1
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Han BY, Liu Z, Hu X, Ling H. HNRNPU promotes the progression of triple-negative breast cancer via RNA transcription and alternative splicing mechanisms. Cell Death Dis 2022; 13:940. [PMID: 36347834 PMCID: PMC9643420 DOI: 10.1038/s41419-022-05376-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 10/25/2022] [Accepted: 10/25/2022] [Indexed: 11/09/2022]
Abstract
Triple-negative breast cancer (TNBC) is a great detriment to women's health due to the lack of effective therapeutic targets. In this study, we employed an integrated genetic screen to identify a pivotal oncogenic factor, heterogeneous nuclear ribonucleoprotein U (HNRNPU), which is required for the progression of TNBC. We elucidated the pro-oncogenic role of HNRNPU, which can induce the proliferation and migration of TNBC cells via its association with DEAD box helicase 5 (DDX5) protein. Elevated levels of the HNRNPU-DDX5 complex prohibited the intron retention of minichromosome maintenance protein 10 (MCM10) pre-mRNA, decreased nonsense-mediated mRNA decay, and activated Wnt/β-catenin signalling; on the other hand, HNRNPU-DDX5 is located in the transcriptional start sites (TSS) of LIM domain only protein 4 (LMO4) and its upregulation promoted the transcription of LMO4, consequently activating PI3K-Akt-mTOR signalling. Our data highlight the synergetic effects of HNRNPU in RNA transcription and splicing in regulating cancer progression and suggest that HNRNPU may act as a potential molecular target in the treatment of TNBC.
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Affiliation(s)
- Bo-yue Han
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Zhebin Liu
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Xin Hu
- Key Laboratory of Breast Cancer in Shanghai, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
| | - Hong Ling
- Department of Breast Surgery, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, 200032 China ,grid.8547.e0000 0001 0125 2443Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, 200032 China
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2
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Lucas AT, Moody A, Schorzman AN, Zamboni WC. Importance and Considerations of Antibody Engineering in Antibody-Drug Conjugates Development from a Clinical Pharmacologist's Perspective. Antibodies (Basel) 2021; 10:30. [PMID: 34449544 PMCID: PMC8395454 DOI: 10.3390/antib10030030] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 07/04/2021] [Accepted: 07/16/2021] [Indexed: 12/12/2022] Open
Abstract
Antibody-drug conjugates (ADCs) appear to be in a developmental boom, with five FDA approvals in the last two years and a projected market value of over $4 billion by 2024. Major advancements in the engineering of these novel cytotoxic drug carriers have provided a few early success stories. Although the use of these immunoconjugate agents are still in their infancy, valuable lessons in the engineering of these agents have been learned from both preclinical and clinical failures. It is essential to appreciate how the various mechanisms used to engineer changes in ADCs can alter the complex pharmacology of these agents and allow the ADCs to navigate the modern-day therapeutic challenges within oncology. This review provides a global overview of ADC characteristics which can be engineered to alter the interaction with the immune system, pharmacokinetic and pharmacodynamic profiles, and therapeutic index of ADCs. In addition, this review will highlight some of the engineering approaches being explored in the creation of the next generation of ADCs.
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Affiliation(s)
- Andrew T. Lucas
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (A.T.L.); (A.N.S.)
- Carolina Center of Cancer Nanotechnology Excellence, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Amber Moody
- Carolina Center of Cancer Nanotechnology Excellence, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
| | - Allison N. Schorzman
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (A.T.L.); (A.N.S.)
| | - William C. Zamboni
- Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; (A.T.L.); (A.N.S.)
- Carolina Center of Cancer Nanotechnology Excellence, UNC Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA;
- Glolytics, LLC, Chapel Hill, NC 27517, USA
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3
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Dai X, Yu L, Chen X, Zhang J. SNRPD1 confers diagnostic and therapeutic values on breast cancers through cell cycle regulation. Cancer Cell Int 2021; 21:229. [PMID: 33879154 PMCID: PMC8059192 DOI: 10.1186/s12935-021-01932-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 04/13/2021] [Indexed: 01/05/2023] Open
Abstract
Background SNRPD1 is a spliceosome-associated protein and has previously been implicated with important roles in cancer development. Methods Through analyzing the differential expression patterns and clinical association of splicing associated genes among tumor and tumor adjacent samples across different tumors and among different breast cancer subtypes, we identify the tumor promotive role of SNRPD1 using multiple publicly available datasets. Through pathway, gene ontology enrichment analysis and network construction, we linked the onco-therapeutic role of SNRPD1 with cell cycle. Via a series of experimental studies including knockdown assay, qPCR, western blotting, cell cycle, drug response assay, we confirmed the higher expression of SNPRD1 at both gene and protein expression levels in triple negative breast cancer cells, as well as its roles in promoting cell cycle and chemotherapy response. Results Our study revealed that SNRPD1 over-expression was significantly associated with genes involved in cell cycle, cell mitosis and chromatin replication, and silencing SNRPD1 in breast cancer cells could lead to halted tumor cell growth and cell cycle arrest at the G0/G1 stage. We also found that triple negative breast cancer cells with reduced SNRPD1 expression lost certain sensitivity to doxorubicin whereas luminal cancer cells did not. Conclusions Our results suggested the prognostic value of SNRPD1 on breast cancer survival, its potential as the therapeutic target halting cell cycle progression for breast cancer control, and warranted special attention on the combined use of doxorubicin and drugs targeting SNRPD1. Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-01932-w.
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Affiliation(s)
- Xiaofeng Dai
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China.
| | - Lihui Yu
- Wuxi School of Medicine, Jiangnan University, Wuxi, Jiangsu, China
| | - Xiao Chen
- School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Jianying Zhang
- Henan Academy of Medical and Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
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4
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Yoshimoto R, Chhipi-Shrestha JK, Schneider-Poetsch T, Furuno M, Burroughs AM, Noma S, Suzuki H, Hayashizaki Y, Mayeda A, Nakagawa S, Kaida D, Iwasaki S, Yoshida M. Spliceostatin A interaction with SF3B limits U1 snRNP availability and causes premature cleavage and polyadenylation. Cell Chem Biol 2021; 28:1356-1365.e4. [PMID: 33784500 DOI: 10.1016/j.chembiol.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Revised: 01/07/2021] [Accepted: 03/09/2021] [Indexed: 12/01/2022]
Abstract
RNA splicing, a highly conserved process in eukaryotic gene expression, is seen as a promising target for anticancer agents. Splicing is associated with other RNA processing steps, such as transcription and nuclear export; however, our understanding of the interaction between splicing and other RNA regulatory mechanisms remains incomplete. Moreover, the impact of chemical splicing inhibition on long non-coding RNAs (lncRNAs) has been poorly understood. Here, we demonstrate that spliceostatin A (SSA), a chemical splicing modulator that binds to the SF3B subcomplex of the U2 small nuclear ribonucleoprotein particle (snRNP), limits U1 snRNP availability in splicing, resulting in premature cleavage and polyadenylation of MALAT1, a nuclear lncRNA, as well as protein-coding mRNAs. Therefore, truncated transcripts are exported into the cytoplasm and translated, resulting in aberrant protein products. Our work demonstrates that active recycling of the splicing machinery maintains homeostasis of RNA processing beyond intron excision.
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Affiliation(s)
- Rei Yoshimoto
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Jagat K Chhipi-Shrestha
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tilman Schneider-Poetsch
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan
| | - Masaaki Furuno
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - A Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Shohei Noma
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Harukazu Suzuki
- RIKEN Center for Integrative Medical Sciences, Tsurumi-ku, Yokohama 230-0045, Japan
| | - Yoshihide Hayashizaki
- RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako, Saitama 351-0198, Japan
| | - Akila Mayeda
- Division of Gene Expression Mechanism, Institute for Comprehensive Medical Science, Fujita Health University, Toyoake, Aichi 470-1192, Japan
| | - Shinichi Nakagawa
- RNA Biology Laboratory, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Hokkaido 060-0812, Japan
| | - Daisuke Kaida
- Department of Gene Expression and Regulation, Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, Sugitani, Toyama 930-0194, Japan
| | - Shintaro Iwasaki
- RNA Systems Biochemistry Laboratory, RIKEN Cluster for Pioneering Research, Wako, Saitama 351-0198, Japan; Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Chiba 277-8561, Japan; AMED-CREST, Japan Agency for Medical Research and Development, Chiyoda-ku, Tokyo 100-0004 Japan.
| | - Minoru Yoshida
- Chemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama 351-0198, Japan; Department of Biotechnology, Graduate School of Agricultural Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan; Collaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan.
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5
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Darrigrand R, Pierson A, Rouillon M, Renko D, Boulpicante M, Bouyssié D, Mouton-Barbosa E, Marcoux J, Garcia C, Ghosh M, Alami M, Apcher S. Isoginkgetin derivative IP2 enhances the adaptive immune response against tumor antigens. Commun Biol 2021; 4:269. [PMID: 33649389 PMCID: PMC7921396 DOI: 10.1038/s42003-021-01801-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 02/05/2021] [Indexed: 11/25/2022] Open
Abstract
The success of cancer immunotherapy relies on the induction of an immunoprotective response targeting tumor antigens (TAs) presented on MHC-I molecules. We demonstrated that the splicing inhibitor isoginkgetin and its water-soluble and non-toxic derivative IP2 act at the production stage of the pioneer translation products (PTPs). We showed that IP2 increases PTP-derived antigen presentation in cancer cells in vitro and impairs tumor growth in vivo. IP2 action is long-lasting and dependent on the CD8+ T cell response against TAs. We observed that the antigen repertoire displayed on MHC-I molecules at the surface of MCA205 fibrosarcoma is modified upon treatment with IP2. In particular, IP2 enhances the presentation of an exon-derived epitope from the tumor suppressor nischarin. The combination of IP2 with a peptide vaccine targeting the nischarin-derived epitope showed a synergistic antitumor effect in vivo. These findings identify the spliceosome as a druggable target for the development of epitope-based immunotherapies.
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Affiliation(s)
- Romain Darrigrand
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie des tumeurs et Immunothérapie, Villejuif, France
| | - Alison Pierson
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie des tumeurs et Immunothérapie, Villejuif, France
| | - Marine Rouillon
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie des tumeurs et Immunothérapie, Villejuif, France
- SATT Paris Saclay, Orsay, France
| | - Dolor Renko
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Mathilde Boulpicante
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie des tumeurs et Immunothérapie, Villejuif, France
| | - David Bouyssié
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Emmanuelle Mouton-Barbosa
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Julien Marcoux
- Institut de Pharmacologie et de Biologie Structurale (IPBS), Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Camille Garcia
- Institut Jacques Monod, CNRS U7592 Université Paris Diderot, Paris, France
- Institut Pasteur, Unité de Spectrométrie de Masse pour la Biologie (MSBio), Centre de Ressources et Recherches Technologiques (C2RT), USR 2000 CNRS, Paris, France
| | - Michael Ghosh
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Mouad Alami
- Université Paris-Saclay, CNRS, BioCIS, Châtenay-Malabry, France
| | - Sébastien Apcher
- Université Paris-Saclay, Institut Gustave Roussy, Inserm, Immunologie des tumeurs et Immunothérapie, Villejuif, France.
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6
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Cao Y, Di X, Zhang Q, Li R, Wang K. RBM10 Regulates Tumor Apoptosis, Proliferation, and Metastasis. Front Oncol 2021; 11:603932. [PMID: 33718153 PMCID: PMC7943715 DOI: 10.3389/fonc.2021.603932] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
The RNA-binding motif protein 10 (RBM10) is involved in alternative splicing and modifies mRNA post-transcriptionally. RBM10 is abnormally expressed in the lung, breast, and colorectal cancer, female genital tumors, osteosarcoma, and other malignant tumors. It can inhibit proliferation, promote apoptosis, and inhibit invasion and metastasis. RBM10 has long been considered a tumor suppressor because it promotes apoptosis through the regulation of the MDM2-p53 negative feedback loop, Bcl-2, Bax, and other apoptotic proteins and inhibits proliferation through the Notch signaling and rap1a/Akt/CREB pathways. However, it has been recently demonstrated that RBM10 can also promote cancer. Given these different views, it is necessary to summarize the research progress of RBM10 in various fields to reasonably analyze the underlying molecular mechanisms, and provide new ideas and directions for the clinical research of RBM10 in various cancer types. In this review, we provide a new perspective on the reasons for these opposing effects on cancer biology, molecular mechanisms, research progress, and clinical value of RBM10.
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Affiliation(s)
- Yingshu Cao
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Xin Di
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Qinghua Zhang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
| | - Ranwei Li
- Department of Urinary Surgery, The Second Hospital of Jilin University, Changchun, China
| | - Ke Wang
- Department of Respiratory Medicine, The Second Hospital of Jilin University, Changchun, China
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7
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Schneider-Poetsch T, Chhipi-Shrestha JK, Yoshida M. Splicing modulators: on the way from nature to clinic. J Antibiot (Tokyo) 2021; 74:603-616. [PMID: 34345042 PMCID: PMC8472923 DOI: 10.1038/s41429-021-00450-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Over the course of more than two decades, natural products isolated from various microorganisms and plants have built the foundation for chemical biology research into the mechanism of pre-mRNA splicing. Hand in hand with advances in scientific methodology small molecule splicing modulators have become powerful tools for investigating, not just the splicing mechanism, but also the cellular effect of altered mRNA processing. Based on thorough structure-activity studies, synthetic analogues have moved on from scientific tool compounds to experimental drugs. With current advances in drug discovery methodology and new means of attacking targets previously thought undruggable, we can expect further advances in both research and therapeutics based on small molecule splicing modulators.
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Affiliation(s)
- Tilman Schneider-Poetsch
- grid.509461.fChemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan
| | | | - Minoru Yoshida
- grid.509461.fChemical Genomics Research Group, RIKEN Center for Sustainable Resource Science, Wako, Saitama Japan ,grid.26999.3d0000 0001 2151 536XDepartment of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo Japan ,grid.26999.3d0000 0001 2151 536XCollaborative Research Institute for Innovative Microbiology, The University of Tokyo, Bunkyo-ku, Tokyo Japan
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8
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Liu S, Yang Z, Li G, Li C, Luo Y, Gong Q, Wu X, Li T, Zhang Z, Xing B, Xu X, Lu X. Multi-omics Analysis of Primary Cell Culture Models Reveals Genetic and Epigenetic Basis of Intratumoral Phenotypic Diversity. GENOMICS PROTEOMICS & BIOINFORMATICS 2020; 17:576-589. [PMID: 32205176 PMCID: PMC7212478 DOI: 10.1016/j.gpb.2018.07.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/29/2018] [Accepted: 07/24/2018] [Indexed: 12/27/2022]
Abstract
Uncovering the functionally essential variations related to tumorigenesis and tumor progression from cancer genomics data is still challenging due to the genetic diversity among patients, and extensive inter- and intra-tumoral heterogeneity at different levels of gene expression regulation, including but not limited to the genomic, epigenomic, and transcriptional levels. To minimize the impact of germline genetic heterogeneities, in this study, we establish multiple primary cultures from the primary and recurrent tumors of a single patient with hepatocellular carcinoma (HCC). Multi-omics sequencing was performed for these cultures that encompass the diversity of tumor cells from the same patient. Variations in the genome sequence, epigenetic modification, and gene expression are used to infer the phylogenetic relationships of these cell cultures. We find the discrepancy among the relationships revealed by single nucleotide variations (SNVs) and transcriptional/epigenomic profiles from the cell cultures. We fail to find overlap between sample-specific mutated genes and differentially expressed genes (DEGs), suggesting that most of the heterogeneous SNVs among tumor stages or lineages of the patient are functionally insignificant. Moreover, copy number alterations (CNAs) and DNA methylation variation within gene bodies, rather than promoters, are significantly correlated with gene expression variability among these cell cultures. Pathway analysis of CNA/DNA methylation-related genes indicates that a single cell clone from the recurrent tumor exhibits distinct cellular characteristics and tumorigenicity, and such an observation is further confirmed by cellular experiments both in vitro and in vivo. Our systematic analysis reveals that CNAs and epigenomic changes, rather than SNVs, are more likely to contribute to the phenotypic diversity among subpopulations in the tumor. These findings suggest that new therapeutic strategies targeting gene dosage and epigenetic modification should be considered in personalized cancer medicine. This culture model may be applied to the further identification of plausible determinants of cancer metastasis and relapse.
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Affiliation(s)
- Sixue Liu
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (2)University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zuyu Yang
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (3)Invasive Pathogens Laboratory, Institute of Environmental Science and Research, Porirua 5022, Wellington, New Zealand
| | - Guanghao Li
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (2)University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunyan Li
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (2)University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yanting Luo
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (2)University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiang Gong
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xin Wu
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Tao Li
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (2)University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiqian Zhang
- (4)Department of Cell Biology, Key Laboratory of Carcinogenesis and Translational Research, Center for Molecular and Translational Medicine, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Baocai Xing
- (5)Department of Hepatobiliary Surgery I, Peking University Cancer Hospital and Institute, Beijing 100142, China
| | - Xiaolan Xu
- (6)National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
| | - Xuemei Lu
- (1)CAS Key Laboratory of Genomics and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China; (2)University of Chinese Academy of Sciences, Beijing 100049, China; (7)CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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9
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Robert T, Johnson JL, Guichaoua R, Yaron TM, Bach S, Cantley LC, Colas P. Development of a CDK10/CycM in vitro Kinase Screening Assay and Identification of First Small-Molecule Inhibitors. Front Chem 2020; 8:147. [PMID: 32175313 PMCID: PMC7056863 DOI: 10.3389/fchem.2020.00147] [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: 10/25/2019] [Accepted: 02/17/2020] [Indexed: 12/31/2022] Open
Abstract
Cyclin-dependent kinases (CDKs) constitute a family of 20 serine/threonine protein kinases that play pivotal roles in the regulation of numerous important molecular and cellular processes. CDKs have long been considered promising therapeutic targets in a variety of pathologies, and the recent therapeutic success of CDK4/6 inhibitors in breast cancers has renewed interest in their therapeutic potential. Small-molecule inhibitors have been identified for every human CDK, except for CDK10. The only recent discovery of an activating cyclin (CycM) for CDK10 enabled us to identify its first phosphorylation substrates and gain insights into its biological functions. Yet, our knowledge of this kinase remains incomplete, despite it being the only member of its family that causes severe human developmental syndromes, when mutated either on the cyclin or the CDK moiety. CDK10 small-molecule inhibitors would be useful in exploring the functions of this kinase and gauging its potential as a therapeutic target for some cancers. Here, we report the identification of an optimized peptide phosphorylation substrate of CDK10/CycM and the development of the first homogeneous, miniaturized CDK10/CycM in vitro kinase assay. We reveal the ability of known CDK inhibitors, among which clinically tested SNS-032, riviciclib, flavopiridol, dinaciclib, AZD4573 and AT7519, to potently inhibit CDK10/CycM. We also show that NVP-2, a strong, remarkably selective CDK9 inhibitor is an equally potent CDK10/CycM inhibitor. Finally, we validate this kinase assay for applications in high-throughput screening campaigns to discover new, original CDK10 inhibitors.
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Affiliation(s)
- Thomas Robert
- Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université/CNRS, Roscoff, France.,Kinase Inhibitor Specialized Screening Facility (KISSf), Station Biologique de Roscoff, Sorbonne Université/CNRS, Roscoff, France
| | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Roxane Guichaoua
- Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université/CNRS, Roscoff, France
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Stéphane Bach
- Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université/CNRS, Roscoff, France.,Kinase Inhibitor Specialized Screening Facility (KISSf), Station Biologique de Roscoff, Sorbonne Université/CNRS, Roscoff, France
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, United States
| | - Pierre Colas
- Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université/CNRS, Roscoff, France
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10
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Zhang Y, Yuan Z, Jiang Y, Shen R, Gu M, Xu W, Gu X. Inhibition of Splicing Factor 3b Subunit 1 (SF3B1) Reduced Cell Proliferation, Induced Apoptosis and Resulted in Cell Cycle Arrest by Regulating Homeobox A10 (HOXA10) Splicing in AGS and MKN28 Human Gastric Cancer Cells. Med Sci Monit 2020; 26:e919460. [PMID: 31927557 PMCID: PMC6977614 DOI: 10.12659/msm.919460] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Background Small nuclear ribonucleoproteins (snRNPs) complexes of protein and noncoding RNA accumulate in the cell nucleus and catalyze pre-mRNA splicing to form the spliceosome. This study aimed to investigate the role of the spliceosome, splicing factor 3b subunit 1 (SF3B1), in AGS and MKN28 human gastric cancer cells in vitro, including gene knockdown with small interfering RNA (siRNA), and the use of the selective mRNA splicing inhibitor of SF3B1, pladienolide B. Material/Methods In AGS and MKN28 human gastric cancer cells, SF3B1expression was inhibited with siRNA and pladienolide B. Following SF3B1 inhibition, the Cell Counting Kit-8 (CCK-8) assay measured cell proliferation, and flow cytometry was used to investigate cell apoptosis and cell cycle arrest. The downstream HOXA10 and AKT pathways were studied by quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and Western blot. The presence of alternative splicing, or differential splicing, of single-gene coding for multiple proteins, was analyzed using The Cancer Genome Atlas (TCGA) SpliceSeq. Results Inhibition of SF3B1 reduced the proliferation rate of AGS and MKN28 human gastric cancer cells by inducing apoptosis and G2/M phase arrest. SF3B1 knockdown resulted in reduced homeobox A10 (HOXA10) mRNA expression and expression of long noncoding RNA (lncRNA) isoforms of HOXA10 (exons 1 and 3) and HOXA10 (exons 2 and 3). SF3B1 inhibition increased PTEN levels and reduced AKT protein phosphorylation. Conclusions In AGS and MKN28 human gastric cancer cells in vitro, inhibition of SF3B1 reduced cell proliferation, induced apoptosis, and resulted in cell cycle arrest by regulating HOXA10 splicing.
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Affiliation(s)
- Yan Zhang
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
| | - Zhen Yuan
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
| | - Yannan Jiang
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
| | - Renbin Shen
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
| | - Menghui Gu
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
| | - Wei Xu
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
| | - Xinhua Gu
- Department of Gastrointestinal Surgery, Suzhou Municipal Hospital, Nanjing Medical University, Suzhou, Jiangsu, China (mainland)
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11
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Harris C, Xu W, Grassi L, Wang C, Markle A, Hardman C, Stevens R, Miro-Quesada G, Hatton D, Wang J. Identification and characterization of an IgG sequence variant with an 11 kDa heavy chain C-terminal extension using a combination of mass spectrometry and high-throughput sequencing analysis. MAbs 2019; 11:1452-1463. [PMID: 31570042 PMCID: PMC6816433 DOI: 10.1080/19420862.2019.1667740] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Protein primary structure is a potential critical quality attribute for biotherapeutics. Identifying and characterizing any sequence variants present is essential for product development. A sequence variant ~11 kDa larger than the expected IgG mass was observed by size-exclusion chromatography and two-dimensional liquid chromatography coupled with online mass spectrometry. Further characterization indicated that the 11 kDa was added to the heavy chain (HC) Fc domain. Despite the relatively large mass addition, only one unknown peptide was detected by peptide mapping. To decipher the sequence, the transcriptome of the manufacturing cell line was characterized by Illumina RNA-seq. Transcriptome reconstruction detected an aberrant fusion transcript, where the light chain (LC) constant domain sequence was fused to the 3ʹ end of the HC transcript. Translation of this fusion transcript generated an extended peptide sequence at the HC C-terminus corresponding to the observed 11 kDa mass addition. Nanopore-based genome sequencing showed multiple copies of the plasmid had integrated in tandem with one copy missing the 5ʹ end of the plasmid, deleting the LC variable domain. The fusion transcript was due to read-through of the HC terminator sequence into the adjacent partial LC gene and an unexpected splicing event between a cryptic splice-donor site at the 3ʹ end of the HC and the splice acceptor site at the 5ʹ end of the LC constant domain. Our study demonstrates that combining protein physicochemical characterization with genomic and transcriptomic analysis of the manufacturing cell line greatly improves the identification of sequence variants and understanding of the underlying molecular mechanisms.
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Affiliation(s)
- Claire Harris
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Weichen Xu
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Luigi Grassi
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Chunlei Wang
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Abigail Markle
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Colin Hardman
- Data Science & Artificial Intelligence, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Richard Stevens
- Antibody Discovery and Protein Engineering, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Guillermo Miro-Quesada
- Data & Quantitative Sciences, Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
| | - Diane Hatton
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Cambridge , UK
| | - Jihong Wang
- Biopharmaceutical Development, BioPharmaceuticals R&D, AstraZeneca , Gaithersburg , MD , USA
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12
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El-Athman R, Knezevic D, Fuhr L, Relógio A. A Computational Analysis of Alternative Splicing across Mammalian Tissues Reveals Circadian and Ultradian Rhythms in Splicing Events. Int J Mol Sci 2019; 20:E3977. [PMID: 31443305 PMCID: PMC6721216 DOI: 10.3390/ijms20163977] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/03/2019] [Accepted: 08/10/2019] [Indexed: 02/07/2023] Open
Abstract
Mounting evidence points to a role of the circadian clock in the temporal regulation of post-transcriptional processes in mammals, including alternative splicing (AS). In this study, we carried out a computational analysis of circadian and ultradian rhythms on the transcriptome level to characterise the landscape of rhythmic AS events in published datasets covering 76 tissues from mouse and olive baboon. Splicing-related genes with 24-h rhythmic expression patterns showed a bimodal distribution of peak phases across tissues and species, indicating that they might be controlled by the circadian clock. On the output level, we identified putative oscillating AS events in murine microarray data and pairs of differentially rhythmic splice isoforms of the same gene in baboon RNA-seq data that peaked at opposing times of the day and included oncogenes and tumour suppressors. We further explored these findings using a new circadian RNA-seq dataset of human colorectal cancer cell lines. Rhythmic isoform expression patterns differed between the primary tumour and the metastatic cell line and were associated with cancer-related biological processes, indicating a functional role of rhythmic AS that might be implicated in tumour progression. Our data shows that rhythmic AS events are widespread across mammalian tissues and might contribute to a temporal diversification of the proteome.
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Affiliation(s)
- Rukeia El-Athman
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Dora Knezevic
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Luise Fuhr
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, 10117 Berlin, Germany.
- Medical Department of Hematology, Oncology and Tumor Immunology, and Molekulares Krebsforschungszentrum (MKFZ), Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, 10117 Berlin, Germany.
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13
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Chegni H, Hassan ZM, Nisini R, Ebrahimi M, Sabouni F. Preliminary In Vitro Effects of CD8+ T Lymphocyte Specific for the CD20 Alternative Splicing D393-CD20 Peptide Expressed on Burkitt Lymphoma Cells. Asian Pac J Cancer Prev 2019; 20:2563-2568. [PMID: 31450932 PMCID: PMC6852797 DOI: 10.31557/apjcp.2019.20.8.2563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Indexed: 12/22/2022] Open
Abstract
The effective discovery of clinically relevant tumor antigens holds a fundamental role for the development of new diagnostic tools and anticancer immunotherapies. D393-CD20 mRNA is absent from normal resting B cells but present in various malignant or transformed B cells. CD8+T lymphocytes play a central role in immunity to cancer. In this study, we want use from T CD8+ against D393-CD20 for effect in RAMOS cell line. After isolation and expanding of specific TCD8 + Lymphocyte against D393-CD20 antigen, for examining the effect of specialized T lymphocyte clone of D393-CD20 antigen on RAMOS cell line, we co-cultured them together, and the rate of apoptosis were examined by flow cytometry and cytotoxicity techniques by using MTT technique. We observed that specialized TCD8+ lymphocyte of D393-CD20 antigen can induce apoptosis in malignant B-lymphocytes, and this antigen can be a proper target for immunotherapy.
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Affiliation(s)
- Hamid Chegni
- Department of Immunology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Zuhair M Hassan
- Department of Immunology, School of Medical Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Roberto Nisini
- Department of Infectious, Parasitic and Immune-Mediated Diseases, National Institute of Health, Viale Regina Elena 299, 00161 Rome, Italy
| | - Marzieh Ebrahimi
- Department of Stem Cells and Developmental Biology, Cell Science Research Centre, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Farzaneh Sabouni
- National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
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14
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Schissler AG, Aberasturi D, Kenost C, Lussier YA. A Single-Subject Method to Detect Pathways Enriched With Alternatively Spliced Genes. Front Genet 2019; 10:414. [PMID: 31143202 PMCID: PMC6521780 DOI: 10.3389/fgene.2019.00414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2018] [Accepted: 04/16/2019] [Indexed: 01/25/2023] Open
Abstract
RNA-Sequencing data offers an opportunity to enable precision medicine, but most methods rely on gene expression alone. To date, no methodology exists to identify and interpret alternative splicing patterns within pathways for an individual patient. This study develops methodology and conducts computational experiments to test the hypothesis that pathway aggregation of subject-specific alternatively spliced genes (ASGs) can inform upon disease mechanisms and predict survival. We propose the N-of-1-pathways Alternatively Spliced (N1PAS) method that takes an individual patient’s paired-sample RNA-Seq isoform expression data (e.g., tumor vs. non-tumor, before-treatment vs. during-therapy) and pathway annotations as inputs. N1PAS quantifies the degree of alternative splicing via Hellinger distances followed by two-stage clustering to determine pathway enrichment. We provide a clinically relevant “odds ratio” along with statistical significance to quantify pathway enrichment. We validate our method in clinical samples and find that our method selects relevant pathways (p < 0.05 in 4/6 data sets). Extensive Monte Carlo studies show N1PAS powerfully detects pathway enrichment of ASGs while adequately controlling false discovery rates. Importantly, our studies also unveil highly heterogeneous single-subject alternative splicing patterns that cohort-based approaches overlook. Finally, we apply our patient-specific results to predict cancer survival (FDR < 20%) while providing diagnostics in pursuit of translating transcriptome data into clinically actionable information. Software available at https://github.com/grizant/n1pas/tree/master.
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Affiliation(s)
- Alfred Grant Schissler
- Department of Mathematics and Statistics, University of Nevada, Reno, Reno, NV, United States.,Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, United States
| | - Dillon Aberasturi
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, United States.,Department of Medicine, The University of Arizona, Tucson, AZ, United States.,The Graduate Interdisciplinary Program in Statistics, The University of Arizona, Tucson, AZ, United States
| | - Colleen Kenost
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, United States.,Department of Medicine, The University of Arizona, Tucson, AZ, United States
| | - Yves A Lussier
- Center for Biomedical Informatics and Biostatistics, The University of Arizona, Tucson, AZ, United States.,Department of Medicine, The University of Arizona, Tucson, AZ, United States.,BIO5 Institute, The University of Arizona, Tucson, AZ, United States.,Cancer Center, The University of Arizona, Tucson, AZ, United States.,University of Arizona Health Sciences, The University of Arizona, Tucson, AZ, United States
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15
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Yin LL, Wen XM, Li M, Xu YM, Zhao XF, Li J, Wang XW. A gene mutation in RNA-binding protein 10 is associated with lung adenocarcinoma progression and poor prognosis. Oncol Lett 2018; 16:6283-6292. [PMID: 30405763 PMCID: PMC6202477 DOI: 10.3892/ol.2018.9496] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 04/27/2018] [Indexed: 01/20/2023] Open
Abstract
RBM10 regulates the expression of various genes, which are often mutated in male lung adenocarcinoma. The present study confirmed the association of the RBM10 mutation at exon 10 with the clinicopathological data and prognosis of lung adenocarcinoma. The effect of mutant RBM10 on regulating lung cancer cell growth and invasion was investigated in vitro. Tissue specimens from 50 patients with lung adenocarcinoma were subjected to Sanger sequencing for RBM10 exon 10 mutations. Lung adenocarcinoma cells were transfected with pcDNA3.1 carrying wild type RBM10 cDNA or exon mutation cDNA for cell viability, apoptosis and invasion assays. RBM10 exon 10 mutations were identified in 11 out of 50 patients, with a high frequency in male patients [c.763 C>T, p.Arg241Cys for 33.3% (10/30)] and were significantly associated with the American Joint Committee on Cancer stage (P=0.005), lymph node metastasis (P=0.019) and shorter 5-year survival rate compared with the wild type RBM10 (36.4% vs. 46.5%; P=0.019). Multivariate analysis revealed that RBM10 exon 10 mutation was an independent prognostic factor (HR=3.787; P=0.033). RBM10 exon 10 mutation at c.763 C>T significantly promoted tumor cell proliferation and invasion capacity, whereas wild type RBM10 inhibited tumor cell invasion in vitro. In conclusion, RBM 10 mutation at exon 10 (c.763 C>T) occurs frequently and is an independent prognostic predictor in lung adenocarcinoma.
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Affiliation(s)
- Lin-Lin Yin
- Department of Oncology, Qilu Hospital, Shandong University, Jinan, Shandong 250000, P.R. China.,Department of Hematology and Oncology, The Fourth Hospital of Jinan, Jinan, Shandong 250031, P.R. China
| | - Xin-Mian Wen
- Department of Clinical Laboratory, The Fourth Hospital of Jinan, Jinan, Shandong 250031, P.R. China
| | - Ming Li
- Department of Chest Surgery, Shandong Chest Hospital, Jinan, Shandong 250013, P.R. China
| | - Yan-Mei Xu
- Department of Pathology, Shandong Shanxian Central Hospital, Heze, Shandong 274300, P.R. China
| | - Xiao-Feng Zhao
- The Joint Laboratory for Translational Medical Research, Liaocheng People's Hospital, Liaocheng, Shandong 252000, P.R. China
| | - Jing Li
- Department of Hematology and Oncology, The Fourth Hospital of Jinan, Jinan, Shandong 250031, P.R. China
| | - Xiu-Wen Wang
- Department of Oncology, Qilu Hospital, Shandong University, Jinan, Shandong 250000, P.R. China
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16
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El-Athman R, Fuhr L, Relógio A. A Systems-Level Analysis Reveals Circadian Regulation of Splicing in Colorectal Cancer. EBioMedicine 2018; 33:68-81. [PMID: 29936137 PMCID: PMC6085510 DOI: 10.1016/j.ebiom.2018.06.012] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/28/2018] [Accepted: 06/11/2018] [Indexed: 12/26/2022] Open
Abstract
Accumulating evidence points to a significant role of the circadian clock in the regulation of splicing in various organisms, including mammals. Both dysregulated circadian rhythms and aberrant pre-mRNA splicing are frequently implicated in human disease, in particular in cancer. To investigate the role of the circadian clock in the regulation of splicing in a cancer progression context at the systems-level, we conducted a genome-wide analysis and compared the rhythmic transcriptional profiles of colon carcinoma cell lines SW480 and SW620, derived from primary and metastatic sites of the same patient, respectively. We identified spliceosome components and splicing factors with cell-specific circadian expression patterns including SRSF1, HNRNPLL, ESRP1, and RBM 8A, as well as altered alternative splicing events and circadian alternative splicing patterns of output genes (e.g., VEGFA, NCAM1, FGFR2, CD44) in our cellular model. Our data reveals a remarkable interplay between the circadian clock and pre-mRNA splicing with putative consequences in tumor progression and metastasis.
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Affiliation(s)
- Rukeia El-Athman
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Luise Fuhr
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany
| | - Angela Relógio
- Institute for Theoretical Biology (ITB), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany; Medical Department of Hematology, Oncology, and Tumor Immunology, Molekulares Krebsforschungszentrum (MKFZ), Charité - Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität zu Berlin, Berlin Institute of Health, Germany.
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17
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The Role of scaRNAs in Adjusting Alternative mRNA Splicing in Heart Development. J Cardiovasc Dev Dis 2018; 5:jcdd5020026. [PMID: 29738469 PMCID: PMC6023535 DOI: 10.3390/jcdd5020026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Revised: 04/27/2018] [Accepted: 05/03/2018] [Indexed: 12/19/2022] Open
Abstract
Congenital heart disease (CHD) is a leading cause of death in children <1 year of age. Despite intense effort in the last 10 years, most CHDs (~70%) still have an unknown etiology. Conotruncal based defects, such as Tetralogy of Fallot (TOF), a common complex of devastating heart defects, typically requires surgical intervention in the first year of life. We reported that the noncoding transcriptome in myocardial tissue from children with TOF is characterized by significant variation in levels of expression of noncoding RNAs, and more specifically, a significant reduction in 12 small cajal body-associated RNAs (scaRNAs) in the right ventricle. scaRNAs are essential for the biochemical modification and maturation of small nuclear RNAs (spliceosomal RNAs), which in turn are critical components of the spliceosome. This is particularly important because we also documented that splicing of mRNAs that are critical for heart development was dysregulated in the heart tissue of infants with TOF. Furthermore, we went on to show, using the zebrafish model, that altering the expression of these same scaRNAs led to faulty mRNA processing and heart defects in the developing embryo. This review will examine how scaRNAs may influence spliceosome fidelity in exon retention during heart development and thus contribute to regulation of heart development.
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18
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Wahba A, Ryan MC, Shankavaram UT, Camphausen K, Tofilon PJ. Radiation-induced alternative transcripts as detected in total and polysome-bound mRNA. Oncotarget 2017; 9:691-705. [PMID: 29416646 PMCID: PMC5787501 DOI: 10.18632/oncotarget.21672] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 09/16/2017] [Indexed: 12/20/2022] Open
Abstract
Alternative splicing is a critical event in the posttranscriptional regulation of gene expression. To investigate whether this process influences radiation-induced gene expression we defined the effects of ionizing radiation on the generation of alternative transcripts in total cellular mRNA (the transcriptome) and polysome-bound mRNA (the translatome) of the human glioblastoma stem-like cell line NSC11. For these studies, RNA-Seq profiles from control and irradiated cells were compared using the program SpliceSeq to identify transcripts and splice variations induced by radiation. As compared to the transcriptome (total RNA) of untreated cells, the radiation-induced transcriptome contained 92 splice events suggesting that radiation induced alternative splicing. As compared to the translatome (polysome-bound RNA) of untreated cells, the radiation-induced translatome contained 280 splice events of which only 24 were overlapping with the radiation-induced transcriptome. These results suggest that radiation not only modifies alternative splicing of precursor mRNA, but also results in the selective association of existing mRNA isoforms with polysomes. Comparison of radiation-induced alternative transcripts to radiation-induced gene expression in total RNA revealed little overlap (about 3%). In contrast, in the radiation-induced translatome, about 38% of the induced alternative transcripts corresponded to genes whose expression level was affected in the translatome. This study suggests that whereas radiation induces alternate splicing, the alternative transcripts present at the time of irradiation may play a role in the radiation-induced translational control of gene expression and thus cellular radioresponse.
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Affiliation(s)
- Amy Wahba
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | | | - Uma T Shankavaram
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Kevin Camphausen
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
| | - Philip J Tofilon
- Radiation Oncology Branch, National Cancer Institute, Bethesda, MD 20892, USA
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19
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D'Souza M, Sulakhe D, Wang S, Xie B, Hashemifar S, Taylor A, Dubchak I, Conrad Gilliam T, Maltsev N. Strategic Integration of Multiple Bioinformatics Resources for System Level Analysis of Biological Networks. Methods Mol Biol 2017; 1613:85-99. [PMID: 28849559 DOI: 10.1007/978-1-4939-7027-8_5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Recent technological advances in genomics allow the production of biological data at unprecedented tera- and petabyte scales. Efficient mining of these vast and complex datasets for the needs of biomedical research critically depends on a seamless integration of the clinical, genomic, and experimental information with prior knowledge about genotype-phenotype relationships. Such experimental data accumulated in publicly available databases should be accessible to a variety of algorithms and analytical pipelines that drive computational analysis and data mining.We present an integrated computational platform Lynx (Sulakhe et al., Nucleic Acids Res 44:D882-D887, 2016) ( http://lynx.cri.uchicago.edu ), a web-based database and knowledge extraction engine. It provides advanced search capabilities and a variety of algorithms for enrichment analysis and network-based gene prioritization. It gives public access to the Lynx integrated knowledge base (LynxKB) and its analytical tools via user-friendly web services and interfaces. The Lynx service-oriented architecture supports annotation and analysis of high-throughput experimental data. Lynx tools assist the user in extracting meaningful knowledge from LynxKB and experimental data, and in the generation of weighted hypotheses regarding the genes and molecular mechanisms contributing to human phenotypes or conditions of interest. The goal of this integrated platform is to support the end-to-end analytical needs of various translational projects.
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Affiliation(s)
- Mark D'Souza
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA.
- Argonne National Laboratory, Building 221, Room: A142, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Dinanath Sulakhe
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
| | - Sheng Wang
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, 60637, USA
| | - Bing Xie
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Department of Computer Science, Illinois Institute of Technology, Chicago, IL, 60616, USA
| | - Somaye Hashemifar
- Toyota Technological Institute at Chicago, 6045 S. Kenwood Avenue, Chicago, IL, 60637, USA
| | - Andrew Taylor
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
| | - Inna Dubchak
- Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America, Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - T Conrad Gilliam
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
| | - Natalia Maltsev
- Department of Human Genetics, University of Chicago, 920 E. 58th Street, Chicago, IL, 60637, USA
- Computation Institute, University of Chicago, 5735 S. Ellis Avenue, Chicago, IL, 60637, USA
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20
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Webster NJG. Alternative RNA Splicing in the Pathogenesis of Liver Disease. Front Endocrinol (Lausanne) 2017; 8:133. [PMID: 28680417 PMCID: PMC5478874 DOI: 10.3389/fendo.2017.00133] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 05/30/2017] [Indexed: 12/27/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is becoming increasingly prevalent due to the worldwide obesity epidemic and currently affects one-third of adults or about one billion people worldwide. NAFLD is predicted to affect over 50% of the world's population by the end of the next decade. It is the most common form of liver disease and is associated with increased risk for progression to a more severe form non-alcoholic steatohepatitis, as well as insulin resistance, type 2 diabetes mellitus, cirrhosis, and eventually hepatocellular carcinoma. This review article will focus on the role of alternative splicing in normal liver physiology and dysregulation in liver disease.
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Affiliation(s)
- Nicholas J. G. Webster
- Medical Research Service, VA San Diego Healthcare System, San Diego, CA, United States
- Department of Medicine, School of Medicine, Moores Cancer Center, University of California San Diego, La Jolla, CA, United States
- *Correspondence: Nicholas J. G. Webster,
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21
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Hernández J, Bechara E, Schlesinger D, Delgado J, Serrano L, Valcárcel J. Tumor suppressor properties of the splicing regulatory factor RBM10. RNA Biol 2016; 13:466-72. [PMID: 26853560 PMCID: PMC4841610 DOI: 10.1080/15476286.2016.1144004] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
RBM10 is an RNA binding protein and alternative splicing regulator frequently mutated in lung adenocarcinomas. Recent results indicate that RBM10 inhibits proliferation of lung cancer cells by promoting skipping of exon 9 of the gene NUMB, a frequent alternative splicing change in lung cancer generating a negative regulator of Notch signaling. Complementing these observations, we show that knock down of RBM10 in human cancer cells enhances growth of mouse tumor xenografts, confirming that RBM10 acts as a tumor suppressor, while knock down of an oncogenic mutant version of RBM10 reduces xenograft tumor growth. A RBM10 mutation found in lung cancer cells, V354E, disrupts RBM10-mediated regulation of NUMB alternative splicing, inducing the cell proliferation-promoting isoform. We now show that 2 natural RBM10 isoforms that differ by the presence or absence of V354 in the second RNA Recognition Motif (RRM2), display similar regulatory effects on NUMB alternative splicing, suggesting that V354E actively disrupts RBM10 activity. Structural modeling localizes V354 in the outside surface of one α-helix opposite to the RNA binding surface of RBM10, and we show that the mutation does not compromise binding of the RRM2 domain to NUMB RNA regulatory sequences. We further show that other RBM10 mutations found in lung adenocarcinomas also compromise regulation of NUMB exon 9. Collectively, our previous and current results reveal that RBM10 is a tumor suppressor that represses Notch signaling and cell proliferation through the regulation of NUMB alternative splicing.
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Affiliation(s)
- Jordi Hernández
- a Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology , Dr. Aiguader 88, 08003 Barcelona , Spain.,b Universitat Pompeu Fabra , Dr. Aiguader 88, 08003 Barcelona , Spain
| | - Elias Bechara
- a Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology , Dr. Aiguader 88, 08003 Barcelona , Spain.,b Universitat Pompeu Fabra , Dr. Aiguader 88, 08003 Barcelona , Spain
| | - Doerte Schlesinger
- a Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology , Dr. Aiguader 88, 08003 Barcelona , Spain
| | - Javier Delgado
- a Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology , Dr. Aiguader 88, 08003 Barcelona , Spain.,b Universitat Pompeu Fabra , Dr. Aiguader 88, 08003 Barcelona , Spain
| | - Luis Serrano
- a Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology , Dr. Aiguader 88, 08003 Barcelona , Spain.,b Universitat Pompeu Fabra , Dr. Aiguader 88, 08003 Barcelona , Spain.,c Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluis Companys 23, 08010 Barcelona , Spain
| | - Juan Valcárcel
- a Centre de Regulació Genòmica, The Barcelona Institute of Science and Technology , Dr. Aiguader 88, 08003 Barcelona , Spain.,b Universitat Pompeu Fabra , Dr. Aiguader 88, 08003 Barcelona , Spain.,c Institució Catalana de Recerca i Estudis Avançats (ICREA) , Passeig Lluis Companys 23, 08010 Barcelona , Spain
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22
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Sumi D, Takeda C, Yasuoka D, Himeno S. Hydrogen peroxide triggers a novel alternative splicing of arsenic (+3 oxidation state) methyltransferase gene. Biochem Biophys Res Commun 2016; 480:18-22. [PMID: 27721063 DOI: 10.1016/j.bbrc.2016.10.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 10/06/2016] [Indexed: 11/20/2022]
Abstract
We previously reported that two splicing variants of human AS3MT mRNA, exon-3 skipping form (Δ3) and exons-4 and -5 skipping form (Δ4,5), were detected in HepG2 cells and that both variants lacked arsenic methylation activity (Sumi et al., 2011). Here we studied whether hydrogen peroxide (H2O2) triggers alternative splicing of AS3MT mRNA. The results showed that exposure of HepG2 cells to H2O2 resulted in increased levels of a novel spliced form skipping exon-3 to exon-10 (Δ3-10) in an H2O2-concentration-dependent manner, although no change was detected in the mRNA levels of Δ3 AS3MT. We found decreased protein levels of serine/arginine-rich 40 (SRp40), which we determined to be a candidate splice factor for controlling the splicing of AS3MT mRNA. We next compared the amounts of methylated arsenic metabolites between control and H2O2-exposed HepG2 cells after the addition of arsenite as a substance. The results showed lower levels of methylated arsenic metabolites in HepG2 cells exposed to H2O2. These data suggest that the splicing of AS3MT pre-mRNA was disconcerted by oxidative stress and that abnormal alternative splicing of AS3MT mRNA may affect arsenic methylation ability.
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Affiliation(s)
- Daigo Sumi
- Laboratory of Molecular Nutrition and Toxicology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Chieri Takeda
- Laboratory of Molecular Nutrition and Toxicology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Daiki Yasuoka
- Laboratory of Molecular Nutrition and Toxicology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan
| | - Seiichiro Himeno
- Laboratory of Molecular Nutrition and Toxicology, Faculty of Pharmaceutical Sciences, Tokushima Bunri University, Yamashiro-cho, Tokushima 770-8514, Japan.
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Weighted gene co-expression network analysis of pneumocytes under exposure to a carcinogenic dose of chloroprene. Life Sci 2016; 151:339-347. [PMID: 26916823 DOI: 10.1016/j.lfs.2016.02.074] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 02/16/2016] [Accepted: 02/20/2016] [Indexed: 02/06/2023]
Abstract
AIMS Occupational exposure to chloroprene via inhalation may lead to acute toxicity and chronic pulmonary diseases, including lung cancer. Currently, most research is focused on epidemiological studies of chloroprene production workers. The specific molecular mechanism of carcinogenesis by chloroprene in lung tissues still remains obscure, and specific candidate therapeutic targets for lung cancer are lacking. The present study identifies specific gene modules and valuable hubs associated with lung cancer. MAIN METHODS We downloaded the dataset GSE40795 from the Gene Expression Omnibus (GEO) and divided the dataset into the non-carcinogenic dose chloroprene exposed mice group and the carcinogenic dose chloroprene exposed mice group. With a systemic biological view, we discovered significantly altered gene modules between the two groups and identified hub genes in the carcinogenic dose exposed group using weighted co-expression network analysis (WGCNA). KEY FINDINGS A total of 2434 differentially expressed genes were identified. Twelve gene modules with multiple biological activities were related to the carcinogenesis of chloroprene in lung tissue. Seven hub genes that were critical for the carcinogenesis of chloroprene in lung tissue were ultimately identified, including Cftr, Hip1, Tbl1x, Ephx1, Cbr3, Antxr2 and Ccnd2. They were implicated in inflammatory response, cell transformation, gene transcription regulation, phase II detoxification, angiogenesis, cell adhesion, motility and the cell cycle. SIGNIFICANCE The seven hub genes may become valuable candidates for risk assessment biomarkers and therapeutic targets in lung cancer.
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24
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Expression of SRPK1 in gliomas and its role in glioma cell lines viability. Tumour Biol 2016; 37:8699-707. [PMID: 26738865 DOI: 10.1007/s13277-015-4738-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Accepted: 12/22/2015] [Indexed: 12/30/2022] Open
Abstract
Among factors regulating the splicing of major importance is serine/arginine protein kinase 1 (SRPK1) that phosphorylates SR splicing factors. SRPK1 is expressed in the mammalian central nervous system in a region- and neuron-specific manner. Based on previous observations that glial cells are practically devoid of SRPK1 and reports showing aberrant expression of SRPK1 in numerous tumors, but with conflicting roles, this study aims to investigate the expression of SRPK1 in glioma and its influence on tumor cell biological features. As shown by immunohistochemical analysis, malignant glioma cells express SRPK1 in glioblastomas with significant association between SRPK1 expression and patients' survival. SRPK1 expression was also significantly upregulated at the messenger RNA (mRNA) and protein level in glioma cell lines. Small interfering RNA-mediated downregulation of SRPK1 had little effect on cell viability, while it slightly enhanced the sensitivity of cells to killing by cisplatin. These results support the idea that at least in vitro, the effect of SRPK1 knockdown on the viability of glioma cell lines is rather limited, while the in vivo effects could be attributed to the modulation of angiogenesis by SRPK1.
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25
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Hayakawa A, Saitoh M, Miyazawa K. Dual Roles for Epithelial Splicing Regulatory Proteins 1 (ESRP1) and 2 (ESRP2) in Cancer Progression. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 925:33-40. [DOI: 10.1007/5584_2016_50] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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26
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Kataoka K, Nagata Y, Kitanaka A, Shiraishi Y, Shimamura T, Yasunaga JI, Totoki Y, Chiba K, Sato-Otsubo A, Nagae G, Ishii R, Muto S, Kotani S, Watatani Y, Takeda J, Sanada M, Tanaka H, Suzuki H, Sato Y, Shiozawa Y, Yoshizato T, Yoshida K, Makishima H, Iwanaga M, Ma G, Nosaka K, Hishizawa M, Itonaga H, Imaizumi Y, Munakata W, Ogasawara H, Sato T, Sasai K, Muramoto K, Penova M, Kawaguchi T, Nakamura H, Hama N, Shide K, Kubuki Y, Hidaka T, Kameda T, Nakamaki T, Ishiyama K, Miyawaki S, Yoon SS, Tobinai K, Miyazaki Y, Takaori-Kondo A, Matsuda F, Takeuchi K, Nureki O, Aburatani H, Watanabe T, Shibata T, Matsuoka M, Miyano S, Shimoda K, Ogawa S. Integrated molecular analysis of adult T cell leukemia/lymphoma. Nat Genet 2015; 47:1304-15. [PMID: 26437031 DOI: 10.1038/ng.3415] [Citation(s) in RCA: 575] [Impact Index Per Article: 63.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 09/09/2015] [Indexed: 12/11/2022]
Abstract
Adult T cell leukemia/lymphoma (ATL) is a peripheral T cell neoplasm of largely unknown genetic basis, associated with human T cell leukemia virus type-1 (HTLV-1) infection. Here we describe an integrated molecular study in which we performed whole-genome, exome, transcriptome and targeted resequencing, as well as array-based copy number and methylation analyses, in a total of 426 ATL cases. The identified alterations overlap significantly with the HTLV-1 Tax interactome and are highly enriched for T cell receptor-NF-κB signaling, T cell trafficking and other T cell-related pathways as well as immunosurveillance. Other notable features include a predominance of activating mutations (in PLCG1, PRKCB, CARD11, VAV1, IRF4, FYN, CCR4 and CCR7) and gene fusions (CTLA4-CD28 and ICOS-CD28). We also discovered frequent intragenic deletions involving IKZF2, CARD11 and TP73 and mutations in GATA3, HNRNPA2B1, GPR183, CSNK2A1, CSNK2B and CSNK1A1. Our findings not only provide unique insights into key molecules in T cell signaling but will also guide the development of new diagnostics and therapeutics in this intractable tumor.
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Affiliation(s)
- Keisuke Kataoka
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yasunobu Nagata
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Kitanaka
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yuichi Shiraishi
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Teppei Shimamura
- Division of Systems Biology, Center for Neurological Disease and Cancer, Graduate School of Medicine, Nagoya University, Nagoya, Japan
| | - Jun-Ichirou Yasunaga
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Yasushi Totoki
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kenichi Chiba
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Aiko Sato-Otsubo
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Genta Nagae
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Ryohei Ishii
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Satsuki Muto
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Shinichi Kotani
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yosaku Watatani
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - June Takeda
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masashi Sanada
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan.,Department of Advanced Diagnosis, Clinical Research Center, Nagoya Medical Center, Nagoya, Japan
| | - Hiroko Tanaka
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Hiromichi Suzuki
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Sato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Yusuke Shiozawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Tetsuichi Yoshizato
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kenichi Yoshida
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hideki Makishima
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masako Iwanaga
- Department of Frontier Life Science, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Guangyong Ma
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Kisato Nosaka
- Department of Hematology, Kumamoto University School of Medicine, Kumamoto, Japan
| | - Masakatsu Hishizawa
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hidehiro Itonaga
- Department of Hematology, Sasebo City General Hospital, Sasebo, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Wataru Munakata
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | | | | | - Ken Sasai
- KAN Research Institute, Inc., Kobe, Japan
| | | | - Marina Penova
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takahisa Kawaguchi
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hiromi Nakamura
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Natsuko Hama
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Kotaro Shide
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Yoko Kubuki
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tomonori Hidaka
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Takuro Kameda
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Tsuyoshi Nakamaki
- Division of Hematology, Department of Medicine, Showa University School of Medicine, Tokyo, Japan
| | - Ken Ishiyama
- Department of Hematology and Oncology, Kanazawa University Hospital, Kanazawa, Japan
| | - Shuichi Miyawaki
- Division of Hematology, Department of Internal Medicine, Tokyo Metropolitan Ohtsuka Hospital, Tokyo, Japan
| | - Sung-Soo Yoon
- Department of Internal Medicine, Seoul National University College of Medicine, Seoul, Korea
| | - Kensei Tobinai
- Department of Hematology, National Cancer Center Hospital, Tokyo, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Atomic Bomb Disease and Hibakusya Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, Japan
| | - Akifumi Takaori-Kondo
- Department of Hematology and Oncology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kengo Takeuchi
- Pathology Project for Molecular Targets, Cancer Institute, Japanese Foundation for Cancer Research, Tokyo, Japan
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Hiroyuki Aburatani
- Genome Science Division, Research Center for Advanced Science and Technology, The University of Tokyo, Tokyo, Japan
| | - Toshiki Watanabe
- Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan.,Laboratory of Molecular Medicine, Human Genome Center, The institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Masao Matsuoka
- Laboratory of Virus Control, Institute for Virus Research, Kyoto University, Kyoto, Japan
| | - Satoru Miyano
- Laboratory of DNA Information Analysis, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
| | - Kazuya Shimoda
- Department of Gastroenterology and Hematology, Faculty of Medicine, University of Miyazaki, Miyazaki, Japan
| | - Seishi Ogawa
- Department of Pathology and Tumor Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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Tang Y, Yan G, Song X, Wu K, Li Z, Yang C, Deng T, Sun Y, Hu X, Yang C, Bai H, Li H, Tan W, Ye M, Liu J. STIP overexpression confers oncogenic potential to human non-small cell lung cancer cells by regulating cell cycle and apoptosis. J Cell Mol Med 2015; 19:2806-17. [PMID: 26354852 PMCID: PMC4687698 DOI: 10.1111/jcmm.12670] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/17/2015] [Indexed: 01/17/2023] Open
Abstract
Sip1/tuftelin‐interacting protein (STIP), a multidomain nuclear protein, is a novel factor associated with the spliceosome, yet its role and molecular function in cancer remain unknown. In this study, we show, for the first time, that STIP is overexpressed in non‐small cell lung cancer (NSCLC) tissues compared to adjacent normal lung tissues. The depletion of endogenous STIP inhibited NSCLC cell proliferation in vitro and in vivo, caused cell cycle arrest and induced apoptosis. Cell cycle arrest at the G2/M phase was associated with the expression and activity of the cyclin B1‐CDK1 (cyclin‐dependent kinase 1) complex. We also provide evidence that STIP knockdown induced apoptosis by activating both caspase‐9 and caspase‐3 and by altering the Bcl‐2/Bax expression ratio. RNA sequencing data indicated that the MAPK mitogen‐activated protein kinases, Wnt, PI3K/AKT, and NF‐κB (nuclear factor kappa‐light‐chain‐enhancer of activated B cells) signalling pathways might be involved in STIP‐mediated tumour regulation. Collectively, these results suggest that STIP may be a novel potential diagnostic and therapeutic target for NSCLC.
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Affiliation(s)
- Yani Tang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Guobei Yan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Xin Song
- Cancer Biotherapy Center, Tumour Hospital of Yunnan Province Affiliated with Kunming Medical University, Kunming, Yunnan, China
| | - Kuangpei Wu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Zhen Li
- Cancer Biotherapy Center, Tumour Hospital of Yunnan Province Affiliated with Kunming Medical University, Kunming, Yunnan, China
| | - Chao Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Tanggang Deng
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Yang Sun
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Xiaoxiao Hu
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Cai Yang
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Huarong Bai
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Hui Li
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
| | - Weihong Tan
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Mao Ye
- Molecular Science and Biomedicine Laboratory, State Key Laboratory for Chemo/Biosensing and Chemometrics, College of Biology, College of Chemistry and Chemical Engineering, Collaborative Innovation Center for Molecular Engineering for Theranostics, Hunan University, Changsha, Hunan, China
| | - Jing Liu
- School of Life Sciences, State Key Laboratory of Medical Genetics, Central South University, Changsha, Hunan, China
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28
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RQN-18690A (18-deoxyherboxidiene) targets SF3b, a spliceosome component, and inhibits angiogenesis. J Antibiot (Tokyo) 2015; 69:121-3. [PMID: 26350783 DOI: 10.1038/ja.2015.94] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 08/11/2015] [Accepted: 08/20/2015] [Indexed: 01/05/2023]
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29
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Koga M, Hayashi M, Kaida D. Splicing inhibition decreases phosphorylation level of Ser2 in Pol II CTD. Nucleic Acids Res 2015. [PMID: 26202968 PMCID: PMC4787822 DOI: 10.1093/nar/gkv740] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Phosphorylation of the C-terminal domain of the largest subunit of RNA polymerase II (Pol II), especially Ser2 and Ser5 residues, plays important roles in transcription and mRNA processing, including 5′ end capping, splicing and 3′ end processing. These phosphorylation events stimulate mRNA processing, however, it is not clear whether splicing activity affects the phosphorylation status of Pol II. In this study, we found that splicing inhibition by potent splicing inhibitors spliceostatin A (SSA) and pladienolide B or by antisense oligos against snRNAs decreased phospho-Ser2 level, but had little or no effects on phospho-Ser5 level. In contrast, transcription and translation inhibitors did not decrease phospho-Ser2 level, therefore inhibition of not all the gene expression processes cause the decrease of phospho-Ser2. SSA treatment caused early dissociation of Pol II and decrease in phospho-Ser2 level of chromatin-bound Pol II, suggesting that splicing inhibition causes downregulation of phospho-Ser2 through at least these two mechanisms.
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Affiliation(s)
- Mitsunori Koga
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Megumi Hayashi
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-0194, Japan
| | - Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Toyama 930-0194, Japan
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30
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Zheng KL, He TL, Ji WP, Jiang H, Shen Y, Li G, Zhu SB, Tong BL, Zhang YJ. Alternative splicing of NUMB, APP and VEGFA as the features of pancreatic ductal carcinoma. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2015; 8:6181-91. [PMID: 26261495 PMCID: PMC4525829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/17/2015] [Indexed: 06/04/2023]
Abstract
BACKGROUND Pancreatic ductal adenocarcinoma (PDAC) is the most common form of malignancy in pancreatic carcinoma. Here we report our discovery on the correlations between transcriptional alternative splicing (AS) of NUMB, APP, VEGFA and PDAC in patients. METHODS The expression of NUMB, APP, VEGFA from patient samples was determined by qRT-PCR. AS of these genes was examined through laser induced fluorescence capillary electrophoresis. Correlation between the AS of the genes and results from clinical laboratory examinations were analyzed. Expression of NOTHC1 and NOTCH4 as downstream target genes was examined by qRT-PCR and Western blot. RESULTS Quantitative results indicated that expression of NUMB was significantly lower in tumor tissues (TT) than in para-tumor tissues (TP) (P<0.05), while APP (P<0.01) and VEGFA (P<0.05) were significantly higher. AS transcript percentage of NUMB PRR(S) was lower in TT than TP (P<0.05). AS transcript percentage of VEGFA (105+185) was significantly lower in TT than TP (P<0.05) compared to higher expression of VEGFA (206+338) (P<0.05). Regression analysis indicated that AS transcript of NUMB PRR(L) correlated with tumor size (P<0.01), while AS transcripts of APP and VEGFA correlated with results of laboratory examinations. To reveal the correlation between AS and its downstream targets, NOTCH1 and NOTCH4 were selected as NUMB gene targets and detected to be significantly higher in TT than TP (P<0.05). CONCLUSION Alternative splicing of APP, VEGFA and NUMB may play an important role in pathogenesis of pancreatic ductal adenocarcinoma. Among the 3 genes, PRR(L) form of NUMB gene is highly expressed in TT and positively correlated with tumor size, while PRR(S) is lacking in TT and negatively correlated with NOTCH expression suggesting that PRR(S) might be protective in tumorogenesis and shows NOTCH pathway down regulation ability.
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MESH Headings
- Alternative Splicing
- Amyloid beta-Protein Precursor/genetics
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Blotting, Western
- Carcinoma, Pancreatic Ductal/chemistry
- Carcinoma, Pancreatic Ductal/genetics
- Carcinoma, Pancreatic Ductal/pathology
- Gene Expression Regulation, Neoplastic
- Humans
- Membrane Proteins/genetics
- Nerve Tissue Proteins/genetics
- Pancreatic Neoplasms/chemistry
- Pancreatic Neoplasms/genetics
- Pancreatic Neoplasms/pathology
- Proto-Oncogene Proteins/analysis
- Proto-Oncogene Proteins/genetics
- RNA, Messenger/genetics
- Real-Time Polymerase Chain Reaction
- Receptor, Notch1/analysis
- Receptor, Notch1/genetics
- Receptor, Notch4
- Receptors, Notch/analysis
- Receptors, Notch/genetics
- Tumor Burden
- Vascular Endothelial Growth Factor A/genetics
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Affiliation(s)
- Kai-Lian Zheng
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
| | - Tian-Lin He
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
| | - Wei-ping Ji
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
| | - Hui Jiang
- R & D Department of Cinoasia InstituteShanghai 200437, China
| | - Ye Shen
- Department of General Surgery, Ao Young HospitalSuzhou 215617, China
| | - Gang Li
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
| | - Si-Bo Zhu
- R & D Department of Cinoasia InstituteShanghai 200437, China
| | - Bing-Lei Tong
- R & D Department of Cinoasia InstituteShanghai 200437, China
| | - Yi-Jie Zhang
- Department of Pancreatic Surgery, Changhai Hospital, Second Military Medical UniversityShanghai 200433, China
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Ohe K, Hagiwara M. Modulation of alternative splicing with chemical compounds in new therapeutics for human diseases. ACS Chem Biol 2015; 10:914-24. [PMID: 25560473 DOI: 10.1021/cb500697f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Alternative splicing is a critical step where a limited number of human genes generate a complex and diverse proteome. Various diseases, including inherited diseases with abnormalities in the "genome code," have been found to result in an aberrant mis-spliced "transcript code" with correlation to the resulting phenotype. Chemical compound-based and nucleic acid-based strategies are trying to target this mis-spliced "transcript code". We will briefly mention about how to obtain splicing-modifying-compounds by high-throughput screening and overview of what is known about compounds that modify splicing pathways. The main focus will be on RNA-binding protein kinase inhibitors. In the main text, we will refer to diseases where splicing-modifying-compounds have been intensively investigated, with comparison to nucleic acid-based strategies. The information on their involvement in mis-splicing as well as nonsplicing events will be helpful in finding better compounds with less off-target effects for future implications in mis-splicing therapy.
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Affiliation(s)
- Kenji Ohe
- †Department of Anatomy and Developmental Biology and ‡Training Program of Leaders for Integrated Medical System for Fruitful Healthy-Longevity Society (LIMS), Kyoto University Graduate School of Medicine, Kyoto 606-8315, Japan
| | - Masatoshi Hagiwara
- †Department of Anatomy and Developmental Biology and ‡Training Program of Leaders for Integrated Medical System for Fruitful Healthy-Longevity Society (LIMS), Kyoto University Graduate School of Medicine, Kyoto 606-8315, Japan
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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: 38] [Impact Index Per Article: 3.8] [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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Vauchy C, Gamonet C, Ferrand C, Daguindau E, Galaine J, Beziaud L, Chauchet A, Henry Dunand CJ, Deschamps M, Rohrlich PS, Borg C, Adotevi O, Godet Y. CD20 alternative splicing isoform generates immunogenic CD4 helper T epitopes. Int J Cancer 2014; 137:116-26. [DOI: 10.1002/ijc.29366] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Revised: 11/12/2014] [Accepted: 11/18/2014] [Indexed: 12/22/2022]
Affiliation(s)
- Charline Vauchy
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
| | - Clementine Gamonet
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
| | - Christophe Ferrand
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
| | - Etienne Daguindau
- Department of Hematology; University Hospital of Besançon, F25020 Besançon cedex; France
| | - Jeanne Galaine
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
| | - Laurent Beziaud
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
| | - Adrien Chauchet
- Department of Hematology; University Hospital of Besançon, F25020 Besançon cedex; France
| | - Carole J. Henry Dunand
- The Department of Medicine; Section of Rheumatology, The Knapp Center for Lupus and Immunology Research, The University of Chicago; Chicago IL
| | - Marina Deschamps
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
| | - Pierre Simon Rohrlich
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- Department of Pediatrics; University Hospital of Besançon, F25020 Besançon cedex; France
| | - Christophe Borg
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
- Department of Medical Oncology; University Hospital of Besançon, F25020 Besançon cedex; France
| | - Olivier Adotevi
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
- Department of Medical Oncology; University Hospital of Besançon, F25020 Besançon cedex; France
| | - Yann Godet
- INSERM UMR1098, F25020 Besançon cedex; France
- Université de Franche-Comté, F25020 Besançon cedex; France
- EFS Bourgogne Franche-Comté, F25020 Besançon cedex; France
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The impact of SF3B1 mutations in CLL on the DNA-damage response. Leukemia 2014; 29:1133-42. [DOI: 10.1038/leu.2014.318] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/03/2014] [Accepted: 10/23/2014] [Indexed: 01/16/2023]
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Spliceostatin hemiketal biosynthesis in Burkholderia spp. is catalyzed by an iron/α-ketoglutarate-dependent dioxygenase. Proc Natl Acad Sci U S A 2014; 111:E3376-85. [PMID: 25097259 DOI: 10.1073/pnas.1408300111] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Spliceostatins are potent spliceosome inhibitors biosynthesized by a hybrid nonribosomal peptide synthetase-polyketide synthase (NRPS-PKS) system of the trans-acyl transferase (AT) type. Burkholderia sp. FERM BP-3421 produces hemiketal spliceostatins, such as FR901464, as well as analogs containing a terminal carboxylic acid. We provide genetic and biochemical evidence for hemiketal biosynthesis by oxidative decarboxylation rather than the previously hypothesized Baeyer-Villiger oxidative release postulated to be catalyzed by a flavin-dependent monooxygenase (FMO) activity internal to the last module of the PKS. Inactivation of Fe(II)/α-ketoglutarate-dependent dioxygenase gene fr9P led to loss of hemiketal congeners, whereas the mutant was still able to produce all major carboxylic acid-type compounds. FMO mutants, on the other hand, produced both hemiketal and carboxylic acid analogs containing an exocyclic methylene instead of an epoxide, indicating that the FMO is involved in epoxidation rather than Baeyer-Villiger oxidation. Moreover, recombinant Fr9P enzyme was shown to catalyze hydroxylation to form β-hydroxy acids, which upon decarboxylation led to hemiketal FR901464. Finally, a third oxygenase activity encoded in the biosynthetic gene cluster, the cytochrome P450 monooxygenase Fr9R, was assigned as a 4-hydroxylase based on gene inactivation results. Identification and deletion of the gene involved in hemiketal formation allowed us to generate a strain--the dioxygenase fr9P(-) mutant--that accumulates only the carboxylic acid-type spliceostatins, which are as potent as the hemiketal analogs, when derivatized to increase cell permeability, but are chemically more stable.
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Multifunctional RNA processing protein SRm160 induces apoptosis and regulates eye and genital development in Drosophila. Genetics 2014; 197:1251-65. [PMID: 24907259 DOI: 10.1534/genetics.114.164434] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
SRm160 is an SR-like protein implicated in multiple steps of RNA processing and nucleocytoplasmic export. Although its biochemical functions have been extensively described, its genetic interactions and potential participation in signaling pathways remain largely unknown, despite the fact that it is highly phosphorylated in both mammalian cells and Drosophila. To begin elucidating the functions of the protein in signaling and its potential role in developmental processes, we characterized mutant and overexpression SRm160 phenotypes in Drosophila and their interactions with the locus encoding the LAMMER protein kinase, Doa. SRm160 mutations are recessive lethal, while its overexpression generates phenotypes including roughened eyes and highly disorganized internal eye structure, which are due at least in part to aberrantly high levels of apoptosis. SRm160 is required for normal somatic sex determination, since its alleles strongly enhance a subtle sex transformation phenotype induced by Doa kinase alleles. Moreover, modification of SRm160 by DOA kinase appears to be necessary for its activity, since Doa alleles suppress phenotypes induced by SRm160 overexpression in the eye and enhance those in genital discs. Modification of SRm160 may occur through direct interaction because DOA kinase phosphorylates it in vitro. Remarkably, SRm160 protein was concentrated in the nuclei of precellular embryos but was very rapidly excluded from nuclei or degraded coincident with cellularization. Also of interest, transcripts are restricted almost exclusively to the developing nervous system in mature embryos.
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37
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Chu X, Zhang T, Wang J, Li M, Zhang X, Tu J, Sun S, Chen X, Lu F. Alternative splicing variants of human Fbx4 disturb cyclin D1 proteolysis in human cancer. Biochem Biophys Res Commun 2014; 447:158-64. [DOI: 10.1016/j.bbrc.2014.03.129] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2014] [Accepted: 03/25/2014] [Indexed: 11/15/2022]
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38
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Berasain C, Elizalde M, Urtasun R, Castillo J, García-Irigoyen O, Uriarte I, Latasa MU, Prieto J, Avila MA. Alterations in the expression and activity of pre-mRNA splicing factors in hepatocarcinogenesis. Hepat Oncol 2014; 1:241-252. [PMID: 30190958 DOI: 10.2217/hep.13.17] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Hepatocellular carcinoma (HCC) is a molecularly complex tumor that is resistant to standard and targeted therapies, and thus a deadly disease. In this context, the identification of key alterations driving HCC development is therefore essential. The implementation of next-generation sequencing techniques has underscored earlier realizations of the marked dysregulation of pre-mRNA splicing in HCC. Impairments in alternative splicing may lead to the expression of protumorigenic protein isoforms and to the generation of unstable mRNA species. Mechanistically, mutations in key nucleotides are responsible for many of these alterations in different types of tumors. However, changes in the expression of factors involved in the regulation of the splicing machinery are also important determinants in the derangement of pre-mRNA splicing. Here we discuss recent reports on the alteration of splicing factors in HCC, the pathological significance of these changes, and the identification of cell signaling pathways leading to the missplicing of genes in hepatocarcinogenesis.
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Affiliation(s)
- Carmen Berasain
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - María Elizalde
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Raquel Urtasun
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Josefa Castillo
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain
| | - Oihane García-Irigoyen
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Iker Uriarte
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Maria U Latasa
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Prieto
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
| | - Matías A Avila
- Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain.,Division of Hepatology & Gene Therapy, Centro de Investigación Médica Aplicada (CIMA), Universidad de Navarra, CIMA, Avda, Pio XII, n55, 31008 Pamplona, Spain.,CIBERehd, Instituto de Salud Carlos III, Madrid, Spain
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Supek F, Miñana B, Valcárcel J, Gabaldón T, Lehner B. Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers. Cell 2014; 156:1324-1335. [DOI: 10.1016/j.cell.2014.01.051] [Citation(s) in RCA: 331] [Impact Index Per Article: 33.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2013] [Revised: 11/20/2013] [Accepted: 01/15/2014] [Indexed: 01/05/2023]
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40
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Fant X, Durieu E, Chicanne G, Payrastre B, Sbrissa D, Shisheva A, Limanton E, Carreaux F, Bazureau JP, Meijer L. cdc-like/dual-specificity tyrosine phosphorylation-regulated kinases inhibitor leucettine L41 induces mTOR-dependent autophagy: implication for Alzheimer's disease. Mol Pharmacol 2014; 85:441-50. [PMID: 24366666 PMCID: PMC6067634 DOI: 10.1124/mol.113.090837] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Accepted: 12/23/2013] [Indexed: 12/26/2022] Open
Abstract
Leucettines, a family of pharmacological inhibitors of dual-specificity tyrosine phosphorylation regulated kinases and cdc-like kinases (CLKs), are currently under investigation for their potential therapeutic application to Down syndrome and Alzheimer's disease. We here report that leucettine L41 triggers bona fide autophagy in osteosarcoma U-2 OS cells and immortalized mouse hippocampal HT22 cells, characterized by microtubule-associated protein light chain 3 membrane translocation and foci formation. Leucettine L41-triggered autophagy requires the Unc-51-like kinase and is sensitive to the phosphatidylinositol 3-kinase (PI3K) inhibitors wortmannin and 3-methyladenine, suggesting that it acts through the mammalian target of rapamycin (mTOR)/PI3K-dependent pathway. Leucettine L41 does not act by modifying the autophagic flux of vesicles. Leucettine L41-induced autophagy correlates best with inhibition of CLKs. Leucettine L41 modestly inhibited phosphatidylinositol-3-phosphate 5-kinase, FYVE domain-containing activity as tested both in vitro and in vivo, which may also contribute to autophagy induction. Altogether these results demonstrate that leucettines can activate the autophagic mTOR/PI3K pathway, a characteristic that may turn advantageous in the context of Alzheimer's disease treatment.
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Affiliation(s)
- Xavier Fant
- Centre National de la Recherche Scientifique (CNRS), USR3151, "Protein Phosphorylation and Human Disease," Station Biologique, Roscoff cedex, France (X.F., E.D.); Institut National de la Santé et de la Recherche Médicale/Université Paul Sabatier Unité Mixte de Recherche (UMR) 1048, "Production et fonctions plaquettaires: signalisation et phosphoinositides" group, Institut des Maladies Métaboliques et Cardiovasculaires (I2MC), Toulouse cedex, France (G.C., B.P.); Department of Physiology, Wayne State University School of Medicine, Detroit, Michigan (D.S., A.S.); Laboratoire Sciences Chimiques de Rennes, UMR CNRS 6226, Groupe Ingénierie Chimique et Molécules pour le Vivant (ICMV), Université de Rennes, Campus de Beaulieu, Rennes cedex, France (E.L., F.C., J.-P.B.); and ManRos Therapeutics, Perharidy Research Center, Roscoff, Bretagne, France (L.M.)
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Bechara EG, Sebestyén E, Bernardis I, Eyras E, Valcárcel J. RBM5, 6, and 10 differentially regulate NUMB alternative splicing to control cancer cell proliferation. Mol Cell 2013; 52:720-33. [PMID: 24332178 DOI: 10.1016/j.molcel.2013.11.010] [Citation(s) in RCA: 238] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 09/18/2013] [Accepted: 10/22/2013] [Indexed: 12/25/2022]
Abstract
RBM5, a regulator of alternative splicing of apoptotic genes, and its highly homologous RBM6 and RBM10 are RNA-binding proteins frequently deleted or mutated in lung cancer. We report that RBM5/6 and RBM10 antagonistically regulate the proliferative capacity of cancer cells and display distinct positional effects in alternative splicing regulation. We identify the Notch pathway regulator NUMB as a key target of these factors in the control of cell proliferation. NUMB alternative splicing, which is frequently altered in lung cancer, can regulate colony and xenograft tumor formation, and its modulation recapitulates or antagonizes the effects of RBM5, 6, and 10 in cell colony formation. RBM10 mutations identified in lung cancer cells disrupt NUMB splicing regulation to promote cell growth. Our results reveal a key genetic circuit in the control of cancer cell proliferation.
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Affiliation(s)
- Elias G Bechara
- Centre de Regulació Genòmica, Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Endre Sebestyén
- Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003 Barcelona, Spain
| | | | - Eduardo Eyras
- Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Dr. Aiguader, 88, 08003 Barcelona, Spain
| | - Juan Valcárcel
- Centre de Regulació Genòmica, Dr. Aiguader, 88, 08003 Barcelona, Spain; Universitat Pompeu Fabra, Dr. Aiguader, 88, 08003 Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Dr. Aiguader, 88, 08003 Barcelona, Spain.
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Sato M, Muguruma N, Nakagawa T, Okamoto K, Kimura T, Kitamura S, Yano H, Sannomiya K, Goji T, Miyamoto H, Okahisa T, Mikasa H, Wada S, Iwata M, Takayama T. High antitumor activity of pladienolide B and its derivative in gastric cancer. Cancer Sci 2013; 105:110-6. [PMID: 24635824 PMCID: PMC4317874 DOI: 10.1111/cas.12317] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 10/21/2013] [Accepted: 10/29/2013] [Indexed: 12/26/2022] Open
Abstract
The antitumor activity of pladienolide B, a novel splicing inhibitor, against gastric cancer is totally unknown and no predictive biomarker of pladienolide B efficacy has been reported. We investigated the antitumor activity of pladienolide B and its derivative on gastric cancer cell lines and primary cultured cancer cells from carcinomatous ascites of gastric cancer patients. The effect of pladienolide B and its derivative on six gastric cancer cell lines was investigated using a MTT assay and the mean IC50 values determined to be 1.6 ± 1.2 (range, 0.6-4.0) and 1.2 ± 1.1 (range, 0.4-3.4) nM, respectively, suggesting strong antitumor activity against gastric cancer. The mean IC50 value of pladienolide B derivative against primary cultured cells from 12 gastric cancer patients was 4.9 ± 4.7 nM, indicative of high antitumor activity. When 18 SCID mice xenografted with primary cultured cells from three patients were administered the pladienolide B derivative intraperitoneally, all tumors completely disappeared within 2 weeks after treatment. Histological examination revealed a pathological complete response for all tumors. In the xenograft tumors after treatment with pladienolide B derivative, immature mRNA were detected and apoptotic cells were observed. When the expressions of cell-cycle proteins p16 and cyclin E in biopsied gastric cancer specimens were examined using immunohisctochemistry, positivities for p16 and cyclin E were significantly and marginally higher, respectively, in the low-IC50 group compared with the high-IC50 group, suggesting the possibility that they might be useful as predictive biomarkers for pladienolide B. In conclusion, pladienolide B was very active against gastric cancer via a mechanism involving splicing impairment and apoptosis induction.
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Affiliation(s)
- Momoko Sato
- Department of Gastroenterology and Oncology, Institutes of Health Biosciences, University of Tokushima Graduate School, Tokushima, Japan
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43
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Abstract
UNLABELLED Alternative splicing of mRNA precursors enables one gene to produce multiple protein isoforms with differing functions. Under normal conditions, this mechanism is tightly regulated in order for the human genome to generate proteomic diversity sufficient for the functional requirements of complex tissues. When deregulated, however, cancer cells take advantage of this mechanism to produce aberrant proteins with added, deleted, or altered functional domains that contribute to tumorigenesis. Here, we discuss aspects of alternative splicing misregulation in cancer, focusing on splicing events affected by deregulation of regulatory splicing factors and also recent studies identifying mutated components of the splicing machinery. SIGNIFICANCE An increasing body of evidence indicates that aberrant splicing of mRNA precursors leads to production of aberrant proteins that contribute to tumorigenesis. Recent studies show that alterations in cellular concentrations of regulatory splicing factors and mutations in components of the core splicing machinery provide major mechanisms of misregulation of mRNA splicing in cancer. A better understanding of this misregulation will potentially reveal a group of novel drug targets for therapeutic intervention.
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Affiliation(s)
- Jian Zhang
- Department of Biological Sciences, Columbia University, New York, New York
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44
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Abstract
An oncogenic splice variant of the transcription factor KLF6 is associated with metastasis and poor survival in node-negative breast cancer patients and promotes the epithelial-to-mesenchymal transition by regulating Twist.
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Affiliation(s)
- Oakley C Olson
- Cancer Biology and Genetics Program, Memorial Sloan-Kettering Cancer Center, New York, NY 10065, USA
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45
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Tang JY, Lee JC, Hou MF, Wang CL, Chen CC, Huang HW, Chang HW. Alternative splicing for diseases, cancers, drugs, and databases. ScientificWorldJournal 2013; 2013:703568. [PMID: 23766705 PMCID: PMC3674688 DOI: 10.1155/2013/703568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/30/2013] [Indexed: 01/05/2023] Open
Abstract
Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 807, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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46
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Bywater MJ, Pearson RB, McArthur GA, Hannan RD. Dysregulation of the basal RNA polymerase transcription apparatus in cancer. Nat Rev Cancer 2013; 13:299-314. [PMID: 23612459 DOI: 10.1038/nrc3496] [Citation(s) in RCA: 163] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mutations that directly affect transcription by RNA polymerases rank among the most central mediators of malignant transformation, but the frequency of new anticancer drugs that selectively target defective transcription apparatus entering the clinic has been limited. This is because targeting the large protein-protein and protein-DNA interfaces that control both generic and selective aspects of RNA polymerase transcription has proved extremely difficult. However, recent technological advances have led to a 'quantum leap' in our comprehension of the structure and function of the core RNA polymerase components, how they are dysregulated in a broad range of cancers and how they may be targeted for 'transcription therapy'.
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Affiliation(s)
- Megan J Bywater
- Division of Cancer Research, Peter MacCallum Cancer Centre, Melbourne 8006, Victoria, Australia
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47
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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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48
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Sengupta N, Yau C, Sakthianandeswaren A, Mouradov D, Gibbs P, Suraweera N, Cazier JB, Polanco-Echeverry G, Ghosh A, Thaha M, Ahmed S, Feakins R, Propper D, Dorudi S, Sieber O, Silver A, Lai C. Analysis of colorectal cancers in British Bangladeshi identifies early onset, frequent mucinous histotype and a high prevalence of RBFOX1 deletion. Mol Cancer 2013; 12:1. [PMID: 23286373 PMCID: PMC3544714 DOI: 10.1186/1476-4598-12-1] [Citation(s) in RCA: 59] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Accepted: 12/26/2012] [Indexed: 12/13/2022] Open
Abstract
Background Prevalence of colorectal cancer (CRC) in the British Bangladeshi population (BAN) is low compared to British Caucasians (CAU). Genetic background may influence mutations and disease features. Methods We characterized the clinicopathological features of BAN CRCs and interrogated their genomes using mutation profiling and high-density single nucleotide polymorphism (SNP) arrays and compared findings to CAU CRCs. Results Age of onset of BAN CRC was significantly lower than for CAU patients (p=3.0 x 10-5) and this difference was not due to Lynch syndrome or the polyposis syndromes. KRAS mutations in BAN microsatellite stable (MSS) CRCs were comparatively rare (5.4%) compared to CAU MSS CRCs (25%; p=0.04), which correlates with the high percentage of mucinous histotype observed (31%) in the BAN samples. No BRAF mutations was seen in our BAN MSS CRCs (CAU CRCs, 12%; p=0.08). Array data revealed similar patterns of gains (chromosome 7 and 8q), losses (8p, 17p and 18q) and LOH (4q, 17p and 18q) in BAN and CAU CRCs. A small deletion on chromosome 16p13.2 involving the alternative splicing factor RBFOX1 only was found in significantly more BAN (50%) than CAU CRCs (15%) cases (p=0.04). Focal deletions targeting the 5’ end of the gene were also identified. Novel RBFOX1 mutations were found in CRC cell lines and tumours; mRNA and protein expression was reduced in tumours. Conclusions KRAS mutations were rare in BAN MSS CRC and a mucinous histotype common. Loss of RBFOX1 may explain the anomalous splicing activity associated with CRC.
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Affiliation(s)
- Neel Sengupta
- Centre for Digestive Diseases, Blizard Institute of Cell and Molecular Science, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St, Whitechapel, London, E1 2AT, UK
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49
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Kajiwara T, Matsushita K, Itoga S, Tamura M, Tanaka N, Tomonaga T, Matsubara H, Shimada H, Habara Y, Matsuo M, Nomura F. SAP155-mediated c-myc suppressor far-upstream element-binding protein-interacting repressor splicing variants are activated in colon cancer tissues. Cancer Sci 2012; 104:149-56. [PMID: 23113893 DOI: 10.1111/cas.12058] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2012] [Revised: 10/23/2012] [Accepted: 10/28/2012] [Indexed: 12/12/2022] Open
Abstract
The c-myc transcriptional suppressor, far-upstream element (FUSE)-binding protein (FBP)-interacting repressor (FIR), is alternatively spliced in colorectal cancer tissue (Matsushita et al., Cancer Res 2006). Recently, the knockdown of SAP155 pre-mRNA-splicing factor, a subunit of SF3b, was reported to disturb FIR pre-mRNA splicing and yield FIRΔexon2, an exon 2-spliced variant of FIR, which lacks c-myc repression activity. In the present study, novel splicing variants of FIR, Δ3 and Δ4, were also generated by SAP155 siRNA, and these variants were found to be activated in human colorectal cancer tissue. Furthermore, the expression levels of FIR variant mRNA were examined in the peripheral blood of colorectal cancer patients and healthy volunteers to assess its potency for tumor detection. As expected, circulating FIR variant mRNA in the peripheral blood of cancer patients were significantly overexpressed compared to that in healthy volunteers. In particular, the area under the receiving operating characteristic curve of FIR, FIRΔexon2 or FIRΔexon2/FIR, was greater than those of conventional carcinoembryonic antigen or carbohydrate antigen 19-9. In addition, FIRΔexon2 or FIR mRNA expression in the peripheral blood was significantly reduced after operative removal of colorectal tumors. Thus, circulating FIR and FIRΔexon2 mRNA are potential novel screening markers for colorectal cancer testing with conventional carcinoembryonic antigen and or carbohydrate antigen 19-9. Taken together, our results indicate that overexpression of FIR and its splicing variants in colorectal cancer directs feed-forward or addicted circuit c-myc transcriptional activation. Clinical implications for colorectal cancers of novel FIR splicing variants are also discussed in the present paper.
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Affiliation(s)
- Toshiko Kajiwara
- Department of Molecular Diagnosis, Chiba University Graduate School of Medicine, Chiba, Japan
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50
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Kaida D, Schneider-Poetsch T, Yoshida M. Splicing in oncogenesis and tumor suppression. Cancer Sci 2012; 103:1611-6. [PMID: 22691055 DOI: 10.1111/j.1349-7006.2012.02356.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2012] [Revised: 06/04/2012] [Accepted: 06/07/2012] [Indexed: 12/23/2022] Open
Abstract
Post-transcriptional modifications, such as 5' end capping, 3' end polyadenylation and splicing, are necessary for the precise regulation of gene expression and transcriptome integrity. Therefore, it is not surprising that abnormalities of these post-transcriptional modifications prompt numerous diseases, including cancer. In fact, many studies revealed that misregulation of mRNA processing, especially splicing, are observed in a variety of cancer cells. In this review we describe how changes within RNA splicing regulatory elements or mutations in the processing factors alter the expression of tumor suppressors or oncogenes with pathological consequences. In addition, we show how several small molecules that bind to spliceosomal components and splicing regulators inhibit or modulate splicing activity. These compounds have anticancer activity and further development of small molecule modulators has potential in next generation cancer therapy.
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Affiliation(s)
- Daisuke Kaida
- Frontier Research Core for Life Sciences, University of Toyama, Japan
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