1
|
Ono Y, Doi N, Shindo M, Pánico P, Salazar AM. Cryptic splicing events result in unexpected protein products from calpain-10 (CAPN10) cDNA. Biochim Biophys Acta Mol Cell Res 2022; 1869:119188. [PMID: 34906616 DOI: 10.1016/j.bbamcr.2021.119188] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 11/13/2021] [Accepted: 12/05/2021] [Indexed: 06/14/2023]
Abstract
Calpain-10 (CAPN10) belongs to the calpain superfamily. Genetic polymorphisms of the CAPN10 gene are associated with susceptibility to develop type 2 diabetes mellitus. Although the role of CAPN10 in the pathophysiology of diabetes has been extensively investigated, its biochemical properties are largely unknown. In this report, we made the surprising discovery that CAPN10 cDNA transcripts are subject to cryptic splicing and unexpected protein products were expressed. The same set of splicing products was reproducibly detected in four types of cultured cells including the primary culture of mouse myoblast. At least, one of the products was identical to a natural splicing variant. Sequence analysis of the splicing potential of CAPN10 cDNA, together with mutagenesis studies, resulted in the identification of a powerful splicing acceptor site at the junction of the sequences encoded by exons 9 and 10. We successfully extended the analysis to create expression construct resistant to splicing for both human and mouse CAPN10. The construct allowed us to analyze two major CAPN10 isoforms and reveal their difference in substrate proteolysis and potential cell functions. These results demonstrate that proteins produced from cDNA do not necessarily reflect the original nucleotide sequence. We provide insight into the property of recombinantly expressed CAPN10 proteins in cultured cells circumventing unexpected protein products.
Collapse
Affiliation(s)
- Yasuko Ono
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science (TMiMS), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 1568506, Japan.
| | - Naoko Doi
- Calpain Project, Department of Basic Medical Sciences, Tokyo Metropolitan Institute of Medical Science (TMiMS), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 1568506, Japan
| | - Mayumi Shindo
- Advanced Technical Support Department, Center for Basic Technology Research, Tokyo Metropolitan Institute of Medical Science (TMiMS), 2-1-6 Kamikitazawa, Setagaya-ku, Tokyo 1568506, Japan
| | - Pablo Pánico
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico; Department of Cognitive Neurosciences, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Ana María Salazar
- Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| |
Collapse
|
2
|
Hujová P, Souček P, Radová L, Kramárek M, Kováčová T, Freiberger T. Nucleotides in both donor and acceptor splice sites are responsible for choice in NAGNAG tandem splice sites. Cell Mol Life Sci 2021; 78:6979-6993. [PMID: 34596691 PMCID: PMC11072513 DOI: 10.1007/s00018-021-03943-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 09/08/2021] [Accepted: 09/15/2021] [Indexed: 12/31/2022]
Abstract
Among alternative splicing events in the human transcriptome, tandem NAGNAG acceptor splice sites represent an appreciable proportion. Both proximal and distal NAG can be used to produce two splicing isoforms differing by three nucleotides. In some cases, the upstream exon can be alternatively spliced as well, which further increases the number of possible transcripts. In this study, we showed that NAG choice in tandem splice site depends considerably not only on the concerned acceptor, but also on the upstream donor splice site sequence. Using an extensive set of experiments with systematically modified two-exonic minigene systems of AFAP1L2 or CSTD gene, we recognized the third and fifth intronic upstream donor splice site position and the tandem acceptor splice site region spanning from -10 to +2, including NAGNAG itself, as the main drivers. In addition, competition between different branch points and their composition were also shown to play a significant role in NAG choice. All these nucleotide effects appeared almost additive, which explained the high variability in proximal versus distal NAG usage.
Collapse
Affiliation(s)
- Pavla Hujová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Přemysl Souček
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic.
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic.
| | - Lenka Radová
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Michal Kramárek
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
| | - Tatiana Kováčová
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| | - Tomáš Freiberger
- Centre for Cardiovascular Surgery and Transplantation, 65691, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, 62500, Brno, Czech Republic
| |
Collapse
|
3
|
Huang J, Hu M, Niu H, Wang J, Si Y, Cheng S, Ding W. Osteopontin isoform c promotes the survival of cisplatin-treated NSCLC cells involving NFATc2-mediated suppression on calcium-induced ROS levels. BMC Cancer 2021; 21:750. [PMID: 34187410 PMCID: PMC8243455 DOI: 10.1186/s12885-021-08495-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 06/09/2021] [Indexed: 12/31/2022] Open
Abstract
Background Tumor microenvironment (TME) critically contributed to the malignant progression of transformed cells and the chemical responses to chemotherapy reagents. Osteopontin (OPN) is a secretory onco-protein with several splicing isoforms, all of which were known to regulate tumor growth and able to alter cell-cell or cell-TME communication, however, the exact role and regulation of the OPN splicing isoforms was not well understood. Methods In this study, the effects of conditioned medium from the culture of OPN splicing isoforms overexpressing cells on cell functions were evaluated. The methods of nuclear calcium reporter assays and subcellular distribution of nuclear factor of activated T cells c2 (NFATc2) assays were used to investigate the molecular mechanism underlining the roles of OPN splicing isoforms. Results We found that the survival of NSCLC cells treated with cisplatin was increased by secretory OPNc in the condition medium, where reduction of apoptosis by OPNc was associated with the activation of cellular calcium signals and subsequent nuclear translocation of NFATc2. Conclusions The results revealed a mechanism of OPN and downstream signal for tumor cells to survive in chemo-stressed TME, which emphasized the importance of secretory proteins in alternative splicing isoforms. Our study not only demonstrated the importance of OPN neutralization for anti-tumor effects, but also implied that modulation in calcium/NFATc2/ROS axis could be a novel approach for improving the long-term outcome of NSCLC treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12885-021-08495-z.
Collapse
Affiliation(s)
- Jing Huang
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Mu Hu
- Department of Thoracic Surgery, Beijing Friendship Hospital, Capital Medical University, Beijing, 100050, China
| | - Huan Niu
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Jing Wang
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Yang Si
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China
| | - Shan Cheng
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
| | - Wei Ding
- School of Basic Medical Sciences, Capital Medical University, Beijing, 100069, China.
| |
Collapse
|
4
|
Oka M, Xu L, Suzuki T, Yoshikawa T, Sakamoto H, Uemura H, Yoshizawa AC, Suzuki Y, Nakatsura T, Ishihama Y, Suzuki A, Seki M. Aberrant splicing isoforms detected by full-length transcriptome sequencing as transcripts of potential neoantigens in non-small cell lung cancer. Genome Biol 2021; 22:9. [PMID: 33397462 PMCID: PMC7780684 DOI: 10.1186/s13059-020-02240-8] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 12/14/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Long-read sequencing of full-length cDNAs enables the detection of structures of aberrant splicing isoforms in cancer cells. These isoforms are occasionally translated, presented by HLA molecules, and recognized as neoantigens. This study used a long-read sequencer (MinION) to construct a comprehensive catalog of aberrant splicing isoforms in non-small-cell lung cancers, by which novel isoforms and potential neoantigens are identified. RESULTS Full-length cDNA sequencing is performed using 22 cell lines, and a total of 2021 novel splicing isoforms are identified. The protein expression of some of these isoforms is then validated by proteome analysis. Ablations of a nonsense-mediated mRNA decay (NMD) factor, UPF1, and a splicing factor, SF3B1, are found to increase the proportion of aberrant transcripts. NetMHC evaluation of the binding affinities to each type of HLA molecule reveals that some of the isoforms potentially generate neoantigen candidates. We also identify aberrant splicing isoforms in seven non-small-cell lung cancer specimens. An enzyme-linked immune absorbent spot assay indicates that approximately half the peptide candidates have the potential to activate T cell responses through their interaction with HLA molecules. Finally, we estimate the number of isoforms in The Cancer Genome Atlas (TCGA) datasets by referring to the constructed catalog and found that disruption of NMD factors is significantly correlated with the number of splicing isoforms found in the TCGA-Lung Adenocarcinoma data collection. CONCLUSIONS Our results indicate that long-read sequencing of full-length cDNAs is essential for the precise identification of aberrant transcript structures in cancer cells.
Collapse
Affiliation(s)
- Miho Oka
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
- Ono Pharmaceutical Co., Ltd., Ibaraki, Japan
| | - Liu Xu
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Toshihiro Suzuki
- General Medical Education and Research Center, Teikyo University, Tokyo, Japan
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Toshiaki Yoshikawa
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Hiromi Sakamoto
- Department of Clinical Genomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Hayato Uemura
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Akiyasu C. Yoshizawa
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Chiba, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Ayako Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| | - Masahide Seki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan
| |
Collapse
|
5
|
Ding D, Sun X, Pang MYH, An L, Huen MSY, Hu T, Ishibashi T. RECQL5 KIX domain splicing isoforms have distinct functions in transcription repression and DNA damage response. DNA Repair (Amst) 2020; 97:103007. [PMID: 33197722 DOI: 10.1016/j.dnarep.2020.103007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 10/27/2020] [Accepted: 10/29/2020] [Indexed: 11/17/2022]
Abstract
RecQL5, a mammalian RecQ family protein, is involved in the regulation of transcription elongation, DNA damage response, and DNA replication. Here, we identified and characterized an alternative splicing isoform of RECQL5 (RECQL5β1), which contains 17 additional amino acid residues within the RECQL5 KIX domain when compared with the canonical isoform (RECQL5β). RECQL5β1 had a markedly decreased binding affinity to RNA polymerase II (Pol II) and poorly competed with the transcription elongation factor TFIIS for binding to Pol II. As a result, this isoform has a weaker activity for repression of transcription elongation. In contrast, we discovered that RECQL5β1 could bind stronger to MRE11, which is a primary sensor of DNA double-strand breaks (DSBs). Furthermore, we found that RECQL5β1 promoted DNA repair in the RECQL5β1 rescue cells. These results suggest that RECQL5β mainly functions as a transcription repressor, while the newly discovered RECQL5β1 has a specialized role in DNA damage response. Taken together, our data suggest a cellular-functional specialization for each KIX splicing isoform in the cell.
Collapse
Affiliation(s)
- Dongbo Ding
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong SAR, China
| | - Xulun Sun
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong SAR, China
| | - Matthew Y H Pang
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong SAR, China
| | - Liwei An
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Michael S Y Huen
- School of Biomedical Sciences, LKS Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, Hong Kong SAR, China
| | - Taobo Hu
- Center of Breast Diseases, Peking University People's Hospital, Peking University, Beijing, China
| | - Toyotaka Ishibashi
- Division of Life Science, The Hong Kong University of Science and Technology, Clear Water Bay, NT, Hong Kong SAR, China.
| |
Collapse
|
6
|
Wang X, Wang J, Cheng Y, Wang J, Tian Y, Zhang J, Xiong J, Yang Y, Wu W, He P, Liu G, Xu Y, Liu L, Ren B, Ruan Y, Jian R. Identification and functional comparison of Bcl2 splicing isoforms in mouse embryonic stem cells. Biochem Biophys Res Commun 2020; 524:502-509. [PMID: 32008743 DOI: 10.1016/j.bbrc.2020.01.140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/24/2020] [Indexed: 10/25/2022]
Abstract
Embryonic stem cells (ESCs) provide an ideal model for investigating developmental processes and are great sources for developing regenerative medicine. Harnessing apoptosis facilitates accurate recapitulation of signalling events during embryogenesis and allows efficient expansion of the ESCs during differentiation. Bcl2, a key regulator of intrinsic anti-apoptotic pathway, encodes two splicing isoforms. However, the identification and functional comparison of Bcl2 splicing isoforms in mouse ESCs (mESCs) remains to be elucidated. Here, we provide the evidence that both Bcl2 splicing variants are expressed in mESCs. Despite the structural difference, they have similar subcellular localisation. Both Bcl2α and Bcl2β enhance differentiation efficiency of the ESCs and effectively improve the survival and growth of ESCs under serum-free conditions. However, the functional effect of Bcl2α was more potent than that of Bcl2β. Moreover, only Bcl2α could maintain the long-term expansion and pluripotency of ESCs cultured in serum-free medium. Taken together, our results demonstrate previously unknown functional differences in Bcl2 alternative splicing isoforms in ESCs, and lay the foundation for future efforts to engineer ESCs for regenerative medicine.
Collapse
Affiliation(s)
- Xueyue Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaqi Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yuda Cheng
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiali Wang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yanping Tian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Junlei Zhang
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Jiaxiang Xiong
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yi Yang
- Experimental Center of Basic Medicine, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Wei Wu
- Thoracic Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Ping He
- Cardiac Surgery Department, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Gaoke Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Yixiao Xu
- Southwest Eye Hospital, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Lianlian Liu
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China
| | - Bangqi Ren
- Southwest Eye Hospital, Southwest Hospital, The First Hospital Affiliated to Army Medical University, Chongqing, 400038, China
| | - Yan Ruan
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| | - Rui Jian
- Laboratory of Stem Cell & Developmental Biology, Department of Histology and Embryology, College of Basic Medical Sciences, Army Medical University, Chongqing, 400038, China.
| |
Collapse
|
7
|
Granata F, Mendez M, Brancaleoni V, Castelbon FJ, Graziadei G, Ventura P, Di Pierro E. Molecular characterization, by digital PCR analysis of four HMBS gene mutations affecting the ubiquitous isoform of Porphobilinogen Deaminase (PBGD) in patients with Acute Intermittent Porphyria (AIP). Mol Genet Metab 2018; 125:295-301. [PMID: 30201327 DOI: 10.1016/j.ymgme.2018.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/03/2018] [Accepted: 09/03/2018] [Indexed: 12/12/2022]
Abstract
Genetic variants in promoters and alternative-splicing lesions require to be experimentally tested in order to validate them as causatives of a disease. The digital PCR (dPCR) approach, which is an alternative to the classical qPCR, is an innovative and a more sensitive method for the detection and quantification of nucleic acids. In the present study, we identified four HMBS gene mutations affecting the ubiquitous isoform of porphobilinogen deaminase (PBGD) and established a dPCR protocol which would be able to detect the different transcripts of this gene. With the application of this method, we were able to characterize the functional roles of these four genetic variants, demonstrating that all these mutations were causatives of the non-erythroid variant of the acute intermittent porphyria (AIP) disease.
Collapse
Affiliation(s)
- Francesca Granata
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale, Milano, Italy
| | - Manuel Mendez
- Instituto de Investigación, Hospital 12 de Octubre, Madrid, Spain
| | - Valentina Brancaleoni
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale, Milano, Italy
| | | | - Giovanna Graziadei
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale, Milano, Italy
| | - Paolo Ventura
- Division of Internal Medicine 2 - Centre for Porphyrias, Dept. of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Policlinico Hospital, Modena, Italy
| | - Elena Di Pierro
- Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, U.O.C. Medicina Generale, Milano, Italy.
| |
Collapse
|
8
|
Kamei S, Fujikawa H, Nohara H, Ueno-Shuto K, Maruta K, Nakashima R, Kawakami T, Matsumoto C, Sakaguchi Y, Ono T, Suico MA, Boucher RC, Gruenert DC, Takeo T, Nakagata N, Li JD, Kai H, Shuto T. Zinc Deficiency via a Splice Switch in Zinc Importer ZIP2/SLC39A2 Causes Cystic Fibrosis-Associated MUC5AC Hypersecretion in Airway Epithelial Cells. EBioMedicine 2017; 27:304-316. [PMID: 29289532 PMCID: PMC5828551 DOI: 10.1016/j.ebiom.2017.12.025] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 12/15/2017] [Accepted: 12/19/2017] [Indexed: 01/02/2023] Open
Abstract
Airway mucus hyperproduction and fluid imbalance are important hallmarks of cystic fibrosis (CF), the most common life-shortening genetic disorder in Caucasians. Dysregulated expression and/or function of airway ion transporters, including cystic fibrosis transmembrane conductance regulator (CFTR) and epithelial sodium channel (ENaC), have been implicated as causes of CF-associated mucus hypersecretory phenotype. However, the contributory roles of other substances and transporters in the regulation of CF airway pathogenesis remain unelucidated. Here, we identified a novel connection between CFTR/ENaC expression and the intracellular Zn2 + concentration in the regulation of MUC5AC, a major secreted mucin that is highly expressed in CF airway. CFTR-defective and ENaC-hyperactive airway epithelial cells specifically and highly expressed a unique, alternative splice isoform of the zinc importer ZIP2/SLC39A2 (ΔC-ZIP2), which lacks the C-terminal domain. Importantly, ΔC-ZIP2 levels correlated inversely with wild-type ZIP2 and intracellular Zn2 + levels. Moreover, the splice switch to ΔC-ZIP2 as well as decreased expression of other ZIPs caused zinc deficiency, which is sufficient for induction of MUC5AC; while ΔC-ZIP2 expression per se induced ENaC expression and function. Thus, our findings demonstrate that the novel splicing switch contributes to CF lung pathology via the novel interplay of CFTR, ENaC, and ZIP2 transporters. Zinc deficiency is a common feature in both CFTR-defective (CF) and ENaC-hyperactive (CF-like) airway epithelial cells. A splice switch from WT-ZIP2 to ΔC-ZIP2 as well as other ZIPs down-regulation caused zinc deficiency in CF and CF-like cells. Lower intracellular Zn2 + levels contributed to CF-associated MUC5AC hypersecretion in airway epithelial cells.
The role of zinc in the pathogenesis of CF lung disease is not well understood. We utilized human CF patient-derived cell lines and primary cells as well as murine CF model, and identified zinc deficiency as a common characteristic in CF models. Down-regulation of several zinc importers (ZIPs) in CF cells caused zinc deficiency, which is sufficient for induction of MUC5AC, a major secreted mucin that exacerbates CF pathogenesis. Especially, strong contribution of ΔC-ZIP2, a novel ZIP2 splice isoform, in the regulation of CF-associated MUC5AC hypersecretion was clearly demonstrated. The study refined the importance of zinc in airway homeostasis.
Collapse
Affiliation(s)
- Shunsuke Kamei
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Haruka Fujikawa
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Hirofumi Nohara
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan; Program for Leading Graduate Schools "HIGO (Health life science: Interdisciplinary and Glocal Oriented) Program", Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Keiko Ueno-Shuto
- Laboratory of Pharmacology, Division of Life Science, Faculty of Pharmaceutical Sciences, Sojo University, 4-22-1 Ikeda, Nishi-ku, Kumamoto 860-0082, Japan
| | - Kasumi Maruta
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Ryunosuke Nakashima
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Taisei Kawakami
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Chizuru Matsumoto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Yuki Sakaguchi
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Tomomi Ono
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Mary Ann Suico
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan
| | - Richard C Boucher
- Marsico Lung Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Dieter C Gruenert
- Head and Neck Stem Cell Lab, University of California, San Francisco, 2340 Sutter St, Box 1330, N331, San Francisco, CA 94115, USA
| | - Toru Takeo
- Division of Reproductive Engineering, Center for Animal Resources and Development (CARD), Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Naomi Nakagata
- Division of Reproductive Engineering, Center for Animal Resources and Development (CARD), Kumamoto University, 2-2-1 Honjo, Chuo-ku, Kumamoto 860-0811, Japan
| | - Jian-Dong Li
- Center for Inflammation, Immunity & Infection, Institute for Biomedical Sciences, Georgia State University, 714 Petit Science Center, 100 Piedmont Ave SE, Atlanta GA30303, USA
| | - Hirofumi Kai
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
| | - Tsuyoshi Shuto
- Department of Molecular Medicine, Graduate School of Pharmaceutical Sciences, Kumamoto University, 5-1 Oe-Honmachi, Chuo-ku, Kumamoto 862-0973, Japan.
| |
Collapse
|
9
|
Tang S, Liu Y, Wang X, Liang Z, Cai H, Mo L, Xiao D, Guo S, Ouyang Y, Sun B, Lu C, Li X. Characterization of overexpression of the alternatively spliced isoform of the protein phosphatase 2A catalytic subunit in cells. Biochem Biophys Res Commun 2017; 494:491-498. [PMID: 29066346 DOI: 10.1016/j.bbrc.2017.10.093] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 12/18/2022]
Abstract
PP2Acα2 is a recently discovered PP2Acα alternative splicing isoform that can be induced following serum withdrawal. It shows enhanced binding to immunoglobulin binding protein 1 and is overexpressed in chronic lymphocytic leukemia patients. Current knowledge concerning PP2Acα2 is limited. In this study, we induced and cloned PP2Acα2 from HL-60 cells and human lymphocytes, transfected them into human embryonic kidney 293 cells and constructed a stable overexpression cell line. We found that PP2Acα2 mRNA inhibits expression of its longer isoform PP2Acα mRNA but had no effect on the final protein expression and modification of this longer isoform. Moreover, PP2Acα2-overexpressed cells demonstrated increased expression of IGBP1, activated mTORC1 signaling to reduce basal autophagy and increased anchorage-independent growth. Our study provides new insights into the complex mechanisms of PP2A regulation.
Collapse
Affiliation(s)
- Shen Tang
- School of Preclinical medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Yuyang Liu
- Hunan Provincial Center for Disease Control and Prevention, Changsha, Hunan, 410005, China
| | - Xinhang Wang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Ziwei Liang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Haiqing Cai
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Laiming Mo
- School of Preclinical medicine, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Deqiang Xiao
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China
| | - Songchao Guo
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China
| | - Yiqiang Ouyang
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China
| | - Bin Sun
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China
| | - Cailing Lu
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| | - Xiyi Li
- Guangxi Colleges and Universities Key Laboratory of Prevention and Control of Highly Prevalent Diseases, China; School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, China.
| |
Collapse
|
10
|
Wang B, Liu Y, Sun Z, Liu X, Mi Y, Liu D, Xu X, Hou Q, Wang F, Hu C. A splicing isoform of Ctenopharyngodon idella ADAR1 (CiADAR1-like): Genome organization, tissue specific expression and transcriptional regulation. Fish Shellfish Immunol 2015; 47:535-544. [PMID: 26455664 DOI: 10.1016/j.fsi.2015.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/30/2015] [Accepted: 09/30/2015] [Indexed: 06/05/2023]
Abstract
Catalyzing the deamination of adenosine to inosine in RNA, ADAR1 (adenosine deaminase that act on RNA 1) belongs to ADAR family. In our previous work, we have cloned the complete genomic sequence of ADAR1 from grass carp (Ctenopharyngodon idella), named CiADAR1. In the process, we found a splicing isoform of CiADAR1 (CiADAR1-like). CiADAR1 and CiADAR1-like are possessed by different promoters but share a common exon 2. The complete genomic CiADAR1-like has 9 exons and 8 introns. Its full-length cDNA is comprised of a 5' UTR (417 bp), a 3' UTR (118 bp) and a 3324 bp-long ORF encoding a polypeptide of 1107 amino acids. The deduced amino acid sequence of CiADAR1-like contains two Z-DNA binding domains, three dsRNA binding motifs and a truncate catalytic domain. CiADAR1-like shared higher homology with Danio rerio ADAR1 and lower homology with HsADAR1-like in phylogenetic tree. qRT-PCR showed that CiADAR1-like were ubiquitously expressed and significantly up-regulated after stimulation with Poly I:C. Its mRNA reached the peak at 12 h post-stimulation in all tested tissues. Western-blotting experiment proved CiADAR1-like was factually expressed in C. idella kidney (CIK) cells. To further study the transcriptional regulatory mechanism of CiADAR1-like, we cloned its promoter sequence. CiADAR1-like promoter is 1173 bp in length containing 3 ISRE and 8 IRF-E. Subsequently, grass carp IRF1 (CiIRF1) and IRF3 (CiIRF3) were expressed in Escherichia coli BL21 and purified by affinity chromatography with the Ni-NTA His-Bind Resin. In vitro, CiIRF1 and CiIRF3 were able to bind to CiADAR1-like promoter with high affinity in gel mobility shift assays, revealing that IRF1 and IRF3 could be the potential transcriptional regulatory factors for CiADAR1-like. In vivo, Co-transfection of pcDNA3.1-IRF1 (or pcDNA3.1-IRF3) with pGL3-CiADAR1-like promoter into CIK cells showed that both IRF1 and IRF3 significantly increased the luciferase activity, suggesting that they play a positive role in CiADAR1-like transcription.
Collapse
Affiliation(s)
- Binhua Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yong Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Zhicheng Sun
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Xiancheng Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Yichuan Mi
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Dan Liu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Xiaowen Xu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Qunhao Hou
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Fang Wang
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China
| | - Chengyu Hu
- Department of Bioscience, College of Life Science, Nanchang University, Nanchang 330031, China.
| |
Collapse
|
11
|
Abstract
Alternative splicing contributes to the complexity of proteome by producing multiple mRNAs from a single gene. Affymetrix exon arrays and experiments in vivo or in vitro demonstrated that alternative splicing was regulated by mechanical stress. Expression of mechano-growth factor (MGF) which is the splicing isoform of insulin-like growth factor 1(IGF-1) and vascular endothelial growth factor (VEGF) splicing variants such as VEGF121, VEGF165, VEGF206, VEGF189, VEGF165 and VEGF145 are regulated by mechanical stress. However, the mechanism of this process is not yet clear. Increasing evidences showed that the possible mechanism is related to Ca2+ signal pathway and phosphorylation signal pathway. This review proposes possible mechanisms of mechanical splicing regulation. This will contribute to the biomechanical study of alternative splicing.
Collapse
Affiliation(s)
- Huan Liu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing 400044, China
| | | |
Collapse
|