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Damberger F, Krepl M, Arora R, Beusch I, Maris C, Dorn G, Šponer J, Ravindranathan S, Allain FT. N-terminal domain of polypyrimidine-tract binding protein is a dynamic folding platform for adaptive RNA recognition. Nucleic Acids Res 2024; 52:10683-10704. [PMID: 39180402 PMCID: PMC11417363 DOI: 10.1093/nar/gkae713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 08/14/2024] [Indexed: 08/26/2024] Open
Abstract
The N-terminal RNA recognition motif domain (RRM1) of polypyrimidine tract binding protein (PTB) forms an additional C-terminal helix α3, which docks to one edge of the β-sheet upon binding to a stem-loop RNA containing a UCUUU pentaloop. Importantly, α3 does not contact the RNA. The α3 helix therefore represents an allosteric means to regulate the conformation of adjacent domains in PTB upon binding structured RNAs. Here we investigate the process of dynamic adaptation by stem-loop RNA and RRM1 using NMR and MD in order to obtain mechanistic insights on how this allostery is achieved. Relaxation data and NMR structure determination of the free protein show that α3 is partially ordered and interacts with the domain transiently. Stem-loop RNA binding quenches fast time scale dynamics and α3 becomes ordered, however microsecond dynamics at the protein-RNA interface is observed. MD shows how RRM1 binding to the stem-loop RNA is coupled to the stabilization of the C-terminal helix and helps to transduce differences in RNA loop sequence into changes in α3 length and order. IRES assays of full length PTB and a mutant with altered dynamics in the α3 region show that this dynamic allostery influences PTB function in cultured HEK293T cells.
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Affiliation(s)
- Fred F Damberger
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Miroslav Krepl
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 00, Czech Republic
| | - Rajika Arora
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Irene Beusch
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | | | - Georg Dorn
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, Brno 612 00, Czech Republic
| | | | - Frédéric H-T Allain
- Institute of Biochemistry, ETH Zurich, 8093 Zurich, Switzerland
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
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2
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Wu Y, Wang J, Zhao J, Su Y, Li X, Chen Z, Wu X, Huang S, He X, Liang L. LTR retrotransposon-derived LncRNA LINC01446 promotes hepatocellular carcinoma progression and angiogenesis by regulating the SRPK2/SRSF1/VEGF axis. Cancer Lett 2024; 598:217088. [PMID: 38945203 DOI: 10.1016/j.canlet.2024.217088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 06/15/2024] [Accepted: 06/25/2024] [Indexed: 07/02/2024]
Abstract
The causal link between long terminal repeat (LTR) retrotransposon-derived lncRNAs and hepatocellular carcinoma (HCC) remains elusive and whether these cancer-exclusive lncRNAs contribute to the effectiveness of current HCC therapies is yet to explore. Here, we investigated the activation of LTR retrotransposon-derived lncRNAs in a broad range of liver diseases. We found that LTR retrotransposon-derived lncRNAs are mainly activated in HCC and is correlated with the proliferation status of HCC. Furthermore, we discovered that an LTR retrotransposon-derived lncRNA, LINC01446, exhibits specific expression in HCC. HCC patients with higher LINC01446 expression had shorter overall survival times. In vitro and in vivo assays showed that LINC01446 promoted HCC growth and angiogenesis. Mechanistically, LINC01446 bound to serine/arginine protein kinase 2 (SRPK2) and activated its downstream target, serine/arginine splicing factor 1 (SRSF1). Furthermore, activation of the SRPK2-SRSF1 axis increased the splicing and expression of VEGF isoform A165 (VEGFA165). Notably, inhibiting LINC01446 expression dramatically impaired tumor growth in vivo and resulted in better therapeutic outcomes when combined with antiangiogenic agents. In addition, we found that the transcription factor MESI2 bound to the cryptic MLT2B3 LTR promoter and drove LINC01446 transcription in HCC cells. Taken together, our findings demonstrate that LTR retrotransposon-derived LINC01446 promotes the progression of HCC by activating the SRPK2/SRSF1/VEGFA165 axis and highlight targeting LINC01446 as a potential therapeutic strategy for HCC patients.
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MESH Headings
- Animals
- Female
- Humans
- Male
- Mice
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Cell Line, Tumor
- Cell Proliferation/genetics
- Disease Progression
- Gene Expression Regulation, Neoplastic
- Liver Neoplasms/genetics
- Liver Neoplasms/pathology
- Liver Neoplasms/metabolism
- Mice, Inbred BALB C
- Mice, Nude
- Neovascularization, Pathologic/genetics
- Protein Serine-Threonine Kinases/genetics
- Protein Serine-Threonine Kinases/metabolism
- Retroelements/genetics
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- Serine-Arginine Splicing Factors/genetics
- Serine-Arginine Splicing Factors/metabolism
- Signal Transduction
- Terminal Repeat Sequences/genetics
- Vascular Endothelial Growth Factor A/genetics
- Vascular Endothelial Growth Factor A/metabolism
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Affiliation(s)
- Yangjun Wu
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jiajia Wang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jingjing Zhao
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yue Su
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xinrong Li
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhiao Chen
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
| | - Xiaohua Wu
- Department of Gynecologic Oncology, Fudan University Shanghai Cancer Center, Fudan University, Shanghai, China; Department of Oncology, Shanghai Medical College, Fudan University, Shanghai, China
| | - Shenglin Huang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China; Department of Integrative Oncology, Fudan University Shanghai Cancer Center, China
| | - Xianghuo He
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
| | - Linhui Liang
- Fudan University Shanghai Cancer Center and Institutes of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China.
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Wang B, Li J, Song Y, Qin X, Lu X, Huang W, Peng C, Wei J, Huang D, Wang W. CLK2 Condensates Reorganize Nuclear Speckles and Induce Intron Retention. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2309588. [PMID: 39119950 DOI: 10.1002/advs.202309588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 07/28/2024] [Indexed: 08/10/2024]
Abstract
Intron retention (IR) constitutes a less explored form of alternative splicing, wherein introns are retained within mature mRNA transcripts. This investigation demonstrates that the cell division cycle (CDC)-like kinase 2 (CLK2) undergoes liquid-liquid phase separation (LLPS) within nuclear speckles in response to heat shock (HS). The formation of CLK2 condensates depends on the intrinsically disordered region (IDR) located within the N-terminal amino acids 1-148. Phosphorylation at residue T343 sustains CLK2 kinase activity and promotes overall autophosphorylation, which inhibits the LLPS activity of the IDR. These CLK2 condensates initiate the reorganization of nuclear speckles, transforming them into larger, rounded structures. Moreover, these condensates facilitate the recruitment of splicing factors into these compartments, restricting their access to mRNA for intron splicing and promoting the IR. The retained introns lead to the sequestration of transcripts within the nucleus. These findings extend to the realm of glioma stem cells (GSCs), where a physiological state mirroring HS stress inhibits T343 autophosphorylation, thereby inducing the formation of CLK2 condensates and subsequent IR. Notably, expressing the CLK2 condensates hampers the maintenance of GSCs. In conclusion, this research unveils a mechanism by which IR is propelled by CLK2 condensates, shedding light on its role in coping with cellular stress.
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Affiliation(s)
- Bing Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Jing Li
- Department of Integrated Traditional Chinese and Western Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yanyang Song
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Xuhui Qin
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Xia Lu
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Wei Huang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Chentai Peng
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Jinxia Wei
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
| | - Donghui Huang
- Institute of Reproduction Health Research, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Wei Wang
- Department of Human Anatomy, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430070, China
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Wang A, Zeng Y, Zhang W, Zhao J, Gao L, Li J, Zhu J, Liu Z, Huang JA. N 6-methyladenosine-modified SRPK1 promotes aerobic glycolysis of lung adenocarcinoma via PKM splicing. Cell Mol Biol Lett 2024; 29:106. [PMID: 39095708 PMCID: PMC11295518 DOI: 10.1186/s11658-024-00622-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/17/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND The RNA N6-methyladenosine (m6A) modification has become an essential hotspot in epigenetic modulation. Serine-arginine protein kinase 1 (SRPK1) is associated with the pathogenesis of various cancers. However, the m6A modification of SRPK1 and its association with the mechanism of in lung adenocarcinoma (LUAD) remains unclear. METHODS Western blotting and polymerase chain reaction (PCR) analyses were carried out to identify gene and protein expression. m6A epitranscriptomic microarray was utilized to the assess m6A profile. Loss and gain-of-function assays were carried out elucidate the impact of METTL3 and SRPK1 on LUAD glycolysis and tumorigenesis. RNA immunoprecipitation (RIP), m6A RNA immunoprecipitation (MeRIP), and RNA stability tests were employed to elucidate the SRPK1's METTL3-mediated m6A modification mechanism in LUAD. Metabolic quantification and co-immunoprecipitation assays were applied to investigate the molecular mechanism by which SRPK1 mediates LUAD metabolism. RESULTS The epitranscriptomic microarray assay revealed that SRPK1 could be hypermethylated and upregulated in LUAD. The main transmethylase METTL3 was upregulated and induced the aberrant high m6A levels of SRPK1. Mechanistically, SRPK1's m6A sites were directly methylated by METTL3, which also stabilized SRPK1 in an IGF2BP2-dependent manner. Methylated SRPK1 subsequently promoted LUAD progression through enhancing glycolysis. Further metabolic quantification, co-immunoprecipitation and western blot assays revealed that SRPK1 interacts with hnRNPA1, an important modulator of PKM splicing, and thus facilitates glycolysis by upregulating PKM2 in LUAD. Nevertheless, METTL3 inhibitor STM2457 can reverse the above effects in vitro and in vivo by suppressing SRPK1 and glycolysis in LUAD. CONCLUSION It was revealed that in LUAD, aberrantly expressed METTL3 upregulated SRPK1 levels via an m6A-IGF2BP2-dependent mechanism. METTL3-induced SRPK1 fostered LUAD cell proliferation by enhancing glycolysis, and the small-molecule inhibitor STM2457 of METTL3 could be an alternative novel therapeutic strategy for individuals with LUAD.
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Affiliation(s)
- Anqi Wang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
| | - Yuanyuan Zeng
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
- Suzhou Key Laboratory for Respiratory Diseases, Suzhou, 215006, China
| | - Weijie Zhang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
| | - Jian Zhao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
| | - Lirong Gao
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
| | - Jianjun Li
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
- Suzhou Key Laboratory for Respiratory Diseases, Suzhou, 215006, China
| | - Jianjie Zhu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China
- Suzhou Key Laboratory for Respiratory Diseases, Suzhou, 215006, China
| | - Zeyi Liu
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China.
- Suzhou Key Laboratory for Respiratory Diseases, Suzhou, 215006, China.
| | - Jian-An Huang
- Department of Pulmonary and Critical Care Medicine, The First Affiliated Hospital of Soochow University, Suzhou, 215006, China.
- Institute of Respiratory Diseases, Soochow University, Suzhou, 215006, China.
- Suzhou Key Laboratory for Respiratory Diseases, Suzhou, 215006, China.
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5
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Roychaudhury A, Lee YR, Choi TI, Thomas MG, Khan TN, Yousaf H, Skinner C, Maconachie G, Crosier M, Horak H, Constantinescu CS, Kim TY, Lee KH, Kyung JJ, Wang T, Ku B, Chodirker BN, Hammer MF, Gottlob I, Norton WHJ, Gerlai R, Kim HG, Graziano C, Pippucci T, Iovino E, Montanari F, Severi G, Toro C, Boerkoel CF, Cha HS, Choi CY, Kim S, Yoon JH, Gilmore K, Vora NL, Davis EE, Chudley AE, Schwartz CE, Kim CH. SRPK3 Is Essential for Cognitive and Ocular Development in Humans and Zebrafish, Explaining X-Linked Intellectual Disability. Ann Neurol 2024. [PMID: 39073169 DOI: 10.1002/ana.27037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 07/30/2024]
Abstract
OBJECTIVE Intellectual disability is often the outcome of neurodevelopmental disorders and is characterized by significant impairments in intellectual and adaptive functioning. X-linked intellectual disability (XLID) is a subset of these disorders caused by genetic defects on the X chromosome, affecting about 2 out of 1,000 males. In syndromic form, it leads to a broad range of cognitive, behavioral, ocular, and physical disabilities. METHODS Employing exome or genome sequencing, here we identified 4 missense variants (c.475C > G; p.H159D, c.1373C > A; p.T458N, and c.1585G > A; p.E529K, c.953C > T; p.S318L) and a putative truncating variant (c.1413_1414del; p.Y471*) in the SRPK3 gene in 9 XLID patients from 5 unrelated families. To validate SRPK3 as a novel XLID gene, we established a knockout (KO) model of the SRPK3 orthologue in zebrafish. RESULTS The 8 patients ascertained postnatally shared common clinical features including intellectual disability, agenesis of the corpus callosum, abnormal eye movement, and ataxia. A ninth case, ascertained prenatally, had a complex structural brain phenotype. Together, these data indicate a pathological role of SRPK3 in neurodevelopmental disorders. In post-fertilization day 5 larvae (free swimming stage), KO zebrafish exhibited severe deficits in eye movement and swim bladder inflation, mimicking uncontrolled ocular movement and physical clumsiness observed in human patients. In adult KO zebrafish, cerebellar agenesis and behavioral abnormalities were observed, recapitulating human phenotypes of cerebellar atrophy and intellectual disability. INTERPRETATION Overall, these results suggest a crucial role of SRPK3 in the pathogenesis of syndromic X-linked intellectual disability and provide new insights into brain development, cognitive and ocular dysfunction in both humans and zebrafish. ANN NEUROL 2024.
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Affiliation(s)
| | - Yu-Ri Lee
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Mervyn G Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
| | - Tahir N Khan
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Hammad Yousaf
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Gail Maconachie
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
- Division of Ophthalmology and Orthoptics, Health Science School, University of Sheffield, Sheffield, UK
| | - Moira Crosier
- Human Developmental Biology Resource, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Holli Horak
- Department of Neurology, University of Arizona, Tucson, AZ, USA
| | - Cris S Constantinescu
- Academic Unit of Mental Health and Clinical Neuroscience, University of Nottingham, Nottingham, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ, USA
| | - Tae-Yoon Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Kang-Han Lee
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Jae-Jun Kyung
- Department of Biology, Chungnam National University, Daejeon, South Korea
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Bernard N Chodirker
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | | | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behavior, University of Leicester, Leicester, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ, USA
| | - William H J Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | - Robert Gerlai
- Department of Psychology, University of Toronto Mississauga, Mississauga, ON, Canada
| | - Hyung-Goo Kim
- Neurological Disorders Research Center, Qatar Biomedical Research Institute, Hamad Bin Khalifa University, Doha, Qatar
| | | | - Tommaso Pippucci
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Emanuela Iovino
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | | | - Giulia Severi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Bologna, Italy
| | - Camilo Toro
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Cornelius F Boerkoel
- NIH Undiagnosed Diseases Program, NIH Office of Rare Diseases Research and NHGRI, Bethesda, MD, USA
| | - Hyo Sun Cha
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Cheol Yong Choi
- Department of Biological Sciences, Sungkyunkwan University, Suwon, South Korea
| | - Sungjin Kim
- Department of Microbiology & Molecular Biology, Chungnam National University, Daejeon, South Korea
| | - Je-Hyun Yoon
- Department of Oncology Science, University of Oklahoma, Oklahoma City, OK, USA
| | - Kelly Gilmore
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Neeta L Vora
- Division of Maternal Fetal Medicine, Department of Ob/Gyn, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica E Davis
- Stanley Manne Children's Research Institute, Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
- Department of Pediatrics, Cell and Developmental Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Albert E Chudley
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Charles E Schwartz
- Greenwood Genetic Center, Greenwood, SC, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon, South Korea
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6
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Cai G, Bao Y, Li Q, Hsu PH, Xia J, Ngo JCK. Design of a covalent protein-protein interaction inhibitor of SRPKs to suppress angiogenesis and invasion of cancer cells. Commun Chem 2024; 7:144. [PMID: 38937565 PMCID: PMC11211491 DOI: 10.1038/s42004-024-01230-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 06/19/2024] [Indexed: 06/29/2024] Open
Abstract
Serine-arginine (SR) proteins are splicing factors that play essential roles in both constitutive and alternative pre-mRNA splicing. Phosphorylation of their C-terminal RS domains by SR protein kinases (SRPKs) regulates their localization and diverse cellular activities. Dysregulation of phosphorylation has been implicated in many human diseases, including cancers. Here, we report the development of a covalent protein-protein interaction inhibitor, C-DBS, that targets a lysine residue within the SRPK-specific docking groove to block the interaction and phosphorylation of the prototypic SR protein SRSF1. C-DBS exhibits high specificity and conjugation efficiency both in vitro and in cellulo. This self-cell-penetrating inhibitor attenuates the phosphorylation of endogenous SR proteins and subsequently inhibits the angiogenesis, migration, and invasion of cancer cells. These findings provide a new foundation for the development of covalent SRPK inhibitors for combatting diseases such as cancer and viral infections and overcoming the resistance encountered by ATP-competitive inhibitors.
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Affiliation(s)
- Gongli Cai
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Yishu Bao
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Qingyun Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
- College of Food Science and Engineering, Henan University of Technology, Zhengzhou, 450001, China
| | - Pang-Hung Hsu
- Department of Bioscience and Biotechnology, National Taiwan Ocean University, Keelung, Taiwan
- Center of Excellence for the Oceans, National Taiwan Ocean University, Keelung, Taiwan
- Institute of Biochemistry and Molecular Biology, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Jacky Chi Ki Ngo
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center of Novel Biomaterials, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
- Center for Protein Science and Crystallography, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China.
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7
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Lin P, Cao W, Chen X, Zhang N, Xing Y, Yang N. Role of mRNA-binding proteins in retinal neovascularization. Exp Eye Res 2024; 242:109870. [PMID: 38514023 DOI: 10.1016/j.exer.2024.109870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Revised: 03/06/2024] [Accepted: 03/18/2024] [Indexed: 03/23/2024]
Abstract
Retinal neovascularization (RNV) is a pathological process that primarily occurs in diabetic retinopathy, retinopathy of prematurity, and retinal vein occlusion. It is a common yet debilitating clinical condition that culminates in blindness. Urgent efforts are required to explore more efficient and less limiting therapeutic strategies. Key RNA-binding proteins (RBPs), crucial for post-transcriptional regulation of gene expression by binding to RNAs, are closely correlated with RNV development. RBP-RNA interactions are altered during RNV. Here, we briefly review the characteristics and functions of RBPs, and the mechanism of RNV. Then, we present insights into the role of the regulatory network of RBPs in RNV. HuR, eIF4E, LIN28B, SRSF1, METTL3, YTHDF1, Gal-1, HIWI1, and ZFR accelerate RNV progression, whereas YTHDF2 and hnRNPA2B1 hinder it. The mechanisms elucidated in this review provide a reference to guide the design of therapeutic strategies to reverse abnormal processes.
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Affiliation(s)
- Pei Lin
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Wenye Cao
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Xuemei Chen
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China; Department of Ophthalmology, Aier Eye Hospital of Wuhan University, Hubei, China.
| | - Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
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8
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Saini T, Gupta P, Raut R, Nayak V, Bharathnaveen P, Mishra P, Misra A. AR-V7 expression facilitates accelerated G2/M phase transition in castration-resistant prostate cancer. Exp Cell Res 2024; 438:114026. [PMID: 38604522 DOI: 10.1016/j.yexcr.2024.114026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/13/2024]
Abstract
The emergence of AR-V7, a truncated isoform of AR upon androgen deprivation therapy treatment, leads to the development of castration resistant prostate cancer (CRPC). Understanding mechanisms that regulate AR-V7 expression is critical for developing newer therapeutic strategies. In this study, we have investigated the regulation of AR-V7 during cell cycle and identified a distinct pattern of periodic fluctuation, peaking during G2/M phase. This fluctuation correlates with the expression of Cdc-2 like kinase 1 (CLK1) and phosphorylated serine/arginine-rich splicing factor 1 (p-SRSF1) during these phases, pointing towards their role in AR-V7 generation. Functional assays reveal that CLK1 knockdown prolongs the S phase, leading to altered cell cycle distribution and increased accumulation of AR-V7 and pSRSF1 in G1/S phase. Conversely, CLK1 overexpression rescues AR-V7 and p-SRSF1 levels in the G2/M phase, consistent with observed cell cycle alterations upon AR-V7 knockdown and overexpression in CRPC cells. Furthermore, overexpression of kinase-deficient CLK1 mutant leads to diminished AR-V7 levels during G2/M, underlining the essential contribution of CLK1's kinase activity in modulating AR-V7 expression. Collectively, our findings, for the first time, show periodic regulation of AR-V7 expression, its effect on cell cycle progression and the critical role of CLK1-pSRSF1 axis in modulating AR-V7 expression throughout the cell cycle.
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Affiliation(s)
- Taruna Saini
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Parth Gupta
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Rajnikant Raut
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Vinayak Nayak
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Pabbithi Bharathnaveen
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India
| | - Parul Mishra
- Department of Animal Biology, School of Life Sciences, University of Hyderabad, Hyderabad, 500046, India
| | - Ashish Misra
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Sangareddy, 502284, India.
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9
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Rahimian R, Guruswamy R, Boutej H, Cordeau P, Weng YC, Kriz J. Targeting SRSF3 restores immune mRNA translation in microglia/macrophages following cerebral ischemia. Mol Ther 2024; 32:783-799. [PMID: 38196192 PMCID: PMC10928149 DOI: 10.1016/j.ymthe.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 10/20/2023] [Accepted: 01/05/2024] [Indexed: 01/11/2024] Open
Abstract
We recently described a novel ribosome-based regulatory mechanism/checkpoint that controls innate immune gene translation and microglial activation in non-sterile inflammation orchestrated by RNA binding protein SRSF3. Here we describe a role of SRSF3 in the regulation of microglia/macrophage activation phenotypes after experimental stroke. Using a model-system for analysis of the dynamic translational state of microglial ribosomes we show that 24 h after stroke highly upregulated immune mRNAs are not translated resulting in a marked dissociation of mRNA and protein networks in activated microglia/macrophages. Next, microglial activation after stroke was characterized by a robust increase in pSRSF3/SRSF3 expression levels. Targeted knockdown of SRSF3 using intranasal delivery of siRNA 24 h after stroke caused a marked knockdown of endogenous protein. Further analyses revealed that treatment with SRSF3-siRNA alleviated translational arrest of selected genes and induced a transient but significant increase in innate immune signaling and IBA1+ immunoreactivity peaking 5 days after initial injury. Importantly, delayed SRSF3-mediated increase in immune signaling markedly reduced the size of ischemic lesion measured 7 days after stroke. Together, our findings suggest that targeting SRSF3 and immune mRNA translation may open new avenues for molecular/therapeutic reprogramming of innate immune response after ischemic injury.
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Affiliation(s)
- Reza Rahimian
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Université Laval, Québec, QC G1J 2G3, Canada
| | - Revathy Guruswamy
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Université Laval, Québec, QC G1J 2G3, Canada
| | - Hejer Boutej
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Université Laval, Québec, QC G1J 2G3, Canada
| | - Pierre Cordeau
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Université Laval, Québec, QC G1J 2G3, Canada
| | - Yuan Cheng Weng
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Université Laval, Québec, QC G1J 2G3, Canada
| | - Jasna Kriz
- CERVO Brain Research Centre and Department of Psychiatry and Neuroscience, Université Laval, Québec, QC G1J 2G3, Canada; Faculty of Medicine, Université Laval, Québec, QC G1J 2G3, Canada.
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10
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Varineau JE, Calo E. A common cellular response to broad splicing perturbations is characterized by metabolic transcript downregulation driven by the Mdm2-p53 axis. Dis Model Mech 2024; 17:dmm050356. [PMID: 38426258 PMCID: PMC10924232 DOI: 10.1242/dmm.050356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 01/09/2024] [Indexed: 03/02/2024] Open
Abstract
Disruptions in core cellular processes elicit stress responses that drive cell-state changes leading to organismal phenotypes. Perturbations in the splicing machinery cause widespread mis-splicing, resulting in p53-dependent cell-state changes that give rise to cell-type-specific phenotypes and disease. However, a unified framework for how cells respond to splicing perturbations, and how this response manifests itself in nuanced disease phenotypes, has yet to be established. Here, we show that a p53-stabilizing Mdm2 alternative splicing event and the resulting widespread downregulation of metabolic transcripts are common events that arise in response to various splicing perturbations in both cellular and organismal models. Together, our results classify a common cellular response to splicing perturbations, put forth a new mechanism behind the cell-type-specific phenotypes that arise when splicing is broadly disrupted, and lend insight into the pleiotropic nature of the effects of p53 stabilization in disease.
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Affiliation(s)
- Jade E. Varineau
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Eliezer Calo
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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11
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Liang X, Diao E, Qian S, Song H, Xiang X, Gou X, Hu X. Comparative metabolomic analysis and antigenicity comparison of cow milk and enzymatically treated cow milk. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024; 104:536-545. [PMID: 37621148 DOI: 10.1002/jsfa.12927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 08/09/2023] [Accepted: 08/25/2023] [Indexed: 08/26/2023]
Abstract
BACKGROUND Amino acids (AAs) are important protein building blocks that play a critical role in the function of the immune system. However, comprehensive comparative metabolomics and antigenicity analyses of cow milk (CM) and enzymatically treated CM are relatively scarce. This study analyzed the AAs in the CM and Flavourzyme-treated milk groups (FT), and their antigenicity was also explored. RESULTS Overall, 50 AAs were detected in the CM and FT groups, with 23 significantly different AAs. The interaction network of these significantly different AAs was analyzed, and 34 significantly different metabolic pathways were found to be involved. It was also found that the antigenicity of the FT group was significantly reduced in comparison with that of the CM group. CONCLUSION These results enhance our understanding of AAs and antigenicity regarding CM and FT, and provide new ideas and directions for the development of high-quality hypoallergenic dairy products. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Xiaona Liang
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Huaiyin Normal University, Huaian, China
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Enjie Diao
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Huaiyin Normal University, Huaian, China
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Shiquan Qian
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Huaiyin Normal University, Huaian, China
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Huwei Song
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Huaiyin Normal University, Huaian, China
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Xinran Xiang
- Jiangsu Collaborative Innovation Center of Regional Modern Agriculture & Environmental Protection, Huaiyin Normal University, Jiangsu Key Laboratory for Food Safety & Nutrition Function Evaluation, Huaiyin Normal University, Huaian, China
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Xiurong Gou
- School of Life Science, Huaiyin Normal University, Huaian, China
| | - Xiumin Hu
- School of Life Science, Huaiyin Normal University, Huaian, China
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12
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Wahid M, Pratoomthai B, Egbuniwe IU, Evans HR, Babaei-Jadidi R, Amartey JO, Erdelyi V, Yacqub-Usman K, Jackson AM, Morris JC, Patel PM, Bates DO. Targeting alternative splicing as a new cancer immunotherapy-phosphorylation of serine arginine-rich splicing factor (SRSF1) by SR protein kinase 1 (SRPK1) regulates alternative splicing of PD1 to generate a soluble antagonistic isoform that prevents T cell exhaustion. Cancer Immunol Immunother 2023; 72:4001-4014. [PMID: 37973660 PMCID: PMC10700477 DOI: 10.1007/s00262-023-03534-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 08/21/2023] [Indexed: 11/19/2023]
Abstract
BACKGROUND Regulation of alternative splicing is a new therapeutic approach in cancer. The programmed cell death receptor 1 (PD-1) is an immunoinhibitory receptor expressed on immune cells that binds to its ligands, PD-L1 and PD-L2 expressed by cancer cells forming a dominant immune checkpoint pathway in the tumour microenvironment. Targeting this pathway using blocking antibodies (nivolumab and pembrolizumab) is the mainstay of anti-cancer immunotherapies, restoring the function of exhausted T cells. PD-1 is alternatively spliced to form isoforms that are either transmembrane signalling receptors (flPD1) that mediate T cell death by binding to the ligand, PD-L1 or an alternatively spliced, soluble, variant that lacks the transmembrane domain. METHODS We used PCR and western blotting on primary peripheral blood mononuclear cells (PBMCs) and Jurkat T cells, IL-2 ELISA, flow cytometry, co-culture of melanoma and cholangiocarcinoma cells, and bioinformatics analysis and molecular cloning to examine the mechanism of splicing of PD1 and its consequence. RESULTS The soluble form of PD-1, generated by skipping exon 3 (∆Ex3PD1), was endogenously expressed in PBMCs and T cells and prevents cancer cell-mediated T cell repression. Multiple binding sites of SRSF1 are adjacent to PD-1 exon 3 splicing sites. Overexpression of phosphomimic SRSF1 resulted in preferential expression of flPD1. Inhibition of SRSF1 phosphorylation both by SRPK1 shRNA knockdown and by a selective inhibitor, SPHINX31, resulted in a switch in splicing to ∆Ex3PD1. Cholangiocarcinoma cell-mediated repression of T cell IL-2 expression was reversed by SPHINX31 (equivalent to pembrolizumab). CONCLUSIONS These results indicate that switching of the splicing decision from flPD1 to ∆Ex3PD1 by targeting SRPK1 could represent a potential novel mechanism of immune checkpoint inhibition in cancer.
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Affiliation(s)
- Mussarat Wahid
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Benjamart Pratoomthai
- Department of Basic Medical Science, Faculty of Medicine Vajira Hospital, Navamindradhiraj University, 681 Samsen Road, Dusit, 10300, Bangkok, Thailand
| | - Isioma U Egbuniwe
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Hannah R Evans
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Roya Babaei-Jadidi
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Jason O Amartey
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Viola Erdelyi
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Kiren Yacqub-Usman
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Andrew M Jackson
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - Jonathan C Morris
- School of Chemistry, University of New South Wales, Sydney, Australia
| | - Poulam M Patel
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK
| | - David O Bates
- Division of Cancer and Stem Cells, School of Medicine, Centre for Cancer Science, Biodiscovery Institute, University of Nottingham, Nottingham, NG2 7UH, UK.
- COMPARE University of Birmingham and University of Nottingham, Midlands, UK.
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13
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Luo SH, Tian JM, Chu Y, Zhu HY, Ni JD, Huang J. The BRD4-SRPK2-SRSF2 signal modulates the splicing efficiency of ACSL3 pre-mRNA and influences erastin-induced ferroptosis in osteosarcoma cells. Cell Death Dis 2023; 14:760. [PMID: 37993451 PMCID: PMC10665344 DOI: 10.1038/s41419-023-06273-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 10/25/2023] [Accepted: 11/06/2023] [Indexed: 11/24/2023]
Abstract
Lipid metabolism is the key to ferroptosis susceptibility. However, little is known about the underlying mechanisms in osteosarcoma cells. Functional restriction of bromodomain-containing protein 4 (BRD4) reduced the susceptibility to erastin-induced ferroptosis of osteosarcoma cells both in vitro and in vivo. Mechanically, BRD4 controls the splicing efficiency of the RNA precursor (pre-mACSL3) of ACSL3 (ACSL3) by recruiting serinerich/threonine protein kinase 2 (SRPK2) to assemble the splicing catalytic platform. Moreover, the AMP-binding domain of ACSL3 significantly influences arachidonic acid synthesis and thus determines the susceptibility to erastin-induced ferroptosis. Overall, we found a BRD4-mediated pre-mACSL3 splicing influences erastin-induced ferroptosis by affecting arachidonic acid synthesis in osteosarcoma cells. Data in this study fills some of the gap in understanding the post-transcriptional regulatory mechanisms of ACSL3 and provides new insights into the mechanisms of lipid metabolism regulation and its effect on susceptibility to ferroptosis in osteosarcoma cells.
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Affiliation(s)
- Shun-Hong Luo
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jia-Ming Tian
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yi Chu
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Hong-Yi Zhu
- Department of Gastroenterology, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiang-Dong Ni
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jun Huang
- Department of Orthopedics, The Second Xiangya Hospital, Central South University, Changsha, Hunan, China.
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14
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Yao X, Wang C, Yu W, Sun L, Lv Z, Xie X, Tian S, Yan L, Zhang H, Liu J. SRSF1 is essential for primary follicle development by regulating granulosa cell survival via mRNA alternative splicing. Cell Mol Life Sci 2023; 80:343. [PMID: 37907803 PMCID: PMC11072053 DOI: 10.1007/s00018-023-04979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 09/14/2023] [Accepted: 09/24/2023] [Indexed: 11/02/2023]
Abstract
Granulosa cell abnormalities are characteristics of premature ovarian insufficiency (POI). Abnormal expression of serine/arginine-rich splicing factor 1 (SRSF1) can cause various diseases, but the role of SRSF1 in mouse granulosa cells remains largely unclear. In this study, we found that SRSF1 was expressed in the nuclei of both mouse oocytes and granulosa cells. The specific knockout of Srsf1 in granulosa cells led to follicular development inhibition, decreased granulosa cell proliferation, and increased apoptosis. Gene Ontology (GO) analysis of RNA-seq results revealed abnormal expression of genes involved in DNA repair, cell killing and other signalling pathways. Alternative splicing (AS) analysis showed that SRSF1 affected DNA damage in granulosa cells by regulating genes related to DNA repair. In summary, SRSF1 in granulosa cells controls follicular development by regulating AS of genes associated with DNA repair, thereby affecting female reproduction.
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Affiliation(s)
- Xiaohong Yao
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Chaofan Wang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Weiran Yu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Longjie Sun
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Zheng Lv
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Xiaomei Xie
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Shuang Tian
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Lu Yan
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Hua Zhang
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - Jiali Liu
- State Key Laboratory of Animal Biotech Breeding, College of Biological Sciences, China Agricultural University, Beijing, 100193, China.
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15
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Dahal S, Clayton K, Cabral T, Cheng R, Jahanshahi S, Ahmed C, Koirala A, Villasmil Ocando A, Malty R, Been T, Hernandez J, Mangos M, Shen D, Babu M, Calarco J, Chabot B, Attisano L, Houry WA, Cochrane A. On a path toward a broad-spectrum anti-viral: inhibition of HIV-1 and coronavirus replication by SR kinase inhibitor harmine. J Virol 2023; 97:e0039623. [PMID: 37706687 PMCID: PMC10617549 DOI: 10.1128/jvi.00396-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/14/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE This study highlights the crucial role RNA processing plays in regulating viral gene expression and replication. By targeting SR kinases, we identified harmine as a potent inhibitor of HIV-1 as well as coronavirus (HCoV-229E and multiple SARS-CoV-2 variants) replication. Harmine inhibits HIV-1 protein expression and reduces accumulation of HIV-1 RNAs in both cell lines and primary CD4+ T cells. Harmine also suppresses coronavirus replication post-viral entry by preferentially reducing coronavirus sub-genomic RNA accumulation. By focusing on host factors rather than viral targets, our study offers a novel approach to combating viral infections that is effective against a range of unrelated viruses. Moreover, at doses required to inhibit virus replication, harmine had limited toxicity and minimal effect on the host transcriptome. These findings support the viability of targeting host cellular processes as a means of developing broad-spectrum anti-virals.
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Affiliation(s)
- Subha Dahal
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Kiera Clayton
- Department of Pathology, University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Tyler Cabral
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Ran Cheng
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Shahrzad Jahanshahi
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Choudhary Ahmed
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Amrit Koirala
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas, USA
- Dan L. Duncan Cancer Comprehensive Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Ramy Malty
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - Terek Been
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Javier Hernandez
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Maria Mangos
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - David Shen
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Mohan Babu
- Research and Innovation Centre, Department of Biochemistry, University of Regina, Regina, Saskatchewan, Canada
| | - John Calarco
- Department of Cell and Systems Biology, University of Toronto, Toronto, Ontario, Canada
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Liliana Attisano
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Walid A. Houry
- Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
- Department of Chemistry, University of Toronto, Toronto, Ontario, Canada
| | - Alan Cochrane
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
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16
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Hogg EKJ, Findlay GM. Functions of SRPK, CLK and DYRK kinases in stem cells, development, and human developmental disorders. FEBS Lett 2023; 597:2375-2415. [PMID: 37607329 PMCID: PMC10952393 DOI: 10.1002/1873-3468.14723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 07/08/2023] [Accepted: 07/18/2023] [Indexed: 08/24/2023]
Abstract
Human developmental disorders encompass a wide range of debilitating physical conditions and intellectual disabilities. Perturbation of protein kinase signalling underlies the development of some of these disorders. For example, disrupted SRPK signalling is associated with intellectual disabilities, and the gene dosage of DYRKs can dictate the pathology of disorders including Down's syndrome. Here, we review the emerging roles of the CMGC kinase families SRPK, CLK, DYRK, and sub-family HIPK during embryonic development and in developmental disorders. In particular, SRPK, CLK, and DYRK kinase families have key roles in developmental signalling and stem cell regulation, and can co-ordinate neuronal development and function. Genetic studies in model organisms reveal critical phenotypes including embryonic lethality, sterility, musculoskeletal errors, and most notably, altered neurological behaviours arising from defects of the neuroectoderm and altered neuronal signalling. Further unpicking the mechanisms of specific kinases using human stem cell models of neuronal differentiation and function will improve our understanding of human developmental disorders and may provide avenues for therapeutic strategies.
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Affiliation(s)
- Elizabeth K. J. Hogg
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeUK
| | - Greg M. Findlay
- The MRC Protein Phosphorylation and Ubiquitylation Unit, School of Life SciencesUniversity of DundeeUK
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17
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Li D, Yu W, Lai M. Targeting serine- and arginine-rich splicing factors to rectify aberrant alternative splicing. Drug Discov Today 2023; 28:103691. [PMID: 37385370 DOI: 10.1016/j.drudis.2023.103691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/30/2023] [Accepted: 06/21/2023] [Indexed: 07/01/2023]
Abstract
Serine- and arginine-rich splicing factors are pivotal modulators of constitutive splicing and alternative splicing that bind to the cis-acting elements in precursor mRNAs and facilitate the recruitment and assembly of the spliceosome. Meanwhile, SR proteins shuttle between the nucleus and cytoplasm with a broad implication in multiple RNA-metabolizing events. Recent studies have demonstrated the positive correlation of overexpression and/or hyperactivation of SR proteins and development of the tumorous phenotype, indicating the therapeutic potentials of targeting SR proteins. In this review, we highlight key findings concerning the physiological and pathological roles of SR proteins. We have also investigated small molecules and oligonucleotides that effectively modulate the functions of SR proteins, which could benefit future studies of SR proteins.
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Affiliation(s)
- Dianyang Li
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China.
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China.
| | - Maode Lai
- Department of Pharmacology, China Pharmaceutical University, Nanjing 210009, China; Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Science (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, Zhejiang, China.
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18
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Li D, Yu W, Lai M. Towards understandings of serine/arginine-rich splicing factors. Acta Pharm Sin B 2023; 13:3181-3207. [PMID: 37655328 PMCID: PMC10465970 DOI: 10.1016/j.apsb.2023.05.022] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 04/13/2023] [Accepted: 05/06/2023] [Indexed: 09/02/2023] Open
Abstract
Serine/arginine-rich splicing factors (SRSFs) refer to twelve RNA-binding proteins which regulate splice site recognition and spliceosome assembly during precursor messenger RNA splicing. SRSFs also participate in other RNA metabolic events, such as transcription, translation and nonsense-mediated decay, during their shuttling between nucleus and cytoplasm, making them indispensable for genome diversity and cellular activity. Of note, aberrant SRSF expression and/or mutations elicit fallacies in gene splicing, leading to the generation of pathogenic gene and protein isoforms, which highlights the therapeutic potential of targeting SRSF to treat diseases. In this review, we updated current understanding of SRSF structures and functions in RNA metabolism. Next, we analyzed SRSF-induced aberrant gene expression and their pathogenic outcomes in cancers and non-tumor diseases. The development of some well-characterized SRSF inhibitors was discussed in detail. We hope this review will contribute to future studies of SRSF functions and drug development targeting SRSFs.
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Affiliation(s)
- Dianyang Li
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
| | - Wenying Yu
- State Key Laboratory of Natural Medicines, China Pharmaceutical University, Nanjing 210009, China
| | - Maode Lai
- School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing 210009, China
- Department of Pathology, Research Unit of Intelligence Classification of Tumor Pathology and Precision Therapy, Chinese Academy of Medical Science (2019RU042), Key Laboratory of Disease Proteomics of Zhejiang Province, Zhejiang University School of Medicine, Hangzhou 310058, China
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19
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Chowdhury I, Dashi G, Keskitalo S. CMGC Kinases in Health and Cancer. Cancers (Basel) 2023; 15:3838. [PMID: 37568654 PMCID: PMC10417348 DOI: 10.3390/cancers15153838] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 07/18/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
CMGC kinases, encompassing cyclin-dependent kinases (CDKs), mitogen-activated protein kinases (MAPKs), glycogen synthase kinases (GSKs), and CDC-like kinases (CLKs), play pivotal roles in cellular signaling pathways, including cell cycle regulation, proliferation, differentiation, apoptosis, and gene expression regulation. The dysregulation and aberrant activation of these kinases have been implicated in cancer development and progression, making them attractive therapeutic targets. In recent years, kinase inhibitors targeting CMGC kinases, such as CDK4/6 inhibitors and BRAF/MEK inhibitors, have demonstrated clinical success in treating specific cancer types. However, challenges remain, including resistance to kinase inhibitors, off-target effects, and the need for better patient stratification. This review provides a comprehensive overview of the importance of CMGC kinases in cancer biology, their involvement in cellular signaling pathways, protein-protein interactions, and the current state of kinase inhibitors targeting these kinases. Furthermore, we discuss the challenges and future perspectives in targeting CMGC kinases for cancer therapy, including potential strategies to overcome resistance, the development of more selective inhibitors, and novel therapeutic approaches, such as targeting protein-protein interactions, exploiting synthetic lethality, and the evolution of omics in the study of the human kinome. As our understanding of the molecular mechanisms and protein-protein interactions involving CMGC kinases expands, so too will the opportunities for the development of more selective and effective therapeutic strategies for cancer treatment.
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Affiliation(s)
- Iftekhar Chowdhury
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Giovanna Dashi
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, 00014 Helsinki, Finland; (I.C.)
- Helsinki Institute of Life Science, University of Helsinki, 00014 Helsinki, Finland
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20
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Sandoval-Castellanos AM, Bhargava A, Zhao M, Xu J, Ning K. Serine and arginine rich splicing factor 1: a potential target for neuroprotection and other diseases. Neural Regen Res 2023; 18:1411-1416. [PMID: 36571335 PMCID: PMC10075106 DOI: 10.4103/1673-5374.360243] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Alternative splicing is the process of producing variably spliced mRNAs by choosing distinct combinations of splice sites within a messenger RNA precursor. This splicing enables mRNA from a single gene to synthesize different proteins, which have different cellular properties and functions and yet arise from the same single gene. A family of splicing factors, Serine-arginine rich proteins, are needed to initiate the assembly and activation of the spliceosome. Serine and arginine rich splicing factor 1, part of the arginine/serine-rich splicing factor protein family, can either activate or inhibit the splicing of mRNAs, depending on the phosphorylation status of the protein and its interaction partners. Considering that serine and arginine rich splicing factor 1 is either an activator or an inhibitor, this protein has been studied widely to identify its various roles in different diseases. Research has found that serine and arginine rich splicing factor 1 is a key target for neuroprotection, showing its promising potential use in therapeutics for neurodegenerative disorders. Furthermore, serine and arginine rich splicing factor 1 might be used to regulate cancer development and autoimmune diseases. In this review, we highlight how serine and arginine rich splicing factor 1 has been studied concerning neuroprotection. In addition, we draw attention to how serine and arginine rich splicing factor 1 is being studied in cancer and immunological disorders, as well as how serine and arginine rich splicing factor 1 acts outside the central or peripheral nervous system.
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Affiliation(s)
- Ana M Sandoval-Castellanos
- Sheffield Institute of Translational Neuroscience, SITraN, The University of Sheffield, Sheffield, UK; Department of Ophthalmology & Vision Science, and Department of Dermatology, Institute for Regenerative Cures, University of California at Davis, School of Medicine, Sacramento, CA, USA
| | - Anushka Bhargava
- Sheffield Institute of Translational Neuroscience, SITraN, The University of Sheffield, Sheffield, UK
| | - Min Zhao
- Department of Ophthalmology & Vision Science, and Department of Dermatology, Institute for Regenerative Cures, University of California at Davis, School of Medicine, Sacramento, CA, USA
| | - Jun Xu
- East Hospital, Tongji University School of Medicine, Shanghai, China
| | - Ke Ning
- Sheffield Institute of Translational Neuroscience, SITraN, The University of Sheffield, Sheffield, UK; East Hospital, Tongji University School of Medicine, Shanghai, China
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21
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Piazzi M, Bavelloni A, Salucci S, Faenza I, Blalock WL. Alternative Splicing, RNA Editing, and the Current Limits of Next Generation Sequencing. Genes (Basel) 2023; 14:1386. [PMID: 37510291 PMCID: PMC10379330 DOI: 10.3390/genes14071386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 06/27/2023] [Accepted: 06/28/2023] [Indexed: 07/30/2023] Open
Abstract
The advent of next generation sequencing (NGS) has fostered a shift in basic analytic strategies of a gene expression analysis in diverse pathologies for the purposes of research, pharmacology, and personalized medicine. What was once highly focused research on individual signaling pathways or pathway members has, from the time of gene expression arrays, become a global analysis of gene expression that has aided in identifying novel pathway interactions, the discovery of new therapeutic targets, and the establishment of disease-associated profiles for assessing progression, stratification, or a therapeutic response. But there are significant caveats to this analysis that do not allow for the construction of the full picture. The lack of timely updates to publicly available databases and the "hit and miss" deposition of scientific data to these databases relegate a large amount of potentially important data to "garbage", begging the question, "how much are we really missing?" This brief perspective aims to highlight some of the limitations that RNA binding/modifying proteins and RNA processing impose on our current usage of NGS technologies as relating to cancer and how not fully appreciating the limitations of current NGS technology may negatively affect therapeutic strategies in the long run.
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Affiliation(s)
- Manuela Piazzi
- "Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Alberto Bavelloni
- Laboratorio di Oncologia Sperimentale, IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
| | - Sara Salucci
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, 40126 Bologna, Italy
| | - Irene Faenza
- Dipartimento di Scienze Biomediche e Neuromotorie (DIBINEM), Università di Bologna, 40126 Bologna, Italy
| | - William L Blalock
- "Luigi Luca Cavalli-Sforza" Istituto di Genetica Molecolare, Consiglio Nazionale delle Ricerche (IGM-CNR), 40136 Bologna, Italy
- IRCCS, Istituto Ortopedico Rizzoli, 40136 Bologna, Italy
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22
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Zheng K, Ren Z, Wang Y. Serine-arginine protein kinases and their targets in viral infection and their inhibition. Cell Mol Life Sci 2023; 80:153. [PMID: 37198350 PMCID: PMC10191411 DOI: 10.1007/s00018-023-04808-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/10/2023] [Accepted: 05/12/2023] [Indexed: 05/19/2023]
Abstract
Accumulating evidence has consolidated the interaction between viral infection and host alternative splicing. Serine-arginine (SR) proteins are a class of highly conserved splicing factors critical for the spliceosome maturation, alternative splicing and RNA metabolism. Serine-arginine protein kinases (SRPKs) are important kinases that specifically phosphorylate SR proteins to regulate their distribution and activities in the central pre-mRNA splicing and other cellular processes. In addition to the predominant SR proteins, other cytoplasmic proteins containing a serine-arginine repeat domain, including viral proteins, have been identified as substrates of SRPKs. Viral infection triggers a myriad of cellular events in the host and it is therefore not surprising that viruses explore SRPKs-mediated phosphorylation as an important regulatory node in virus-host interactions. In this review, we briefly summarize the regulation and biological function of SRPKs, highlighting their involvement in the infection process of several viruses, such as viral replication, transcription and capsid assembly. In addition, we review the structure-function relationships of currently available inhibitors of SRPKs and discuss their putative use as antivirals against well-characterized viruses or newly emerging viruses. We also highlight the viral proteins and cellular substrates targeted by SRPKs as potential antiviral therapeutic candidates.
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Affiliation(s)
- Kai Zheng
- School of Pharmacy, Shenzhen University Medical School, Shenzhen, 518055, China.
| | - Zhe Ren
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
| | - Yifei Wang
- Institute of Biomedicine, College of Life Science and Technology, Guangdong Province Key Laboratory of Bioengineering Medicine, Key Laboratory of Innovative Technology Research On Natural Products and Cosmetics Raw Materials, Jinan University, Guangzhou, 510632, China
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23
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Luther CH, Brandt P, Vylkova S, Dandekar T, Müller T, Dittrich M. Integrated analysis of SR-like protein kinases Sky1 and Sky2 links signaling networks with transcriptional regulation in Candida albicans. Front Cell Infect Microbiol 2023; 13:1108235. [PMID: 37082713 PMCID: PMC10111165 DOI: 10.3389/fcimb.2023.1108235] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 03/01/2023] [Indexed: 04/07/2023] Open
Abstract
Fungal infections are a major global health burden where Candida albicans is among the most common fungal pathogen in humans and is a common cause of invasive candidiasis. Fungal phenotypes, such as those related to morphology, proliferation and virulence are mainly driven by gene expression, which is primarily regulated by kinase signaling cascades. Serine-arginine (SR) protein kinases are highly conserved among eukaryotes and are involved in major transcriptional processes in human and S. cerevisiae. Candida albicans harbors two SR protein kinases, while Sky2 is important for metabolic adaptation, Sky1 has similar functions as in S. cerevisiae. To investigate the role of these SR kinases for the regulation of transcriptional responses in C. albicans, we performed RNA sequencing of sky1Δ and sky2Δ and integrated a comprehensive phosphoproteome dataset of these mutants. Using a Systems Biology approach, we study transcriptional regulation in the context of kinase signaling networks. Transcriptomic enrichment analysis indicates that pathways involved in the regulation of gene expression are downregulated and mitochondrial processes are upregulated in sky1Δ. In sky2Δ, primarily metabolic processes are affected, especially for arginine, and we observed that arginine-induced hyphae formation is impaired in sky2Δ. In addition, our analysis identifies several transcription factors as potential drivers of the transcriptional response. Among these, a core set is shared between both kinase knockouts, but it appears to regulate different subsets of target genes. To elucidate these diverse regulatory patterns, we created network modules by integrating the data of site-specific protein phosphorylation and gene expression with kinase-substrate predictions and protein-protein interactions. These integrated signaling modules reveal shared parts but also highlight specific patterns characteristic for each kinase. Interestingly, the modules contain many proteins involved in fungal morphogenesis and stress response. Accordingly, experimental phenotyping shows a higher resistance to Hygromycin B for sky1Δ. Thus, our study demonstrates that a combination of computational approaches with integration of experimental data can offer a new systems biological perspective on the complex network of signaling and transcription. With that, the investigation of the interface between signaling and transcriptional regulation in C. albicans provides a deeper insight into how cellular mechanisms can shape the phenotype.
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Affiliation(s)
- Christian H. Luther
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Philipp Brandt
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Slavena Vylkova
- Septomics Research Center, Friedrich Schiller University and Leibniz Institute for Natural Product Research and Infection Biology – Hans Knöll Institute, Jena, Germany
| | - Thomas Dandekar
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Tobias Müller
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
| | - Marcus Dittrich
- University of Würzburg, Department of Bioinformatics, Biocenter/Am Hubland 97074, Würzburg, Germany
- University of Würzburg, Institut of Human Genetics, Biocenter/Am Hubland 97074, Würzburg, Germany
- *Correspondence: Marcus Dittrich,
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24
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Lee YR, Thomas MG, Roychaudhury A, Skinner C, Maconachie G, Crosier M, Horak H, Constantinescu CS, Choi TI, Kyung JJ, Wang T, Ku B, Chodirker BN, Hammer MF, Gottlob I, Norton WHJ, Chudley AE, Schwartz CE, Kim CH. Eye movement defects in KO zebrafish reveals SRPK3 as a causative gene for an X-linked intellectual disability. RESEARCH SQUARE 2023:rs.3.rs-2683050. [PMID: 36993381 PMCID: PMC10055661 DOI: 10.21203/rs.3.rs-2683050/v1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/31/2023]
Abstract
Intellectual disability (ID) is a common neurodevelopmental disorder characterized by significantly impaired intellectual and adaptive functioning. X-linked ID (XLID) disorders, caused by defects in genes on the X chromosome, affect 1.7 out of 1,000 males. Employing exome sequencing, we identified three missense mutations (c.475C>G; p.H159D, c.1373C>A; p.T458N, and c.1585G>A; p.E529K) in the SRPK3 gene in seven XLID patients from three independent families. Clinical features common to the patients are intellectual disability, agenesis of the corpus callosum, abnormal smooth pursuit eye movement, and ataxia. SRPK proteins are known to be involved in mRNA processing and, recently, synaptic vesicle and neurotransmitter release. In order to validate SRPK3 as a novel XLID gene, we established a knockout (KO) model of the SRPK3 orthologue in zebrafish. In day 5 of larval stage, KO zebrafish showed significant defects in spontaneous eye movement and swim bladder inflation. In adult KO zebrafish, we found agenesis of cerebellar structures and impairments in social interaction. These results suggest an important role of SRPK3 in eye movements, which might reflect learning problems, intellectual disability, and other psychiatric disorders.
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Affiliation(s)
- Yu-Ri Lee
- Department of Biology, Chungnam National University, Daejeon 34134, South Korea
- KM Convergence Research Division, Korea Institute of Oriental Medicine, Daejeon 34054, South Korea
- These authors contributed equally: Yu-Ri Lee, Mervyn G. Thomas, Arkaprava Roychaudhury
| | - Mervyn G. Thomas
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- These authors contributed equally: Yu-Ri Lee, Mervyn G. Thomas, Arkaprava Roychaudhury
| | - Arkaprava Roychaudhury
- Department of Biology, Chungnam National University, Daejeon 34134, South Korea
- These authors contributed equally: Yu-Ri Lee, Mervyn G. Thomas, Arkaprava Roychaudhury
| | | | - Gail Maconachie
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- Division of Ophthalmology and Orthoptics, Health Science School, University of Sheffield, UK
| | - Moira Crosier
- Human Developmental Biology Resource, Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne NE1 4EP, UK
| | - Holli Horak
- Department of Neurology, University of Arizona, Tucson, AZ 85724, USA
| | - Cris S. Constantinescu
- Academic Unit of Mental Health and Clinical Neuroscience, University of Nottingham, NG7 2UH, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ 08013, USA
| | - Tae-Ik Choi
- Department of Biology, Chungnam National University, Daejeon 34134, South Korea
| | - Jae-Jun Kyung
- Department of Biology, Chungnam National University, Daejeon 34134, South Korea
| | - Tao Wang
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Bonsu Ku
- Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, South Korea
| | - Bernard N Chodirker
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
| | | | - Irene Gottlob
- The University of Leicester Ulverscroft Eye Unit, Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, UK
- Cooper Neurological Institute and Cooper Medical School of Rowan University, Camden, NJ 08013, USA
| | - William H. J. Norton
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Albert E. Chudley
- Department of Pediatrics and Child Health, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba R3A 1R9, Canada
| | - Charles E. Schwartz
- Greenwood Genetic Center, Greenwood, SC 29646, USA
- Department of Pediatrics and Human Development, College of Human Medicine, Michigan State University, Grand Rapids, MI 49503, USA
| | - Cheol-Hee Kim
- Department of Biology, Chungnam National University, Daejeon 34134, South Korea
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25
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Mercier J, Nagengast AA, DiAngelo JR. The role of SR protein kinases in regulating lipid storage in the Drosophila fat body. Biochem Biophys Res Commun 2023; 649:10-15. [PMID: 36738578 DOI: 10.1016/j.bbrc.2023.01.093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/28/2023] [Indexed: 01/31/2023]
Abstract
The survival of animals during periods of limited nutrients is dependent on the organism's ability to store lipids during times of nutrient abundance. However, the increased availability of food in modern western society has led to an excess storage of lipids resulting in metabolic diseases. To better understand the genes involved in regulating lipid storage, genome-wide RNAi screens were performed in cultured Drosophila cells and one group of genes identified includes mRNA splicing factor genes. Our lab has previously shown that a group of splicing factors important for intron/exon border recognition known as SR proteins are involved in controlling lipid storage in Drosophila; however, how these SR proteins are regulated to control lipid storage is not fully understood. Here, we focus on two SR protein kinases (SRPKs) in Drosophila: SRPK and SRPK79D. Decreasing the expression of these genes specifically in the adult fat body using RNAi resulted in lower levels of triglycerides and this is due to a decrease in the amount of fat stored per cell, despite having more fat cells, when compared to control flies. Decreasing SRPK and SRPK79D levels in the fat body leads to altered splicing of the β-oxidation gene, carnitine palmitoyltransferase 1 (CPT1), resulting in increased production of a more active enzyme, which would increase lipid breakdown and be consistent with the lean phenotype observed in these flies. In addition, flies with decreased SRPK and SRPK79D levels in their fat bodies eat less, which may also contribute to the decreased triglyceride phenotype. Together, these findings provide evidence to support that lipid storage is controlled by the phosphorylation of factors involved in mRNA splicing.
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Affiliation(s)
| | - Alexis A Nagengast
- Departments of Chemistry and Biochemistry, Widener University, Chester, PA, USA.
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26
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Zhang N, Lv F, Qiu F, Han D, Xu Y, Liang W. Pathogenic fungi neutralize plant-derived ROS via Srpk1 deacetylation. EMBO J 2023; 42:e112634. [PMID: 36891678 PMCID: PMC10152141 DOI: 10.15252/embj.2022112634] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 02/06/2023] [Accepted: 02/20/2023] [Indexed: 03/10/2023] Open
Abstract
In response to infection, plants can induce the production of reactive oxygen species (ROS) to restrict pathogen invasion. In turn, adapted pathogens have evolved a counteracting mechanism of enzymatic ROS detoxification, but how it is activated remains elusive. Here, we show that in the tomato vascular wilt pathogen Fusarium oxysporum f. sp. lycopersici (Fol) this process is initiated by deacetylation of the FolSrpk1 kinase. Upon ROS exposure, Fol decreases FolSrpk1 acetylation on the K304 residue by altering the expression of the acetylation-controlling enzymes. Deacetylated FolSrpk1 disassociates from the cytoplasmic FolAha1 protein, thus enabling its nuclear translocation. Increased accumulation of FolSrpk1 in the nucleus allows for hyperphosphorylation of its phosphorylation target FolSr1 that subsequently enhances transcription of different types of antioxidant enzymes. Secretion of these enzymes removes plant-produced H2 O2 , and enables successful Fol invasion. Deacetylation of FolSrpk1 homologs has a similar function in Botrytis cinerea and likely other fungal pathogens. These findings reveal a conserved mechanism for initiation of ROS detoxification upon plant fungal infection.
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Affiliation(s)
- Ning Zhang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Fangjiao Lv
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Fahui Qiu
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Dehai Han
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Yang Xu
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
| | - Wenxing Liang
- College of Plant Health and Medicine, Engineering Research Center for Precision Pest Management for Fruits and Vegetables of Qingdao, Shandong Engineering Research Center for Environment-Friendly Agricultural Pest Management, Shandong Province Key Laboratory of Applied Mycology, Qingdao Agricultural University, Qingdao, China
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27
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Pimentel DC, Leopoldo JR, Teixeira LF, Barros MVDA, de Souza APM, Onofre TS, de Carvalho RL, Machado SA, Messias IG, Pinto CCDS, Poleto MD, Diogo MA, Mariotini-Moura C, Bressan GC, Teixeira RR, Fietto JLR, Vasconcellos RDS. First evidence of a serine arginine protein kinase (SRPK) in leishmania braziliensis and its potential as therapeutic target. Acta Trop 2023; 238:106801. [PMID: 36563831 DOI: 10.1016/j.actatropica.2022.106801] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Revised: 12/17/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022]
Abstract
Leishmaniasis is a parasitic disease found in tropical and subtropical regions around the world, caused by parasites of the genus Leishmania. The disease is a public health concern and presents clinical manifestations that can cause death, disability, and mutilation. The parasite has promastigote (vector) and amastigote (vertebrate host) forms and kinase enzymes are involved in this differentiation process. In the present investigation, we show, for the first time, evidence of a serine/arginine protein kinase in Leshmania braziliensis (LbSRPK). Our results show that amastigotes express more LbSRPK than promastigotes. Analogues of SRPIN340 (a known inhibitor of SRPK) were evaluated for their leishmanicidal activity and two of them, namely SRVIC22 and SRVIC32 showed important leishmanicidal activity in vitro. SRVIC22 and SRVIC32 were able to reduce the infection rate in macrophages and the number of intracellular amastigotes by 55 and 60%, respectively. Bioinformatics analysis revealed the existence of two different amino acid residues in the active site of LbSRPK compared to their human homologue (Tyr/Leu-and Ser/Tyr), which could explain the absence of leishmanicidal activity of SRPIN340 on infected macrophages. In order to enhance leishmanicidal activity of the analogues, optimizations were proposed in the structures of the ligands, suggesting strong interactions with the catalytic site of LbSRPK. Although the evidence on the action of inhibitors upon LbSRPK is only indirect, our studies not only reveal, for the first time, evidence of a SRPK in Leishmania, but also shed light on a new therapeutic target for drug development.
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Affiliation(s)
- Débora Cristina Pimentel
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Juliana Rodrigues Leopoldo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Leilane Ferreira Teixeira
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Marcus Vinícius de Andrade Barros
- Departamento de Química, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Ana Paula Martins de Souza
- Departamento de Química, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Thiago Souza Onofre
- Department of Microbiology and Molecular Genetics, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Rayane Luiza de Carvalho
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Sara Andrade Machado
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Isabelly Gonçalves Messias
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Carla Cristina de Souza Pinto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Marcelo Depolo Poleto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Marcel Arruda Diogo
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Christiane Mariotini-Moura
- FAMINAS Muriaé, Bairro Universitário Muriaé, Av. Cristiano Ferreira Varella, 655, CEP, MG 36888-233, Brazil
| | - Gustavo Costa Bressan
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Robson Ricardo Teixeira
- Departamento de Química, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Juliana Lopes Rangel Fietto
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil
| | - Raphael de Souza Vasconcellos
- Departamento de Bioquímica e Biologia Molecular, Universidade Federal de Viçosa, Av. P. H. Rolfs, s/n, Campus Universitário, CEP, Viçosa, MG 36570-900, Brazil.
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Wodi C, Belali T, Morse R, Porazinski S, Ladomery M. SPHINX-Based Combination Therapy as a Potential Novel Treatment Strategy for Acute Myeloid Leukaemia. Br J Biomed Sci 2023; 80:11041. [PMID: 36895328 PMCID: PMC9988938 DOI: 10.3389/bjbs.2023.11041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 02/08/2023] [Indexed: 02/23/2023]
Abstract
Introduction: Dysregulated alternative splicing is a prominent feature of cancer. The inhibition and knockdown of the SR splice factor kinase SRPK1 reduces tumour growth in vivo. As a result several SPRK1 inhibitors are in development including SPHINX, a 3-(trifluoromethyl)anilide scaffold. The objective of this study was to treat two leukaemic cell lines with SPHINX in combination with the established cancer drugs azacitidine and imatinib. Materials and Methods: We selected two representative cell lines; Kasumi-1, acute myeloid leukaemia, and K562, BCR-ABL positive chronic myeloid leukaemia. Cells were treated with SPHINX concentrations up to 10μM, and in combination with azacitidine (up to 1.5 μg/ml, Kasumi-1 cells) and imatinib (up to 20 μg/ml, K562 cells). Cell viability was determined by counting the proportion of live cells and those undergoing apoptosis through the detection of activated caspase 3/7. SRPK1 was knocked down with siRNA to confirm SPHINX results. Results: The effects of SPHINX were first confirmed by observing reduced levels of phosphorylated SR proteins. SPHINX significantly reduced cell viability and increased apoptosis in Kasumi-1 cells, but less prominently in K562 cells. Knockdown of SRPK1 by RNA interference similarly reduced cell viability. Combining SPHINX with azacitidine augmented the effect of azacitidine in Kasumi-1 cells. In conclusion, SPHINX reduces cell viability and increases apoptosis in the acute myeloid leukaemia cell line Kasumi-1, but less convincingly in the chronic myeloid leukaemia cell line K562. Conclusion: We suggest that specific types of leukaemia may present an opportunity for the development of SRPK1-targeted therapies to be used in combination with established chemotherapeutic drugs.
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Affiliation(s)
- Chigeru Wodi
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Tareg Belali
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Ruth Morse
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
| | - Sean Porazinski
- Garvan Institute of Medical Research, Darlinghurst, NSW, Australia.,St Vincent's Clinical School, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Michael Ladomery
- Centre for Research in Bioscience, Faculty of Health and Applied Sciences, University of the West of England, Bristol, United Kingdom
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Shi W, Yang J, Chen D, Yin C, Zhang H, Xu X, Pan X, Wang R, Fei L, Li M, Qi L, Bhadauria V, Liu J, Peng YL. The rice blast fungus SR protein 1 regulates alternative splicing with unique mechanisms. PLoS Pathog 2022; 18:e1011036. [PMID: 36480554 PMCID: PMC9767378 DOI: 10.1371/journal.ppat.1011036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 12/20/2022] [Accepted: 11/30/2022] [Indexed: 12/13/2022] Open
Abstract
Serine/arginine-rich (SR) proteins are well known as splicing factors in humans, model animals and plants. However, they are largely unknown in regulating pre-mRNA splicing of filamentous fungi. Here we report that the SR protein MoSrp1 enhances and suppresses alternative splicing in a model fungal plant pathogen Magnaporthe oryzae. Deletion of MoSRP1 caused multiple defects, including reduced virulence and thousands of aberrant alternative splicing events in mycelia, most of which were suppressed or enhanced intron splicing. A GUAG consensus bound by MoSrp1 was identified in more than 94% of the intron or/and proximate exons having the aberrant splicing. The dual functions of regulating alternative splicing of MoSrp1 were exemplified in enhancing and suppressing the consensus-mediated efficient splicing of the introns in MoATF1 and MoMTP1, respectively, which both were important for mycelial growth, conidiation, and virulence. Interestingly, MoSrp1 had a conserved sumoylation site that was essential to nuclear localization and enhancing GUAG binding. Further, we showed that MoSrp1 interacted with a splicing factor and two components of the exon-joining complex via its N-terminal RNA recognition domain, which was required to regulate mycelial growth, development and virulence. In contrast, the C-terminus was important only for virulence and stress responses but not for mycelial growth and development. In addition, only orthologues from Pezizomycotina species could completely rescue defects of the deletion mutants. This study reveals that the fungal conserved SR protein Srp1 regulates alternative splicing in a unique manner.
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Affiliation(s)
- Wei Shi
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Jun Yang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Deng Chen
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Changfa Yin
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Huixia Zhang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiaozhou Xu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Xiao Pan
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Ruijin Wang
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- MARA Key Laboratory of Surveillance and Management for Plant Quarantine Pests, Department of Plant Biosecurity, College of Plant Protection, China Agricultural University, Beijing, China
| | - Liwang Fei
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Mengfei Li
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Linlu Qi
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Vijai Bhadauria
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - Junfeng Liu
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
| | - You-Liang Peng
- State Key Laboratory of Agrobiotechnology, China Agricultural University, Beijing, China
- MARA Key Laboratory of Pest Monitoring and Green Management, Department of Plant Pathology, College of Plant Protection, China Agricultural University, Beijing, China
- * E-mail:
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Aubol BE, Adams JA. SRPK1 regulates RNA binding in a pre-spliceosomal complex using a catalytic bypass mechanism. FEBS J 2022; 289:7428-7445. [PMID: 35730996 DOI: 10.1111/febs.16560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 05/10/2022] [Accepted: 06/21/2022] [Indexed: 01/14/2023]
Abstract
Serine-arginine protein kinase 1 (SRPK1) phosphorylates serine-arginine (SR) proteins in the cytoplasm, directing them to the nucleus for splicing function. SRPK1 has also been detected in the nucleus but its function here is still not fully understood. We now demonstrate that nuclear SRPK1 can regulate U1-70K, a protein component of the uridine-rich 1 small nuclear ribonucleoprotein (U1 snRNP) that binds SR proteins and facilitates 5' splice-site selection in precursor mRNA. We found that SRPK1 uses a large, disordered domain to bind U1-70K, regulating the interaction of an exonic splicing enhancer (ESE) to the associated SR protein. Surprisingly, the catalytic activity of SRPK1 is not required for this phenomenon. Instead, SRPK1 associates directly with the N-terminus of U1-70K and alters the regulatory function of the distal C-terminus, modifying interactions between the U1-70K:SR protein complex and the ESE. Disruption of SRPK1 binding to this complex affects the alternative splicing of genes modulated by the C-terminus of U1-70K. Such findings suggest that, in addition to operating as a traditional serine-modifying catalyst, SRPK1 can also bypass this intrinsic activity to regulate RNA contacts in an early pre-spliceosomal complex.
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Affiliation(s)
- Brandon E Aubol
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
| | - Joseph A Adams
- Department of Pharmacology, University of California San Diego, La Jolla, CA, USA
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31
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Pan Y, Huo F, Kang M, Liu B, Wu M, Pei D. Alternative splicing of HSPA12A pre-RNA by SRSF11 contributes to metastasis potential of colorectal cancer. Clin Transl Med 2022; 12:e1113. [PMID: 36394206 PMCID: PMC9670187 DOI: 10.1002/ctm2.1113] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Dysregulation of alternative splicing (AS) induced by serine/arginine-rich proteins has recently been linked to cancer metastasis. Nonetheless, as a member of the serine/arginine-rich protein family, the involvement of SRSF11 in colorectal cancer (CRC) is unknown. METHODS The TCGA dataset and clinical samples were used to assess SRSF11 expression levels in CRC. For SRSF11, functional experiments were conducted both in vitro and in vivo. RNA-seq technology was used to analyze and screen SRSF11-triggered AS events, which were then confirmed by in vivo UV crosslinking and immunoprecipitation (CLIP) and mini-gene reporter assays. Jalview software was used to determine the preferential binding motif with relation to exon skipping (ES) events. Furthermore, coimmunoprecipitation (Co-IP) and Phospho-tag SDS-PAGE experiments were used to investigate PAK5-mediated phosphorylation regulation on SRSF11, and in vitro kinase experiments validated the interaction. RESULTS In CRC, SRSF11 was discovered to be overexpressed and associated with a poor prognosis. And SRSF11 played a pro-metastatic role in vitro and in vivo. By screening SRSF11-regulated AS events, we identified the binding motif of SRSF11-triggered splicing-switching of HSPA12A AS, which specifically regulated HSPA12A AS by directly binding to a motif in exon 2. Mechanistically, the HSPA12A transcript with exon 2 retention increased N-cadherin expression by promoting RNA stability. Furthermore, the oncogenic kinase PAK5 phosphorylated SRSF11 at serine 287, protecting it from ubiquitination degradation. CONCLUSIONS SRSF11 exerts pro-metastatic effects in CRC by inhibiting the AS of HSPA12A pre-RNA. Our findings point to SRSF11-regulated HSPA12A splicing as a novel relationship between SRSF11-regulated splicing and CRC metastasis and suggest a PAK5/SRSF11/HSPA12A axis as a potential therapeutic target and prognostic biomarker in CRC.
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Affiliation(s)
- Yao‐Jie Pan
- Laboratory of Clinical and Experimental PathologyXuzhou Medical UniversityXuzhouChina
| | - Fu‐Chun Huo
- Laboratory of Clinical and Experimental PathologyXuzhou Medical UniversityXuzhouChina
| | - Meng‐Jie Kang
- Laboratory of Clinical and Experimental PathologyXuzhou Medical UniversityXuzhouChina
| | - Bo‐Wen Liu
- Department of General SurgeryXuzhou Medical UniversityXuzhouChina
| | - Meng‐Di Wu
- Laboratory of Clinical and Experimental PathologyXuzhou Medical UniversityXuzhouChina
| | - Dong‐Sheng Pei
- Laboratory of Clinical and Experimental PathologyXuzhou Medical UniversityXuzhouChina
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32
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Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022; 22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
Abstract
Nearly 60 - 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - D Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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33
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Muehlbauer LK, Wei T, Shishkova E, Coon JJ, Lambert PF. IQGAP1 and RNA Splicing in the Context of Head and Neck via Phosphoproteomics. J Proteome Res 2022; 21:2211-2223. [PMID: 35980772 PMCID: PMC9833422 DOI: 10.1021/acs.jproteome.2c00309] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
IQGAP1 (IQ motif-containing GTPase-activating protein 1) scaffolds several signaling pathways in mammalian cells that are implicated in carcinogenesis, including the RAS and PI3K pathways that involve multiple protein kinases. IQGAP1 has been shown to promote head and neck squamous cell carcinoma (HNSCC); however, the underlying mechanism(s) remains unclear. Here, we report a mass spectrometry-based analysis identifying differences in phosphorylation of cellular proteins in vivo and in vitro in the presence or absence of IQGAP1. By comparing the esophageal phosphoproteome profiles between Iqgap1+/+ and Iqgap1-/- mice, we identified RNA splicing as one of the most altered cellular processes. Serine/arginine-rich splicing factor 6 (SRSF6) was the protein with the most downregulated levels of phosphorylation in Iqgap1-/- tissue. We confirmed that the absence of IQGAP1 reduced SRSF6 phosphorylation both in vivo and in vitro. We then expanded our analysis to human normal oral keratinocytes. Again, we found factors involved in RNA splicing to be highly altered in the phosphoproteome profile upon genetic disruption of IQGAP1. Both the Clinical Proteomic Tumor Analysis Consortium (CPTAC) and the Cancer Genome Atlas (TCGA) data sets indicate that phosphorylation of splicing-related proteins is important in HNSCC prognosis. The Biological General Repository for Interaction Datasets (BioGRID) repository also suggested multiple interactions between IQGAP1 and splicing-related proteins. Based on these collective observations, we propose that IQGAP1 regulates the phosphorylation of splicing proteins, which potentially affects their splicing activities and, therefore, contributes to HNSCC. Raw data are available from the MassIVE database with identifier MSV000087770.
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Affiliation(s)
- Laura K. Muehlbauer
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Tao Wei
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Evgenia Shishkova
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Joshua J. Coon
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- Department of Biomolecular Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
- National Center for Quantitative Biology of Complex Systems, University of Wisconsin-Madison, Madison, WI 53706, USA
- Morgridge Institute for Research, Madison, WI 53706, USA
| | - Paul F. Lambert
- McArdle Laboratory for Cancer Research, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, 53705, USA
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Sun M, Jin Y, Zhang Y, Gregorich ZR, Ren J, Ge Y, Guo W. SR Protein Kinases Regulate the Splicing of Cardiomyopathy-Relevant Genes via Phosphorylation of the RSRSP Stretch in RBM20. Genes (Basel) 2022; 13:1526. [PMID: 36140694 PMCID: PMC9498672 DOI: 10.3390/genes13091526] [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: 07/06/2022] [Revised: 08/22/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
(1) Background: RNA binding motif 20 (RBM20) regulates mRNA splicing specifically in muscle tissues. Missense mutations in the arginine/serine (RS) domain of RBM20 lead to abnormal gene splicing and have been linked to severe dilated cardiomyopathy (DCM) in human patients and animal models. Interestingly, many of the reported DCM-linked missense mutations in RBM20 are in a highly conserved RSRSP stretch within the RS domain. Recently, it was found that the two Ser residues within this stretch are constitutively phosphorylated, yet the identity of the kinase(s) responsible for phosphorylating these residues, as well as the function of RSRSP phosphorylation, remains unknown. (2) Methods: The ability of three known SR protein kinases (SRPK1, CLK1, and AKT2) to phosphorylate the RBM20 RSRSP stretch and regulate target gene splicing was evaluated by using both in vitro and in vivo approaches. (3) Results: We found that all three kinases phosphorylated S638 and S640 in the RSRSP stretch and regulated RBM20 target gene splicing. While SRPK1 and CLK1 were both capable of directly phosphorylating the RS domain in RBM20, whether AKT2-mediated control of the RS domain phosphorylation is direct or indirect could not be determined. (4) Conclusions: Our results indicate that SR protein kinases regulate the splicing of a cardiomyopathy-relevant gene by modulating phosphorylation of the RSRSP stretch in RBM20. These findings suggest that SR protein kinases may be potential targets for the treatment of RBM20 cardiomyopathy.
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Affiliation(s)
- Mingming Sun
- Department of Zoology and Physiology, University of Wyoming, Laramie, WY 82071, USA
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Yanghai Zhang
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Zachery R Gregorich
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Jun Ren
- Department of Cardiology, Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital Fudan University, Shanghai 200032, China
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53706, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Wei Guo
- Department of Animal and Dairy Sciences, University of Wisconsin-Madison, Madison, WI 53706, USA
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Lei P, Zhang J, Liao P, Ren C, Wang J, Wang Y. Current progress and novel strategies that target CDK12 for drug discovery. Eur J Med Chem 2022; 240:114603. [PMID: 35868123 DOI: 10.1016/j.ejmech.2022.114603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/08/2022] [Accepted: 07/08/2022] [Indexed: 02/05/2023]
Abstract
CDK12 is a cyclin-dependent kinase that plays critical roles in DNA replication, transcription, mRNA splicing, and DNA damage repair. CDK12 genomic changes, including mutation, amplification, deletion, and fusion, lead to various cancers, such as colorectal cancer, gastric cancer, and ovarian cancer. An increasing number of CDK12 inhibitors have been reported since CDK12 was identified as a biomarker and cancer therapeutic target. A major challenge lies in that CDK12 and CDK13 share highly similar sequences, which leads to great difficulties in the development of highly selective CDK12 inhibitors. In recent years, great efforts were made in developing selective CDK12 blockers. Techniques including PROTAC and molecular glue degraders were also applied to facilitate their development. Also, the drug combination strategy of CDK12 small molecule inhibitors were studied. This review discusses the latest studies on CDK12 inhibitors and analyzes their structure-activity relationships, shedding light on their further development.
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Affiliation(s)
- Peng Lei
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Jifa Zhang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China
| | - Peiyu Liao
- School of Pharmacy, Chengdu Medical College, Chengdu, 610500, Sichuan, China
| | - Changyu Ren
- Department of Pharmacy, Chengdu Fifth People's Hospital, Chengdu, 611130, Sichuan, China
| | - Jiaxing Wang
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, Memphis, 38163, Tennessee, United States
| | - Yuxi Wang
- Targeted Tracer Research and Development Laboratory, Institute of Respiratory Health, Frontiers Science Center for Disease-related Molecular Network, Joint Research Institution of Altitude Health, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; State Key Laboratory of Biotherapy and Cancer Center, Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, Chengdu, 610041, Sichuan, China; Tianfu Jincheng Laboratory, Chengdu, 610041, Sichuan, China.
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A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
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p53 Isoforms as Cancer Biomarkers and Therapeutic Targets. Cancers (Basel) 2022; 14:cancers14133145. [PMID: 35804915 PMCID: PMC9264937 DOI: 10.3390/cancers14133145] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary The well-known tumor suppressor protein p53 plays important roles in tumor prevention through transcriptional regulation of its target genes. Reactivation of p53 activity has been a potent strategy for cancer treatment. Accumulating evidences indicate that p53 isoforms truncated/modified in the N- or C-terminus can modulate the p53 pathway in a p53-dependent or p53-independent manner. It is thus imperative to characterize the roles of the p53 isoforms in cancer development. This review illustrates how p53 isoforms participate in tumor development and/or suppression. It also summarizes the knowledge about the p53 isoforms as promising cancer biomarkers and therapeutic targets. Abstract This review aims to summarize the implications of the major isoforms of the tumor suppressor protein p53 in aggressive cancer development. The current knowledge of p53 isoforms, their involvement in cell-signaling pathways, and their interactions with other cellular proteins or factors suggests the existence of an intricate molecular network that regulates their oncogenic function. Moreover, existing literature about the involvement of the p53 isoforms in various cancers leads to the proposition of therapeutic solutions by altering the cellular levels of the p53 isoforms. This review thus summarizes how the major p53 isoforms Δ40p53α/β/γ, Δ133p53α/β/γ, and Δ160p53α/β/γ might have clinical relevance in the diagnosis and effective treatments of cancer.
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Sewell AK, Poss ZC, Ebmeier CC, Jacobsen JR, Old WM, Han M. The TORC1 phosphoproteome in C. elegans reveals roles in transcription and autophagy. iScience 2022; 25:104186. [PMID: 35479415 PMCID: PMC9036118 DOI: 10.1016/j.isci.2022.104186] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 03/14/2022] [Accepted: 03/29/2022] [Indexed: 11/13/2022] Open
Abstract
The protein kinase complex target of rapamycin complex 1 (TORC1) is a critical mediator of nutrient sensing that has been widely studied in cultured cells and yeast, yet our understanding of the regulatory activities of TORC1 in the context of a whole, multi-cellular organism is still very limited. Using Caenorhabditis elegans, we analyzed the DAF-15/Raptor-dependent phosphoproteome by quantitative mass spectrometry and characterized direct kinase targets by in vitro kinase assays. Here, we show new targets of TORC1 that indicate previously unknown regulation of transcription and autophagy. Our results further show that DAF-15/Raptor is differentially expressed during postembryonic development, suggesting a dynamic role for TORC1 signaling throughout the life span. This study provides a comprehensive view of the TORC1 phosphoproteome, reveals more than 100 DAF-15/Raptor-dependent phosphosites that reflect the complex function of TORC1 in a whole, multi-cellular organism, and serves as a rich resource to the field.
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Affiliation(s)
- Aileen K. Sewell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - Zachary C. Poss
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - Christopher C. Ebmeier
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - Jeremy R. Jacobsen
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - William M. Old
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
| | - Min Han
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA
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Serine-Arginine Protein Kinase 1 (SRPK1): a systematic review of its multimodal role in oncogenesis. Mol Cell Biochem 2022; 477:2451-2467. [PMID: 35583632 PMCID: PMC9499919 DOI: 10.1007/s11010-022-04456-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 04/27/2022] [Indexed: 11/13/2022]
Abstract
Alternative splicing is implicated in each of the hallmarks of cancer, and is mechanised by various splicing factors. Serine-Arginine Protein Kinase 1 (SRPK1) is an enzyme which moderates the activity of splicing factors rich in serine/arginine domains. Here we review SRPK1’s relationship with various cancers by performing a systematic review of all relevant published data. Elevated SRPK1 expression correlates with advanced disease stage and poor survival in many epithelial derived cancers. Numerous pre-clinical studies investigating a host of different tumour types; have found increased SRPK1 expression to be associated with proliferation, invasion, migration and apoptosis in vitro as well as tumour growth, tumourigenicity and metastasis in vivo. Aberrant SRPK1 expression is implicated in various signalling pathways associated with oncogenesis, a number of which, such as the PI3K/AKT, NF-КB and TGF-Beta pathway, are implicated in multiple different cancers. SRPK1-targeting micro RNAs have been identified in a number of studies and shown to have an important role in regulating SRPK1 activity. SRPK1 expression is also closely related to the response of various tumours to platinum-based chemotherapeutic agents. Future clinical applications will likely focus on the role of SRPK1 as a biomarker of treatment resistance and the potential role of its inhibition.
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Murphy AJ, Li AH, Li P, Sun H. Therapeutic Targeting of Alternative Splicing: A New Frontier in Cancer Treatment. Front Oncol 2022; 12:868664. [PMID: 35463320 PMCID: PMC9027816 DOI: 10.3389/fonc.2022.868664] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 03/11/2022] [Indexed: 01/05/2023] Open
Abstract
The ability for cells to harness alternative splicing enables them to diversify their proteome in order to carry out complex biological functions and adapt to external and internal stimuli. The spliceosome is the multiprotein-RNA complex charged with the intricate task of alternative splicing. Aberrant splicing can arise from abnormal spliceosomes or splicing factors and drive cancer development and progression. This review will provide an overview of the alternative splicing process and aberrant splicing in cancer, with a focus on serine/arginine-rich (SR) proteins and their recently reported roles in cancer development and progression and beyond. Recent mapping of the spliceosome, its associated splicing factors, and their relationship to cancer have opened the door to novel therapeutic approaches that capitalize on the widespread influence of alternative splicing. We conclude by discussing small molecule inhibitors of the spliceosome that have been identified in an evolving era of cancer treatment.
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Affiliation(s)
- Anthony J. Murphy
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Alex H. Li
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
| | - Peichao Li
- Department of Thoracic Surgery, The Second Hospital, Cheeloo College of Medicine, Shandong University, Jinan, China
| | - Hong Sun
- Department of Environmental Medicine, New York University School of Medicine, New York, NY, United States
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Miranda J, Bringas R, Fernandez-de-Cossio J, Perera-Negrin Y. Targeting CK2 mediated signaling to impair/tackle SARS-CoV-2 infection: a computational biology approach. Mol Med 2021; 27:161. [PMID: 34930105 PMCID: PMC8686809 DOI: 10.1186/s10020-021-00424-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 12/13/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Similarities in the hijacking mechanisms used by SARS-CoV-2 and several types of cancer, suggest the repurposing of cancer drugs to treat Covid-19. CK2 kinase antagonists have been proposed for cancer treatment. A recent study in cells infected with SARS-CoV-2 found a significant CK2 kinase activity, and the use of a CK2 inhibitor showed antiviral responses. CIGB-300, originally designed as an anticancer peptide, is an antagonist of CK2 kinase activity that binds to the CK2 phospho-acceptor sites. Recent preliminary results show the antiviral activity of CIGB-300 using a surrogate model of coronavirus. Here we present a computational biology study that provides evidence, at the molecular level, of how CIGB-300 may interfere with the SARS-CoV-2 life cycle within infected human cells. METHODS Sequence analyses and data from phosphorylation studies were combined to predict infection-induced molecular mechanisms that can be interfered by CIGB-300. Next, we integrated data from multi-omics studies and data focusing on the antagonistic effect on the CK2 kinase activity of CIGB-300. A combination of network and functional enrichment analyses was used. RESULTS Firstly, from the SARS-CoV studies, we inferred the potential incidence of CIGB-300 in SARS-CoV-2 interference on the immune response. Afterwards, from the analysis of multiple omics data, we proposed the action of CIGB-300 from the early stages of viral infections perturbing the virus hijacking of RNA splicing machinery. We also predicted the interference of CIGB-300 in virus-host interactions that are responsible for the high infectivity and the particular immune response to SARS-CoV-2 infection. Furthermore, we provided evidence of how CIGB-300 may participate in the attenuation of phenotypes related to muscle, bleeding, coagulation and respiratory disorders. CONCLUSIONS Our computational analysis proposes putative molecular mechanisms that support the antiviral activity of CIGB-300.
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Affiliation(s)
- Jamilet Miranda
- Division of Informatics, Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Ricardo Bringas
- Division of Informatics, Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Jorge Fernandez-de-Cossio
- Division of Informatics, Department of Bioinformatics, Center for Genetic Engineering and Biotechnology, Havana, Cuba
| | - Yasser Perera-Negrin
- Laboratory of Molecular Oncology, Division of Biomedical Research, Department of Pharmaceuticals, Center for Genetic Engineering and Biotechnology, Havana, Cuba
- China-Cuba Biotechnology Joint Innovation Center, Yongzhou Zhong Gu Biotechnology Co., Yongzhou, Hunan People’s Republic of China
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Naro C, Bielli P, Sette C. Oncogenic dysregulation of pre-mRNA processing by protein kinases: challenges and therapeutic opportunities. FEBS J 2021; 288:6250-6272. [PMID: 34092037 PMCID: PMC8596628 DOI: 10.1111/febs.16057] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/13/2021] [Accepted: 06/04/2021] [Indexed: 12/12/2022]
Abstract
Alternative splicing and polyadenylation represent two major steps in pre-mRNA-processing, which ensure proper gene expression and diversification of human transcriptomes. Deregulation of these processes contributes to oncogenic programmes involved in the onset, progression and evolution of human cancers, which often result in the acquisition of resistance to existing therapies. On the other hand, cancer cells frequently increase their transcriptional rate and develop a transcriptional addiction, which imposes a high stress on the pre-mRNA-processing machinery and establishes a therapeutically exploitable vulnerability. A prominent role in fine-tuning pre-mRNA-processing mechanisms is played by three main families of protein kinases: serine arginine protein kinase (SRPK), CDC-like kinase (CLK) and cyclin-dependent kinase (CDK). These kinases phosphorylate the RNA polymerase, splicing factors and regulatory proteins involved in cleavage and polyadenylation of the nascent transcripts. The activity of SRPKs, CLKs and CDKs can be altered in cancer cells, and their inhibition was shown to exert anticancer effects. In this review, we describe key findings that have been reported on these topics and discuss challenges and opportunities of developing therapeutic approaches targeting splicing factor kinases.
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Affiliation(s)
- Chiara Naro
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Policlinico Universitario A. GemelliIRCCSRomeItaly
| | - Pamela Bielli
- Department of Biomedicine and PreventionUniversity of Rome Tor VergataItaly
- Fondazione Santa LuciaIRCCSRomeItaly
| | - Claudio Sette
- Department of NeuroscienceSection of Human AnatomyCatholic University of the Sacred HeartRomeItaly
- Fondazione Santa LuciaIRCCSRomeItaly
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Baker M, Petasny M, Taqatqa N, Bentata M, Kay G, Engal E, Nevo Y, Siam A, Dahan S, Salton M. KDM3A regulates alternative splicing of cell-cycle genes following DNA damage. RNA (NEW YORK, N.Y.) 2021; 27:1353-1362. [PMID: 34321328 PMCID: PMC8522690 DOI: 10.1261/rna.078796.121] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/26/2021] [Indexed: 06/13/2023]
Abstract
Changes in the cellular environment result in chromatin structure alteration, which in turn regulates gene expression. To learn about the effect of the cellular environment on the transcriptome, we studied the H3K9 demethylase KDM3A. Using RNA-seq, we found that KDM3A regulates the transcription and alternative splicing of genes associated with cell cycle and DNA damage. We showed that KDM3A undergoes phosphorylation by PKA at serine 265 following DNA damage, and that the phosphorylation is important for proper cell-cycle regulation. We demonstrated that SAT1 alternative splicing, regulated by KDM3A, plays a role in cell-cycle regulation. Furthermore we found that KDM3A's demethylase activity is not needed for SAT1 alternative splicing regulation. In addition, we identified KDM3A's protein partner ARID1A, the SWI/SNF subunit, and SRSF3 as regulators of SAT1 alternative splicing and showed that KDM3A is essential for SRSF3 binding to SAT1 pre-mRNA. These results suggest that KDM3A serves as a sensor of the environment and an adaptor for splicing factor binding. Our work reveals chromatin sensing of the environment in the regulation of alternative splicing.
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Affiliation(s)
- Mai Baker
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mayra Petasny
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Nadeen Taqatqa
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Mercedes Bentata
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Gillian Kay
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Eden Engal
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Yuval Nevo
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Ahmad Siam
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Sara Dahan
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
| | - Maayan Salton
- Department of Biochemistry and Molecular Biology, the Institute for Medical Research Israel Canada, Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem 91120, Israel
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Lenard AJ, Hutten S, Zhou Q, Usluer S, Zhang F, Bourgeois BMR, Dormann D, Madl T. Phosphorylation Regulates CIRBP Arginine Methylation, Transportin-1 Binding and Liquid-Liquid Phase Separation. Front Mol Biosci 2021; 8:689687. [PMID: 34738012 PMCID: PMC8562343 DOI: 10.3389/fmolb.2021.689687] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 10/01/2021] [Indexed: 12/20/2022] Open
Abstract
Arginine-glycine(-glycine) (RG/RGG) regions are highly abundant in RNA-binding proteins and involved in numerous physiological processes. Aberrant liquid-liquid phase separation (LLPS) and stress granule (SGs) association of RG/RGG regions in the cytoplasm have been implicated in several neurodegenerative disorders. LLPS and SG association of these proteins is regulated by the interaction with nuclear import receptors, such as transportin-1 (TNPO1), and by post-translational arginine methylation. Strikingly, many RG/RGG proteins harbour potential phosphorylation sites within or close to their arginine methylated regions, indicating a regulatory role. Here, we studied the role of phosphorylation within RG/RGG regions on arginine methylation, TNPO1-binding and LLPS using the cold-inducible RNA-binding protein (CIRBP) as a paradigm. We show that the RG/RGG region of CIRBP is in vitro phosphorylated by serine-arginine protein kinase 1 (SRPK1), and discovered two novel phosphorylation sites in CIRBP. SRPK1-mediated phosphorylation of the CIRBP RG/RGG region impairs LLPS and binding to TNPO1 in vitro and interferes with SG association in cells. Furthermore, we uncovered that arginine methylation of the CIRBP RG/RGG region regulates in vitro phosphorylation by SRPK1. In conclusion, our findings indicate that LLPS and TNPO1-mediated chaperoning of RG/RGG proteins is regulated through an intricate interplay of post-translational modifications.
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Affiliation(s)
- Aneta J. Lenard
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Saskia Hutten
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany
- BioMedical Center, Cell Biology, Ludwig-Maximilians-Universität (LMU) München, Martinsried, Germany
| | - Qishun Zhou
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Sinem Usluer
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Fangrong Zhang
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Benjamin M. R. Bourgeois
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Dorothee Dormann
- Johannes Gutenberg-Universität (JGU) Mainz, Faculty of Biology, Mainz, Germany
- BioMedical Center, Cell Biology, Ludwig-Maximilians-Universität (LMU) München, Martinsried, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
- Munich Cluster for Systems Neurology (SyNergy), Munich, Germany
| | - Tobias Madl
- Gottfried Schatz Research Center for Cell Signaling, Metabolism and Aging, Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
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Qin Z, Qin L, Feng X, Li Z, Bian J. Development of Cdc2-like Kinase 2 Inhibitors: Achievements and Future Directions. J Med Chem 2021; 64:13191-13211. [PMID: 34519506 DOI: 10.1021/acs.jmedchem.1c00985] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cdc2-like kinases (CLKs; CLK1-4) are associated with various neurodegenerative disorders, metabolic regulation, and viral infection and have been recognized as potential drug targets. Human CLK2 has received increasing attention as a regulator that phosphorylates serine- and arginine-rich (SR) proteins and subsequently modulates the alternative splicing of precursor mRNA (pre-mRNA), which is an attractive target for degenerative disease and cancer. Numerous CLK2 inhibitors have been identified, with several molecules currently in clinical development. The first CLK2 inhibitor Lorecivivint (compound 1) has recently entered phase 3 clinical trials. However, highly selective CLK2 inhibitors are rarely reported. This Perspective summarizes the biological roles and therapeutic potential of CLK2 along with progress on the development of CLK2 inhibitors and discusses the achievements and future prospects of CLK2 inhibitors for therapeutic applications.
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Affiliation(s)
- Zhen Qin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Lian Qin
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Xi Feng
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Zhiyu Li
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
| | - Jinlei Bian
- Jiangsu Key Laboratory of Drug Design and Optimization, Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211100, P. R. China
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Pan XW, Xu D, Chen WJ, Chen JX, Chen WJ, Ye JQ, Gan SS, Zhou W, Song X, Shi L, Cui XG. USP39 promotes malignant proliferation and angiogenesis of renal cell carcinoma by inhibiting VEGF-A 165b alternative splicing via regulating SRSF1 and SRPK1. Cancer Cell Int 2021; 21:486. [PMID: 34544400 PMCID: PMC8454004 DOI: 10.1186/s12935-021-02161-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 08/18/2021] [Indexed: 01/01/2023] Open
Abstract
Background The benefit of targeted therapy for renal cell carcinoma (RCC) is largely crippled by drug resistance. Rapid disease progression and poor prognosis occur in patients with drug resistance. New treatments demand prompt exploration for clinical therapies. Ubiquitin-specific peptidase 39 (USP39) serves as the pro-tumor factor in several previous studies of other malignant tumors. To investigate the function and mechanism of USP39 in promoting malignant proliferation and angiogenesis of RCC. Methods We applied ONCOMINE database to analyze the correlation between USP39 expression level and the clinical characteristics of RCC. USP39 knockdown or overexpression plasmids were transfected into 786-O and ACHN cells. The HUVEC received cell supernatants of 786-O and ACHN cells with knockdown or overexpression USP39.The effect of USP39 on RCC was evaluated by MTT assay, cell cycle analysis, colony formation assay and tubule formation assay. The interaction between USP39 and VEGF-A alternative splicing was assessed by affinity purification and mass spectrometry, co-immunoprecipitation and Western blot assays. Results The mRNA expression level of USP39 in RCC was significantly higher than that in normal renal tissue (P < 0.001), and negatively correlated with the survival rate of RCC patients (P < 0.01). Silencing of USP39 in 786-O and ACHN cells inhibited cell proliferation and colony formation, and induced S phase arrest. USP39 overexpression significantly increased the number of tubules (P < 0.05) and branches (P < 0.01) formed by HUVEC cells, and USP39 knockdown produced an opposite effect (P < 0.05). The USP39 (101–565) fragment directly mediated its binding to SRSF1 and SRPK1, and promoted the phosphorylation of SRSF1 to regulate VEGF-A alternative splicing. USP39 knockdown upregulated the expression of VEGF-A165b, and USP39 overexpression downregulated the expression of VEGF-A165b significantly (both P < 0.05). Conclusion USP39 acted as a pro-tumor factor by motivating the malignant biological processes of RCC, probably through inhibiting VEGF-A165b alternative splicing and regulating SRSF1 and SRPK1. USP39 may prove to be a potential therapeutic target for RCC. Graphic abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s12935-021-02161-x.
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Affiliation(s)
- Xiu-Wu Pan
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.,Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Da Xu
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wen-Jin Chen
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Jia-Xin Chen
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wei-Jie Chen
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Jian-Qing Ye
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Si-Shun Gan
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China
| | - Wang Zhou
- Depanrtment of Urology, Third Affiliated Hospital of the Second Military Medical University, Shanghai, 201805, China.
| | - Xu Song
- Department of Urology, Shanghai Seventh People's Hospital, Shandong, 200137, China.
| | - Lei Shi
- Department of Urology, Yantai Yuhuangding Hospital of Qingdao University Medical College, Shandong, 264000, China.
| | - Xin-Gang Cui
- Department of Urology, Xinhua Hospital, School of Medicine, Shanghai Jiaotong University, 1665 Kongjiang Road, Shanghai, 200092, China.
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Deshmukh V, Seo T, O'Green A, Ibanez M, Hofilena B, KC S, Stewart J, Dellamary L, Chiu K, Ghias A, Barroga C, Kennedy S, Tambiah J, Hood J, Yazici Y. SM04755, a small-molecule inhibitor of the Wnt pathway, as a potential topical treatment for tendinopathy. J Orthop Res 2021; 39:2048-2061. [PMID: 33104243 PMCID: PMC8451793 DOI: 10.1002/jor.24898] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 10/01/2020] [Accepted: 10/21/2020] [Indexed: 02/04/2023]
Abstract
The Wnt pathway is upregulated in tendinopathy, affecting inflammation and tenocyte differentiation. Given its potential role in tendinopathy, this signaling pathway may be a relevant target for treatment. The current study examined the therapeutic potential of SM04755, a topical, small-molecule Wnt pathway inhibitor, for the treatment of tendinopathy using in vitro assays and animal models. In vitro, SM04755 decreased Wnt pathway activity, induced tenocyte differentiation, and inhibited catabolic enzymes and pro-inflammatory cytokines in human mesenchymal stem cells, rat tendon-derived stem cells, and human peripheral blood mononuclear cells. Evaluation of the mechanism of action of SM04755 by biochemical profiling and computational modeling identified CDC-like kinase 2 (CLK2) and dual-specificity tyrosine phosphorylation-regulated kinase 1A (DYRK1A) as molecular targets. CLK and DYRK1A inhibition by siRNA knockdown or pharmacological inhibition induced tenocyte differentiation and reduced tenocyte catabolism. In vivo, topically applied SM04755 showed therapeutically relevant exposure in tendons with low systemic exposure and no detectable toxicity in rats. Moreover, SM04755 showed reduced tendon inflammation and evidence of tendon regeneration, decreased pain, and improved weight-bearing function in rat collagenase-induced tendinopathy models compared with vehicle control. Together, these data demonstrate that CLK2 and DYRK1A inhibition by SM04755 resulted in Wnt pathway inhibition, enhanced tenocyte differentiation and protection, and reduced inflammation. SM04755 has the potential to benefit symptoms and modify disease processes in tendinopathy.
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Affiliation(s)
| | - Tim Seo
- Samumed, LLCSan DiegoCaliforniaUSA
| | | | | | | | - Sunil KC
- Samumed, LLCSan DiegoCaliforniaUSA
| | | | | | | | | | | | | | | | - John Hood
- Formerly Samumed, LLCSan DiegoCaliforniaUSA
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Huang JQ, Li HF, Zhu J, Song JW, Zhang XB, Gong P, Liu QY, Zhou CH, Wang L, Gong LY. SRPK1/AKT axis promotes oxaliplatin-induced anti-apoptosis via NF-κB activation in colon cancer. J Transl Med 2021; 19:280. [PMID: 34193174 PMCID: PMC8243872 DOI: 10.1186/s12967-021-02954-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2021] [Accepted: 06/19/2021] [Indexed: 12/28/2022] Open
Abstract
Background Colorectal cancer is the third most common diagnosis. Oxaliplatin is used as first-line treatment of colon cancer. However, oxaliplatin resistance greatly reduces its therapeutic effect. SRPK1 involves in pre-mRNA splicing and tumorigenesis. How SRPK1 mediates drug resistance in colon cancer is unknown. Methods The expression of SRPK1 was analyzed in the TCGA and the CPTAC pan-cancer samples and detected in colon cancer cell lines and tissues by IHC and western blot. The MTT and TUNEL assay were used to verify the anti-apoptosis ability of colon cancer cell. The activation of NF-κB was determined by luciferase assay and qRT-PCR. AKT, IKK, IκB and their phosphorylation level were verified by western blot. Results We found that SRPK1 expression was the second highest in TCGA and the CPTAC pan-cancer samples. The mRNA and protein levels of SRPK1 were increased in tissues from patients with colon cancer. SRPK1 was associated with clinical stage and TNM classifications in 148 cases of colon cancer patients. High SRPK1 levels correlated with poor prognosis (p < 0.001). SRPK1 overexpression enhanced the anti-apoptosis ability of colon cancer cells, whereas SRPK1 silencing had the opposite effect under oxaliplatin treatment. Mechanistically, SRPK1 enhances IKK kinase and IκB phosphorylation to promote NF-κB nuclear translocation to confer oxaliplatin resistance. Conclusions Our findings suggest that SRPK1 participates in colon cancer progression and enhances the anti-apoptosis capacity to induce drug resistance in colon cancer cells via NF-κB pathway activation, and thus might be a potential pharmaceutically target for colon cancer treatment. Supplementary Information The online version contains supplementary material available at 10.1186/s12967-021-02954-8.
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Affiliation(s)
- Jing-Qiang Huang
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
| | - He-Feng Li
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China.,School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
| | - Jing Zhu
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China
| | - Jun-Wei Song
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China.,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Health Science Center, Shenzhen University, Shenzhen, 518060, Guangdong, China
| | - Xian-Bin Zhang
- Department of General Surgery, Shenzhen University General Hospital, Shenzhen, Guangdong, 518060, P. R. China
| | - Peng Gong
- Department of General Surgery, Shenzhen University General Hospital, Shenzhen, Guangdong, 518060, P. R. China
| | - Qiu-Yu Liu
- Department of Pathology, Henan Provincial People's Hospital, Zhengzhou, Henan, 450003, P. R. China
| | - Chun-Hui Zhou
- Department of Pathology, Guangzhou Health Science College, Guangzhou, Guangdong, 510520, P. R. China
| | - Liang Wang
- Department of Cell Biology and Medical Genetics, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China.
| | - Li-Yun Gong
- Guangdong Key Laboratory for Genome Stability and Human Disease Prevention, Department of Biochemistry and Molecular Biology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518060, P. R. China.
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p53/p73 Protein Network in Colorectal Cancer and Other Human Malignancies. Cancers (Basel) 2021; 13:cancers13122885. [PMID: 34207603 PMCID: PMC8227208 DOI: 10.3390/cancers13122885] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 06/02/2021] [Accepted: 06/03/2021] [Indexed: 12/16/2022] Open
Abstract
Simple Summary The p53 family of proteins comprises p53, p63, and p73, which share high structural and functional similarity. The two distinct promoters of each locus, the alternative splicing, and the alternative translation initiation sites enable the generation of numerous isoforms with different protein-interacting domains and distinct activities. The co-expressed p53/p73 isoforms have significant but distinct roles in carcinogenesis. Their activity is frequently impaired in human tumors including colorectal carcinoma due to dysregulated expression and a dominant-negative effect accomplished by some isoforms and p53 mutants. The interactions between isoforms are particularly important to understand the onset of tumor formation, progression, and therapeutic response. The understanding of the p53/p73 network can contribute to the development of new targeted therapies. Abstract The p53 tumor suppressor protein is crucial for cell growth control and the maintenance of genomic stability. Later discovered, p63 and p73 share structural and functional similarity with p53. To understand the p53 pathways more profoundly, all family members should be considered. Each family member possesses two promoters and alternative translation initiation sites, and they undergo alternative splicing, generating multiple isoforms. The resulting isoforms have important roles in carcinogenesis, while their expression is dysregulated in several human tumors including colorectal carcinoma, which makes them potential targets in cancer treatment. Their activities arise, at least in part, from the ability to form tetramers that bind to specific DNA sequences and activate the transcription of target genes. In this review, we summarize the current understanding of the biological activities and regulation of the p53/p73 isoforms, highlighting their role in colorectal tumorigenesis. The analysis of the expression patterns of the p53/p73 isoforms in human cancers provides an important step in the improvement of cancer therapy. Furthermore, the interactions among the p53 family members which could modulate normal functions of the canonical p53 in tumor tissue are described. Lastly, we emphasize the importance of clinical studies to assess the significance of combining the deregulation of different members of the p53 family to define the outcome of the disease.
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Hamey JJ, Nguyen A, Wilkins MR. Discovery of Arginine Methylation, Phosphorylation, and Their Co-occurrence in Condensate-Associated Proteins in Saccharomyces cerevisiae. J Proteome Res 2021; 20:2420-2434. [PMID: 33856219 DOI: 10.1021/acs.jproteome.0c00927] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The formation of condensates in membraneless organelles is thought to be driven by protein phase separation. Arginine methylation and serine/threonine phosphorylation are important in the phase separation process; however, these post-translational modifications are often present in intrinsically disordered regions that are difficult to analyze with standard proteomic techniques. To understand their presence and co-occurrence in condensate-associated proteins, here, we use a multiprotease and multi-tandem mass spectrometry (MS/MS) fragmentation approach, coupled with heavy methyl stable isotope labeling of amino acids in cell culture (SILAC) and phospho- or methyl-peptide enrichment. For Saccharomyces cerevisiae, we report a 50% increase in the known arginine methylproteome, involving 15 proteins that are all condensate-associated. Importantly, some of these proteins have arginine methylation on all predicted sites-providing evidence that this modification can be pervasive. We explored whether arginine-methylated, condensate-associated proteins are also phosphorylated and found 12 such proteins to carry phosphorylated serine or threonine. In Npl3, Ded1, and Sbp1, single peptides were found to carry both modifications, indicating a co-occurrence in close proximity and on the same protein molecule. These co-modifications occur in regions of disorder, whereas arginine methylation is typically on regions of disorder that are also basic. For phosphorylation, its association with charged regions of condensate-associated proteins was less consistent, although some regions with multisite phosphorylation sites were strongly acidic. We conclude that arginine-methylated proteins associated with condensates are typically also modified with protein phosphorylation.
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Affiliation(s)
- Joshua J Hamey
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Amy Nguyen
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Marc R Wilkins
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW 2052, Australia
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