Care MedicineTaipei Medical University HospitalTaiwan
| | - Ya‐Sian Chang
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
- Center for Precision MedicineChina Medical University HospitalTaichungTaiwan
| | - Jinn‐Moon Yang
- TIGP‐BioinformaticsInstitute of Information ScienceAcademia SinicaTaipeiTaiwan
- Institute of Bioinformatics and Systems BiologyNational Chiao Tung UniversityHsinchuTaiwan
- Department of Biological Science and TechnologyNational Chiao Tung UniversityHsinchuTaiwan
| | - Chih‐Shiang Chang
- Graduate Institute of Pharmaceutical ChemistryChina Medical UniversityTaichungTaiwan
| | - Kai‐Cheng Hsu
- Graduate Institute of Cancer Molecular Biology and Drug DiscoveryCollege of Medical Science and TechnologyTaipei Medical UniversityTaiwan
| | - Yun‐Ti Chen
- Institute of Bioinformatics and Systems BiologyNational Chiao Tung UniversityHsinchuTaiwan
| | - Ting‐Yuan Liu
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Yu‐Chia Chen
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
| | - Shyr‐Yi Lin
- Department of Primary Care MedicineTaipei Medical University HospitalTaiwan
- Department of General MedicineSchool of MedicineCollege of MedicineTaipei Medical UniversityTaiwan
- TMU Research Center of Cancer Translational MedicineTaipei Medical UniversityTaiwan
| | - Yang‐Chang Wu
- Graduate Institute of Natural ProductsKaohsiung Medical UniversityTaiwan
- Research Center for Natural Products and Drug DevelopmentKaohsiung Medical UniversityTaiwan
- Department of Medical ResearchKaohsiung Medical University HospitalTaiwan
- Chinese Medicine Research and Development CenterChina Medical University HospitalTaichungTaiwan
| | - Jan‐Gowth Chang
- Epigenome Research CenterChina Medical University HospitalTaichungTaiwan
- Department of Primary Care MedicineTaipei Medical University HospitalTaiwan
- Department of Laboratory MedicineChina Medical University HospitalTaichungTaiwan
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20
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Sun Q, Li S, Li J, Fu Q, Wang Z, Li B, Liu SS, Su Z, Song J, Lu D. Homoharringtonine regulates the alternative splicing of Bcl-x and caspase 9 through a protein phosphatase 1-dependent mechanism. BMC COMPLEMENTARY AND ALTERNATIVE MEDICINE 2018; 18:164. [PMID: 29788973 PMCID: PMC5964699 DOI: 10.1186/s12906-018-2233-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/15/2018] [Indexed: 12/31/2022]
Abstract
BACKGROUND Homoharringtonine (HHT) is a natural alkaloid with potent antitumor activity, but its precise mechanism of action is still poorly understood. METHODS We examined the effect of HHT on alternative splicing of Bcl-x and Caspase 9 in various cells using semi-quantitative reverse transcriptase-polymerase chain reaction (RT-PCR). The mechanism of HHT-affected alternative splicing in these cells was investigated by treatment with protein phosphatase inhibitors and overexpression of a protein phosphatase. RESULTS Treatment with HHT downregulated the levels of anti-apoptotic Bcl-xL and Caspase 9b mRNA with a concomitant increase in the mRNA levels of pro-apoptotic Bcl-xS and Caspase 9a in a dose- and time-dependent manner. Calyculin A, an inhibitor of protein phosphatase 1 (PP1) and protein phosphatase 2A (PP2A), significantly inhibited the effects of HHT on the alternative splicing of Bcl-x and Caspase 9, in contrast to okadaic acid, a specific inhibitor of PP2A. Overexpression of PP1 resulted in a decrease in the ratio of Bcl-xL/xS and an increase in the ratio of Caspase 9a/9b. Moreover, the effects of HHT on Bcl-x and Caspase 9 splicing were enhanced in response to PP1 overexpression. These results suggest that HHT-induced alternative splicing of Bcl-x and Caspase 9 is dependent on PP1 activation. In addition, overexpression of PP1 could induce apoptosis and sensitize MCF7 cells to apoptosis induced by HHT. CONCLUSION Homoharringtonine regulates the alternative splicing of Bcl-x and Caspase 9 through a PP1-dependent mechanism. Our study reveals a novel mechanism underlying the antitumor activities of HHT.
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Qureshi AA, Zuvanich EG, Khan DA, Mushtaq S, Silswal N, Qureshi N. Proteasome inhibitors modulate anticancer and anti-proliferative properties via NF-kB signaling, and ubiquitin-proteasome pathways in cancer cell lines of different organs. Lipids Health Dis 2018; 17:62. [PMID: 29606130 PMCID: PMC5879737 DOI: 10.1186/s12944-018-0697-5] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Accepted: 03/04/2018] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cancer is second most common cause of death in the United State. There are over 100 different types of cancer associated with different human organs, predominantly breast, liver, pancreas, prostate, colon, rectum, lung, and stomach. We have recently reported properties of pro-inflammatory (for treatment of various types of cancers), and anti-inflammatory (for cardiovascular disease and diabetes) compounds. The major problem associated with development of anticancer drugs is their lack of solubility in aqueous solutions and severe side effects in cancer patients. Therefore, the present study was carried out to check anticancer properties of selected compounds, mostly aqueous soluble, in cancer cell lines from different organs. METHODS The anticancer properties, anti-proliferative, and pro-apoptotic activity of novel naturally occurring or FDA approved, nontoxic, proteasome inhibitors/activators were compared. In addition to that, effect of δ-tocotrienol on expression of proteasome subunits (X, Y, Z, LMP7, LMP2, LMP10), ICAM-1, VCAM-1, and TNF-α using total RNAs derived from plasmas of hepatitis C patients was investigated. RESULTS Our data demonstrated that following compounds are very effective in inducing apoptosis of cancer cells: Thiostrepton, dexamethasone, 2-methoxyestradiol, δ-tocotrienol, quercetin, amiloride, and quinine sulfate have significant anti-proliferation properties in Hela cells (44% - 87%) with doses of 2.5-20 μM, compared to respective controls. Anti-proliferation properties of thiostrepton, 2-methoxyestradiol, δ-tocotrienol, and quercetin were 70% - 92%. However, thiostrepton, dexamethasone, 2-methoxyestradiol, δ-tocotrienol, quercetin, and quinine sulphate were effective in pancreatic, prostate, breast, lungs, melanoma, Β-lymphocytes, and T-cells (Jurkat: 40% to 95%) compared to respective controls. In lung cancer cells, these compounds were effective between 5 and 40 μM. The IC50 values of anti-proliferation properties of thiostrepton in most of these cell lines were between doses of 2.5-5 μM, dexamethasone 2.5-20 μM, 2-methoxyestradiol 2.5-10 μM, δ-tocotrienol 2.5-20 μM, quercetin 10-40 μM, and (-) Corey lactone 40-80 μM. In hepatitis C patients, δ-tocotrienol treatment resulted in significant decrease in the expression of pro-inflammatory cytokines. CONCLUSIONS These data demonstrate effectiveness of several natural-occurring compounds with anti-proliferative properties against cancer cells of several organs of humans. Thiostrepton, dexamethasone, 2-methoxyestradiol, δ-tocotrienol and quercetin are very effective for apoptosis of cancer cells in liver, pancreas, prostate, breast, lung, melanoma, Β-lymphocytes and T-cells. The results have provided an opportunity to test these compounds either individually or in combination as dietary supplements in humans for treatment of various types of cancers.
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Affiliation(s)
- Asaf A Qureshi
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.
| | - Eleanor G Zuvanich
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Dilshad A Khan
- Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology and National University of Medical Science, Rawalpindi, 64000, Pakistan
| | - Shahida Mushtaq
- Department of Chemical Pathology and Endocrinology, Armed Forces Institute of Pathology and National University of Medical Science, Rawalpindi, 64000, Pakistan
| | - Neerupma Silswal
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA
| | - Nilofer Qureshi
- Department of Basic Medical Science, School of Medicine, University of Missouri-Kansas City, 2411 Holmes Street, Kansas City, MO, 64108, USA.,Pharmacology and Toxicology, School of Pharmacy, University of Missouri-Kansas City, 2464 Charlotte Street, Kansas City, MO, 64108, USA
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22
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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23
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Yhee JY, Yoon HY, Kim H, Jeon S, Hergert P, Im J, Panyam J, Kim K, Nho RS. The effects of collagen-rich extracellular matrix on the intracellular delivery of glycol chitosan nanoparticles in human lung fibroblasts. Int J Nanomedicine 2017; 12:6089-6105. [PMID: 28860768 PMCID: PMC5573064 DOI: 10.2147/ijn.s138129] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
Recent progress in nanomedicine has shown a strong possibility of targeted therapy for obstinate chronic lung diseases including idiopathic pulmonary fibrosis (IPF). IPF is a fatal lung disease characterized by persistent fibrotic fibroblasts in response to type I collagen-rich extracellular matrix. As a pathological microenvironment is important in understanding the biological behavior of nanoparticles, in vitro cellular uptake of glycol chitosan nanoparticles (CNPs) in human lung fibroblasts was comparatively studied in the presence or absence of type I collagen matrix. Primary human lung fibroblasts from non-IPF and IPF patients (n=6/group) showed significantly increased cellular uptake of CNPs (>33.6-78.1 times) when they were cultured on collagen matrix. To elucidate the underlying mechanism of enhanced cellular delivery of CNPs in lung fibroblasts on collagen, cells were pretreated with chlorpromazine, genistein, and amiloride to inhibit clathrin-mediated endocytosis, caveolae-mediated endocytosis, and macropinocytosis, respectively. Amiloride pretreatment remarkably reduced the cellular uptake of CNPs, suggesting that lung fibroblasts mainly utilize the macropinocytosis-dependent mechanism when interacted with collagen. In addition, the internalization of CNPs was predominantly suppressed by a phosphoinositide 3-kinase (PI3K) inhibitor in IPF fibroblasts, indicating that enhanced PI3K activity associated with late-stage macropinocytosis can be particularly important for the enhanced cellular delivery of CNPs in IPF fibroblasts. Our study strongly supports the concept that a pathological microenvironment which surrounds lung fibroblasts has a significant impact on the intracellular delivery of nanoparticles. Based on the property of enhanced intracellular delivery of CNPs when fibroblasts are made to interact with a collagen-rich matrix, we suggest that CNPs may have great potential as a drug-carrier system for targeting fibrotic lung fibroblasts.
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Affiliation(s)
- Ji Young Yhee
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Hong Yeol Yoon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Hyunjoon Kim
- Department of Pharmaceutics, University of Minnesota, Minneapolis, MN, USA
| | - Sangmin Jeon
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea
| | - Polla Hergert
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Jintaek Im
- Department of Medicine, University of Minnesota, Minneapolis, MN, USA
| | - Jayanth Panyam
- Department of Pharmaceutics, University of Minnesota, Minneapolis, MN, USA
| | - Kwangmeyung Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul, Republic of Korea.,Korea University-Korea Institute of Science and Technology (KU-KIST) Graduate School of Converging Science and Technology, Korea University, Seoul, Republic of Korea
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Amiloride, An Old Diuretic Drug, Is a Potential Therapeutic Agent for Multiple Myeloma. Clin Cancer Res 2017; 23:6602-6615. [DOI: 10.1158/1078-0432.ccr-17-0678] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 06/30/2017] [Accepted: 07/28/2017] [Indexed: 11/16/2022]
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25
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Soemedi R, Cygan KJ, Rhine CL, Glidden DT, Taggart AJ, Lin CL, Fredericks AM, Fairbrother WG. The effects of structure on pre-mRNA processing and stability. Methods 2017; 125:36-44. [PMID: 28595983 DOI: 10.1016/j.ymeth.2017.06.001] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 05/31/2017] [Accepted: 06/01/2017] [Indexed: 12/16/2022] Open
Abstract
Pre-mRNA molecules can form a variety of structures, and both secondary and tertiary structures have important effects on processing, function and stability of these molecules. The prediction of RNA secondary structure is a challenging problem and various algorithms that use minimum free energy, maximum expected accuracy and comparative evolutionary based methods have been developed to predict secondary structures. However, these tools are not perfect, and this remains an active area of research. The secondary structure of pre-mRNA molecules can have an enhancing or inhibitory effect on pre-mRNA splicing. An example of enhancing structure can be found in a novel class of introns in zebrafish. About 10% of zebrafish genes contain a structured intron that forms a bridging hairpin that enforces correct splice site pairing. Negative examples of splicing include local structures around splice sites that decrease splicing efficiency and potentially cause mis-splicing leading to disease. Splicing mutations are a frequent cause of hereditary disease. The transcripts of disease genes are significantly more structured around the splice sites, and point mutations that increase the local structure often cause splicing disruptions. Post-splicing, RNA secondary structure can also affect the stability of the spliced intron and regulatory RNA interference pathway intermediates, such as pre-microRNAs. Additionally, RNA secondary structure has important roles in the innate immune defense against viruses. Finally, tertiary structure can also play a large role in pre-mRNA splicing. One example is the G-quadruplex structure, which, similar to secondary structure, can either enhance or inhibit splicing through mechanisms such as creating or obscuring RNA binding protein sites.
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Affiliation(s)
- Rachel Soemedi
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Kamil J Cygan
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Christy L Rhine
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - David T Glidden
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
| | - Allison J Taggart
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - Chien-Ling Lin
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - Alger M Fredericks
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA.
| | - William G Fairbrother
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, 70 Ship Street, Providence, RI 02903, USA; Center for Computational Molecular Biology, Brown University, 115 Waterman Street, Providence, RI 02912, USA.
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Bates DO, Morris JC, Oltean S, Donaldson LF. Pharmacology of Modulators of Alternative Splicing. Pharmacol Rev 2017; 69:63-79. [PMID: 28034912 PMCID: PMC5226212 DOI: 10.1124/pr.115.011239] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
More than 95% of genes in the human genome are alternatively spliced to form multiple transcripts, often encoding proteins with differing or opposing function. The control of alternative splicing is now being elucidated, and with this comes the opportunity to develop modulators of alternative splicing that can control cellular function. A number of approaches have been taken to develop compounds that can experimentally, and sometimes clinically, affect splicing control, resulting in potential novel therapeutics. Here we develop the concepts that targeting alternative splicing can result in relatively specific pathway inhibitors/activators that result in dampening down of physiologic or pathologic processes, from changes in muscle physiology to altering angiogenesis or pain. The targets and pharmacology of some of the current inhibitors/activators of alternative splicing are demonstrated and future directions discussed.
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Affiliation(s)
- David O Bates
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Jonathan C Morris
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Sebastian Oltean
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Lucy F Donaldson
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
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27
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Chang WH, Niu DM, Lu CY, Lin SY, Liu TC, Chang JG. Modulation the alternative splicing of GLA (IVS4+919G>A) in Fabry disease. PLoS One 2017; 12:e0175929. [PMID: 28430823 PMCID: PMC5400244 DOI: 10.1371/journal.pone.0175929] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/03/2017] [Indexed: 12/31/2022] Open
Abstract
While a base substitution in intron 4 of GLA (IVS4+919G>A) that causes aberrant alternative splicing resulting in Fabry disease has been reported, its molecular mechanism remains unclear. Here we reported that upon IVS4+919G>A transversion, H3K36me3 was enriched across the alternatively spliced region. PSIP1, an adapter of H3K36me3, together with Hsp70 and NONO were recruited and formed a complex with SF2/ASF and SRp20, which further promoted GLA splicing. Amiloride, a splicing regulator in cancer cells, could reverse aberrant histone modification patterns and disrupt the association of splicing complex with GLA. It could also reverse aberrant GLA splicing in a PP1-dependant manner. Our findings revealed the alternative splicing mechanism of GLA (IVS4+919G>A), and a potential treatment for this specific genetic type of Fabry disease by amiloride in the future.
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Affiliation(s)
- Wen-Hsin Chang
- Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei, Taiwan
| | - Dau-Ming Niu
- Institute of Clinical Medicine, National Yang-Ming University, Taipei, Taiwan
- Department of Pediatrics, Taipei Veterans General Hospital, Taipei, Taiwan
| | - Chi-Yu Lu
- Department of Biochemistry, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Research Center for Environmental Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Shyr-Yi Lin
- Department of Primary Care Medicine, Taipei Medical University Hospital, Taipei, Taiwan
- Department of General Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- * E-mail: (SYL); (TCL); (JGC)
| | - Ta-Chih Liu
- Graduate Institute of Clinical Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
- Division of Hematology and Oncology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung, Taiwan
- * E-mail: (SYL); (TCL); (JGC)
| | - Jan-Gowth Chang
- Epigenome Research Center, China Medical University Hospital, Taichung, Taiwan
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
- School of Medicine, China Medical University, Taichung, Taiwan
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan
- * E-mail: (SYL); (TCL); (JGC)
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28
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Kędzierska H, Piekiełko-Witkowska A. Splicing factors of SR and hnRNP families as regulators of apoptosis in cancer. Cancer Lett 2017; 396:53-65. [PMID: 28315432 DOI: 10.1016/j.canlet.2017.03.013] [Citation(s) in RCA: 149] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Revised: 03/08/2017] [Accepted: 03/08/2017] [Indexed: 12/19/2022]
Abstract
SR and hnRNP proteins were initially discovered as regulators of alternative splicing: the process of controlled removal of introns and selective joining of exons through which multiple transcripts and, subsequently, proteins can be expressed from a single gene. Alternative splicing affects genes involved in all crucial cellular processes, including apoptosis. During cancerogenesis impaired apoptotic control facilitates survival of cells bearing molecular aberrations, contributing to their unrestricted proliferation and chemoresistance. Apparently, SR and hnRNP proteins regulate all levels of expression of apoptotic genes, including transcription initiation and elongation, alternative splicing, mRNA stability, translation, and protein degradation. The frequently disturbed expressions of SR/hnRNP proteins in cancers lead to impaired functioning of target apoptotic genes, including regulators of the extrinsic (Fas, caspase-8, caspase-2, c-FLIP) and the intrinsic pathway (Apaf-1, caspase-9, ICAD), genes encoding Bcl-2 proteins, IAPs, and p53 tumor suppressor. Prototypical members of SR/hnRNP families, SRSF1 and hnRNP A1, promote synthesis of anti-apoptotic splice variants of Bcl-x and Mcl-1, which results in attenuation of programmed cell death in breast cancer and chronic myeloid leukemia. SR/hnRNP proteins significantly affect responses to chemotherapy, acting as mediators or modulators of drug-induced apoptosis. Aberrant expression of SRSF1 and hnRNP K can interfere with tumor responses to chemotherapy in pancreatic and liver cancers. Currently, a number of splicing factor inhibitors is being tested in pre-clinical and clinical trials. In this review we discuss recent findings on the role of SR and hnRNP proteins in apoptotic control in cancer cells as well as their significance in anticancer treatments.
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Affiliation(s)
- Hanna Kędzierska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland
| | - Agnieszka Piekiełko-Witkowska
- Department of Biochemistry and Molecular Biology, Centre of Postgraduate Medical Education, ul. Marymoncka 99/103, 01-813 Warsaw, Poland.
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29
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Abstract
Alternative splicing (AS) has emerged in the postgenomic era as one of the main drivers of proteome diversity, with ≥94% of multiexon genes alternatively spliced in humans. AS is therefore one of the main control mechanisms for cell phenotype, and is a process deregulated in disease. Numerous reports describe pathogenic mutations in splice factors, splice sites, or regulatory sequences. Additionally, compared with the physiologic state, disease often associates with an abnormal proportion of splice isoforms (or novel isoforms), without an apparent driver mutation. It is therefore essential to study how AS is regulated in physiology, how it contributes to pathogenesis, and whether we can manipulate faulty splicing for therapeutic advantage. Although the disease most commonly linked to deregulation of AS in several genes is cancer, many reports detail pathogenic splice variants in diseases ranging from neuromuscular disorders to diabetes or cardiomyopathies. A plethora of splice variants have been implicated in CKDs as well. In this review, we describe examples of these CKD-associated splice variants and ideas on how to manipulate them for therapeutic benefit.
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Affiliation(s)
- Megan Stevens
- School of Physiology and Pharmacology, Faculty of Biomedical Sciences, and Academic Renal Unit, School of Clinical Sciences, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Sebastian Oltean
- School of Physiology and Pharmacology, Faculty of Biomedical Sciences, and Academic Renal Unit, School of Clinical Sciences, Faculty of Health Sciences, University of Bristol, Bristol, United Kingdom
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Branduardi P. Synthetic Biology for Cellular Remodelling to Elicit Industrially Relevant Microbial Phenotypes. Synth Biol (Oxf) 2016. [DOI: 10.1007/978-3-319-22708-5_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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31
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Small Molecule Modulators of Pre-mRNA Splicing in Cancer Therapy. Trends Mol Med 2015; 22:28-37. [PMID: 26700537 DOI: 10.1016/j.molmed.2015.11.005] [Citation(s) in RCA: 125] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 11/09/2015] [Accepted: 11/13/2015] [Indexed: 12/24/2022]
Abstract
Pre-mRNA splicing is a fundamental process in mammalian gene expression and alternative RNA splicing plays a considerable role in generating protein diversity. RNA splicing events are also key to the pathology of numerous diseases, particularly cancers. Some tumors are molecularly addicted to specific RNA splicing isoforms making interference with pre-mRNA processing a viable therapeutic strategy. Several RNA splicing modulators have recently been characterized, some showing promise in preclinical studies. While the targets of most splicing modulators are constitutive RNA processing components, possibly leading to undesirable side effects, selectivity for individual splicing events has been observed. Given the high prevalence of splicing defects in cancer, small molecule modulators of RNA processing represent a potentially promising novel therapeutic strategy in cancer treatment. Here, we review their reported effects, mechanisms, and limitations.
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32
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Liu J, Lin J, Huang LF, Huang B, Xu YM, Li J, Wang Y, Zhang J, Yang WM, Min QH, Wang XZ. Differential expression and alternative splicing of cell cycle genes in imatinib-treated K562 cells. Tumour Biol 2015; 36:8127-36. [DOI: 10.1007/s13277-015-3493-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2014] [Accepted: 04/23/2015] [Indexed: 02/01/2023] Open
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Rehman SU, Husain MA, Sarwar T, Ishqi HM, Tabish M. Modulation of alternative splicing by anticancer drugs. WILEY INTERDISCIPLINARY REVIEWS-RNA 2015; 6:369-79. [DOI: 10.1002/wrna.1283] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 03/20/2015] [Accepted: 03/20/2015] [Indexed: 01/04/2023]
Affiliation(s)
- Sayeed Ur Rehman
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Mohammed Amir Husain
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Tarique Sarwar
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Hassan Mubarak Ishqi
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
| | - Mohammad Tabish
- Department of Biochemistry, Faculty of Life Sciences; Aligarh Muslim University; Aligarh India
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Shilo A, Siegfried Z, Karni R. The role of splicing factors in deregulation of alternative splicing during oncogenesis and tumor progression. Mol Cell Oncol 2015; 2:e970955. [PMID: 27308389 PMCID: PMC4905244 DOI: 10.4161/23723548.2014.970955] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2014] [Revised: 09/13/2014] [Accepted: 09/15/2014] [Indexed: 04/18/2023]
Abstract
In past decades, cancer research has focused on genetic alterations that are detected in malignant tissues and contribute to the initiation and progression of cancer. These changes include mutations, copy number variations, and translocations. However, it is becoming increasingly clear that epigenetic changes, including alternative splicing, play a major role in cancer development and progression. There are relatively few studies on the contribution of alternative splicing and the splicing factors that regulate this process to cancer development and progression. Recently, multiple studies have revealed altered splicing patterns in cancers and several splicing factors were found to contribute to tumor development. Studies using high-throughput genomic analysis have identified mutations in components of the core splicing machinery and in splicing factors in several cancers. In this review, we will highlight new findings on the role of alternative splicing and its regulators in cancer initiation and progression, in addition to novel approaches to correct oncogenic splicing.
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Affiliation(s)
- Asaf Shilo
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology; Institute for Medical Research Israel-Canada; Hebrew University-Hadassah Medical School; Ein Karem, Jerusalem, Israel
- Correspondence to: Rotem Karni;
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Wojtuszkiewicz A, Assaraf YG, Maas MJP, Kaspers GJL, Jansen G, Cloos J. Pre-mRNA splicing in cancer: the relevance in oncogenesis, treatment and drug resistance. Expert Opin Drug Metab Toxicol 2014; 11:673-89. [PMID: 25495223 DOI: 10.1517/17425255.2015.993316] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
INTRODUCTION Aberrant pre-mRNA splicing in cancer is emerging as an important determinant of oncogenesis, response to treatment and anticancer drug resistance. At the same time, the spliceosome has become a target for a novel class of pre-clinical chemotherapeutics with a potential future application in cancer treatment. Taken together, these findings offer novel opportunities for the enhancement of the efficacy of cancer therapy. AREAS COVERED This review presents a comprehensive overview of the molecular mechanisms involved in splicing and current developments regarding splicing aberrations in relation to several aspects of cancer formation and therapy. Identified mutations in the various components of the spliceosome and their implications for cancer prognosis are delineated. Moreover, the contribution of abnormal splicing patterns as well as deregulated splicing factors to chemoresistance is discussed, along with novel splicing-based therapeutic approaches. EXPERT OPINION Significant progress has been made in deciphering the role of splicing factors in cancer including carcinogenesis and drug resistance. Splicing-based prognostic tools as well as therapeutic options hold great potential towards improvements in cancer therapy. However, gaining more in-depth molecular insight into the consequences of mutations in various components of the splicing machinery as well as of cellular effects of spliceosome inhibition is a prerequisite to establish the role of splicing in tumor progression and treatment options, respectively.
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Affiliation(s)
- Anna Wojtuszkiewicz
- VU University Medical Center, Department of Pediatric Oncology/Hematology , Amsterdam , The Netherlands
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Naryshkin NA, Weetall M, Dakka A, Narasimhan J, Zhao X, Feng Z, Ling KKY, Karp GM, Qi H, Woll MG, Chen G, Zhang N, Gabbeta V, Vazirani P, Bhattacharyya A, Furia B, Risher N, Sheedy J, Kong R, Ma J, Turpoff A, Lee CS, Zhang X, Moon YC, Trifillis P, Welch EM, Colacino JM, Babiak J, Almstead NG, Peltz SW, Eng LA, Chen KS, Mull JL, Lynes MS, Rubin LL, Fontoura P, Santarelli L, Haehnke D, McCarthy KD, Schmucki R, Ebeling M, Sivaramakrishnan M, Ko CP, Paushkin SV, Ratni H, Gerlach I, Ghosh A, Metzger F. Motor neuron disease. SMN2 splicing modifiers improve motor function and longevity in mice with spinal muscular atrophy. Science 2014; 345:688-93. [PMID: 25104390 DOI: 10.1126/science.1250127] [Citation(s) in RCA: 359] [Impact Index Per Article: 35.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Spinal muscular atrophy (SMA) is a genetic disease caused by mutation or deletion of the survival of motor neuron 1 (SMN1) gene. A paralogous gene in humans, SMN2, produces low, insufficient levels of functional SMN protein due to alternative splicing that truncates the transcript. The decreased levels of SMN protein lead to progressive neuromuscular degeneration and high rates of mortality. Through chemical screening and optimization, we identified orally available small molecules that shift the balance of SMN2 splicing toward the production of full-length SMN2 messenger RNA with high selectivity. Administration of these compounds to Δ7 mice, a model of severe SMA, led to an increase in SMN protein levels, improvement of motor function, and protection of the neuromuscular circuit. These compounds also extended the life span of the mice. Selective SMN2 splicing modifiers may have therapeutic potential for patients with SMA.
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Affiliation(s)
| | - Marla Weetall
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Amal Dakka
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Jana Narasimhan
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Xin Zhao
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Zhihua Feng
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Karen K Y Ling
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Gary M Karp
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Hongyan Qi
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Matthew G Woll
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Guangming Chen
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Nanjing Zhang
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | | | - Priya Vazirani
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | | | - Bansri Furia
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Nicole Risher
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Josephine Sheedy
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Ronald Kong
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Jiyuan Ma
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Anthony Turpoff
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Chang-Sun Lee
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Xiaoyan Zhang
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Young-Choon Moon
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | | | - Ellen M Welch
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Joseph M Colacino
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - John Babiak
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Neil G Almstead
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA
| | - Stuart W Peltz
- PTC Therapeutics, 100 Corporate Court, South Plainfield, NJ 07080, USA.
| | - Loren A Eng
- SMA Foundation, 888 Seventh Avenue, Suite 400, New York, NY 10019, USA
| | - Karen S Chen
- SMA Foundation, 888 Seventh Avenue, Suite 400, New York, NY 10019, USA
| | - Jesse L Mull
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Maureen S Lynes
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Lee L Rubin
- Department of Stem Cell and Regenerative Biology and the Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
| | - Paulo Fontoura
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Luca Santarelli
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Daniel Haehnke
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | | | - Roland Schmucki
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Martin Ebeling
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Manaswini Sivaramakrishnan
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Chien-Ping Ko
- Section of Neurobiology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Paushkin
- SMA Foundation, 888 Seventh Avenue, Suite 400, New York, NY 10019, USA
| | - Hasane Ratni
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Irene Gerlach
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Anirvan Ghosh
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland
| | - Friedrich Metzger
- Roche Pharmaceutical Research and Early Development, Roche Innovation Center Basel, F. Hoffmann-La Roche, Grenzacherstrasse 124, 4070 Basel, Switzerland.
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Chang YC, Khanal Lamichhane A, Garraffo HM, Walter PJ, Leerkes M, Kwon-Chung KJ. Molecular mechanisms of hypoxic responses via unique roles of Ras1, Cdc24 and Ptp3 in a human fungal pathogen Cryptococcus neoformans. PLoS Genet 2014; 10:e1004292. [PMID: 24762475 PMCID: PMC3998916 DOI: 10.1371/journal.pgen.1004292] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 02/21/2014] [Indexed: 12/26/2022] Open
Abstract
Cryptococcus neoformans encounters a low oxygen environment when it enters the human host. Here, we show that the conserved Ras1 (a small GTPase) and Cdc24 (the guanine nucleotide exchange factor for Cdc42) play an essential role in cryptococcal growth in hypoxia. Suppressor studies indicate that PTP3 functions epistatically downstream of both RAS1 and CDC24 in regulating hypoxic growth. Ptp3 shares sequence similarity to the family of phosphotyrosine-specific protein phosphatases and the ptp3Δ strain failed to grow in 1% O2. We demonstrate that RAS1, CDC24 and PTP3 function in parallel to regulate thermal tolerance but RAS1 and CDC24 function linearly in regulating hypoxic growth while CDC24 and PTP3 reside in compensatory pathways. The ras1Δ and cdc24Δ strains ceased to grow at 1% O2 and became enlarged but viable single cells. Actin polarization in these cells, however, was normal for up to eight hours after transferring to hypoxic conditions. Double deletions of the genes encoding Rho GTPase Cdc42 and Cdc420, but not of the genes encoding Rac1 and Rac2, caused a slight growth retardation in hypoxia. Furthermore, growth in hypoxia was not affected by the deletion of several central genes functioning in the pathways of cAMP, Hog1, or the two-component like phosphorylation system that are critical in the cryptococcal response to osmotic and genotoxic stresses. Interestingly, although deletion of HOG1 rescued the hypoxic growth defect of ras1Δ, cdc24Δ, and ptp3Δ, Hog1 was not hyperphosphorylated in these three mutants in hypoxic conditions. RNA sequencing analysis indicated that RAS1, CDC24 and PTP3 acted upon the expression of genes involved in ergosterol biosynthesis, chromosome organization, RNA processing and protein translation. Moreover, growth of the wild-type strain under low oxygen conditions was affected by sub-inhibitory concentrations of the compounds that inhibit these biological processes, demonstrating the importance of these biological processes in the cryptococcal hypoxia response. When Cryptococcus neoformans, an environmental fungal pathogen, enters the human host, it encounters a low oxygen condition. The well conserved Ras1 and Cdc24 proteins are known for their key roles in maintenance of the actin cytoskeletal integrity in eukaryotic cells. In this work, we show a unique role of RAS1 and CDC24 in the growth of C. neoformans in a low oxygen environment. Actin polarization, however, appeared normal in the ras1Δ and cdc24Δ strains under hypoxic conditions for up to eight hours. We show that PTP3 is required for hypoxic growth and it can rescue the hypoxic growth defect in ras1Δ and cdc24Δ. Genetic analysis suggested that RAS1 and CDC24 function linearly while CDC24 and PTP3 function parallelly in regulating hypoxic growth. RNA sequencing combined with analysis by small molecular inhibitors revealed that RAS1, CDC24 and PTP3 regulate several biological processes such as ergosterol biosynthesis, chromosome organization, RNA processing and protein translation which are required in the cryptococcal response to hypoxic conditions.
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Affiliation(s)
- Yun C. Chang
- Molecular Microbiology Section, Laboratory of Clinical Infectious Diseases, NIAID, NIH Bethesda, Maryland, United States of America
- * E-mail:
| | - Ami Khanal Lamichhane
- Molecular Microbiology Section, Laboratory of Clinical Infectious Diseases, NIAID, NIH Bethesda, Maryland, United States of America
| | - H. Martin Garraffo
- Clinical Mass Spectrometry Core, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Peter J. Walter
- Clinical Mass Spectrometry Core, NIDDK, NIH, Bethesda, Maryland, United States of America
| | - Maarten Leerkes
- Bioinformatics and Computational Biosciences Branch, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Kyung J. Kwon-Chung
- Molecular Microbiology Section, Laboratory of Clinical Infectious Diseases, NIAID, NIH Bethesda, Maryland, United States of America
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Martínez-Montiel N, Rosas-Murrieta N, Martínez-Contreras R. [Alternative splicing regulation: implications in cancer diagnosis and treatment]. Med Clin (Barc) 2014; 144:317-23. [PMID: 24725854 DOI: 10.1016/j.medcli.2014.02.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Revised: 02/07/2014] [Accepted: 02/13/2014] [Indexed: 12/31/2022]
Abstract
The accurate expression of the genetic information is regulated by processes like mRNA splicing, proposed after the discoveries of Phil Sharp and Richard Roberts, who demonstrated the existence of intronic sequences, present in almost every structural eukaryotic gene, which should be precisely removed. This intron removal is called "splicing", which generates different proteins from a single mRNA, with different or even antagonistic functions. We currently know that alternative splicing is the most important source of protein diversity, given that 70% of the human genes undergo splicing and that mutations causing defects in this process could originate up to 50% of genetic diseases, including cancer. When these defects occur in genes involved in cell adhesion, proliferation and cell cycle regulation, there is an impact on cancer progression, rising the opportunity to diagnose and treat some types of cancer according to a particular splicing profile.
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Affiliation(s)
- Nancy Martínez-Montiel
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Nora Rosas-Murrieta
- Laboratorio de Bioquímica y Biología Molecular, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México
| | - Rebeca Martínez-Contreras
- Laboratorio de Ecología Molecular Microbiana, Centro de Investigaciones en Ciencias Microbiológicas, Instituto de Ciencias, Benemérita Universidad Autónoma de Puebla, Puebla, México.
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Dardis A, Zanin I, Zampieri S, Stuani C, Pianta A, Romanello M, Baralle FE, Bembi B, Buratti E. Functional characterization of the common c.-32-13T>G mutation of GAA gene: identification of potential therapeutic agents. Nucleic Acids Res 2013; 42:1291-302. [PMID: 24150945 PMCID: PMC3902950 DOI: 10.1093/nar/gkt987] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Glycogen storage disease type II is a lysosomal storage disorder due to mutations of the GAA gene, which causes lysosomal alpha-glucosidase deficiency. Clinically, glycogen storage disease type II has been classified in infantile and late-onset forms. Most late-onset patients share the leaky splicing mutation c.-32-13T>G. To date, the mechanism by which the c.-32-13T>G mutation affects the GAA mRNA splicing is not fully known. In this study, we demonstrate that the c.-32-13T>G mutation abrogates the binding of the splicing factor U2AF65 to the polypyrimidine tract of exon 2 and that several splicing factors affect exon 2 inclusion, although the only factor capable of acting in the c.-32-13 T>G context is the SR protein family member, SRSF4 (SRp75). Most importantly, a preliminary screening using small molecules described to be able to affect splicing profiles, showed that resveratrol treatment resulted in a significant increase of normal spliced GAA mRNA, GAA protein content and activity in cells transfected with a mutant minigene and in fibroblasts from patients carrying the c-32-13T>G mutation. In conclusion, this work provides an in-depth functional characterization of the c.-32-13T>G mutation and, most importantly, an in vitro proof of principle for the use of small molecules to rescue normal splicing of c.-32-13T>G mutant alleles.
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Affiliation(s)
- Andrea Dardis
- Regional Centre for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy and International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Trieste, Italy
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40
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Naro C, Sette C. Phosphorylation-mediated regulation of alternative splicing in cancer. Int J Cell Biol 2013; 2013:151839. [PMID: 24069033 PMCID: PMC3771450 DOI: 10.1155/2013/151839] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
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Affiliation(s)
- Chiara Naro
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
| | - Claudio Sette
- Department of Biomedicine and Prevention, University of Rome “Tor Vergata”, 00133 Rome, Italy
- Laboratories of Neuroembryology and of Cellular and Molecular Neurobiology, Fondazione Santa Lucia IRCCS, 00143 Rome, Italy
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Lee HC, Rudy Y, Chen PY, Sheu SH, Chang JG, Cui J. Modulation of KCNQ1 alternative splicing regulates cardiac IKs and action potential repolarization. Heart Rhythm 2013; 10:1220-8. [PMID: 23608591 PMCID: PMC3771516 DOI: 10.1016/j.hrthm.2013.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Indexed: 10/26/2022]
Abstract
BACKGROUND Slow delayed-rectifier potassium current (IKs) channels, made of the pore-forming KCNQ1 and auxiliary KCNE1 subunits, play a key role in determining action potential duration (APD) in cardiac myocytes. The consequences of drug-induced KCNQ1 splice alteration remain unknown. OBJECTIVE To study the modulation of KCNQ1 alternative splicing by amiloride and the consequent changes in IKs and action potentials (APs) in ventricular myocytes. METHODS Canine endocardial, midmyocardial, and epicardial ventricular myocytes were isolated. Levels of KCNQ1a and KCNQ1b as well as a series of splicing factors were quantified by using the reverse transcriptase-polymerase chain reaction and Western blot. The effect of amiloride-induced changes in the KCNQ1b/total KCNQ1 ratio on AP was measured by using whole-cell patch clamp with and without isoproterenol. RESULTS With 50 μmol/L of amiloride for 6 hours, KCNQ1a at transcriptional and translational levels increased in midmyocardial myocytes but decreased in endo- and epicardial myocytes. Likewise, changes in splicing factors in midmyocardial were opposite to that in endo- and epicardial myocytes. In midmyocardial myocytes amiloride shortened APD and decreased isoproterenol-induced early afterdepolarizations significantly. The same amiloride-induced effects were demonstrated by using human ventricular myocyte model for AP simulations under beta-adrenergic stimulation. Moreover, amiloride reduced the transmural dispersion of repolarization in pseudo-electrocardiogram. CONCLUSIONS Amiloride regulates IKs and APs with transmural differences and reduces arrhythmogenicity through the modulation of KCNQ1 splicing. We suggested that the modulation of KCNQ1 splicing may help prevent arrhythmia.
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Affiliation(s)
- Hsiang-Chun Lee
- Cardiac Bioelectricity and Arrhythmia Center, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Cardiovascular Center, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University
- Graduate institute of Medicine, College of Medicine, Kaohsiung Medical University
- Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Yoram Rudy
- Cardiac Bioelectricity and Arrhythmia Center, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Po-Yuan Chen
- College of Electrical Engineering and Computer Science, National Cheng-Kung University, Tainan, Taiwan
| | - Sheng-Hsiung Sheu
- Cardiovascular Center, Kaohsiung Medical University Chung-Ho Memorial Hospital, Kaohsiung Medical University
- Graduate institute of Medicine, College of Medicine, Kaohsiung Medical University
- Department of Internal Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jan-Gowth Chang
- Department of Laboratory Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Jianmin Cui
- Cardiac Bioelectricity and Arrhythmia Center, Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
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Tang JY, Chang HW, Chang JG. Modulating roles of amiloride in irradiation-induced antiproliferative effects in glioblastoma multiforme cells involving Akt phosphorylation and the alternative splicing of apoptotic genes. DNA Cell Biol 2013; 32:504-10. [PMID: 23822711 DOI: 10.1089/dna.2013.1998] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Apoptosis is a key mechanism for enhanced cellular radiosensitivity in radiation therapy. Studies suggest that Akt signaling may play a role in apoptosis and radioresistance. This study evaluates the possible modulating role of amiloride, an antihypertensive agent with a modulating effect to alternative splicing for regulating apoptosis, in the antiproliferative effects induced by ionizing radiation (IR) in glioblastoma multiforme (GBM) 8401 cells. Analysis of cell viability showed that amiloride treatment significantly inhibited cell proliferation in irradiated GBM8401 cells (p<0.05) in a time-dependent manner, especially in cells treated with amiloride with IR post-treatment. In comparison with GBM8401 cells treated with amiloride alone, with GBM8401 cells treated with IR alone, and with human embryonic lung fibroblast control cells (HEL 299), GBM8401 cells treated with IR combined with amiloride showed increased overexpression of phosphorylated Akt, regardless of whether IR treatment was performed before or after amiloride administration. The alternative splicing pattern of apoptotic protease-activating factor-1 (APAF1) in cells treated with amiloride alone, IR alone, and combined amiloride-IR treatments showed more consistent cell proliferation compared to that in other apoptosis-related genes such as baculoviral IAP repeat containing 5 (BIRC5), Bcl-X, and homeodomain interacting protein kinase-3 (HIPK3). In GBM8401 cells treated with amiloride with IR post-treatment, the ratio of prosurvival (-XL,-LC) to proapoptotic (-LN,-S) splice variants of APAF1 was lower than that seen in cells treated with amiloride with IR pretreatment, suggesting that proapoptotic splice variants of APAF1 (APAF1-LN,-S) were higher in the glioblastoma cells treated with amiloride with IR post-treatment, as compared to glioblastoma cells and fibroblast control cells that had received other treatments. Together, these results suggest that amiloride modulates cell radiosensitivity involving the Akt phosphorylation and the alternative splicing of APAF1, especially for the cells treated with amiloride with IR post-treatment. Therefore, amiloride may improve the effectiveness of radiation therapy for GBMs.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung, Taiwan
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43
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Liu MM, Zack DJ. Alternative splicing and retinal degeneration. Clin Genet 2013; 84:142-9. [PMID: 23647439 DOI: 10.1111/cge.12181] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 04/30/2013] [Accepted: 04/30/2013] [Indexed: 12/27/2022]
Abstract
Alternative splicing is highly regulated in tissue-specific and development-specific patterns, and it has been estimated that 15% of disease-causing point mutations affect pre-mRNA splicing. In this review, we consider the cis-acting splice site and trans-acting splicing factor mutations that affect pre-mRNA splicing and contribute to retinal degeneration. Numerous splice site mutations have been identified in retinitis pigmentosa (RP) and various cone-rod dystrophies. Mutations in alternatively spliced retina-specific exons of the widely expressed RPGR and COL2A1 genes lead primarily to X-linked RP and ocular variants of Stickler syndrome, respectively. Furthermore, mutations in general pre-mRNA splicing factors, such as PRPF31, PRPF8, and PRPF3, predominantly cause autosomal dominant RP. These findings suggest an important role for pre-mRNA splicing in retinal homeostasis and the pathogenesis of retinal degenerative diseases. The development of novel therapeutic strategies to modulate aberrant splicing, including small molecule-based therapies, has the potential to lead to new treatments for retinal degenerative diseases.
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Affiliation(s)
- M M Liu
- Wilmer Eye Institute, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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Havens MA, Duelli DM, Hastings ML. Targeting RNA splicing for disease therapy. WILEY INTERDISCIPLINARY REVIEWS. RNA 2013; 4:247-66. [PMID: 23512601 PMCID: PMC3631270 DOI: 10.1002/wrna.1158] [Citation(s) in RCA: 128] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Splicing of pre-messenger RNA into mature messenger RNA is an essential step for the expression of most genes in higher eukaryotes. Defects in this process typically affect cellular function and can have pathological consequences. Many human genetic diseases are caused by mutations that cause splicing defects. Furthermore, a number of diseases are associated with splicing defects that are not attributed to overt mutations. Targeting splicing directly to correct disease-associated aberrant splicing is a logical approach to therapy. Splicing is a favorable intervention point for disease therapeutics, because it is an early step in gene expression and does not alter the genome. Significant advances have been made in the development of approaches to manipulate splicing for therapy. Splicing can be manipulated with a number of tools including antisense oligonucleotides, modified small nuclear RNAs (snRNAs), trans-splicing, and small molecule compounds, all of which have been used to increase specific alternatively spliced isoforms or to correct aberrant gene expression resulting from gene mutations that alter splicing. Here we describe clinically relevant splicing defects in disease states, the current tools used to target and alter splicing, specific mutations and diseases that are being targeted using splice-modulating approaches, and emerging therapeutics.
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Affiliation(s)
- Mallory A. Havens
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA. No conflicts of interest
| | - Dominik M. Duelli
- Department of Cellular and Molecular Pharmacology, Chicago Medical School, Rosalind Franklin University of Medicine and Science, North Chicago, IL, 60064, USA. No conflicts of interest
| | - Michelle L. Hastings
- Department of Cell Biology and Anatomy, Chicago Medical School, Rosalind Franklin University of Medicine and Science. North Chicago, IL, 60064, USA, Phone: 847-578-8517 Fax: 847-578-3253. No conflicts of interest
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Low expression of the putative tumour suppressor spinophilin is associated with higher proliferative activity and poor prognosis in patients with hepatocellular carcinoma. Br J Cancer 2013; 108:1830-7. [PMID: 23591196 PMCID: PMC3658515 DOI: 10.1038/bjc.2013.165] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
BACKGROUND Spinophilin, a multifunctional intracellular scaffold protein, is reduced in certain types of cancer and is regarded as a novel putative tumour suppressor protein. However, the role of spinophilin in hepatocellular carcinoma (HCC) has never been explored before. METHODS In this study, we determined for the first time the expression pattern of spinophilin in human HCC by immunohistochemistry and quantitative reverse transcriptase-PCR analysis. In addition, we performed immunohistochemical analysis of p53, p14(ARF) and the proliferation marker Ki-67. Kaplan-Meier curves and multivariate Cox proportional models were used to study the impact on clinical outcome. Small interfering RNA (siRNA) was used to silence spinophilin and to explore the effects of reduced spinophilin expression on cellular growth. RESULTS In our study, complete loss of spinophilin immunoreactivity was found in 44 of 104 HCCs (42.3%) and reduced levels were found in an additional 37 (35.6%) cases. After adjusting for other prognostic factors, multivariate Cox regression analysis identified low expression of spinophilin as an independent prognostic factor with respect to disease-free (hazard ratio (HR)=1.8; 95% confidence interval (CI)=1.04-3.40; P=0.043) and cancer-specific survival (HR=2.0; CI=1.1-3.8; P=0.025). Reduced spinophilin expression significantly correlated with higher Ki-67 index in HCC (P=0.014). Reducing spinophilin levels by siRNA induced a higher cellular growth rate and increased cyclin D2 expression in tumour cells (P<0.05). CONCLUSION This is the first study of the expression pattern and distribution of spinophilin in HCC. According to our data, the loss of spinophilin is associated with higher proliferation and might be useful as a prognostic marker in patients with HCC.
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Abstract
Several bacterial fermentation products and their synthetic derivatives display antitumour activities and bind tightly to components of the spliceosome, which is the complex molecular machinery involved in the removal of introns from mRNA precursors in eukaryotic cells. The drugs alter gene expression, including alternative splicing, of genes that are important for cancer progression. A flurry of recent reports has revealed that genes encoding splicing factors, including the drug target splicing factor 3B subunit 1 (SF3B1), are among the most highly mutated in various haematological malignancies such as chronic lymphocytic leukaemia and myelodysplastic syndromes. These observations highlight the role of splicing factors in cancer and suggest that an understanding of the molecular effects of drugs targeting these proteins could open new perspectives for studies of the spliceosome and its role in cancer progression, and for the development of novel antitumour therapies.
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47
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Pre-mRNA splicing in disease and therapeutics. Trends Mol Med 2012; 18:472-82. [PMID: 22819011 DOI: 10.1016/j.molmed.2012.06.006] [Citation(s) in RCA: 325] [Impact Index Per Article: 27.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 06/12/2012] [Accepted: 06/18/2012] [Indexed: 01/18/2023]
Abstract
In metazoans, alternative splicing of genes is essential for regulating gene expression and contributing to functional complexity. Computational predictions, comparative genomics, and transcriptome profiling of normal and diseased tissues indicate that an unexpectedly high fraction of diseases are caused by mutations that alter splicing. Mutations in cis elements cause missplicing of genes that alter gene function and contribute to disease pathology. Mutations of core spliceosomal factors are associated with hematolymphoid neoplasias, retinitis pigmentosa, and microcephalic osteodysplastic primordial dwarfism type 1 (MOPD1). Mutations in the trans regulatory factors that control alternative splicing are associated with autism spectrum disorder, amyotrophic lateral sclerosis (ALS), and various cancers. In addition to discussing the disorders caused by these mutations, this review summarizes therapeutic approaches that have emerged to correct splicing of individual genes or target the splicing machinery.
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Four parameters increase the sensitivity and specificity of the exon array analysis and disclose 25 novel aberrantly spliced exons in myotonic dystrophy. J Hum Genet 2012; 57:368-74. [PMID: 22513715 DOI: 10.1038/jhg.2012.37] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Myotonic dystrophy type 1 (DM1) is an RNA gain-of-function disorder in which abnormally expanded CTG repeats of DMPK sequestrate a splicing trans-factor MBNL1 and upregulate another splicing trans-factor CUGBP1. To identify a diverse array of aberrantly spliced genes, we performed the exon array analysis of DM1 muscles. We analyzed 72 exons by RT-PCR and found that 27 were aberrantly spliced, whereas 45 were not. Among these, 25 were novel and especially splicing aberrations of LDB3 exon 4 and TTN exon 45 were unique to DM1. Retrospective analysis revealed that four parameters efficiently detect aberrantly spliced exons: (i) the signal intensity is high; (ii) the ratio of probe sets with reliable signal intensities (that is, detection above background P-value=0.000) is high within a gene; (iii) the splice index (SI) is high; and (iv) SI is deviated from SIs of the other exons that can be estimated by calculating the deviation value (DV). Application of the four parameters gave rise to a sensitivity of 77.8% and a specificity of 95.6% in our data set. We propose that calculation of DV, which is unique to our analysis, is of particular importance in analyzing the exon array data.
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Liu J, Xiao Y, Xiong HM, Li J, Huang B, Zhang HB, Feng DQ, Chen XM, Wang XZ. Alternative splicing of apoptosis-related genes in imatinib-treated K562 cells identified by exon array analysis. Int J Mol Med 2011; 29:690-8. [PMID: 22211240 PMCID: PMC3577368 DOI: 10.3892/ijmm.2011.872] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2011] [Accepted: 12/02/2011] [Indexed: 01/22/2023] Open
Abstract
Imatinib is the therapeutic standard for newly diagnosed patients with chronic myeloid leukemia (CML). In these patients, imatinib has been shown to induce an apoptotic response specifically in cells expressing the oncogenic fusion protein BCR-ABL. Previous studies in our lab revealed that imatinib-induced apoptosis in K562 cells involves a shift in production of Bcl-x splice isoforms towards the pro-apoptotic Bcl-xS splice variant. Here, we report the findings from our subsequent study to identify other apoptosis-related genes that are differentially spliced in response to imatinib treatment. Gene expression profiling of imatinib-treated K562 cells was performed by the Affymetrix GeneChip® Human Exon 1.0 ST array, and differences in exon-level expression and alternative splicing were analyzed using the easyExon software. Detailed analysis by reverse transcription-PCR (RT-PCR) and sequencing of key genes confirmed the experimental results of the exon array. Our results suggest that imatinib treatment of K562 cells causes a transcriptional shift towards alternative splicing in a large number of apoptotic genes. The present study provides insight into the molecular character of apoptotic leukemia cells and may help to improve the mechanism of imatinib therapy in patients with CML.
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Affiliation(s)
- Jing Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Nanchang University, Nanchang 330006, PR China
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