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Choi S, Cho N, Kim KK. The implications of alternative pre-mRNA splicing in cell signal transduction. Exp Mol Med 2023; 55:755-766. [PMID: 37009804 PMCID: PMC10167241 DOI: 10.1038/s12276-023-00981-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 01/05/2023] [Accepted: 01/27/2023] [Indexed: 04/04/2023] Open
Abstract
Cells produce multiple mRNAs through alternative splicing, which ensures proteome diversity. Because most human genes undergo alternative splicing, key components of signal transduction pathways are no exception. Cells regulate various signal transduction pathways, including those associated with cell proliferation, development, differentiation, migration, and apoptosis. Since proteins produced through alternative splicing can exhibit diverse biological functions, splicing regulatory mechanisms affect all signal transduction pathways. Studies have demonstrated that proteins generated by the selective combination of exons encoding important domains can enhance or attenuate signal transduction and can stably and precisely regulate various signal transduction pathways. However, aberrant splicing regulation via genetic mutation or abnormal expression of splicing factors negatively affects signal transduction pathways and is associated with the onset and progression of various diseases, including cancer. In this review, we describe the effects of alternative splicing regulation on major signal transduction pathways and highlight the significance of alternative splicing.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
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Park JE, Ryoo G, Lee W. Alternative Splicing: Expanding Diversity in Major ABC and SLC Drug Transporters. AAPS JOURNAL 2017; 19:1643-1655. [DOI: 10.1208/s12248-017-0150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2017] [Accepted: 09/10/2017] [Indexed: 01/18/2023]
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McCubrey JA, Rakus D, Gizak A, Steelman LS, Abrams SL, Lertpiriyapong K, Fitzgerald TL, Yang LV, Montalto G, Cervello M, Libra M, Nicoletti F, Scalisi A, Torino F, Fenga C, Neri LM, Marmiroli S, Cocco L, Martelli AM. Effects of mutations in Wnt/β-catenin, hedgehog, Notch and PI3K pathways on GSK-3 activity-Diverse effects on cell growth, metabolism and cancer. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2016; 1863:2942-2976. [PMID: 27612668 DOI: 10.1016/j.bbamcr.2016.09.004] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 08/14/2016] [Accepted: 09/02/2016] [Indexed: 02/07/2023]
Abstract
Glycogen synthase kinase-3 (GSK-3) is a serine/threonine kinase that participates in an array of critical cellular processes. GSK-3 was first characterized as an enzyme that phosphorylated and inactivated glycogen synthase. However, subsequent studies have revealed that this moon-lighting protein is involved in numerous signaling pathways that regulate not only metabolism but also have roles in: apoptosis, cell cycle progression, cell renewal, differentiation, embryogenesis, migration, regulation of gene transcription, stem cell biology and survival. In this review, we will discuss the roles that GSK-3 plays in various diseases as well as how this pivotal kinase interacts with multiple signaling pathways such as: PI3K/PTEN/Akt/mTOR, Ras/Raf/MEK/ERK, Wnt/beta-catenin, hedgehog, Notch and TP53. Mutations that occur in these and other pathways can alter the effects that natural GSK-3 activity has on regulating these signaling circuits that can lead to cancer as well as other diseases. The novel roles that microRNAs play in regulation of the effects of GSK-3 will also be evaluated. Targeting GSK-3 and these other pathways may improve therapy and overcome therapeutic resistance.
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Affiliation(s)
- James A McCubrey
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University Greenville, NC 27858, USA.
| | - Dariusz Rakus
- Department of Animal Molecular Physiology, Institute of Experimental Biology, Wroclaw University, Wroclaw, Poland
| | - Agnieszka Gizak
- Department of Animal Molecular Physiology, Institute of Experimental Biology, Wroclaw University, Wroclaw, Poland
| | - Linda S Steelman
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University Greenville, NC 27858, USA
| | - Steve L Abrams
- Department of Microbiology and Immunology, Brody School of Medicine at East Carolina University Greenville, NC 27858, USA
| | - Kvin Lertpiriyapong
- Department of Comparative Medicine, Brody School of Medicine at East Carolina University, USA
| | - Timothy L Fitzgerald
- Department of Surgery, Brody School of Medicine at East Carolina University, USA
| | - Li V Yang
- Department of Internal Medicine, Hematology/Oncology Section, Brody School of Medicine at East Carolina University, USA
| | - Giuseppe Montalto
- Biomedical Department of Internal Medicine and Specialties, University of Palermo, Palermo, Italy; Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "Alberto Monroy", Palermo, Italy
| | - Melchiorre Cervello
- Consiglio Nazionale delle Ricerche, Istituto di Biomedicina e Immunologia Molecolare "Alberto Monroy", Palermo, Italy
| | - Massimo Libra
- Department of Bio-medical Sciences, University of Catania, Catania, Italy
| | | | - Aurora Scalisi
- Unit of Oncologic Diseases, ASP-Catania, Catania 95100, Italy
| | - Francesco Torino
- Department of Systems Medicine, Chair of Medical Oncology, Tor Vergata University of Rome, Rome, Italy
| | - Concettina Fenga
- Department of Biomedical, Odontoiatric, Morphological and Functional Images, Occupational Medicine Section - Policlinico "G. Martino" - University of Messina, Messina 98125, Italy
| | - Luca M Neri
- Department of Morphology, Surgery and Experimental Medicine, University of Ferrara, Ferrara, Italy
| | - Sandra Marmiroli
- Department of Surgery, Medicine, Dentistry and Morphology, University of Modena and Reggio Emilia, Modena, Italy
| | - Lucio Cocco
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
| | - Alberto M Martelli
- Dipartimento di Scienze Biomediche e Neuromotorie, Università di Bologna, Bologna, Italy
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4
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Discovery of CTCF-sensitive Cis-spliced fusion RNAs between adjacent genes in human prostate cells. PLoS Genet 2015; 11:e1005001. [PMID: 25658338 PMCID: PMC4450057 DOI: 10.1371/journal.pgen.1005001] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 01/13/2015] [Indexed: 11/19/2022] Open
Abstract
Genes or their encoded products are not expected to mingle with each other unless in some disease situations. In cancer, a frequent mechanism that can produce gene fusions is chromosomal rearrangement. However, recent discoveries of RNA trans-splicing and cis-splicing between adjacent genes (cis-SAGe) support for other mechanisms in generating fusion RNAs. In our transcriptome analyses of 28 prostate normal and cancer samples, 30% fusion RNAs on average are the transcripts that contain exons belonging to same-strand neighboring genes. These fusion RNAs may be the products of cis-SAGe, which was previously thought to be rare. To validate this finding and to better understand the phenomenon, we used LNCaP, a prostate cell line as a model, and identified 16 additional cis-SAGe events by silencing transcription factor CTCF and paired-end RNA sequencing. About half of the fusions are expressed at a significant level compared to their parental genes. Silencing one of the in-frame fusions resulted in reduced cell motility. Most out-of-frame fusions are likely to function as non-coding RNAs. The majority of the 16 fusions are also detected in other prostate cell lines, as well as in the 14 clinical prostate normal and cancer pairs. By studying the features associated with these fusions, we developed a set of rules: 1) the parental genes are same-strand-neighboring genes; 2) the distance between the genes is within 30kb; 3) the 5′ genes are actively transcribing; and 4) the chimeras tend to have the second-to-last exon in the 5′ genes joined to the second exon in the 3′ genes. We then randomly selected 20 neighboring genes in the genome, and detected four fusion events using these rules in prostate cancer and non-cancerous cells. These results suggest that splicing between neighboring gene transcripts is a rather frequent phenomenon, and it is not a feature unique to cancer cells. Genes are considered the units of hereditary information; thus, neither genes nor their encoded products are expected to mingle with each other unless in some disease situations. However, the genes are not alone in the genome. Genes have neighbors, some close, some far. With RNA-seq, many fusion RNAs involving neighboring genes are being identified. However, little is done to validate and characterize the fusion RNAs. Using one prostate cell line and a discovery pipeline for cis-splicing between adjacent genes (cis-SAGe), we found 16 new such events. We then developed a set of rules based on the characteristics of these fusion RNAs, and applied them to 20 random neighboring gene pairs. Four turned out to be true. The majority of the fusions are found in cancer cells, as well as in non-cancer cells. These results suggest that the genes are “leaky”, and the fusions are not limited to cancer cells.
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Shargunov AV, Krasnov GS, Ponomarenko EA, Lisitsa AV, Shurdov MA, Zverev VV, Archakov AI, Blinov VM. Tissue-Specific Alternative Splicing Analysis Reveals the Diversity of Chromosome 18 Transcriptome. J Proteome Res 2013; 13:173-82. [DOI: 10.1021/pr400808u] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander V. Shargunov
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
| | - George S. Krasnov
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
| | - Elena A. Ponomarenko
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
- LLC PostGenTech, 10, Pogodinskaya Street, 119121 Moscow, Russia
| | - Andrey V. Lisitsa
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
- LLC PostGenTech, 10, Pogodinskaya Street, 119121 Moscow, Russia
| | | | - Vitaliy V. Zverev
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
| | - Alexander I. Archakov
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
| | - Vladimir M. Blinov
- I. I. Mechnikov Institute of Vaccines and Sera of the Russian Academy of Medical Sciences, 5A, Maly Kazenny per., 105064 Moscow, Russia
- Bioinformatics
and Postgenome Research, V. N. Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, 10, Pogodinskaya
Street, 119121 Moscow, Russia
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Hassan MA, Butty V, Jensen KDC, Saeij JPJ. The genetic basis for individual differences in mRNA splicing and APOBEC1 editing activity in murine macrophages. Genome Res 2013; 24:377-89. [PMID: 24249727 PMCID: PMC3941103 DOI: 10.1101/gr.166033.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Alternative splicing and mRNA editing are known to contribute to transcriptome diversity. Although alternative splicing is pervasive and contributes to a variety of pathologies, including cancer, the genetic context for individual differences in isoform usage is still evolving. Similarly, although mRNA editing is ubiquitous and associated with important biological processes such as intracellular viral replication and cancer development, individual variations in mRNA editing and the genetic transmissibility of mRNA editing are equivocal. Here, we have used linkage analysis to show that both mRNA editing and alternative splicing are regulated by the macrophage genetic background and environmental cues. We show that distinct loci, potentially harboring variable splice factors, regulate the splicing of multiple transcripts. Additionally, we show that individual genetic variability at the Apobec1 locus results in differential rates of C-to-U(T) editing in murine macrophages; with mouse strains expressing mostly a truncated alternative transcript isoform of Apobec1 exhibiting lower rates of editing. As a proof of concept, we have used linkage analysis to identify 36 high-confidence novel edited sites. These results provide a novel and complementary method that can be used to identify C-to-U editing sites in individuals segregating at specific loci and show that, beyond DNA sequence and structural changes, differential isoform usage and mRNA editing can contribute to intra-species genomic and phenotypic diversity.
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Affiliation(s)
- Musa A Hassan
- Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
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Zhu H, Carpenter RL, Han W, Lo HW. The GLI1 splice variant TGLI1 promotes glioblastoma angiogenesis and growth. Cancer Lett 2013; 343:51-61. [PMID: 24045042 DOI: 10.1016/j.canlet.2013.09.014] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/10/2013] [Accepted: 09/11/2013] [Indexed: 01/27/2023]
Abstract
We investigated truncated glioma-associated oncogene homolog 1 (TGLI1) that behaves as gain-of-function GLI1 and promotes tumor cell migration and invasion. Herein, we report that TGLI1 had a higher propensity than GLI1 to enhance glioblastoma angiogenesis and growth, both in vivo and in vitro. TGLI1 has gained the ability to enhance expression of pro-angiogenic heparanase. In patient glioblastomas, TGLI1 levels are correlated with heparanase expression. Together, we report that TGLI1 is a novel mediator of glioblastoma angiogenesis and that heparanase is a novel transcriptional target of TGLI1, shedding new light on the molecular pathways that support tumor angiogenesis and aggressive growth.
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Affiliation(s)
- Hu Zhu
- Department of Surgery, Division of Surgical Sciences, Durham, NC 27710, USA
| | | | - Woody Han
- Department of Surgery, Division of Surgical Sciences, Durham, NC 27710, USA
| | - Hui-Wen Lo
- Department of Surgery, Division of Surgical Sciences, Durham, NC 27710, USA; Duke Center for RNA Biology, Durham, NC 27710, USA; Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA.
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