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Jia R, Zheng ZM. Oncogenic SRSF3 in health and diseases. Int J Biol Sci 2023; 19:3057-3076. [PMID: 37416784 PMCID: PMC10321290 DOI: 10.7150/ijbs.83368] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/30/2023] [Indexed: 07/08/2023] Open
Abstract
Serine/arginine rich splicing factor 3 (SRSF3) is an important multi-functional splicing factor, and has attracted increasing attentions in the past thirty years. The importance of SRSF3 is evidenced by its impressively conserved protein sequences in all animals and alternative exon 4 which represents an autoregulatory mechanism to maintain its proper cellular expression level. New functions of SRSF3 have been continuously discovered recently, especially its oncogenic function. SRSF3 plays essential roles in many cellular processes by regulating almost all aspects of RNA biogenesis and processing of many target genes, and thus, contributes to tumorigenesis when overexpressed or disregulated. This review updates and highlights the gene, mRNA, and protein structure of SRSF3, the regulatory mechanisms of SRSF3 expression, and the characteristics of SRSF3 targets and binding sequences that contribute to SRSF3's diverse molecular and cellular functions in tumorigenesis and human diseases.
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Affiliation(s)
- Rong Jia
- The State Key Laboratory Breeding Base of Basic Science of Stomatology & Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, Hubei, China
| | - Zhi-Ming Zheng
- Tumor Virus RNA Biology Section, HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, Maryland, USA
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2
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Harries LW. Dysregulated RNA processing and metabolism: a new hallmark of ageing and provocation for cellular senescence. FEBS J 2023; 290:1221-1234. [PMID: 35460337 DOI: 10.1111/febs.16462] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 03/28/2022] [Accepted: 04/21/2022] [Indexed: 12/23/2022]
Abstract
The human genome is capable of producing hundreds of thousands of different proteins and non-coding RNAs from <20 000 genes, in a co-ordinated and regulated fashion. This is achieved by a collection of phenomena known as mRNA processing and metabolism, and encompasses events in the life cycle of an RNA from synthesis to degradation. These factors are critical determinants of cellular adaptability and plasticity, which allows the cell to adjust its transcriptomic output in response to its internal and external environment. Evidence is building that dysfunctional RNA processing and metabolism may be a key contributor to the development of cellular senescence. Senescent cells by definition have exited cell cycle, but have gained functional features such as the secretion of the senescence-associated secretory phenotype (SASP), a known driver of chronic disease and perhaps even ageing itself. In this review, I will outline the impact of dysregulated mRNA processing and metabolism on senescence and ageing at the level of genes, cells and systems, and describe the mechanisms by which progressive deterioration in these processes may impact senescence and organismal ageing. Finally, I will present the evidence implicating this important process as a new hallmark of ageing, which could be harnessed in the future to develop new senotherapeutic interventions for chronic disease.
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3
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Coelho OGL, Ribeiro PVM, Alfenas RDCG. Can grape polyphenols affect glycation markers? A systematic review. Crit Rev Food Sci Nutr 2023; 63:1208-1218. [PMID: 34369228 DOI: 10.1080/10408398.2021.1962796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Advanced glycation end-products (AGEs) favor inflammation and oxidative stress, playing a role in chronic diseases pathogenesis. Grape polyphenols exert antiglycative and antioxidant effects which may contribute to prevent chronic diseases. However, clinical evidence of grape polyphenols on chronic disease prevention and treatment by glycation markers modulation are limited. Therefore, we aimed to critically analyze studies about that topic to investigate the antiglycative power of dietary grape polyphenol, and to explore the molecular mechanism involved. This systematic review was conducted and reported according to PRISMA guidelines. The following search terms were used: "grape", "extract", "grape seed extract", "grape skin extract", "polyphenol extract", "grape polyphenol(s)", "grape juice", "resveratrol", "quercetin", "catechin", "epicatechin", "procyanidin(s)", and "anthocyanin(s)". Seven studies were included. Glycated hemoglobin was not affected. The interventions duration may not have been enough to detect changes. Grape polyphenols reduced fructosamine and methylglyoxal (MGO) concentrations, and increased endogenous secretory RAGE (esRAGE) gene expression but did not affect the serum concentration. Resveratrol antiglycative effects are mainly due its ability to trap MGO and downregulate RAGE. In conclusion, grape polyphenols may have a positive impact on early glycation products, AGEs and esRAGE. Future studies are needed to explore how they modulate AGEs and receptors in chronic diseases.
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Affiliation(s)
- Olívia G L Coelho
- Departamento de Nutrição de Saúde, Universidade Federal de Viçosa, Viçosa, Brazil
| | - Priscila V M Ribeiro
- Departamento de Nutrição de Saúde, Universidade Federal de Viçosa, Viçosa, Brazil
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4
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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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5
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Choi S, Cho N, Kim KK. Non-canonical splice junction processing increases the diversity of RBFOX2 splicing isoforms. Int J Biochem Cell Biol 2022; 144:106172. [PMID: 35124219 DOI: 10.1016/j.biocel.2022.106172] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 01/23/2022] [Accepted: 02/01/2022] [Indexed: 12/13/2022]
Abstract
The underlying mechanisms of splicing regulation through non-canonical splice junction processing remain largely unknown. Here, we identified two RBFOX2 splicing isoforms by alternative 3' splice site selection of exon 9; the non-canonical splice junction processed RBFOX2 transcript (RBFOX2-N.C.) was expressed by the selection of the 3' splice GG acceptor sequence. The cytoplasmic localization of RBFOX2-C., a canonical splice junction-processed RBFOX2 transcript, was different from that of RBFOX2-N.C., which showed nuclear localization. In addition, we confirmed that RBFOX2-C. showed a significantly stronger localization into stress granules than RBFOX2-N.C. upon sodium arsenite treatment. Next, we investigated the importance of non-canonical 3' splice GG sequence selection of specific cis-regulatory elements using minigene constructs of the RBFOX2 gene. We found that the non-canonical 3' splice GG sequence and suboptimal branch point site adjacent region were critical for RBFOX2-N.C. expression through a non-canonical 3' splice selection. Our results suggest a regulatory mechanism for the non-canonical 3' splice selection in the RBFOX2 gene, providing a basis for studies related to the regulation of alternative pre-mRNA splicing through non-canonical splice junction processing.
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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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Choi K, Yang A, Baek J, Jeong H, Kang Y, Baek W, Kim JC, Kang M, Choi M, Ham Y, Son MJ, Han SB, Kim J, Jang JH, Ahn JS, Shen H, Woo SH, Kim JH, Cho S. Regulation of Survival Motor Neuron Gene Expression by Calcium Signaling. Int J Mol Sci 2021; 22:ijms221910234. [PMID: 34638572 PMCID: PMC8508836 DOI: 10.3390/ijms221910234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/07/2021] [Accepted: 09/16/2021] [Indexed: 11/21/2022] Open
Abstract
Spinal muscular atrophy (SMA) is caused by homozygous survival of motor neurons 1 (SMN1) gene deletion, leaving a duplicate gene, SMN2, as the sole source of SMN protein. However, a defect in SMN2 splicing, involving exon 7 skipping, results in a low level of functional SMN protein. Therefore, the upregulation of SMN protein expression from the SMN2 gene is generally considered to be one of the best therapeutic strategies to treat SMA. Most of the SMA drug discovery is based on synthetic compounds, and very few natural compounds have been explored thus far. Here, we performed an unbiased mechanism-independent and image-based screen of a library of microbial metabolites in SMA fibroblasts using an SMN-specific immunoassay. In doing so, we identified brefeldin A (BFA), a well-known inhibitor of ER-Golgi protein trafficking, as a strong inducer of SMN protein. The profound increase in SMN protein was attributed to, in part, the rescue of the SMN2 pre-mRNA splicing defect. Intriguingly, BFA increased the intracellular calcium concentration, and the BFA-induced exon 7 inclusion of SMN2 splicing, was abrogated by the depletion of intracellular calcium and by the pharmacological inhibition of calcium/calmodulin-dependent kinases (CaMKs). Moreover, BFA considerably reduced the expression of Tra2-β and SRSF9 proteins in SMA fibroblasts and enhanced the binding of PSF and hnRNP M to an exonic splicing enhancer (ESE) of exon 7. Together, our results demonstrate a significant role for calcium and its signaling on the regulation of SMN splicing, probably through modulating the expression/activity of splicing factors.
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Affiliation(s)
- Kwangman Choi
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- Department of Medical Biotechnology, SoonChunHyang University, Asan 31538, Korea
| | - Ansook Yang
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea;
| | - Jiyeon Baek
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea;
| | - Hyejeong Jeong
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea;
| | - Yura Kang
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (Y.K.); (W.B.)
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Woosun Baek
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (Y.K.); (W.B.)
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
| | - Joon-Chul Kim
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea; (J.-C.K.); (M.-J.S.)
| | - Mingu Kang
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea;
| | - Miri Choi
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea;
| | - Youngwook Ham
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea; (J.-H.J.); (J.S.A.)
| | - Min-Jeong Son
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea; (J.-C.K.); (M.-J.S.)
| | - Sang-Bae Han
- College of Pharmacy, Chungbuk National University, Cheongju 28160, Korea;
| | - Janghwan Kim
- Stem Cell Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Korea;
| | - Jae-Hyuk Jang
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea; (J.-H.J.); (J.S.A.)
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Jong Seog Ahn
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea; (J.-H.J.); (J.S.A.)
- Anticancer Agent Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea
| | - Haihong Shen
- Gwangju Institute of Science and Technology, School of life Sciences, Gwangju 61005, Korea;
| | - Sun-Hee Woo
- College of Pharmacy, Chungnam National University, Daejeon 34134, Korea; (J.-C.K.); (M.-J.S.)
- Correspondence: (S.-H.W.); (J.H.K.); (S.C.); Tel.: +82-42-821-5924 (S.-H.W.); +82-31-920-2204 (J.H.K.); +82-43-240-6105 (S.C.); Fax: +82-42-823-6566 (S.-H.W.); +82-31-920-2006 (J.H.K.); +82-43-240-6159 (S.C)
| | - Jong Heon Kim
- Department of Cancer Biomedical Science, Graduate School of Cancer Science and Policy, National Cancer Center, Goyang 10408, Korea; (Y.K.); (W.B.)
- Cancer Molecular Biology Branch, Division of Cancer Biology, Research Institute, National Cancer Center, Goyang 10408, Korea
- Correspondence: (S.-H.W.); (J.H.K.); (S.C.); Tel.: +82-42-821-5924 (S.-H.W.); +82-31-920-2204 (J.H.K.); +82-43-240-6105 (S.C.); Fax: +82-42-823-6566 (S.-H.W.); +82-31-920-2006 (J.H.K.); +82-43-240-6159 (S.C)
| | - Sungchan Cho
- Natural Medicine Research Center, Korea Research Institute of Bioscience and Biotechnology, Cheongju 28116, Korea; (K.C.); (A.Y.); (J.B.); (H.J.); (M.K.); (M.C.); (Y.H.)
- Department of Biomolecular Science, KRIBB School of Bioscience, Korea University of Science and Technology, Daejeon 34113, Korea; (J.-H.J.); (J.S.A.)
- Correspondence: (S.-H.W.); (J.H.K.); (S.C.); Tel.: +82-42-821-5924 (S.-H.W.); +82-31-920-2204 (J.H.K.); +82-43-240-6105 (S.C.); Fax: +82-42-823-6566 (S.-H.W.); +82-31-920-2006 (J.H.K.); +82-43-240-6159 (S.C)
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Santoro M, Piacentini R, Perna A, Pisano E, Severino A, Modoni A, Grassi C, Silvestri G. Resveratrol corrects aberrant splicing of RYR1 pre-mRNA and Ca 2+ signal in myotonic dystrophy type 1 myotubes. Neural Regen Res 2020; 15:1757-1766. [PMID: 32209783 PMCID: PMC7437583 DOI: 10.4103/1673-5374.276336] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Myotonic dystrophy type 1 (DM1) is a spliceopathy related to the mis-splicing of several genes caused by sequestration of nuclear transcriptional RNA-binding factors from non-coding CUG repeats of DMPK pre-mRNAs. Dysregulation of ryanodine receptor 1 (RYR1), sarcoplasmatic/endoplasmatic Ca2+-ATPase (SERCA) and α1S subunit of voltage-gated Ca2+ channels (Cav1.1) is related to Ca2+ homeostasis and excitation-contraction coupling impairment. Though no pharmacological treatment for DM1 exists, aberrant splicing correction represents one major therapeutic target for this disease. Resveratrol (RES, 3,5,4′-trihydroxy-trans-stilbene) is a promising pharmacological tools for DM1 treatment for its ability to directly bind the DNA and RNA influencing gene expression and alternative splicing. Herein, we analyzed the therapeutic effects of RES in DM1 myotubes in a pilot study including cultured myotubes from two DM1 patients and two healthy controls. Our results indicated that RES treatment corrected the aberrant splicing of RYR1, and this event appeared associated with restoring of depolarization-induced Ca2+ release from RYR1 dependent on the electro-mechanical coupling between RYR1 and Cav1.1. Interestingly, immunoblotting studies showed that RES treatment was associated with a reduction in the levels of CUGBP Elav-like family member 1, while RYR1, Cav1.1 and SERCA1 protein levels were unchanged. Finally, RES treatment did not induce any major changes either in the amount of ribonuclear foci or sequestration of muscleblind-like splicing regulator 1. Overall, the results of this pilot study would support RES as an attractive compound for future clinical trials in DM1. Ethical approval was obtained from the Ethical Committee of IRCCS Fondazione Policlinico Universitario A. Gemelli, Rome, Italy (rs9879/14) on May 20, 2014.
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Affiliation(s)
| | - Roberto Piacentini
- Department of Neuroscience, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Alessia Perna
- Department of Neuroscience, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Eugenia Pisano
- Department of Cardiovascular and Thoracic Sciences, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Anna Severino
- Department of Cardiovascular and Thoracic Sciences, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Anna Modoni
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Claudio Grassi
- Department of Neuroscience, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Gabriella Silvestri
- Department of Neuroscience, Università Cattolica del Sacro Cuore; Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
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Fujita KI, Ishizuka T, Mitsukawa M, Kurata M, Masuda S. Regulating Divergent Transcriptomes through mRNA Splicing and Its Modulation Using Various Small Compounds. Int J Mol Sci 2020; 21:ijms21062026. [PMID: 32188117 PMCID: PMC7139312 DOI: 10.3390/ijms21062026] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/11/2020] [Accepted: 03/12/2020] [Indexed: 12/14/2022] Open
Abstract
Human transcriptomes are more divergent than genes and contribute to the sophistication of life. This divergence is derived from various isoforms arising from alternative splicing. In addition, alternative splicing regulated by spliceosomal factors and RNA structures, such as the RNA G-quadruplex, is important not only for isoform diversity but also for regulating gene expression. Therefore, abnormal splicing leads to serious diseases such as cancer and neurodegenerative disorders. In the first part of this review, we describe the regulation of divergent transcriptomes using alternative mRNA splicing. In the second part, we present the relationship between the disruption of splicing and diseases. Recently, various compounds with splicing inhibitor activity were established. These splicing inhibitors are recognized as a biological tool to investigate the molecular mechanism of splicing and as a potential therapeutic agent for cancer treatment. Food-derived compounds with similar functions were found and are expected to exhibit anticancer effects. In the final part, we describe the compounds that modulate the messenger RNA (mRNA) splicing process and their availability for basic research and future clinical potential.
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Kurata M, Fujiwara N, Fujita KI, Yamanaka Y, Seno S, Kobayashi H, Miyamae Y, Takahashi N, Shibuya Y, Masuda S. Food-Derived Compounds Apigenin and Luteolin Modulate mRNA Splicing of Introns with Weak Splice Sites. iScience 2019; 22:336-352. [PMID: 31809999 PMCID: PMC6909097 DOI: 10.1016/j.isci.2019.11.033] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/23/2019] [Accepted: 11/15/2019] [Indexed: 01/08/2023] Open
Abstract
Cancer cells often exhibit extreme sensitivity to splicing inhibitors. We identified food-derived flavonoids, apigenin and luteolin, as compounds that modulate mRNA splicing at the genome-wide level, followed by proliferation inhibition. They bind to mRNA splicing-related proteins to induce a widespread change of splicing patterns in treated cells. Their inhibitory activity on splicing is relatively moderate, and introns with weak splice sites tend to be sensitive to them. Such introns remain unspliced, and the resulting intron-containing mRNAs are retained in the nucleus, resulting in the nuclear accumulation of poly(A)+ RNAs in these flavonoid-treated cells. Tumorigenic cells are more susceptible to these flavonoids than nontumorigenic cells, both for the nuclear poly(A)+ RNA-accumulating phenotype and cell viability. This study illustrates the possible mechanism of these flavonoids to suppress tumor progression in vivo that were demonstrated by previous studies and provides the potential of daily intake of moderate splicing inhibitors to prevent cancer development. Food-derived compounds, apigenin and luteolin, modulate mRNA splicing The treatment of these flavonoids causes numerous alternative splicing events Splicing of introns with weak splice sites tend to be inhibited by these flavonoids Tumorigenic cells are more sensitive to these flavonoids than non-tumorigenic cells
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Affiliation(s)
- Masashi Kurata
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan; Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan
| | - Naoko Fujiwara
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Ken-Ichi Fujita
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Yasutaka Yamanaka
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan
| | - Shigeto Seno
- Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, Osaka 565-0871, Japan
| | - Hisato Kobayashi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yusaku Miyamae
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki 305-8572, Japan
| | - Nobuyuki Takahashi
- Department of Nutritional Science and Food Safety, Tokyo University of Agriculture, Tokyo 156-8502, Japan
| | - Yasuyuki Shibuya
- Department of Oral and Maxillofacial Surgery, Graduate School of Medical Sciences, Nagoya City University, Nagoya 467-8601, Japan
| | - Seiji Masuda
- Division of Integrated Life Sciences, Graduate School of Biostudies, Kyoto University, Kyoto 606-8502, Japan.
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Mitochondria-targeted hydrogen sulfide attenuates endothelial senescence by selective induction of splicing factors HNRNPD and SRSF2. Aging (Albany NY) 2019; 10:1666-1681. [PMID: 30026406 PMCID: PMC6075431 DOI: 10.18632/aging.101500] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Accepted: 07/15/2018] [Indexed: 12/13/2022]
Abstract
Cellular senescence is a key driver of ageing, influenced by age-related changes to the regulation of alternative splicing. Hydrogen sulfide (H2S) has similarly been described to influence senescence, but the pathways by which it accomplishes this are unclear.We assessed the effects of the slow release H2S donor Na-GYY4137 (100 µg/ml), and three novel mitochondria-targeted H2S donors AP39, AP123 and RT01 (10 ng/ml) on splicing factor expression, cell proliferation, apoptosis, DNA replication, DNA damage, telomere length and senescence-related secretory complex (SASP) expression in senescent primary human endothelial cells.All H2S donors produced up to a 50% drop in senescent cell load assessed at the biochemical and molecular level. Some changes were noted in the composition of senescence-related secretory complex (SASP); IL8 levels increased by 24% but proliferation was not re-established in the culture as a whole. Telomere length, apoptotic index and the extent of DNA damage were unaffected. Differential effects on splicing factor expression were observed depending on the intracellular targeting of the H2S donors. Na-GYY4137 produced a general 1.9 - 3.2-fold upregulation of splicing factor expression, whereas the mitochondria-targeted donors produced a specific 2.5 and 3.1-fold upregulation of SRSF2 and HNRNPD splicing factors only. Knockdown of SRSF2 or HNRNPD genes in treated cells rendered the cells non-responsive to H2S, and increased levels of senescence by up to 25% in untreated cells.Our data suggest that SRSF2 and HNRNPD may be implicated in endothelial cell senescence, and can be targeted by exogenous H2S. These molecules may have potential as moderators of splicing factor expression and senescence phenotypes.
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Vitali M, Sirri R, Zappaterra M, Zambonelli P, Giannini G, Lo Fiego DP, Davoli R. Functional analysis finds differences on the muscle transcriptome of pigs fed an n-3 PUFA-enriched diet with or without antioxidant supplementations. PLoS One 2019; 14:e0212449. [PMID: 30785965 PMCID: PMC6382273 DOI: 10.1371/journal.pone.0212449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 02/01/2019] [Indexed: 12/11/2022] Open
Abstract
Supplementing pig diets with n-3 polyunsaturated fatty acids (n-3 PUFA) may produce meat products with an increased n-3 fatty acid content, and the combined antioxidants addition could prevent lipid oxidation in the feed. However, to date, the effects of these bioactive compounds at the molecular level in porcine skeletal muscle are mostly unknown. This study aimed to analyse changes in the Longissimus thoracis transcriptome of 35 pigs fed three diets supplemented with: linseed (L); linseed, vitamin E and Selenium (LES) or linseed and plant-derived polyphenols (LPE). Pigs were reared from 80.8 ± 5.6 kg to 151.8 ± 9.9 kg. After slaughter, RNA-Seq was performed and 1182 differentially expressed genes (DEGs) were submitted to functional analysis. The L vs LES comparison did not show differences, while L vs LPE showed 1102 DEGs and LES vs LPE 80 DEGs. LPE compared to the other groups showed the highest number of up-regulated genes involved in preserving muscle metabolism and structure. Results enlighten that the combined supplementation of bioactive lipids (n-3 PUFA from linseed) with plant extracts as a source of polyphenols increases, compared to the only addition of linseed, the expression of genes involved in mRNA metabolic processes and transcriptional regulation, glucose uptake and, finally, in supporting muscle development and physiology. These results improve the knowledge of the biological effect of bioactive compounds in Longissimus thoracis muscle, and sustain the growing interest over their use in pig production.
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Affiliation(s)
- Marika Vitali
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
| | - Rubina Sirri
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
| | - Martina Zappaterra
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Paolo Zambonelli
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Giulia Giannini
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Domenico Pietro Lo Fiego
- Department of Life Sciences, University of Modena and Reggio Emilia, Reggio Emilia, Italy
- Interdepartmental Research Centre for Agri-Food Biological Resources Improvement and Valorisation (BIOGEST-SITEIA), University of Modena and Reggio Emilia, Reggio Emilia, Italy
| | - Roberta Davoli
- Interdepartmental Centre for Industrial Agrifood Research (CIRI- AGRO), University of Bologna, Cesena, Italy
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
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Dembic M, Andersen HS, Bastin J, Doktor TK, Corydon TJ, Sass JO, Lopes Costa A, Djouadi F, Andresen BS. Next generation sequencing of RNA reveals novel targets of resveratrol with possible implications for Canavan disease. Mol Genet Metab 2019; 126:64-76. [PMID: 30446350 DOI: 10.1016/j.ymgme.2018.10.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Revised: 10/17/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022]
Abstract
Resveratrol (RSV) is a small compound first identified as an activator of sirtuin 1 (SIRT1), a key factor in mediating the effects of caloric restriction. Since then, RSV received great attention for its widespread beneficial effects on health and in connection to many diseases. RSV improves the metabolism and the mitochondrial function, and more recently it was shown to restore fatty acid β-oxidation (FAO) capacities in patient fibroblasts harboring mutations with residual enzyme activity. Many of RSV's beneficial effects are mediated by the transcriptional coactivator PGC-1α, a direct target of SIRT1 and a master regulator of the mitochondrial fatty acid oxidation. Despite numerous studies RSV's mechanism of action is still not completely elucidated. Our aim was to investigate the effects of RSV on gene regulation on a wide scale, possibly to detect novel genes whose up-regulation by RSV may be of interest with respect to disease treatment. We performed Next Generation Sequencing of RNA on normal fibroblasts treated with RSV. To investigate whether the effects of RSV are mediated through SIRT1 we expanded the analysis to include SIRT1-knockdown fibroblasts. We identified the aspartoacylase (ASPA) gene, mutated in Canavan disease, to be strongly up-regulated by RSV in several cell lines, including Canavan disease fibroblasts. We further link RSV to the up-regulation of other genes involved in myelination including the glial specific transcription factors POU3F1, POU3F2, and myelin basic protein (MBP). We also observe a strong up-regulation by RSV of the riboflavin transporter gene SLC52a1. Mutations in SLC52a1 cause transient multiple acyl-CoA dehydrogenase deficiency (MADD). Our analysis of alternative splicing identified novel metabolically important genes affected by RSV, among which is particularly interesting the α subunit of the stimulatory G protein (Gsα), which regulates the cellular levels of cAMP through adenylyl cyclase. We conclude that in fibroblasts RSV stimulates the PGC-1α and p53 pathways, and up-regulates genes affecting the glucose metabolism, mitochondrial β-oxidation, and mitochondrial biogenesis. We further confirm that RSV might be a relevant treatment in the correction of FAO deficiencies and we suggest that treatment in other metabolic disorders including Canavan disease and MADD might be also beneficial.
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Affiliation(s)
- Maja Dembic
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Henriette S Andersen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Jean Bastin
- INSERM UMR-S 1124, Université Paris Descartes, UFR Biomédicale des Saints-Pères, 45, rue des Saints-Pères, 75270 Paris, cedex 06, France
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
| | - Thomas J Corydon
- Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark; Department of Ophthalmology, Aarhus University Hospital, 8000 Aarhus C, Denmark.
| | - Jörn Oliver Sass
- Research Group Inborn Errors of Metabolism, Department of Natural Sciences & IFGA, University of Applied Sciences, Rheinbach, Germany.
| | - Alexandra Lopes Costa
- INSERM UMR-S 1124, Université Paris Descartes, UFR Biomédicale des Saints-Pères, 45, rue des Saints-Pères, 75270 Paris, cedex 06, France
| | - Fatima Djouadi
- INSERM UMR-S 1124, Université Paris Descartes, UFR Biomédicale des Saints-Pères, 45, rue des Saints-Pères, 75270 Paris, cedex 06, France
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark.
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Lea WA, Parnell SC, Wallace DP, Calvet JP, Zelenchuk LV, Alvarez NS, Ward CJ. Human-Specific Abnormal Alternative Splicing of Wild-Type PKD1 Induces Premature Termination of Polycystin-1. J Am Soc Nephrol 2018; 29:2482-2492. [PMID: 30185468 DOI: 10.1681/asn.2018040442] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/06/2018] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The major form of autosomal dominant polycystic kidney disease is caused by heterozygous mutations in PKD1, the gene that encodes polycystin-1 (PC1). Unlike PKD1 genes in the mouse and most other mammals, human PKD1 is unusual in that it contains two long polypyrimidine tracts in introns 21 and 22 (2.5 kbp and 602 bp, respectively; 97% cytosine and thymine). Although these polypyrimidine tracts have been shown to form thermodynamically stable segments of triplex DNA that can cause DNA polymerase stalling and enhance the local mutation rate, the efficiency of transcription and splicing across these cytosine- and thymine-rich introns has been unexplored. METHODS We used RT-PCR and Western blotting (using an mAb to the N terminus) to probe splicing events over exons 20-24 in the mouse and human PKD1 genes as well as Nanopore sequencing to confirm the presence of multiple splice forms. RESULTS Analysis of PC1 indicates that humans, but not mice, have a smaller than expected protein product, which we call Trunc_PC1. The findings show that Trunc_PC1 is the protein product of abnormal differential splicing across introns 21 and 22 and that 28.8%-61.5% of PKD1 transcripts terminate early. CONCLUSIONS The presence of polypyrimidine tracts decreases levels of full-length PKD1 mRNA from normal alleles. In heterozygous individuals, low levels of full-length PC1 may reduce polycystin signaling below a critical "cystogenic" threshold.
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Affiliation(s)
- Wendy A Lea
- The Jared Grantham Kidney Institute and Departments of.,Internal Medicine
| | - Stephen C Parnell
- The Jared Grantham Kidney Institute and Departments of.,Biochemistry and Molecular Biology
| | - Darren P Wallace
- The Jared Grantham Kidney Institute and Departments of.,Internal Medicine.,Molecular and Integrative Physiology, and
| | - James P Calvet
- The Jared Grantham Kidney Institute and Departments of.,Biochemistry and Molecular Biology
| | - Lesya V Zelenchuk
- The Jared Grantham Kidney Institute and Departments of.,Internal Medicine
| | - Nehemiah S Alvarez
- Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, Kansas; and.,De Novo Genomics, Kansas City, Kansas
| | - Christopher J Ward
- The Jared Grantham Kidney Institute and Departments of .,Internal Medicine.,Biochemistry and Molecular Biology
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Gene Expression of Sirtuin-1 and Endogenous Secretory Receptor for Advanced Glycation End Products in Healthy and Slightly Overweight Subjects after Caloric Restriction and Resveratrol Administration. Nutrients 2018; 10:nu10070937. [PMID: 30037068 PMCID: PMC6073749 DOI: 10.3390/nu10070937] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 07/15/2018] [Accepted: 07/19/2018] [Indexed: 01/09/2023] Open
Abstract
Sirtuin-1 (Sirt-1) and an endogenous secretory receptor for an advanced glycation end product (esRAGE) are associated with vascular protection. The purpose of this study was to examine the effects of resveratrol (RSV) and caloric restriction (CR) on gene expression of Sirt-1 and esRAGE on serum levels of Sirt1 and esRAGE in healthy and slightly overweight subjects. The study included 48 healthy subjects randomized to 30 days of RSV (500 mg/day) or CR (1000 cal/day). Waist circumference (p = 0.011), TC (p = 0.007), HDL (p = 0.031), non-HDL (p = 0.025), ApoA1 (p = 0.011), and ApoB (p = 0.037) decreased in the CR group. However, TC (p = 0.030), non-HDL (p = 0.010), ApoB (p = 0.034), and HOMA-IR (p = 0.038) increased in the RSV group. RSV and CR increased serum levels of Sirt-1, respectively, from 1.06 ± 0.71 ng/mL to 5.75 ± 2.98 ng/mL (p < 0.0001) and from 1.65 ± 1.81 ng/mL to 5.80 ± 2.23 ng/mL (p < 0.0001). esRAGE serum levels were similar in RSV (p = NS) and CR (p = NS) groups. Significant positive correlation was observed between gene expression changes of Sirt-1 and esRAGE in RSV (r = 0.86; p < 0.0001) and in CR (r = 0.71; p < 0.0001) groups, but not for the changes in serum concentrations. CR promoted increases in the gene expression of esRAGE (post/pre). Future long-term studies are needed to evaluate the impact of these outcomes on vascular health.
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15
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Melangath G, Sen T, Kumar R, Bawa P, Srinivasan S, Vijayraghavan U. Functions for fission yeast splicing factors SpSlu7 and SpPrp18 in alternative splice-site choice and stress-specific regulated splicing. PLoS One 2017; 12:e0188159. [PMID: 29236736 PMCID: PMC5728500 DOI: 10.1371/journal.pone.0188159] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2017] [Accepted: 11/01/2017] [Indexed: 01/23/2023] Open
Abstract
Budding yeast spliceosomal factors ScSlu7 and ScPrp18 interact and mediate intron 3'ss choice during second step pre-mRNA splicing. The fission yeast genome with abundant multi-intronic transcripts, degenerate splice signals and SR proteins is an apt unicellular fungal model to deduce roles for core spliceosomal factors in alternative splice-site choice, intron retention and to study the cellular implications of regulated splicing. From our custom microarray data we deduce a stringent reproducible subset of S. pombe alternative events. We examined the role of factors SpSlu7 or SpPrp18 for these splice events and investigated the relationship to growth phase and stress. Wild-type log and stationary phase cells showed ats1+ exon 3 skipped and intron 3 retained transcripts. Interestingly the non-consensus 5'ss in ats1+ intron 3 caused SpSlu7 and SpPrp18 dependent intron retention. We validated the use of an alternative 5'ss in dtd1+ intron 1 and of an upstream alternative 3'ss in DUF3074 intron 1. The dtd1+ intron 1 non-canonical 5'ss yielded an alternative mRNA whose levels increased in stationary phase. Utilization of dtd1+ intron 1 sub-optimal 5' ss required functional SpPrp18 and SpSlu7 while compromise in SpSlu7 function alone hampered the selection of the DUF3074 intron 1 non canonical 3'ss. We analysed the relative abundance of these splice isoforms during mild thermal, oxidative and heavy metal stress and found stress-specific splice patterns for ats1+ and DUF3074 intron 1 some of which were SpSlu7 and SpPrp18 dependent. By studying ats1+ splice isoforms during compromised transcription elongation rates in wild-type, spslu7-2 and spprp18-5 mutant cells we found dynamic and intron context-specific effects in splice-site choice. Our work thus shows the combinatorial effects of splice site strength, core splicing factor functions and transcription elongation kinetics to dictate alternative splice patterns which in turn serve as an additional recourse of gene regulation in fission yeast.
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Affiliation(s)
- Geetha Melangath
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Titash Sen
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Rakesh Kumar
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
| | - Pushpinder Bawa
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Subha Srinivasan
- Institute of Bioinformatics and Applied Biotechnology, Bangalore, Karnataka, India
| | - Usha Vijayraghavan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, Karnataka, India
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16
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Latorre E, Birar VC, Sheerin AN, Jeynes JCC, Hooper A, Dawe HR, Melzer D, Cox LS, Faragher RGA, Ostler EL, Harries LW. Small molecule modulation of splicing factor expression is associated with rescue from cellular senescence. BMC Cell Biol 2017; 18:31. [PMID: 29041897 PMCID: PMC5645932 DOI: 10.1186/s12860-017-0147-7] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 10/09/2017] [Indexed: 12/31/2022] Open
Abstract
Background Altered expression of mRNA splicing factors occurs with ageing in vivo and is thought to be an ageing mechanism. The accumulation of senescent cells also occurs in vivo with advancing age and causes much degenerative age-related pathology. However, the relationship between these two processes is opaque. Accordingly we developed a novel panel of small molecules based on resveratrol, previously suggested to alter mRNA splicing, to determine whether altered splicing factor expression had potential to influence features of replicative senescence. Results Treatment with resveralogues was associated with altered splicing factor expression and rescue of multiple features of senescence. This rescue was independent of cell cycle traverse and also independent of SIRT1, SASP modulation or senolysis. Under growth permissive conditions, cells demonstrating restored splicing factor expression also demonstrated increased telomere length, re-entered cell cycle and resumed proliferation. These phenomena were also influenced by ERK antagonists and agonists. Conclusions This is the first demonstration that moderation of splicing factor levels is associated with reversal of cellular senescence in human primary fibroblasts. Small molecule modulators of such targets may therefore represent promising novel anti-degenerative therapies. Electronic supplementary material The online version of this article (10.1186/s12860-017-0147-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Eva Latorre
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Vishal C Birar
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - Angela N Sheerin
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - J Charles C Jeynes
- Centre for Biomedical Modelling and Analysis, University of Exeter, Exeter, Devon, EX2 5DW, UK
| | - Amy Hooper
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Helen R Dawe
- College of Life and Environmental Sciences, University of Exeter, Exeter, Devon, EX4 4QD, UK
| | - David Melzer
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK
| | - Lynne S Cox
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, UK
| | - Richard G A Faragher
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK
| | - Elizabeth L Ostler
- School of Pharmacy and Biomolecular Sciences, University of Brighton, Cockcroft Building, Moulsecoomb, Brighton, BN2 4GJ, UK.
| | - Lorna W Harries
- Institute of Biomedical and Clinical Sciences, University of Exeter Medical School, University of Exeter, Barrack Road, Exeter, Devon, EX2 5DW, UK.
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17
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Lambert CA, Garbacki N, Colige AC. Chemotherapy induces alternative transcription and splicing: Facts and hopes for cancer treatment. Int J Biochem Cell Biol 2017; 91:84-97. [DOI: 10.1016/j.biocel.2017.04.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Revised: 04/04/2017] [Accepted: 04/15/2017] [Indexed: 01/14/2023]
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18
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Marques FZ, Prestes PR, Byars SG, Ritchie SC, Würtz P, Patel SK, Booth SA, Rana I, Minoda Y, Berzins SP, Curl CL, Bell JR, Wai B, Srivastava PM, Kangas AJ, Soininen P, Ruohonen S, Kähönen M, Lehtimäki T, Raitoharju E, Havulinna A, Perola M, Raitakari O, Salomaa V, Ala-Korpela M, Kettunen J, McGlynn M, Kelly J, Wlodek ME, Lewandowski PA, Delbridge LM, Burrell LM, Inouye M, Harrap SB, Charchar FJ. Experimental and Human Evidence for Lipocalin-2 (Neutrophil Gelatinase-Associated Lipocalin [NGAL]) in the Development of Cardiac Hypertrophy and heart failure. J Am Heart Assoc 2017; 6:e005971. [PMID: 28615213 PMCID: PMC5669193 DOI: 10.1161/jaha.117.005971] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Accepted: 05/02/2017] [Indexed: 12/25/2022]
Abstract
BACKGROUND Cardiac hypertrophy increases the risk of developing heart failure and cardiovascular death. The neutrophil inflammatory protein, lipocalin-2 (LCN2/NGAL), is elevated in certain forms of cardiac hypertrophy and acute heart failure. However, a specific role for LCN2 in predisposition and etiology of hypertrophy and the relevant genetic determinants are unclear. Here, we defined the role of LCN2 in concentric cardiac hypertrophy in terms of pathophysiology, inflammatory expression networks, and genomic determinants. METHODS AND RESULTS We used 3 experimental models: a polygenic model of cardiac hypertrophy and heart failure, a model of intrauterine growth restriction and Lcn2-knockout mouse; cultured cardiomyocytes; and 2 human cohorts: 114 type 2 diabetes mellitus patients and 2064 healthy subjects of the YFS (Young Finns Study). In hypertrophic heart rats, cardiac and circulating Lcn2 was significantly overexpressed before, during, and after development of cardiac hypertrophy and heart failure. Lcn2 expression was increased in hypertrophic hearts in a model of intrauterine growth restriction, whereas Lcn2-knockout mice had smaller hearts. In cultured cardiomyocytes, Lcn2 activated molecular hypertrophic pathways and increased cell size, but reduced proliferation and cell numbers. Increased LCN2 was associated with cardiac hypertrophy and diastolic dysfunction in diabetes mellitus. In the YFS, LCN2 expression was associated with body mass index and cardiac mass and with levels of inflammatory markers. The single-nucleotide polymorphism, rs13297295, located near LCN2 defined a significant cis-eQTL for LCN2 expression. CONCLUSIONS Direct effects of LCN2 on cardiomyocyte size and number and the consistent associations in experimental and human analyses reveal a central role for LCN2 in the ontogeny of cardiac hypertrophy and heart failure.
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Affiliation(s)
- Francine Z Marques
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
- Heart Failure Research Group, Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia
| | - Priscilla R Prestes
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Sean G Byars
- Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Scott C Ritchie
- Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Victoria, Australia
| | - Peter Würtz
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
| | - Sheila K Patel
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
| | - Scott A Booth
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Indrajeetsinh Rana
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Yosuke Minoda
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Stuart P Berzins
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
- Department of Microbiology and Immunology, Peter Doherty Institute, The University of Melbourne, Victoria, Australia
| | - Claire L Curl
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - James R Bell
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Bryan Wai
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
- Department of Cardiology, Austin Health, Heidelberg, Victoria, Australia
| | - Piyush M Srivastava
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
- Department of Cardiology, Austin Health, Heidelberg, Victoria, Australia
| | - Antti J Kangas
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
| | - Pasi Soininen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
| | - Saku Ruohonen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - Terho Lehtimäki
- Fimlab Laboratories, Department of Clinical Chemistry, Pirkanmaa Hospital District, School of Medicine, University of Tampere, Finland
| | - Emma Raitoharju
- Fimlab Laboratories, Department of Clinical Chemistry, Pirkanmaa Hospital District, School of Medicine, University of Tampere, Finland
| | - Aki Havulinna
- National Institute for Health and Welfare, Helsinki, Finland
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Finland
| | - Olli Raitakari
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Finland
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku, Finland
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki, Finland
| | - Mika Ala-Korpela
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- Medical Research Council Integrative Epidemiology Unit, University of Bristol, United Kingdom
- School of Social and Community Medicine, University of Bristol, United Kingdom
| | - Johannes Kettunen
- Computational Medicine, Faculty of Medicine, University of Oulu and Biocenter Oulu, Oulu, Finland
- NMR Metabolomics Laboratory, School of Pharmacy, University of Eastern Finland, Kuopio, Finland
- National Institute for Health and Welfare, Helsinki, Finland
| | - Maree McGlynn
- School of Medicine, Deakin University, Waurn Ponds, Victoria, Australia
| | - Jason Kelly
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
| | - Mary E Wlodek
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
| | | | - Lea M Delbridge
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Louise M Burrell
- Department of Medicine, The University of Melbourne Austin Health, Heidelberg, Victoria, Australia
- Department of Cardiology, Austin Health, Heidelberg, Victoria, Australia
| | - Michael Inouye
- Heart Failure Research Group, Baker Heart and Diabetes Research Institute, Melbourne, Victoria, Australia
- Centre for Systems Genomics, The University of Melbourne, Victoria, Australia
- School of BioSciences, The University of Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Victoria, Australia
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Stephen B Harrap
- Department of Physiology, The University of Melbourne, Victoria, Australia
| | - Fadi J Charchar
- School of Applied and Biomedical Sciences, Faculty of Science and Technology, Federation University Australia, Ballarat, Victoria, Australia
- Department of Physiology, The University of Melbourne, Victoria, Australia
- Department of Cardiovascular Sciences, University of Leicester, United Kingdom
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Mthembu NN, Mbita Z, Hull R, Dlamini Z. Abnormalities in alternative splicing of angiogenesis-related genes and their role in HIV-related cancers. HIV AIDS-RESEARCH AND PALLIATIVE CARE 2017; 9:77-93. [PMID: 28694706 PMCID: PMC5490432 DOI: 10.2147/hiv.s124911] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Alternative splicing of mRNA leads to an increase in proteome biodiversity by allowing the generation of multiple mRNAs, coding for multiple protein isoforms of various structural and functional properties from a single primary pre-mRNA transcript. The protein isoforms produced are tightly regulated in normal development but are mostly deregulated in various cancers. In HIV-infected individuals with AIDS, there is an increase in aberrant alternative splicing, resulting in an increase in HIV/AIDS-related cancers, such as Kaposi’s sarcoma, non-Hodgkin’s lymphoma, and cervical cancer. This aberrant splicing leads to abnormal production of protein and is caused by mutations in cis-acting elements or trans-acting factors in angiogenesis-related genes. Restoring the normal regulation of alternative splicing of angiogenic genes would alter the expression of protein isoforms and may confer normal cell physiology in patients with these cancers. This review highlights the abnormalities in alternative splicing of angiogenesis-related genes and their implication in HIV/AIDS-related cancers. This allows us to gain an insight into the pathogenesis of HIV/AIDS-related cancer and in turn elucidate the therapeutic potential of alternatively spliced genes in HIV/AIDS-related malignancies.
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Affiliation(s)
| | - Zukile Mbita
- Department of Biochemistry, Microbiology and Biotechnology, University of Limpopo, Sovenga, South Africa
| | - Rodney Hull
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
| | - Zodwa Dlamini
- Research, Innovation and Engagements, Mangosuthu University of Technology, Durban
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20
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Kurata M, Murata Y, Momma K, Fouad Ali Mursi I, Takahashi M, Miyamae Y, Kambe T, Nagao M, Narita H, Shibuya Y, Masuda S. The isoflavone fraction from soybean presents mRNA maturation inhibition activity. Biosci Biotechnol Biochem 2017; 81:551-554. [PMID: 27776450 DOI: 10.1080/09168451.2016.1249451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 10/05/2016] [Indexed: 01/29/2023]
Abstract
Recent findings indicate that mRNA splicing inhibitors can be potential anticancer candidates. We have previously established a screening system which monitors mRNA processing in order to identify mRNA processing inhibitors. Among a number of dietary resources, isoflavone fractions showed an inhibitory effect of mRNA processing. These findings demonstrate that a variety of dietary sources have an impact on mRNA biogenesis.
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Affiliation(s)
- Masashi Kurata
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
- b Department of Oral and Maxillofacial Surgery , Graduate School of Medical Sciences, Nagoya City University , Nagoya , Japan
| | - Yuki Murata
- c Department of Food and Nutrition , Kyoto Women's University , Kyoto , Japan
| | - Keiko Momma
- d Department of Living and Welfare , Kyoto Women's University , Kyoto , Japan
| | - Intisar Fouad Ali Mursi
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Masakazu Takahashi
- e Department of Bioscience , Fukui Prefectural University , Fukui , Japan
| | - Yusaku Miyamae
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Taiho Kambe
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Masaya Nagao
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
| | - Hiroshi Narita
- c Department of Food and Nutrition , Kyoto Women's University , Kyoto , Japan
| | - Yasuyuki Shibuya
- b Department of Oral and Maxillofacial Surgery , Graduate School of Medical Sciences, Nagoya City University , Nagoya , Japan
| | - Seiji Masuda
- a Division of Integrated Life Sciences, Graduate School of Biostudies , Kyoto University , Kyoto , Japan
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21
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Resveratrol limits epithelial to mesenchymal transition through modulation of KHSRP/hnRNPA1-dependent alternative splicing in mammary gland cells. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1860:291-298. [PMID: 28088441 DOI: 10.1016/j.bbagrm.2017.01.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 01/03/2017] [Accepted: 01/04/2017] [Indexed: 12/29/2022]
Abstract
Resveratrol (RESV) is a natural polyphenolic compound endowed with anti-inflammatory, anti-proliferative, as well as pro-apoptotic activities that make it a potential anti-tumor compound. Here we show that RESV counteracts the TGF-β-induced Epithelial to Mesenchymal Transition (EMT) phenotype in mammary gland cells and affects the alternative exon usage of pre-mRNAs that encode crucial factors in adhesion and migration -including CD44, ENAH, and FGFR2- in a panel of immortalized and transformed mammary gland cells. RESV causes a shift from the mesenchymal-specific forms of these factors to the respective epithelial forms and increases the expression of the RNA-binding proteins KHSRP and hnRNPA1. From a mechanistic point of view, we show that the combined silencing of KHSRP and hnRNPA1 prevents the RESV-dependent inclusion of the epithelial-type exons in the Cd44 pre-mRNA. Our findings support an unexpected regulatory mechanism where RESV limits EMT by controlling gene expression at post-transcriptional level.
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22
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Paraboschi EM, Cardamone G, Rimoldi V, Gemmati D, Spreafico M, Duga S, Soldà G, Asselta R. Meta-Analysis of Multiple Sclerosis Microarray Data Reveals Dysregulation in RNA Splicing Regulatory Genes. Int J Mol Sci 2015; 16:23463-81. [PMID: 26437396 PMCID: PMC4632709 DOI: 10.3390/ijms161023463] [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: 07/22/2015] [Revised: 09/08/2015] [Accepted: 09/14/2015] [Indexed: 12/12/2022] Open
Abstract
Abnormalities in RNA metabolism and alternative splicing (AS) are emerging as important players in complex disease phenotypes. In particular, accumulating evidence suggests the existence of pathogenic links between multiple sclerosis (MS) and altered AS, including functional studies showing that an imbalance in alternatively-spliced isoforms may contribute to disease etiology. Here, we tested whether the altered expression of AS-related genes represents a MS-specific signature. A comprehensive comparative analysis of gene expression profiles of publicly-available microarray datasets (190 MS cases, 182 controls), followed by gene-ontology enrichment analysis, highlighted a significant enrichment for differentially-expressed genes involved in RNA metabolism/AS. In detail, a total of 17 genes were found to be differentially expressed in MS in multiple datasets, with CELF1 being dysregulated in five out of seven studies. We confirmed CELF1 downregulation in MS (p = 0.0015) by real-time RT-PCRs on RNA extracted from blood cells of 30 cases and 30 controls. As a proof of concept, we experimentally verified the unbalance in alternatively-spliced isoforms in MS of the NFAT5 gene, a putative CELF1 target. In conclusion, for the first time we provide evidence of a consistent dysregulation of splicing-related genes in MS and we discuss its possible implications in modulating specific AS events in MS susceptibility genes.
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Affiliation(s)
- Elvezia Maria Paraboschi
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, Milan 20133, Italy.
| | - Giulia Cardamone
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università degli Studi di Milano, Via Viotti 3/5, Milan 20133, Italy.
| | - Valeria Rimoldi
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
| | - Donato Gemmati
- Center Haemostasis & Thrombosis, Department of Medical Sciences, Corso Giovecca 203, University of Ferrara, Ferrara 44121, Italy.
| | - Marta Spreafico
- Department of Transfusion Medicine and Hematology, Azienda Ospedaliera della Provincia di Lecco, Alessandro Manzoni Hospital, Via dell'Eremo 9/11, Lecco 23900, Italy.
| | - Stefano Duga
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
| | - Giulia Soldà
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
| | - Rosanna Asselta
- Department of Biomedical Sciences, Humanitas University, Via Manzoni 113, Rozzano, Milan 20089, Italy.
- Humanitas Clinical and Research Center, Via Manzoni 56, Rozzano, Milan 20089, Italy.
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Takarada T, Nishida A, Takeuchi A, Lee T, Takeshima Y, Matsuo M. Resveratrol enhances splicing of insulin receptor exon 11 in myotonic dystrophy type 1 fibroblasts. Brain Dev 2015; 37:661-8. [PMID: 25476247 DOI: 10.1016/j.braindev.2014.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 11/07/2014] [Accepted: 11/07/2014] [Indexed: 11/19/2022]
Abstract
INTRODUCTION Myotonic dystrophy type 1 (DM1) is characterized by splicing abnormalities caused by CUG expansion of the DMPK gene transcript. Splicing of exon 11 of the insulin receptor (IR) gene is deregulated to suppress exon 11 inclusion into mRNA in DM1. Consequently, the exon 11-deleted IR isoform that is less sensitive to insulin is predominantly produced, leading to glucose intolerance in DM1. Upregulation of exon 11 retaining full-length IR mRNA is a potential way to recover insulin sensitivity in DM1. METHODS We examined candidate chemicals for their ability to enhance inclusion of exon 11 of the IR gene in cultured cells by reverse transcription-PCR amplification of a fragment extending from exons 10 to 12 of IR mRNA. RESULTS We revealed that resveratrol (RES) enhanced the percentage of exon 11-containing IR mRNA among the total IR mRNA in HeLa cells. The RES-mediated enhancement of exon 11 inclusion was cell-specific and highest in fibroblasts. We tested RES on four fibroblast samples from three generations of one DM1 family. In each sample, RES treatment significantly upregulated the percentage of exon 11-containing IR mRNA to levels higher than that of the control, irrespective of the length of the sample's CTG repeat expansion. DISCUSSION A natural compound, RES, was shown for the first time to upregulate the full-length IR mRNA in fibroblasts from DM1 cases. Our results provide the justification of RES as a leading compound to improve glucose tolerance in DM1.
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Affiliation(s)
- Toru Takarada
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Nishi, Kobe 6512180, Japan; Kobe Pharmaceutical University, Higashinada, Kobe 6588558, Japan
| | - Atsushi Nishida
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Nishi, Kobe 6512180, Japan
| | - Atsuko Takeuchi
- Kobe Pharmaceutical University, Higashinada, Kobe 6588558, Japan
| | - Tomoko Lee
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638131, Japan
| | - Yasuhiro Takeshima
- Department of Pediatrics, Hyogo College of Medicine, Nishinomiya 6638131, Japan
| | - Masafumi Matsuo
- Department of Medical Rehabilitation, Faculty of Rehabilitation, Kobegakuin University, Nishi, Kobe 6512180, Japan.
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Feng D, Su RC, Zou L, Triggs-Raine B, Huang S, Xie J. Increase of a group of PTC(+) transcripts by curcumin through inhibition of the NMD pathway. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2015; 1849:1104-15. [PMID: 25934542 DOI: 10.1016/j.bbagrm.2015.04.002] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/07/2015] [Accepted: 04/22/2015] [Indexed: 12/11/2022]
Abstract
Nonsense-mediated mRNA decay (NMD), an mRNA surveillance mechanism, eliminates premature termination codon-containing (PTC⁺) transcripts. For instance, it maintains the homeostasis of splicing factors and degrades aberrant transcripts of human genetic disease genes. Here we examine the inhibitory effect on the NMD pathway and consequent increase of PTC+ transcripts by the dietary compound curcumin. We have found that several PTC⁺ transcripts including that of serine/arginine-rich splicing factor 1 (SRSF1) were specifically increased in cells by curcumin. We also observed a similar curcumin effect on the PTC⁺ mutant transcript from a Tay-Sachs-causing HEXA allele or from a beta-globin reporter gene. The curcumin effect was accompanied by significantly reduced expression of the NMD factors UPF1, 2, 3A and 3B. Consistently, in chromatin immunoprecipitation assays, curcumin specifically reduced the occupancy of acetyl-histone H3 and RNA polymerase II at the promoter region (-376 to -247nt) of human UPF1, in a time- and dosage-dependent way. Importantly, knocking down UPF1 abolished or substantially reduced the difference of PTC(+) transcript levels between control and curcumin-treated cells. The disrupted curcumin effect was efficiently rescued by expression of exogenous Myc-UPF1 in the knockdown cells. Together, our data demonstrate that a group of PTC⁺ transcripts are stabilized by a dietary compound curcumin through the inhibition of UPF factor expression and the NMD pathway.
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Affiliation(s)
- Dairong Feng
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005, China; Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Ruey-Chyi Su
- Department of Medical Microbiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Liping Zou
- Department of Pediatrics, Chinese PLA General Hospital, Beijing 100853, China
| | - Barbara Triggs-Raine
- Department of Biochemistry & Medical Genetics, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada
| | - Shangzhi Huang
- Department of Medical Genetics, Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences & Peking Union Medical College Beijing 100005, China.
| | - Jiuyong Xie
- Department of Physiology and Pathophysiology, Faculty of Medicine, University of Manitoba, Winnipeg MB R3E 0J9, Canada.
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25
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Gabriel M, Delforge Y, Deward A, Habraken Y, Hennuy B, Piette J, Klinck R, Chabot B, Colige A, Lambert C. Role of the splicing factor SRSF4 in cisplatin-induced modifications of pre-mRNA splicing and apoptosis. BMC Cancer 2015; 15:227. [PMID: 25884497 PMCID: PMC4399393 DOI: 10.1186/s12885-015-1259-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Accepted: 03/25/2015] [Indexed: 12/17/2022] Open
Abstract
Background Modification of splicing by chemotherapeutic drugs has usually been evaluated on a limited number of pre-mRNAs selected for their recognized or potential importance in cell proliferation or apoptosis. However, the pathways linking splicing alterations to the efficiency of cancer therapy remain unclear. Methods Next-generation sequencing was used to analyse the transcriptome of breast carcinoma cells treated by cisplatin. Pharmacological inhibitors, RNA interference, cells deficient in specific signalling pathways, RT-PCR and FACS analysis were used to investigate how the anti-cancer drug cisplatin affected alternative splicing and the cell death pathway. Results We identified 717 splicing events affected by cisplatin, including 245 events involving cassette exons. Gene ontology analysis indicates that cell cycle, mRNA processing and pre-mRNA splicing were the main pathways affected. Importantly, the cisplatin–induced splicing alterations required class I PI3Ks P110β but not components such as ATM, ATR and p53 that are involved in the DNA damage response. The siRNA-mediated depletion of the splicing regulator SRSF4, but not SRSF6, expression abrogated many of the splicing alterations as well as cell death induced by cisplatin. Conclusion Many of the splicing alterations induced by cisplatin are caused by SRSF4 and they contribute to apoptosis in a process requires class I PI3K. Electronic supplementary material The online version of this article (doi:10.1186/s12885-015-1259-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maude Gabriel
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Yves Delforge
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Adeline Deward
- Laboratory of Virology and Immunology, GIGA-Signal Transduction, GIGA B34, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Yvette Habraken
- Laboratory of Virology and Immunology, GIGA-Signal Transduction, GIGA B34, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Benoit Hennuy
- GIGA Genomics Platform, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Jacques Piette
- Laboratory of Virology and Immunology, GIGA-Signal Transduction, GIGA B34, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Roscoe Klinck
- Laboratory of Functional Genomics and Department of Microbiology and Infectiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Benoit Chabot
- Laboratory of Functional Genomics and Department of Microbiology and Infectiology, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada.
| | - Alain Colige
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
| | - Charles Lambert
- Laboratory of Connective Tissues Biology, GIGA-Cancer, University of Liège, avenue de l'Hôpital 1, 4000, Liège, Belgium.
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Naturally occurring plant polyphenols as potential therapies for inherited neuromuscular diseases. Future Med Chem 2014; 5:2091-101. [PMID: 24215348 DOI: 10.4155/fmc.13.165] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
There are several lines of laboratory-based evidence emerging to suggest that purified polyphenol compounds such as resveratrol, found naturally in red grapes, epigallocatechin galate from green tea and curcumin from turmeric, might be useful for the treatment of various inherited neuromuscular diseases, including spinal muscular atrophy, Duchenne muscular dystrophy and Charcot-Marie-Tooth disease. Here, we critically examine the scientific evidence related to the known molecular effects that these polyphenols have on different models of inherited neuromuscular disease, with particular attention to problems with the validity of in vitro evidence. We also present proteomic evidence that polyphenols have in vitro effects on cells related to metal ion chelation in cell-culture media. Although their precise mechanisms of action remain somewhat elusive, polyphenols could be an attractive approach to therapy for inherited neuromuscular disease, especially since they may be safer to use on young children, compared with some of the other drug candidates.
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27
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Dardis A, Zanin I, Zampieri S, Stuani C, Pianta A, Romanello M, Baralle FE, Bembi B, Buratti E. Functional characterization of the common c.-32-13T>G mutation of GAA gene: identification of potential therapeutic agents. Nucleic Acids Res 2013; 42:1291-302. [PMID: 24150945 PMCID: PMC3902950 DOI: 10.1093/nar/gkt987] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Glycogen storage disease type II is a lysosomal storage disorder due to mutations of the GAA gene, which causes lysosomal alpha-glucosidase deficiency. Clinically, glycogen storage disease type II has been classified in infantile and late-onset forms. Most late-onset patients share the leaky splicing mutation c.-32-13T>G. To date, the mechanism by which the c.-32-13T>G mutation affects the GAA mRNA splicing is not fully known. In this study, we demonstrate that the c.-32-13T>G mutation abrogates the binding of the splicing factor U2AF65 to the polypyrimidine tract of exon 2 and that several splicing factors affect exon 2 inclusion, although the only factor capable of acting in the c.-32-13 T>G context is the SR protein family member, SRSF4 (SRp75). Most importantly, a preliminary screening using small molecules described to be able to affect splicing profiles, showed that resveratrol treatment resulted in a significant increase of normal spliced GAA mRNA, GAA protein content and activity in cells transfected with a mutant minigene and in fibroblasts from patients carrying the c-32-13T>G mutation. In conclusion, this work provides an in-depth functional characterization of the c.-32-13T>G mutation and, most importantly, an in vitro proof of principle for the use of small molecules to rescue normal splicing of c.-32-13T>G mutant alleles.
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Affiliation(s)
- Andrea Dardis
- Regional Centre for Rare Diseases, University Hospital Santa Maria della Misericordia, Udine, Italy and International Centre for Genetic Engineering and Biotechnology (ICGEB), Area Science Park, Trieste, Italy
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28
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Pérez-Carro R, Sánchez-Alcudia R, Pérez B, Navarrete R, Pérez-Cerdá C, Ugarte M, Desviat LR. Functional analysis and in vitro correction of splicing FAH mutations causing tyrosinemia type I. Clin Genet 2013; 86:167-71. [PMID: 23895425 DOI: 10.1111/cge.12243] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/08/2013] [Accepted: 07/23/2013] [Indexed: 01/16/2023]
Abstract
Hereditary tyrosinemia type I (HT1) is a rare disease caused by a deficiency of fumarylacetoacetate hydrolase (FAH) in the tyrosine catabolic pathway, resulting mainly in hepatic alterations due to accumulation of the toxic metabolites fumarylacetoacetate, maleylacetoacetate and succinylacetone. We have characterized using minigenes four splicing mutations affecting exonic or intronic nucleotides of the FAH gene identified in two HT1 patients. Two of the mutations are novel, c.82-1G>A and c.913G>C and the other two have been previously associated with a splicing defect (c.836A>G and c.1062+5G>A). All mutations were confirmed to affect splicing in minigenes, resulting in exon skipping or activation of a cryptic splice site. We have analyzed the effect of different compounds known to modulate splicing (valproic acid, phenyl butyrate, M344, EIPA, and resveratrol) and the overexpression of splice factors of the SR protein family on the transcriptional profile of the mutant minigenes. For the c.836A>G mutation, a partial recovery of the correctly spliced transcript was observed. These results confirm the relevance of performing functional studies for mutations potentially affecting the splicing process and open the possibility of supplementary therapeutic approaches to diseases caused by splicing defects.
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Affiliation(s)
- R Pérez-Carro
- Centro de Diagnóstico de Enfermedades Moleculares, Centro de Biología Molecular Severo Ochoa, Universidad Autónoma, CIBERER, IdiPaz, Madrid, Spain
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29
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The role of SIRT1 in ocular aging. Exp Eye Res 2013; 116:17-26. [PMID: 23892278 DOI: 10.1016/j.exer.2013.07.017] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Revised: 07/13/2013] [Accepted: 07/16/2013] [Indexed: 12/27/2022]
Abstract
The sirtuins are a highly conserved family of nicotinamide adenine dinucleotide (NAD+)-dependent histone deacetylases that helps regulate the lifespan of diverse organisms. The human genome encodes seven different sirtuins (SIRT1-7), which share a common catalytic core domain but possess distinct N- and C-terminal extensions. Dysfunction of some sirtuins have been associated with age-related diseases, such as cancer, type II diabetes, obesity-associated metabolic diseases, neurodegeneration, and cardiac aging, as well as the response to environmental stress. SIRT1 is one of the targets of resveratrol, a polyphenolic SIRT1 activator that has been shown to increase the lifespan and to protect various organs against aging. A number of animal studies have been conducted to examine the role of sirtuins in ocular aging. Here we review current knowledge about SIRT1 and ocular aging. The available data indicate that SIRT1 is localized in the nucleus and cytoplasm of cells forming all normal ocular structures, including the cornea, lens, iris, ciliary body, and retina. Upregulation of SIRT1 has been shown to have an important protective effect against various ocular diseases, such as cataract, retinal degeneration, optic neuritis, and uveitis, in animal models. These results suggest that SIRT1 may provide protection against diseases related to oxidative stress-induced ocular damage, including cataract, age-related macular degeneration, and optic nerve degeneration in glaucoma patients.
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30
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Tang JY, Lee JC, Hou MF, Wang CL, Chen CC, Huang HW, Chang HW. Alternative splicing for diseases, cancers, drugs, and databases. ScientificWorldJournal 2013; 2013:703568. [PMID: 23766705 PMCID: PMC3674688 DOI: 10.1155/2013/703568] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/30/2013] [Indexed: 01/05/2023] Open
Abstract
Alternative splicing is a major diversification mechanism in the human transcriptome and proteome. Several diseases, including cancers, have been associated with dysregulation of alternative splicing. Thus, correcting alternative splicing may restore normal cell physiology in patients with these diseases. This paper summarizes several alternative splicing-related diseases, including cancers and their target genes. Since new cancer drugs often target spliceosomes, several clinical drugs and natural products or their synthesized derivatives were analyzed to determine their effects on alternative splicing. Other agents known to have modulating effects on alternative splicing during therapeutic treatment of cancer are also discussed. Several commonly used bioinformatics resources are also summarized.
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Affiliation(s)
- Jen-Yang Tang
- Department of Radiation Oncology, Faculty of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Radiation Oncology, Kaohsiung Medical University Hospital, Kaohsiung 807, Taiwan
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jin-Ching Lee
- Department of Biotechnology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Institute of Clinical Medicine, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Kaohsiung Municipal Ta-Tung Hospital, Kaohsiung 807, Taiwan
| | - Chun-Lin Wang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Chien-Chi Chen
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu 300, Taiwan
| | - Hurng-Wern Huang
- Institute of Biomedical Science, National Sun Yat-Sen University, Kaohsiung 807, Taiwan
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Graduate Institute of Natural Products, Kaohsiung Medical University, Kaohsiung 807, Taiwan
- Department of Biomedical Science and Environmental Biology, Kaohsiung Medical University, Kaohsiung 807, Taiwan
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Hagen RM, Chedea VS, Mintoff CP, Bowler E, Morse HR, Ladomery MR. Epigallocatechin-3-gallate promotes apoptosis and expression of the caspase 9a splice variant in PC3 prostate cancer cells. Int J Oncol 2013; 43:194-200. [PMID: 23615977 DOI: 10.3892/ijo.2013.1920] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Accepted: 01/29/2013] [Indexed: 11/06/2022] Open
Abstract
Growing evidence suggests that the flavonoid epigallocatechin-3-gallate (EGCG), notably abundant in green tea, has health-promoting properties. We examined the effect of EGCG on cell survival and apoptosis in the prostate cancer cell line PC3. Cell survival was reduced and apoptosis increased significantly with a low dose of 1 µM EGCG. The ability of the anticancer drug cisplatin to promote apoptosis was enhanced by EGCG. Furthermore, EGCG, both alone and in combination with cisplatin, promoted the expression of the pro-apoptotic splice isoform of caspase 9.
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Affiliation(s)
- Rachel M Hagen
- Centre for Research in Bioscience, Faculty of Health and Life Sciences, University of the West of England, Coldharbour Lane, Frenchay, Bristol BS16 1QY, UK
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