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Song M, Pang L, Zhang M, Qu Y, Laster KV, Dong Z. Cdc2-like kinases: structure, biological function, and therapeutic targets for diseases. Signal Transduct Target Ther 2023; 8:148. [PMID: 37029108 PMCID: PMC10082069 DOI: 10.1038/s41392-023-01409-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 03/15/2023] [Accepted: 03/20/2023] [Indexed: 04/09/2023] Open
Abstract
The CLKs (Cdc2-like kinases) belong to the dual-specificity protein kinase family and play crucial roles in regulating transcript splicing via the phosphorylation of SR proteins (SRSF1-12), catalyzing spliceosome molecular machinery, and modulating the activities or expression of non-splicing proteins. The dysregulation of these processes is linked with various diseases, including neurodegenerative diseases, Duchenne muscular dystrophy, inflammatory diseases, viral replication, and cancer. Thus, CLKs have been considered as potential therapeutic targets, and significant efforts have been exerted to discover potent CLKs inhibitors. In particular, clinical trials aiming to assess the activities of the small molecules Lorecivivint on knee Osteoarthritis patients, and Cirtuvivint and Silmitasertib in different advanced tumors have been investigated for therapeutic usage. In this review, we comprehensively documented the structure and biological functions of CLKs in various human diseases and summarized the significance of related inhibitors in therapeutics. Our discussion highlights the most recent CLKs research, paving the way for the clinical treatment of various human diseases.
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Affiliation(s)
- Mengqiu Song
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
| | - Luping Pang
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Research Center of Basic Medicine, Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Mengmeng Zhang
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Yingzi Qu
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China
| | - Kyle Vaughn Laster
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China
| | - Zigang Dong
- Department of Pathophysiology, School of Basic Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
- China-US (Henan) Hormel Cancer Institute, No.127, Dongming Road, Jinshui District, Zhengzhou, Henan, 450008, China.
- State Key Laboratory of Esophageal Cancer Prevention and Treatment, Zhengzhou University, Zhengzhou, Henan, China.
- Academy of Medical Sciences, College of Medicine, Zhengzhou University, Zhengzhou, Henan, 450001, China.
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2
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Patel A, Dobbins T, Kong X, Patel R, Carter G, Harding L, Sparks RP, Patel NA, Cooper DR. Induction of beige-like adipocyte markers and functions in 3T3-L1 cells by Clk1 and PKCβII inhibitory molecules. J Cell Mol Med 2022; 26:4183-4194. [PMID: 35801494 PMCID: PMC9344812 DOI: 10.1111/jcmm.17345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 11/29/2022] Open
Abstract
Excessive dietary intake of fat results in its storage in white adipose tissue (WAT). Energy expenditure through lipid oxidation occurs in brown adipose tissue (BAT). Certain WAT depots can undergo a change termed beiging where markers that BAT express are induced. Little is known about signalling pathways inducing beiging. Here, inhibition of a signalling pathway regulating alternative pre‐mRNA splicing is involved in adipocyte beiging. Clk1/2/4 kinases regulate splicing by phosphorylating factors that process pre‐mRNA. Clk1 inhibition by TG003 results in beige‐like adipocytes highly expressing PGC1α and UCP1. SiRNA for Clk1, 2 and 4, demonstrated that Clk1 depletion increased UCP1 and PGC1α expression, whereas Clk2/4 siRNA did not. TG003‐treated adipocytes contained fewer lipid droplets, are smaller, and contain more mitochondria, resulting in proton leak increases. Additionally, inhibition of PKCβII activity, a splice variant regulated by Clk1, increased beiging. PGC1α is a substrate for both Clk1 and PKCβII kinases, and we surmised that inhibition of PGC1α phosphorylation resulted in beiging of adipocytes. We show that TG003 binds Clk1 more than Clk2/4 through direct binding, and PGC1α binds to Clk1 at a site close to TG003. Furthermore, we show that TG003 is highly specific for Clk1 across hundreds of kinases in our activity screen. Hence, Clk1 inhibition becomes a target for induction of beige adipocytes.
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Affiliation(s)
- Achintya Patel
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Tradd Dobbins
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Xiaoyuan Kong
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Rehka Patel
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA
| | - Gay Carter
- J.A. Haley Research Service, Tampa, Florida, USA
| | - Linette Harding
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Robert P Sparks
- Department of Chemistry, University of South Florida, Tampa, Florida, USA
| | - Niketa A Patel
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA.,J.A. Haley Research Service, Tampa, Florida, USA
| | - Denise R Cooper
- Department of Molecular Medicine, University of South Florida Morsani College of Medicine, Tampa, Florida, USA.,J.A. Haley Research Service, Tampa, Florida, USA
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3
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Naro C, Bielli P, Sette C. Oncogenic dysregulation of pre-mRNA processing by protein kinases: challenges and therapeutic opportunities. FEBS J 2021; 288:6250-6272. [PMID: 34092037 PMCID: PMC8596628 DOI: 10.1111/febs.16057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/13/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Alternative splicing and polyadenylation represent two major steps in pre-mRNA-processing, which ensure proper gene expression and diversification of human transcriptomes. Deregulation of these processes contributes to oncogenic programmes involved in the onset, progression and evolution of human cancers, which often result in the acquisition of resistance to existing therapies. On the other hand, cancer cells frequently increase their transcriptional rate and develop a transcriptional addiction, which imposes a high stress on the pre-mRNA-processing machinery and establishes a therapeutically exploitable vulnerability. A prominent role in fine-tuning pre-mRNA-processing mechanisms is played by three main families of protein kinases: serine arginine protein kinase (SRPK), CDC-like kinase (CLK) and cyclin-dependent kinase (CDK). These kinases phosphorylate the RNA polymerase, splicing factors and regulatory proteins involved in cleavage and polyadenylation of the nascent transcripts. The activity of SRPKs, CLKs and CDKs can be altered in cancer cells, and their inhibition was shown to exert anticancer effects. In this review, we describe key findings that have been reported on these topics and discuss challenges and opportunities of developing therapeutic approaches targeting splicing factor kinases.
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Affiliation(s)
- Chiara Naro
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Pamela Bielli
- Department of Biomedicine and PreventionUniversity of Rome Tor VergataItaly
- Fondazione Santa LuciaIRCCSRomeItaly
| | - Claudio Sette
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Santa LuciaIRCCSRomeItaly
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4
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Wang Z, Gao X, Li Q, Zhu H, Zhao X, Garcia-Barrio M, Zhang J, Guo Y, Chen YE, Zeng R, Wu JR, Chang L. Inhibition of a Novel CLK1-THRAP3-PPARγ Axis Improves Insulin Sensitivity. Front Physiol 2021; 12:699578. [PMID: 34526909 PMCID: PMC8435799 DOI: 10.3389/fphys.2021.699578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 08/09/2021] [Indexed: 11/13/2022] Open
Abstract
Increasing energy expenditure by promoting "browning" in adipose tissues is a promising strategy to prevent obesity and associated diabetes. To uncover potential targets of cold exposure, which induces energy expenditure, we performed phosphoproteomics profiling in brown adipose tissue of mice housed in mild cold environment at 16°C. We identified CDC2-like kinase 1 (CLK1) as one of the kinases that were significantly downregulated by mild cold exposure. In addition, genetic knockout of CLK1 or chemical inhibition in mice ameliorated diet-induced obesity and insulin resistance at 22°C. Through proteomics, we uncovered thyroid hormone receptor-associated protein 3 (THRAP3) as an interacting partner of CLK1, further confirmed by co-immunoprecipitation assays. We further demonstrated that CLK1 phosphorylates THRAP3 at Ser243, which is required for its regulatory interaction with phosphorylated peroxisome proliferator-activated receptor gamma (PPARγ), resulting in impaired adipose tissue browning and insulin sensitivity. These data suggest that CLK1 plays a critical role in controlling energy expenditure through the CLK1-THRAP3-PPARγ axis.
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Affiliation(s)
- Zhenguo Wang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Xiaojing Gao
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
- Key Laboratory of Systems Biology, CAS Center for Excellence in Molecular Cell Science, Institute of Biochemistry and Cell Biology, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Qingrun Li
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Hongwen Zhu
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
| | - Xiangjie Zhao
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Minerva Garcia-Barrio
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Jifeng Zhang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Yanhong Guo
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Y. Eugene Chen
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
| | - Rong Zeng
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Jia-Rui Wu
- CAS Key Laboratory of Systems Biology, Hangzhou Institute for Advanced Study, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Hangzhou, China
- School of Life Sciences and Technology, Shanghai Tech University, Shanghai, China
| | - Lin Chang
- Department of Internal Medicine, Cardiovascular Center, University of Michigan Medical Center, Ann Arbor, MI, United States
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5
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Uzor S, Porazinski SR, Li L, Clark B, Ajiro M, Iida K, Hagiwara M, Alqasem AA, Perks CM, Wilson ID, Oltean S, Ladomery MR. CDC2-like (CLK) protein kinase inhibition as a novel targeted therapeutic strategy in prostate cancer. Sci Rep 2021; 11:7963. [PMID: 33846420 PMCID: PMC8041776 DOI: 10.1038/s41598-021-86908-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/16/2021] [Indexed: 11/30/2022] Open
Abstract
Dysregulation of alternative splicing is a feature of cancer, both in aetiology and progression. It occurs because of mutations in splice sites or sites that regulate splicing, or because of the altered expression and activity of splice factors and of splice factor kinases that regulate splice factor activity. Recently the CDC2-like kinases (CLKs) have attracted attention due to their increasing involvement in cancer. We measured the effect of the CLK inhibitor, the benzothiazole TG003, on two prostate cancer cell lines. TG003 reduced cell proliferation and increased apoptosis in PC3 and DU145 cells. Conversely, the overexpression of CLK1 in PC3 cells prevented TG003 from reducing cell proliferation. TG003 slowed scratch closure and reduced cell migration and invasion in a transwell assay. TG003 decisively inhibited the growth of a PC3 cell line xenograft in nude mice. We performed a transcriptomic analysis of cells treated with TG003. We report widespread and consistent changes in alternative splicing of cancer-associated genes including CENPE, ESCO2, CKAP2, MELK, ASPH and CD164 in both HeLa and PC3 cells. Together these findings suggest that targeting CLKs will provide novel therapeutic opportunities in prostate cancer.
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Affiliation(s)
- Simon Uzor
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
- Department of Medical Laboratory Science, Ebonyi State University, P.M.B. 53, Abakaliki, Nigeria
| | - Sean R Porazinski
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
- Garvan Institute of Medical Research, 384 Victoria Street, Darlinghurst, Sydney, NSW, 2010, Australia
| | - Ling Li
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, Exeter, EX1 2LU, UK
| | - Bethany Clark
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Masahiko Ajiro
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kei Iida
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Masatoshi Hagiwara
- Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Abdullah A Alqasem
- IGFs and Metabolic Endocrinology Group, Bristol Medical School, Translational Health Sciences, University of Bristol, Southmead Hospital, Bristol, BS10 5NB, UK
| | - Claire M Perks
- IGFs and Metabolic Endocrinology Group, Bristol Medical School, Translational Health Sciences, University of Bristol, Southmead Hospital, Bristol, BS10 5NB, UK
| | - Ian D Wilson
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Sciences, Medical School, College of Medicine and Health, University of Exeter, Exeter, EX1 2LU, UK.
| | - Michael R Ladomery
- Faculty of Health and Applied Sciences, University of the West of England, Coldharbour Lane, Bristol, BS16 1QY, UK.
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6
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Chao Y, Jiang Y, Zhong M, Wei K, Hu C, Qin Y, Zuo Y, Yang L, Shen Z, Zou C. Regulatory roles and mechanisms of alternative RNA splicing in adipogenesis and human metabolic health. Cell Biosci 2021; 11:66. [PMID: 33795017 PMCID: PMC8017860 DOI: 10.1186/s13578-021-00581-w] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 03/24/2021] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing (AS) regulates gene expression patterns at the post-transcriptional level and generates a striking expansion of coding capacities of genomes and cellular protein diversity. RNA splicing could undergo modulation and close interaction with genetic and epigenetic machinery. Notably, during the adipogenesis processes of white, brown and beige adipocytes, AS tightly interplays with the differentiation gene program networks. Here, we integrate the available findings on specific splicing events and distinct functions of different splicing regulators as examples to highlight the directive biological contribution of AS mechanism in adipogenesis and adipocyte biology. Furthermore, accumulating evidence has suggested that mutations and/or altered expression in splicing regulators and aberrant splicing alterations in the obesity-associated genes are often linked to humans’ diet-induced obesity and metabolic dysregulation phenotypes. Therefore, significant attempts have been finally made to overview novel detailed discussion on the prospects of splicing machinery with obesity and metabolic disorders to supply featured potential management mechanisms in clinical applicability for obesity treatment strategies.
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Affiliation(s)
- Yunqi Chao
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yonghui Jiang
- Department of Genetics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Mianling Zhong
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Kaiyan Wei
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Chenxi Hu
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yifang Qin
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Yiming Zuo
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Lili Yang
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Zheng Shen
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China
| | - Chaochun Zou
- Department of Endocrinology, The Children's Hospital, School of Medicine, Zhejiang University, Hangzhou, 310052, Zhejiang, China.
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7
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Babu N, Pinto SM, Biswas M, Subbannayya T, Rajappa M, Mohan SV, Advani J, Rajagopalan P, Sathe G, Syed N, Radhakrishna VD, Muthusamy O, Navani S, Kumar RV, Gopisetty G, Rajkumar T, Radhakrishnan P, Thiyagarajan S, Pandey A, Gowda H, Majumder P, Chatterjee A. Phosphoproteomic analysis identifies CLK1 as a novel therapeutic target in gastric cancer. Gastric Cancer 2020; 23:796-810. [PMID: 32333232 DOI: 10.1007/s10120-020-01062-8] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 03/12/2020] [Indexed: 02/07/2023]
Abstract
BACKGROUND Phosphorylation is an important regulatory mechanism of protein activity in cells. Studies in various cancers have reported perturbations in kinases resulting in aberrant phosphorylation of oncoproteins and tumor suppressor proteins. METHODS In this study, we carried out quantitative phosphoproteomic analysis of gastric cancer tissues and corresponding xenograft samples. Using these data, we employed bioinformatics analysis to identify aberrant signaling pathways. We further performed molecular inhibition and silencing of the upstream regulatory kinase in gastric cancer cell lines and validated its effect on cellular phenotype. Through an ex vivo technology utilizing patient tumor and blood sample, we sought to understand the therapeutic potential of the kinase by recreating the tumor microenvironment. RESULTS Using mass spectrometry-based high-throughput analysis, we identified 1,344 phosphosites and 848 phosphoproteins, including differential phosphorylation of 177 proteins (fold change cut-off ≥ 1.5). Our data showed that a subset of differentially phosphorylated proteins belonged to splicing machinery. Pathway analysis highlighted Cdc2-like kinase (CLK1) as upstream kinase. Inhibition of CLK1 using TG003 and CLK1 siRNA resulted in a decreased cell viability, proliferation, invasion and migration as well as modulation in the phosphorylation of SRSF2. Ex vivo experiments which utilizes patient's own tumor and blood to recreate the tumor microenvironment validated the use of CLK1 as a potential target for gastric cancer treatment. CONCLUSIONS Our data indicates that CLK1 plays a crucial role in the regulation of splicing process in gastric cancer and that CLK1 can act as a novel therapeutic target in gastric cancer.
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Affiliation(s)
- Niraj Babu
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Sneha M Pinto
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Center for Systems Biology and Molecular Medicine, Yenepoya (Deemed To Be University), Mangalore, 575018, India
| | | | - Tejaswini Subbannayya
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Mitra Biotech, Bangalore, 560100, India
| | | | - Sonali V Mohan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India
| | - Jayshree Advani
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Pavithra Rajagopalan
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Gajanan Sathe
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | - Nazia Syed
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India
| | | | | | | | - Rekha V Kumar
- Department of Pathology, Kidwai Memorial Institute of Oncology, Bangalore, 560029, India
| | - Gopal Gopisetty
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | - Thangarajan Rajkumar
- Department of Molecular Oncology, Cancer Institute (WIA), Chennai, 600020, India
| | | | | | - Akhilesh Pandey
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560029, India
| | - Harsha Gowda
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India.,Manipal Academy of Higher Education, Manipal, 576104, India.,Cancer Precision Medicine, QIMR Berghofer, Royal Brisbane Hospital, Brisbane, QLD, 4029, Australia
| | | | - Aditi Chatterjee
- Institute of Bioinformatics, International Technology Park, Bangalore, Bangalore, 560066, India. .,Manipal Academy of Higher Education, Manipal, 576104, India. .,Mitra Biotech, Bangalore, 560100, India.
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8
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Hasenson SE, Shav‐Tal Y. Speculating on the Roles of Nuclear Speckles: How RNA‐Protein Nuclear Assemblies Affect Gene Expression. Bioessays 2020; 42:e2000104. [DOI: 10.1002/bies.202000104] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/17/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Sarah E. Hasenson
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
| | - Yaron Shav‐Tal
- The Mina & Everard Goodman Faculty of Life Sciences and the Institute of Nanotechnology and Advanced Materials Bar‐Ilan University Ramat Gan 4481400 Israel
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9
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Hochberg-Laufer H, Neufeld N, Brody Y, Nadav-Eliyahu S, Ben-Yishay R, Shav-Tal Y. Availability of splicing factors in the nucleoplasm can regulate the release of mRNA from the gene after transcription. PLoS Genet 2019; 15:e1008459. [PMID: 31765392 PMCID: PMC6901260 DOI: 10.1371/journal.pgen.1008459] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 12/09/2019] [Accepted: 10/04/2019] [Indexed: 11/18/2022] Open
Abstract
Gene expression dynamics can be measured in single living cells. Using a detectable transcriptionally active gene in living cells, we previously found that an mRNA undergoing several splicing events was retained at this gene after transcription until completion of mRNA processing. To determine the reason for this delay in release and whether mRNA retention on the gene might depend on splicing factor availability, we modulated the levels of splicing factors in the nucleus. Increasing the abundance of the diffusing fraction of splicing factors by their overexpression or by Clk1 kinase overexpression to disassemble nuclear speckles, led to a reduction in splicing factor residence times on the active gene, and the retained mRNA was rapidly released from the gene. Other treatments such as overexpression of a mutant inactive Clk1, the downregulation of MALAT1 lncRNA or of the Son protein, or the overexpression of the splicing factor import factor TNPO3, did not affect the dynamics of mRNA release from the gene. We found that the faster release of the mRNA from the gene mediated by increased availability of splicing factors, was dependent on the RS domain of the splicing factors and its phosphorylation state. We propose that the relative abundancies of splicing factors in the nucleoplasm can affect their availability for the splicing events taking place, and regulate the kinetics of mRNA release from the gene after processing. Genetic information is contained in the cell nucleus and encodes proteins. However, protein production takes place in the cytoplasm, and so a molecule is needed to connect between the nucleus and cytoplasm. This messenger molecule is called messenger RNA (mRNA). It is produced and copied from the DNA, and after some processing will travel to the cytoplasm to encode proteins. This study focuses on the timing of mRNA release from the gene after it is copied from the DNA. Processing of mRNA includes the removal of some of its pieces and the stitching back of the remaining parts. This is called splicing. We found that mRNAs undergoing many splicing events are retained on the gene until splicing has completed, and examined what is the cause for this delay. We found that the factors performing the splicing might be limiting the process if their levels are not high enough at the gene locus. By increasing splicing factor levels in the nucleus we show that their abundance increases the rate at which mRNA is released. This means that the cell can regulate gene expression rates by limiting the availability of splicing factors that are free to take part in the processing of mRNA.
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Affiliation(s)
- Hodaya Hochberg-Laufer
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Noa Neufeld
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yehuda Brody
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Shani Nadav-Eliyahu
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Rakefet Ben-Yishay
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
- * E-mail:
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10
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More than a messenger: Alternative splicing as a therapeutic target. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2019; 1862:194395. [PMID: 31271898 DOI: 10.1016/j.bbagrm.2019.06.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 06/18/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
Abstract
Alternative splicing of pre-mRNA is an essential post- and co-transcriptional mechanism of gene expression regulation that produces multiple mature mRNA transcripts from a single gene. Genetic mutations that affect splicing underlie numerous devastating diseases. The complexity of splicing regulation allows for multiple therapeutic approaches to correct disease-associated mis-splicing events. In this review, we first highlight recent findings from therapeutic strategies that have used splice switching antisense oligonucleotides and small molecules that bind directly to RNA. Second, we summarize different genetic and chemical approaches to target components of the spliceosome to correct splicing defects in pathological conditions. Finally, we present an overview of compounds that target kinases and accessory pathways that intersect with the splicing machinery. Advancements in the understanding of disease-specific defects caused by mis-regulation of alternative splicing will certainly increase the development of therapeutic options for the clinic. This article is part of a Special Issue entitled: RNA structure and splicing regulation edited by Francisco Baralle, Ravindra Singh and Stefan Stamm.
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11
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Boschi F, Rizzatti V, Zoico E, Montanari T, Zamboni M, Sbarbati A, Colitti M. Relationship between lipid droplets size and integrated optical density. Eur J Histochem 2019; 63. [PMID: 30907383 PMCID: PMC6444373 DOI: 10.4081/ejh.2019.3017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 03/09/2019] [Indexed: 12/19/2022] Open
Abstract
Lipid accumulation is largely investigated due to its role in many human diseases. The attention is mainly focused on the lipid droplets (LDs), spherical cytoplasmic organelles which are devoted to the storage of the lipids. The amount of lipid content is often evaluated by measuring LDs size and/or the integrated optical density (IOD) in cultured cells. Both evaluations are directly associated to the lipid content and therefore they are correlated to each other, but a lack of theoretical relationship between size and IOD was observed in literature. Here we investigated the size-IOD relationship of LDs observed in microscopical images of cultured cells. The experimental data were obtained from immature and differentiated 3T3-L1 murine cells, which have been extensively used in studies on adipogenesis. A simple model based on the spherical shape of the LDs and the Lambert-Beer law, which describes the light absorption by an optical thick material, leads to a mathematical relationship. Despite only light rays’ absorption was considered in the model, neglecting their scattering, a very good agreement between the theoretical curve and the experimental data was found. Moreover, a computational simulation corroborates the model indicating the validity of the mathematically theoretical relationship between size and IOD. The theoretical model could be used to calculate the absorption coefficient in the LDs population and it could be applied to seek for morphologically and functionally LDs subpopulations. The identification of LDs dynamic by measuring size and IOD could be related to different pathophysiological conditions and useful for understand cellular lipid-associated diseases.
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12
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Zhang T, Zhang X, Han K, Zhang G, Wang J, Xie K, Xue Q, Fan X. Analysis of long noncoding RNA and mRNA using RNA sequencing during the differentiation of intramuscular preadipocytes in chicken. PLoS One 2017; 12:e0172389. [PMID: 28199418 PMCID: PMC5310915 DOI: 10.1371/journal.pone.0172389] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 02/03/2017] [Indexed: 02/04/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) regulate metabolic tissue development and function, including adipogenesis. However, little is known about the function and profile of lncRNAs in intramuscular preadipocyte differentiation in chicken. Here, we identified lncRNAs in chicken intramuscular preadipocytes at different differentiation stages using RNA sequencing. A total of 1,311,382,604 clean reads and 25,435 lncRNAs were obtained from 12 samples. In total, 7,433 differentially expressed genes (4,698 lncRNAs and 2,735 mRNAs) were identified by pairwise comparison. These 7,433 differentially expressed genes were grouped into 11 clusters based on their expression patterns by K-means clustering. Using Weighted Gene Coexpression Network Analysis, we identified four stage-specific modules positively related to I0, I2, I4, and I6 stages and two stage-specific modules negatively related to I0 and I2 stages, respectively. Many well-known and novel pathways associated with intramuscular preadipocyte differentiation were identified. We also identified hub genes in each stage-specific module and visualized them in Cytoscape. Our analysis revealed many highly-connected genes, including XLOC_058593, BMP3, MYOD1, and LAMP3. This study provides a valuable resource for chicken lncRNA study and improves our understanding of the biology of preadipocyte differentiation in chicken.
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Affiliation(s)
- Tao Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Xiangqian Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Kunpeng Han
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Genxi Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Jinyu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
- * E-mail:
| | - Kaizhou Xie
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Qian Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
- Key Laboratory for Animal Genetics, Breeding, Reproduction and Molecular Design of Jiangsu Province, Yangzhou, Jiangsu, China
| | - Xiaomei Fan
- Vazyme Biotech Co.,Ltd., Economic and Technological Development Zone, Nanjing, Jiangsu, China
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13
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Rabiee A, Schwämmle V, Sidoli S, Dai J, Rogowska-Wrzesinska A, Mandrup S, Jensen ON. Nuclear phosphoproteome analysis of 3T3-L1 preadipocyte differentiation reveals system-wide phosphorylation of transcriptional regulators. Proteomics 2016; 17. [PMID: 27717184 DOI: 10.1002/pmic.201600248] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Revised: 09/07/2016] [Accepted: 09/20/2016] [Indexed: 01/16/2023]
Abstract
Adipocytes (fat cells) are important endocrine and metabolic cells critical for systemic insulin sensitivity. Both adipose excess and insufficiency are associated with adverse metabolic function. Adipogenesis is the process whereby preadipocyte precursor cells differentiate into lipid-laden mature adipocytes. This process is driven by a network of transcriptional regulators (TRs). We hypothesized that protein PTMs, in particular phosphorylation, play a major role in activating and propagating signals within TR networks upon induction of adipogenesis by extracellular stimulus. We applied MS-based quantitative proteomics and phosphoproteomics to monitor the alteration of nuclear proteins during the early stages (4 h) of preadipocyte differentiation. We identified a total of 4072 proteins including 2434 phosphorylated proteins, a majority of which were assigned as regulators of gene expression. Our results demonstrate that adipogenic stimuli increase the nuclear abundance and/or the phosphorylation levels of proteins involved in gene expression, cell organization, and oxidation-reduction pathways. Furthermore, proteins acting as negative modulators involved in negative regulation of gene expression, insulin stimulated glucose uptake, and cytoskeletal organization showed a decrease in their nuclear abundance and/or phosphorylation levels during the first 4 h of adipogenesis. Among 288 identified TRs, 49 were regulated within 4 h of adipogenic stimulation including several known and many novel potential adipogenic regulators. We created a kinase-substrate database for 3T3-L1 preadipocytes by investigating the relationship between protein kinases and protein phosphorylation sites identified in our dataset. A majority of the putative protein kinases belong to the cyclin-dependent kinase family and the mitogen-activated protein kinase family including P38 and c-Jun N-terminal kinases, suggesting that these kinases act as orchestrators of early adipogenesis.
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Affiliation(s)
- Atefeh Rabiee
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Veit Schwämmle
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Simone Sidoli
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Jie Dai
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Adelina Rogowska-Wrzesinska
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
| | - Susanne Mandrup
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark
| | - Ole N Jensen
- Department of Biochemistry and Molecular Biology and VILLUM Center for Bioanalytical Sciences, University of Southern Denmark, Odense, Denmark.,Center for Epigenetics, University of Southern Denmark, Odense, Denmark
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14
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Dülk M, Kudlik G, Fekete A, Ernszt D, Kvell K, Pongrácz JE, Merő BL, Szeder B, Radnai L, Geiszt M, Csécsy DE, Kovács T, Uher F, Lányi Á, Vas V, Buday L. The scaffold protein Tks4 is required for the differentiation of mesenchymal stromal cells (MSCs) into adipogenic and osteogenic lineages. Sci Rep 2016; 6:34280. [PMID: 27711054 PMCID: PMC5053279 DOI: 10.1038/srep34280] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 09/08/2016] [Indexed: 12/27/2022] Open
Abstract
The commitment steps of mesenchymal stromal cells (MSCs) to adipogenic and other lineages have been widely studied but not fully understood. Therefore, it is critical to understand which molecules contribute to the conversion of stem cells into differentiated cells. The scaffold protein Tks4 plays a role in podosome formation, EGFR signaling and ROS production. Dysfunction of Tks4 causes a hereditary disease called Frank-ter Haar syndrome with a variety of defects concerning certain mesenchymal tissues (bone, fat and cartilage) throughout embryogenic and postnatal development. In this study, we aimed to analyze how the mutation of Tks4 affects the differentiation potential of multipotent bone marrow MSCs (BM-MSCs). We generated a Tks4 knock-out mouse strain on C57Bl/6 background, and characterized BM-MSCs isolated from wild type and Tks4-/- mice to evaluate their differentiation. Tks4-/- BM-MSCs had reduced ability to differentiate into osteogenic and adipogenic lineages compared to wild type. Studying the expression profile of a panel of lipid-regulated genes during adipogenic induction revealed that the expression of adipogenic transcription factors, genes responsible for lipid droplet formation, sterol and fatty acid metabolism was delayed or reduced in Tks4-/- BM-MSCs. Taken together, these results establish a novel function for Tks4 in the regulation of MSC differentiation.
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Affiliation(s)
- Metta Dülk
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Gyöngyi Kudlik
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Anna Fekete
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Dávid Ernszt
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, Hungary.,Szentagothai Research Center, University of Pecs, Hungary
| | - Krisztián Kvell
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, Hungary.,Szentagothai Research Center, University of Pecs, Hungary
| | - Judit E Pongrácz
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, University of Pecs, Hungary.,Szentagothai Research Center, University of Pecs, Hungary
| | - Balázs L Merő
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Bálint Szeder
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Radnai
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Miklós Geiszt
- Department of Physiology, Semmelweis University Medical School, Budapest, Hungary.,"Momentum" Peroxidase Enzyme Research Group of the Semmelweis University and the Hungarian Academy of Sciences, Budapest, Hungary
| | - Dalma E Csécsy
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Tamás Kovács
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - Ferenc Uher
- Stem Cell Biology, National Blood Service, Budapest, Hungary
| | - Árpád Lányi
- Department of Immunology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Virag Vas
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary
| | - László Buday
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, Hungary.,Department of Medical Chemistry, Semmelweis University Medical School, Budapest, Hungary
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15
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Even Y, Escande ML, Fayet C, Genevière AM. CDK13, a Kinase Involved in Pre-mRNA Splicing, Is a Component of the Perinucleolar Compartment. PLoS One 2016; 11:e0149184. [PMID: 26886422 PMCID: PMC4757566 DOI: 10.1371/journal.pone.0149184] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2015] [Accepted: 01/07/2016] [Indexed: 02/07/2023] Open
Abstract
The perinucleolar compartment (PNC) is a subnuclear stucture forming predominantly in cancer cells; its prevalence positively correlates with metastatic capacity. Although several RNA-binding proteins have been characterized in PNC, the molecular function of this compartment remains unclear. Here we demonstrate that the cyclin-dependent kinase 13 (CDK13) is a newly identified constituent of PNC. CDK13 is a kinase involved in the regulation of gene expression and whose overexpression was found to alter pre-mRNA processing. In this study we show that CDK13 is enriched in PNC and co-localizes all along the cell cycle with the PNC component PTB. In contrast, neither the cyclins K and L, known to associate with CDK13, nor the potential kinase substrates accumulate in PNC. We further show that CDK13 overexpression increases PNC prevalence suggesting that CDK13 may be determinant for PNC formation. This result linked to the finding that CDK13 gene is amplified in different types of cancer indicate that this kinase can contribute to cancer development in human.
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Affiliation(s)
- Yasmine Even
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Marie-Line Escande
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Claire Fayet
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
| | - Anne-Marie Genevière
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650, Banyuls/Mer, France
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16
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Zu M, Li C, Fang JS, Lian WW, Liu AL, Zheng LS, Du GH. Drug Discovery of Host CLK1 Inhibitors for Influenza Treatment. Molecules 2015; 20:19735-47. [PMID: 26540031 PMCID: PMC6332427 DOI: 10.3390/molecules201119653] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Revised: 09/28/2015] [Accepted: 10/21/2015] [Indexed: 11/16/2022] Open
Abstract
The rapid evolution of influenza virus makes antiviral drugs less effective, which is considered to be a major bottleneck in antiviral therapy. The key proteins in the host cells, which are related with the replication cycle of influenza virus, are regarded as potential drug targets due to their distinct advantage of lack of evolution and drug resistance. Cdc2-like kinase 1 (CLK1) in the host cells is responsible for alternative splicing of the M2 gene of influenza virus during influenza infection and replication. In this study, we carried out baculovirus-mediated expression and purification of CLK1 and established a reliable screening assay for CLK1 inhibitors. After a virtual screening of CLK1 inhibitors was performed, the activities of the selected compounds were evaluated. Finally, several compounds with strong inhibitory activity against CLK1 were discovered and their in vitro anti-influenza virus activities were validated using a cytopathic effect (CPE) reduction assay. The assay results showed that clypearin, corilagin, and pinosylvine were the most potential anti-influenza virus compounds as CLK1 inhibitors among the compounds tested. These findings will provide important information for new drug design and development in influenza treatment, and CLK1 may be a potent drug target for anti-influenza drug screening and discovery.
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Affiliation(s)
- Mian Zu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Sciences, Beijing 100049, China.
| | - Chao Li
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Jian-Song Fang
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Wen-Wen Lian
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
| | - Ai-Lin Liu
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
- Beijing Key Laboratory of Drug Target Research and New Drug Screening, Beijing 100050, China.
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China.
| | - Li-Shu Zheng
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China.
| | - Guan-Hua Du
- Institute of Materia Medica, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China.
- Beijing Key Laboratory of Drug Target Research and New Drug Screening, Beijing 100050, China.
- State Key Laboratory of Bioactive Substance and Function of Natural Medicines, Beijing 100050, China.
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17
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Lin JC. Impacts of Alternative Splicing Events on the Differentiation of Adipocytes. Int J Mol Sci 2015; 16:22169-89. [PMID: 26389882 PMCID: PMC4613302 DOI: 10.3390/ijms160922169] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/07/2015] [Accepted: 09/07/2015] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing was found to be a common phenomenon after the advent of whole transcriptome analyses or next generation sequencing. Over 90% of human genes were demonstrated to undergo at least one alternative splicing event. Alternative splicing is an effective mechanism to spatiotemporally expand protein diversity, which influences the cell fate and tissue development. The first focus of this review is to highlight recent studies, which demonstrated effects of alternative splicing on the differentiation of adipocytes. Moreover, use of evolving high-throughput approaches, such as transcriptome analyses (RNA sequencing), to profile adipogenic transcriptomes, is also addressed.
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Affiliation(s)
- Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, 250 Wu-Hsing Street, Taipei 11031, Taiwan.
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18
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Xu P, Fischer-Posovszky P, Bischof J, Radermacher P, Wabitsch M, Henne-Bruns D, Wolf AM, Hillenbrand A, Knippschild U. Gene expression levels of Casein kinase 1 (CK1) isoforms are correlated to adiponectin levels in adipose tissue of morbid obese patients and site-specific phosphorylation mediated by CK1 influences multimerization of adiponectin. Mol Cell Endocrinol 2015; 406:87-101. [PMID: 25724478 DOI: 10.1016/j.mce.2015.02.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 01/29/2015] [Accepted: 02/11/2015] [Indexed: 01/03/2023]
Abstract
White adipose tissue has now been recognized as an important endocrine organ secreting bioactive molecules termed adipocytokines. In obesity, anti-inflammatory adipocytokines like adiponectin are decreased while pro-inflammatory factors are over-produced. These changes contribute to the development of insulin resistance and obesity-associated diseases. Since members of the casein kinase 1 (CK1) family are involved in the regulation of various signaling pathways we ask here whether they are able to modulate the functions of adiponectin. We show that CK1δ and ε are expressed in adipose tissue and that the expression of CK1 isoforms correlates with that of adiponectin. Furthermore, adiponectin co-immunoprecipitates with CK1δ and CK1ε and is phosphorylated by CK1δ at serine 174 and threonine 235, thereby influencing the formation of adiponectin oligomeric complexes. Furthermore, inhibition of CK1δ in human adipocytes by IC261 leads to an increase in basal and insulin-stimulated glucose uptake. In summary, our data indicate that site-specific phosphorylation of adiponectin, especially at sites targeted by CK1δ in vitro, provides an additional regulatory mechanism for modulating adiponectin complex formation and function.
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Affiliation(s)
- Pengfei Xu
- Department of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Pamela Fischer-Posovszky
- Divison of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University of Ulm, Eythstrasse 24, 89075 Ulm, Germany
| | - Joachim Bischof
- Department of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Peter Radermacher
- Institute of Pathophysiology and Process Development in Anesthesia, University of Ulm, Helmholtzstrasse 8/1, 89081 Ulm, Germany
| | - Martin Wabitsch
- Divison of Pediatric Endocrinology and Diabetes, Department of Pediatrics and Adolescent Medicine, University of Ulm, Eythstrasse 24, 89075 Ulm, Germany
| | - Doris Henne-Bruns
- Department of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Anna-Maria Wolf
- Department of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Andreas Hillenbrand
- Department of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany
| | - Uwe Knippschild
- Department of General and Visceral Surgery, University of Ulm, Albert-Einstein-Allee 23, 89081 Ulm, Germany.
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19
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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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20
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Khalouei S, Chow AM, Brown IR. Localization of heat shock protein HSPA6 (HSP70B') to sites of transcription in cultured differentiated human neuronal cells following thermal stress. J Neurochem 2014; 131:743-54. [DOI: 10.1111/jnc.12970] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/05/2014] [Accepted: 10/06/2014] [Indexed: 12/14/2022]
Affiliation(s)
- Sam Khalouei
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
| | - Ari M. Chow
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
| | - Ian R. Brown
- Centre for the Neurobiology of Stress; Department of Biological Sciences; University of Toronto Scarborough; Toronto Ontario Canada
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21
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Long Non-Coding RNA NEAT1 Associates with SRp40 to Temporally Regulate PPARγ2 Splicing during Adipogenesis in 3T3-L1 Cells. Genes (Basel) 2014; 5:1050-63. [PMID: 25437750 PMCID: PMC4276926 DOI: 10.3390/genes5041050] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 10/15/2014] [Accepted: 10/22/2014] [Indexed: 01/18/2023] Open
Abstract
Long non-coding (lnc) RNAs serve a multitude of functions in cells. NEAT1 RNA is a highly abundant 4 kb lncRNA in nuclei, and coincides with paraspeckles, nuclear domains that control sequestration of paraspeckle proteins. We examined NEAT1 RNA levels and its function in 3T3-L1 cells during differentiation to adipocytes. Levels of NEAT1 transcript, measured by RT-PCR, fluctuated in a temporal manner over the course of differentiation that suggested its role in alternative splicing of PPARγ mRNA, the major transcription factor driving adipogenesis. When cells were induced to differentiate by a media cocktail of insulin, dexamethasone, and isobutylmethyxanthine (IBMX) on Day 0, NEAT1 levels dropped on Day 4, when the PPARγ2 variant was spliced and when terminal differentiation occurs The appearance of PPARγ2 coordinates with the PPARγ1 variant to drive differentiation of adipocytes. SiRNA used to deplete NEAT1 resulted in the inability of cells to phosphorylate the serine/arginine-rich splicing protein, SRp40. SiRNA treatment for SRp40 resulted in dysregulation of PPARγ1 and, primarily, PPARγ2 mRNA levels. SRp40 associated with NEAT1, as shown by RNA-IP on days 0 and 8, but decreased on day 4, and concentrations increased over that of IgG control. Overexpression of SRp40 increased PPARγ2, but not γ1. Although lncRNA MALAT1 has been investigated in SR protein function, NEAT1 has not been shown to bind SR proteins for phosphorylation such that alternative splicing results. The ability of cells to increase phosphorylated SR proteins for PPARγ2 splicing suggests that fluxes in NEAT1 levels during adipogenesis regulate alternative splicing events.
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Du C, Ma X, Meruvu S, Hugendubler L, Mueller E. The adipogenic transcriptional cofactor ZNF638 interacts with splicing regulators and influences alternative splicing. J Lipid Res 2014; 55:1886-96. [PMID: 25024404 DOI: 10.1194/jlr.m047555] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Increasing evidence indicates that transcription and alternative splicing are coordinated processes; however, our knowledge of specific factors implicated in both functions during the process of adipocyte differentiation is limited. We have previously demonstrated that the zinc finger protein ZNF638 plays a role as a transcriptional coregulator of adipocyte differentiation via induction of PPARγ in cooperation with CCAAT/enhancer binding proteins (C/EBPs). Here we provide new evidence that ZNF638 is localized in nuclear bodies enriched with splicing factors, and through biochemical purification of ZNF638's interacting proteins in adipocytes and mass spectrometry analysis, we show that ZNF638 interacts with splicing regulators. Functional analysis of the effects of ectopic ZNF638 expression on a minigene reporter demonstrated that ZNF638 is sufficient to promote alternative splicing, a function enhanced through its recruitment to the minigene promoter at C/EBP responsive elements via C/EBP proteins. Structure-function analysis revealed that the arginine/serine-rich motif and the C-terminal zinc finger domain required for speckle localization are necessary for the adipocyte differentiation function of ZNF638 and for the regulation of the levels of alternatively spliced isoforms of lipin1 and nuclear receptor co-repressor 1. Overall, our data demonstrate that ZNF638 participates in splicing decisions and that it may control adipogenesis through regulation of the relative amounts of differentiation-specific isoforms.
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Affiliation(s)
- Chen Du
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Xinran Ma
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sunitha Meruvu
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Lynne Hugendubler
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Elisabetta Mueller
- Genetics of Development and Disease Branch of the National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
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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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24
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Boschi F, Rizzatti V, Zamboni M, Sbarbati A. Lipid droplets fusion in adipocyte differentiated 3T3-L1 cells: A Monte Carlo simulation. Exp Cell Res 2014; 321:201-8. [DOI: 10.1016/j.yexcr.2013.12.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2013] [Revised: 12/09/2013] [Accepted: 12/26/2013] [Indexed: 10/25/2022]
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25
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Phosphorylation-mediated regulation of alternative splicing in cancer. Int J Cell Biol 2013; 2013:151839. [PMID: 24069033 PMCID: PMC3771450 DOI: 10.1155/2013/151839] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 07/26/2013] [Indexed: 12/12/2022] Open
Abstract
Alternative splicing (AS) is one of the key processes involved in the regulation of gene expression in eukaryotic cells. AS catalyzes the removal of intronic sequences and the joining of selected exons, thus ensuring the correct processing of the primary transcript into the mature mRNA. The combinatorial nature of AS allows a great expansion of the genome coding potential, as multiple splice-variants encoding for different proteins may arise from a single gene. Splicing is mediated by a large macromolecular complex, the spliceosome, whose activity needs a fine regulation exerted by cis-acting RNA sequence elements and trans-acting RNA binding proteins (RBP). The activity of both core spliceosomal components and accessory splicing factors is modulated by their reversible phosphorylation. The kinases and phosphatases involved in these posttranslational modifications significantly contribute to AS regulation and to its integration in the complex regulative network that controls gene expression in eukaryotic cells. Herein, we will review the major canonical and noncanonical splicing factor kinases and phosphatases, focusing on those whose activity has been implicated in the aberrant splicing events that characterize neoplastic transformation.
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26
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Rizzatti V, Boschi F, Pedrotti M, Zoico E, Sbarbati A, Zamboni M. Lipid droplets characterization in adipocyte differentiated 3T3-L1 cells: size and optical density distribution. Eur J Histochem 2013; 57:e24. [PMID: 24085273 PMCID: PMC3794355 DOI: 10.4081/ejh.2013.e24] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 06/27/2013] [Accepted: 06/27/2013] [Indexed: 02/02/2023] Open
Abstract
The 3T3-L1 cell line, derived from 3T3 cells, is widely used in biological research on adipose tissue. 3T3-L1 cells have a fibroblast-like morphology, but, under appropriate conditions, they differentiate into an adipocyte-like phenotype. During the differentiation process, 3T3-L1 cells increase the synthesis of triglycerides and acquire the behavior of adipose cells. In particular, triglycerides accumulate in lipid droplets (LDs) embedded in the cytoplasm. The number and the size distribution of the LDs is often correlated with obesity and many other pathologies linked with fat accumulation. The integrated optical density (IOD) of the LDs is related with the amount of triglycerides in the droplets. The aim of this study is the attempt to characterize the size distribution and the IOD of the LDs in 3T3-L1 differentiated cells. The cells were differentiated into adipocytes for 5 days with a standard procedure, stained with Oil Red O and observed with an optical microscope. The diameter, area, optical density of the LDs were measured. We found an asymmetry of the kernel density distribution of the maximum Feret's diameter of the LDs with a tail due to very large LDs. More information regarding the birth of the LDs could help in finding the best mathematical model in order to analyze fat accumulation in adipocytes.
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