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Cheng S, Fahmi NA, Park M, Sun J, Thao K, Yeh HS, Zhang W, Yong J. mTOR Contributes to the Proteome Diversity through Transcriptome-Wide Alternative Splicing. Int J Mol Sci 2022; 23:ijms232012416. [PMID: 36293270 PMCID: PMC9604279 DOI: 10.3390/ijms232012416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/16/2022] Open
Abstract
The mammalian target of rapamycin (mTOR) pathway is crucial in energy metabolism and cell proliferation. Previously, we reported transcriptome-wide 3′-untranslated region (UTR) shortening by alternative polyadenylation upon mTOR activation and its impact on the proteome. Here, we further interrogated the mTOR-activated transcriptome and found that hyperactivation of mTOR promotes transcriptome-wide exon skipping/exclusion, producing short isoform transcripts from genes. This widespread exon skipping confers multifarious regulations in the mTOR-controlled functional proteomics: AS in coding regions widely affects the protein length and functional domains. They also alter the half-life of proteins and affect the regulatory post-translational modifications. Among the RNA processing factors differentially regulated by mTOR signaling, we found that SRSF3 mechanistically facilitates exon skipping in the mTOR-activated transcriptome. This study reveals a role of mTOR in AS regulation and demonstrates that widespread AS is a multifaceted modulator of the mTOR-regulated functional proteome.
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Affiliation(s)
- Sze Cheng
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
| | - Kaitlyn Thao
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55445, USA
- Correspondence: (W.Z.); (J.Y.); Tel.: +1-407-823-2763 (W.Z.); +1-612-626-2420 (J.Y.)
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2
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Riegler S, Servi L, Scarpin MR, Godoy Herz MA, Kubaczka MG, Venhuizen P, Meyer C, Brunkard JO, Kalyna M, Barta A, Petrillo E. Light regulates alternative splicing outcomes via the TOR kinase pathway. Cell Rep 2021; 36:109676. [PMID: 34496244 PMCID: PMC8547716 DOI: 10.1016/j.celrep.2021.109676] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Revised: 05/18/2021] [Accepted: 08/16/2021] [Indexed: 11/29/2022] Open
Abstract
For plants, light is the source of energy and the most relevant regulator of growth and adaptations to the environment by inducing changes in gene expression at various levels, including alternative splicing. Light-triggered chloroplast retrograde signals control alternative splicing in Arabidopsis thaliana. Here, we provide evidence that light regulates the expression of a core set of splicing-related factors in roots. Alternative splicing responses in roots are not directly caused by light but are instead most likely triggered by photo-synthesized sugars. The target of rapamycin (TOR) kinase plays a key role in this shoot-to-root signaling pathway. Knocking down TOR expression or pharmacologically inhibiting TOR activity disrupts the alternative splicing responses to light and exogenous sugars in roots. Consistently, splicing decisions are modulated by mitochondrial activity in roots. In conclusion, by activating the TOR pathway, sugars act as mobile signals to coordinate alternative splicing responses to light throughout the whole plant. Riegler et al. reveal a central role for TOR kinase paired with retrograde signaling in alternative splicing regulation by light in roots and, to a certain extent, in leaves. Activating the TOR pathway, sugars act as mobile signals to coordinate alternative splicing responses to light throughout the whole plant.
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Affiliation(s)
- Stefan Riegler
- Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Lucas Servi
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - M Regina Scarpin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA
| | - Micaela A Godoy Herz
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - María G Kubaczka
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina
| | - Peter Venhuizen
- Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Christian Meyer
- Institut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles, France
| | - Jacob O Brunkard
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Plant Gene Expression Center, US Department of Agriculture, Agricultural Research Service, Albany, CA 94710, USA; Laboratory of Genetics, University of Wisconsin, Madison, Madison, WI 53706, USA
| | - Maria Kalyna
- Department of Applied Genetics and Cell Biology, BOKU - University of Natural Resources and Life Sciences, Muthgasse 18, 1190 Vienna, Austria
| | - Andrea Barta
- Max Perutz Labs, Medical University of Vienna, Vienna Biocenter Campus, 1030 Vienna, Austria
| | - Ezequiel Petrillo
- Universidad de Buenos Aires, Facultad de Ciencias Exactas y Naturales, Departamento de Fisiología, Biología, Molecular, y Celular, Buenos Aires, Argentina; CONICET-Universidad de Buenos Aires, Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE), C1428EHA, Buenos Aires, Argentina.
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Pacheco JM, Canal MV, Pereyra CM, Welchen E, Martínez-Noël GMA, Estevez JM. The tip of the iceberg: emerging roles of TORC1, and its regulatory functions in plant cells. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4085-4101. [PMID: 33462577 DOI: 10.1093/jxb/eraa603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/19/2020] [Indexed: 06/12/2023]
Abstract
Target of Rapamycin (TOR) is an evolutionarily conserved protein kinase that plays a central role in coordinating cell growth with light availability, the diurnal cycle, energy availability, and hormonal pathways. TOR Complex 1 (TORC1) controls cell proliferation, growth, metabolism, and defense in plants. Sugar availability is the main signal for activation of TOR in plants, as it also is in mammals and yeast. Specific regulators of the TOR kinase pathway in plants are inorganic compounds in the form of major nutrients in the soils, and light inputs via their impact on autotrophic metabolism. The lack of TOR is embryo-lethal in plants, whilst dysregulation of TOR signaling causes major alterations in growth and development. TOR exerts control as a regulator of protein translation via the action of proteins such as S6K, RPS6, and TAP46. Phytohormones are central players in the downstream systemic physiological TOR effects. TOR has recently been attributed to have roles in the control of DNA methylation, in the abundance of mRNA splicing variants, and in the variety of regulatory lncRNAs and miRNAs. In this review, we summarize recent discoveries in the plant TOR signaling pathway in the context of our current knowledge of mammalian and yeast cells, and highlight the most important gaps in our understanding of plants that need to be addressed in the future.
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Affiliation(s)
| | - María Victoria Canal
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Cintia M Pereyra
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - Elina Welchen
- Instituto de Agrobiotecnología del Litoral (CONICET-UNL), Cátedra de Biología Celular y Molecular, Facultad de Bioquímica y Ciencias Biológicas,, Universidad Nacional del Litoral, Santa Fe, Argentina
| | - Giselle M A Martínez-Noël
- Instituto de Investigaciones en Biodiversidad y Biotecnología (INBIOTEC-CONICET) and Fundación para Investigaciones Biológicas Aplicadas (FIBA), Vieytes, Mar Del Plata, Argentina
| | - José M Estevez
- Fundación Instituto Leloir and IIBBA-CONICET, Buenos Aires CP, Argentina
- Centro de Biotecnología Vegetal (CBV), Facultad de Ciencias de la Vida (FCsV), Universidad Andres Bello, Santiago, Chile and Millennium Institute for Integrative Biology (iBio), Santiago, Chile
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Fahmi NA, Nassereddeen H, Chang J, Park M, Yeh H, Sun J, Fan D, Yong J, Zhang W. AS-Quant: Detection and Visualization of Alternative Splicing Events with RNA-seq Data. Int J Mol Sci 2021; 22:ijms22094468. [PMID: 33922891 PMCID: PMC8123109 DOI: 10.3390/ijms22094468] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/19/2021] [Accepted: 04/22/2021] [Indexed: 02/06/2023] Open
Abstract
(1) Background: A simplistic understanding of the central dogma falls short in correlating the number of genes in the genome to the number of proteins in the proteome. Post-transcriptional alternative splicing contributes to the complexity of the proteome and is critical in understanding gene expression. mRNA-sequencing (RNA-seq) has been widely used to study the transcriptome and provides opportunity to detect alternative splicing events among different biological conditions. Despite the popularity of studying transcriptome variants with RNA-seq, few efficient and user-friendly bioinformatics tools have been developed for the genome-wide detection and visualization of alternative splicing events. (2) Results: We propose AS-Quant, (Alternative Splicing Quantitation), a robust program to identify alternative splicing events from RNA-seq data. We then extended AS-Quant to visualize the splicing events with short-read coverage plots along with complete gene annotation. The tool works in three major steps: (i) calculate the read coverage of the potential spliced exons and the corresponding gene; (ii) categorize the events into five different categories according to the annotation, and assess the significance of the events between two biological conditions; (iii) generate the short reads coverage plot for user specified splicing events. Our extensive experiments on simulated and real datasets demonstrate that AS-Quant outperforms the other three widely used baselines, SUPPA2, rMATS, and diffSplice for detecting alternative splicing events. Moreover, the significant alternative splicing events identified by AS-Quant between two biological contexts were validated by RT-PCR experiment. (3) Availability: AS-Quant is implemented in Python 3.0. Source code and a comprehensive user's manual are freely available online.
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Affiliation(s)
- Naima Ahmed Fahmi
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA; (N.A.F.); (J.S.)
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
| | - Heba Nassereddeen
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
- Department of Electrical and Computer Engineering, University of Central Florida, Orlando, FL 32816, USA
| | - Jaewoong Chang
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA; (J.C.); (M.P.); (H.Y.)
| | - Meeyeon Park
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA; (J.C.); (M.P.); (H.Y.)
| | - Hsinsung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA; (J.C.); (M.P.); (H.Y.)
| | - Jiao Sun
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA; (N.A.F.); (J.S.)
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
| | - Deliang Fan
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, AZ 85287, USA;
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA; (J.C.); (M.P.); (H.Y.)
- Correspondence: (J.Y.); (W.Z.)
| | - Wei Zhang
- Department of Computer Science, University of Central Florida, Orlando, FL 32816, USA; (N.A.F.); (J.S.)
- Genomics and Bioinformatics Cluster, University of Central Florida, Orlando, FL 32816, USA;
- Correspondence: (J.Y.); (W.Z.)
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Raspin K, FitzGerald LM, Marthick JR, Field MA, Malley RC, Banks A, Donovan S, Thomson RJ, Foley GR, Stanford JL, Dickinson JL. A rare variant in EZH2 is associated with prostate cancer risk. Int J Cancer 2021; 149:1089-1099. [PMID: 33821477 DOI: 10.1002/ijc.33584] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 02/26/2021] [Accepted: 03/09/2021] [Indexed: 11/11/2022]
Abstract
Prostate cancer (PrCa) is highly heritable, and although rare variants contribute significantly to PrCa risk, few have been identified to date. Herein, whole-genome sequencing was performed in a large PrCa family featuring multiple affected relatives spanning several generations. A rare, predicted splice site EZH2 variant, rs78589034 (G > A), was identified as segregating with disease in all but two individuals in the family, one of whom was affected with lymphoma and bowel cancer and a female relative. This variant was significantly associated with disease risk in combined familial and sporadic PrCa datasets (n = 1551; odds ratio [OR] = 3.55, P = 1.20 × 10-5 ). Transcriptome analysis was performed on prostate tumour needle biopsies available for two rare variant carriers and two wild-type cases. Although no allele-dependent differences were detected in EZH2 transcripts, a distinct differential gene expression signature was observed when comparing prostate tissue from the rare variant carriers with the wild-type samples. The gene expression signature comprised known downstream targets of EZH2 and included the top-ranked genes, DUSP1, FOS, JUNB and EGR1, which were subsequently validated by qPCR. These data provide evidence that rs78589034 is associated with increased PrCa risk in Tasmanian men and further, that this variant may be associated with perturbed EZH2 function in prostate tissue. Disrupted EZH2 function is a driver of tumourigenesis in several cancers, including prostate, and is of significant interest as a therapeutic target.
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Affiliation(s)
- Kelsie Raspin
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Liesel M FitzGerald
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - James R Marthick
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Matt A Field
- Australian Institute of Tropical Health and Medicine and Centre for Tropical Bioinformatics and Molecular Biology, James Cook University, Cairns, Queensland, Australia.,John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory, Australia
| | - Roslyn C Malley
- Hobart Pathology, Hobart, Tasmania, Australia.,Tasmanian School of Medicine, University of Tasmania, Hobart, Tasmania, Australia
| | - Annette Banks
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | | | - Russell J Thomson
- Centre for Research in Mathematics and Data Science, Western Sydney University, Sydney, New South Wales, Australia
| | - Georgea R Foley
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
| | - Janet L Stanford
- Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Joanne L Dickinson
- Menzies Institute for Medical Research, University of Tasmania, Hobart, Tasmania, Australia
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Královičová J, Borovská I, Pengelly R, Lee E, Abaffy P, Šindelka R, Grutzner F, Vořechovský I. Restriction of an intron size en route to endothermy. Nucleic Acids Res 2021; 49:2460-2487. [PMID: 33550394 PMCID: PMC7969005 DOI: 10.1093/nar/gkab046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 01/11/2021] [Accepted: 01/15/2021] [Indexed: 11/15/2022] Open
Abstract
Ca2+-insensitive and -sensitive E1 subunits of the 2-oxoglutarate dehydrogenase complex (OGDHC) regulate tissue-specific NADH and ATP supply by mutually exclusive OGDH exons 4a and 4b. Here we show that their splicing is enforced by distant lariat branch points (dBPs) located near the 5' splice site of the intervening intron. dBPs restrict the intron length and prevent transposon insertions, which can introduce or eliminate dBP competitors. The size restriction was imposed by a single dominant dBP in anamniotes that expanded into a conserved constellation of four dBP adenines in amniotes. The amniote clusters exhibit taxon-specific usage of individual dBPs, reflecting accessibility of their extended motifs within a stable RNA hairpin rather than U2 snRNA:dBP base-pairing. The dBP expansion took place in early terrestrial species and was followed by a uridine enrichment of large downstream polypyrimidine tracts in mammals. The dBP-protected megatracts permit reciprocal regulation of exon 4a and 4b by uridine-binding proteins, including TIA-1/TIAR and PUF60, which promote U1 and U2 snRNP recruitment to the 5' splice site and BP, respectively, but do not significantly alter the relative dBP usage. We further show that codons for residues critically contributing to protein binding sites for Ca2+ and other divalent metals confer the exon inclusion order that mirrors the Irving-Williams affinity series, linking the evolution of auxiliary splicing motifs in exons to metallome constraints. Finally, we hypothesize that the dBP-driven selection for Ca2+-dependent ATP provision by E1 facilitated evolution of endothermy by optimizing the aerobic scope in target tissues.
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Affiliation(s)
- Jana Královičová
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Ivana Borovská
- Slovak Academy of Sciences, Centre for Biosciences, 840 05 Bratislava, Slovak Republic
| | - Reuben Pengelly
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
| | - Eunice Lee
- School of Biological Sciences, University of Adelaide, Adelaide 5005, SA, Australia
| | - Pavel Abaffy
- Czech Academy of Sciences, Institute of Biotechnology, 25250 Vestec, Czech Republic
| | - Radek Šindelka
- Czech Academy of Sciences, Institute of Biotechnology, 25250 Vestec, Czech Republic
| | - Frank Grutzner
- School of Biological Sciences, University of Adelaide, Adelaide 5005, SA, Australia
| | - Igor Vořechovský
- University of Southampton, Faculty of Medicine, HDH, Southampton SO16 6YD, UK
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Liu Y, Zheng Y, Zhou Y, Liu Y, Xie M, Meng W, An M. The expression and significance of mTORC1 in diabetic retinopathy. BMC Ophthalmol 2020; 20:297. [PMID: 32689970 PMCID: PMC7370483 DOI: 10.1186/s12886-020-01553-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/06/2020] [Indexed: 01/23/2023] Open
Abstract
Background To investigate the expression and significance of mechanistic target of rapamycin complex 1(mTORC1) in diabetic retinopathy (DR), and to find new targets and new methods for the treatment of DR. Methods A DR rat model was prepared by general feeding combined with intraperitoneal injection of 10% streptozotocin (60 mg/kg). The rats were randomly divided into a control group (NDM group) and a diabetes group (DM group). Three months later, the degrees of retinopathy was determined using hematoxylin and eosin staining, and the levels of p-S6, VEGF, and PEDF proteins were detected by immunohistochemistry and western blotting. Human retinal capillary endothelial cells (HRCECs) were cultured in high glucose (HG) conditions, then treated with rapamycin or transfected with siTSC1.The protein levels of p-S6 were assessed by western blotting. The 5-ethynyl-2′-deoxyuridine assay was used to detect cell proliferation, and the Transwell assay was used to detect cell migration. Results A DM rat model was successfully developed. The expressions of p-S6 and VEGF proteins were significantly increased in the DM group (p < 0.05), and the expression of PEDF protein was significantly decreased compared with the NDM group (p < 0.05). In vitro, the p-S6 protein, as well as cell proliferation and migration, in HG induced HRCECs were increased (p < 0.05) compared with the control (normal glucose) group (p < 0.05). After transfection with siTSC1 to activate mTORC1, the expression of p-S6, as well as cell proliferation and migration, were increased. In contrast, rapamycin decreased p-S6 expression, as well as proliferation and migration, in HG induced HRCECs compared to the control group (p < 0.05). Conclusion mTORC1 plays an important role in DR. After activation, mTORC1 induced expression of the p-S6 protein, regulated the expressions of VEGF and PEDF proteins, and changed the proliferation and migration of endothelial cells. The mTORC1 can therefore be used as a new target,as well as in the treatment of DR.
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Affiliation(s)
- Yanli Liu
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China
| | - Yarong Zheng
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China
| | - Yekai Zhou
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China
| | - Yi Liu
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China
| | - Mengxuan Xie
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China
| | - Wenjing Meng
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China.,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China
| | - Meixia An
- The Third Affiliated Hospital of Southern Medical University, Guangzhou, 510515, China. .,Guangdong Provincial Key Laboratory of Bone and Joint Degeneration Diesases, Guangzhou, China.
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Bhadra M, Howell P, Dutta S, Heintz C, Mair WB. Alternative splicing in aging and longevity. Hum Genet 2019; 139:357-369. [PMID: 31834493 DOI: 10.1007/s00439-019-02094-6] [Citation(s) in RCA: 97] [Impact Index Per Article: 19.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Accepted: 11/24/2019] [Indexed: 12/13/2022]
Abstract
Alternative pre-mRNA splicing increases the complexity of the proteome that can be generated from the available genomic coding sequences. Dysregulation of the splicing process has been implicated in a vast repertoire of diseases. However, splicing has recently been linked to both the aging process itself and pro-longevity interventions. This review focuses on recent research towards defining RNA splicing as a new hallmark of aging. We highlight dysfunctional alternative splicing events that contribute to the aging phenotype across multiple species, along with recent efforts toward deciphering mechanistic roles for RNA splicing in the regulation of aging and longevity. Further, we discuss recent research demonstrating a direct requirement for specific splicing factors in pro-longevity interventions, and specifically how nutrient signaling pathways interface to splicing factor regulation and downstream splicing targets. Finally, we review the emerging potential of using splicing profiles as a predictor of biological age and life expectancy. Understanding the role of RNA splicing components and downstream targets altered in aging may provide opportunities to develop therapeutics and ultimately extend healthy lifespan in humans.
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Affiliation(s)
- Malini Bhadra
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Porsha Howell
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Sneha Dutta
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - Caroline Heintz
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA
| | - William B Mair
- Department of Molecular Metabolism, Harvard T.H. Chan School of Public Health, Boston, MA, 02115, USA.
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9
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Yeh HS, Yong J. mTOR-coordinated Post-Transcriptional Gene Regulations: from Fundamental to Pathogenic Insights. J Lipid Atheroscler 2019; 9:8-22. [PMID: 32821719 PMCID: PMC7379075 DOI: 10.12997/jla.2020.9.1.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2019] [Revised: 09/13/2019] [Accepted: 09/22/2019] [Indexed: 12/26/2022] Open
Abstract
Post-transcriptional regulations of mRNA transcripts such as alternative splicing and alternative polyadenylation can affect the expression of genes without changing the transcript levels. Recent studies have demonstrated that these post-transcriptional events can have significant physiological impacts on various biological systems and play important roles in the pathogenesis of a number of diseases, including cancers. Nevertheless, how cellular signaling pathways control these post-transcriptional processes in cells are not very well explored in the field yet. The mammalian target of rapamycin complex 1 (mTORC1) pathway plays a key role in sensing cellular nutrient and energy status and regulating the proliferation and growth of cells by controlling various anabolic and catabolic processes. Dysregulation of mTORC1 pathway can tip the metabolic balance of cells and is associated with a number of pathological conditions, including various types of cancers, diabetes, and cardiovascular diseases. Numerous reports have shown that mTORC1 controls its downstream pathways through translational and/or transcriptional regulation of the expression of key downstream effectors. And, recent studies have also shown that mTORC1 can control downstream pathways via post-transcriptional regulations. In this review, we will discuss the roles of post-transcriptional processes in gene expression regulations and how mTORC1-mediated post-transcriptional regulations contribute to cellular physiological changes. We highlight post-transcriptional regulation as an additional layer of gene expression control by mTORC1 to steer cellular biology. These emphasize the importance of studying post-transcriptional events in transcriptome datasets for gaining a fuller understanding of gene expression regulations in the biological systems of interest.
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Affiliation(s)
- Hsin-Sung Yeh
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Jeongsik Yong
- Department of Biochemistry, Molecular Biology and Biophysics, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
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