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Holmes ME, Hertel KJ. Interdependent regulation of alternative splicing by SR and hnRNP proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.19.608666. [PMID: 39229091 PMCID: PMC11370404 DOI: 10.1101/2024.08.19.608666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Alternative pre-mRNA splicing is a combinatorial process involving SR and hnRNP splicing factors. These proteins can silence or enhance splicing based on their expression levels and binding positions. To better understand their combinatorial and interdependent regulation, computational analyses were performed using HepG2 and K562 cell knockdown and binding datasets from the ENCODE Project. Analyses of diMerential splicing for 6 SR proteins and 13 hnRNP knockdowns revealed statistically significant exon overlap among most RBP combinations, albeit at diMerent levels. Neither SR proteins nor hnRNPs showed strong preferences for collaborating with specific RBP classes in mediating exon inclusion. While SRSF1, hnRNPK, and hnRNPC stand out as major influencers of alternative splicing, they do so predominantly independent of other RBPs. Meanwhile, minor influencers of alternative splicing such as hnRNPAB and hnRNPA0 predominantly regulate exon inclusion in concert with other RBPs, indicating that inclusion can be mediated by both single and multiple RBPs. Interestingly, the higher the number of RBPs that regulate the inclusion of an exon, the more variable exon inclusion preferences become. Interdependently regulated exons are more modular and have diMerent physical characteristics such as reduced exon length compared to their independent counterparts. A comparison of RBP interdependence between HepG2 and K562 cells provides the framework that explains cell-type-specific alternative splicing. Our study highlights the importance of the interdependent regulation of alternative exons and identifies characteristics of interdependently regulated exons that diMer from independently regulated exons.
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2
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Li F, Li W. Readers of RNA Modification in Cancer and Their Anticancer Inhibitors. Biomolecules 2024; 14:881. [PMID: 39062595 PMCID: PMC11275166 DOI: 10.3390/biom14070881] [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: 06/18/2024] [Revised: 07/19/2024] [Accepted: 07/21/2024] [Indexed: 07/28/2024] Open
Abstract
Cancer treatment has always been a challenge for humanity. The inadequacies of current technologies underscore the limitations of our efforts against this disease. Nevertheless, the advent of targeted therapy has introduced a promising avenue, furnishing us with more efficacious tools. Consequently, researchers have turned their attention toward epigenetics, offering a novel perspective in this realm. The investigation of epigenetics has brought RNA readers to the forefront, as they play pivotal roles in recognizing and regulating RNA functions. Recently, the development of inhibitors targeting these RNA readers has emerged as a focal point in research and holds promise for further strides in targeted therapy. In this review, we comprehensively summarize various types of inhibitors targeting RNA readers, including non-coding RNA (ncRNA) inhibitors, small-molecule inhibitors, and other potential inhibitors. We systematically elucidate their mechanisms in suppressing cancer progression by inhibiting readers, aiming to present inhibitors of readers at the current stage and provide more insights into the development of anticancer drugs.
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Affiliation(s)
| | - Wenjin Li
- Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China;
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3
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Sue SH, Liu ST, Huang SM. Factors affecting the expression and stability of full-length and truncated SRSF3 proteins in human cancer cells. Sci Rep 2024; 14:14397. [PMID: 38909100 PMCID: PMC11193772 DOI: 10.1038/s41598-024-64640-1] [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: 03/04/2024] [Accepted: 06/11/2024] [Indexed: 06/24/2024] Open
Abstract
Alternative splicing plays a crucial role in increasing the diversity of mRNAs expressed in the genome. Serine/arginine-rich splicing factor 3 (SRSF3) is responsible for regulating the alternative splicing of its own mRNA and ensuring that its expression is balanced to maintain homeostasis. Moreover, the exon skipping of SRSF3 leads to the production of a truncated protein instead of a frameshift mutation that generates a premature termination codon (PTC). However, the precise regulatory mechanism involved in the splicing of SRSF3 remains unclear. In this study, we first established a platform for coexpressing full-length SRSF3 (SRSF3-FL) and SRSF3-PTC and further identified a specific antibody against the SRSF3-FL and truncated SRSF3 (SRSF3-TR) proteins. Next, we found that exogenously overexpressing SRSF3-FL or SRSF3-PTC failed to reverse the effects of digoxin, caffeine, or both in combination on this molecule and its targets. Endoplasmic reticulum-related pathways, transcription factors, and chemicals such as palmitic acid and phosphate were found to be involved in the regulation of SRSF3 expression. The downregulation of SRSF3-FL by palmitic acid and phosphate was mediated via different regulatory mechanisms in HeLa cells. In summary, we provide new insights into the altered expression of the SRSF3-FL and SRSF3-TR proteins for the identification of the functions of SRSF3 in cells.
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Affiliation(s)
- Sung-How Sue
- Department of Cardiovascular Surgery, Chung Shan Medical University Hospital, Chung Shan Medical University, Taichung City, 402, Taiwan, Republic of China
- Institute of Medicine, Chung Shan Medical University, Taichung City, 402, Taiwan, Republic of China
| | - Shu-Ting Liu
- Department of Biochemistry, National Defense Medical Center, Taipei City, 114, Taiwan, Republic of China
| | - Shih-Ming Huang
- Department of Biochemistry, National Defense Medical Center, Taipei City, 114, Taiwan, Republic of China.
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4
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Sudhakar SRN, Khan SN, Clark A, Hendrickson-Rebizant T, Patel S, Lakowski TM, Davie JR. Protein arginine methyltransferase 1, a major regulator of biological processes. Biochem Cell Biol 2024; 102:106-126. [PMID: 37922507 DOI: 10.1139/bcb-2023-0212] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023] Open
Abstract
Protein arginine methyltransferase 1 (PRMT1) is a major type I arginine methyltransferase that catalyzes the formation of monomethyl and asymmetric dimethylarginine in protein substrates. It was first identified to asymmetrically methylate histone H4 at the third arginine residue forming the H4R3me2a active histone mark. However, several protein substrates are now identified as being methylated by PRMT1. As a result of its association with diverse classes of substrates, PRMT1 regulates several biological processes like chromatin dynamics, transcription, RNA processing, and signal transduction. The review provides an overview of PRMT1 structure, biochemical features, specificity, regulation, and role in cellular functions. We discuss the genomic distribution of PRMT1 and its association with tRNA genes. Further, we explore the different substrates of PRMT1 involved in splicing. In the end, we discuss the proteins that interact with PRMT1 and their downstream effects in diseased states.
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Affiliation(s)
- Sadhana R N Sudhakar
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Shahper N Khan
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ariel Clark
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | | | - Shrinal Patel
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
| | - Ted M Lakowski
- College of Pharmacy Pharmaceutical Analysis Laboratory, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - James R Davie
- Department of Biochemistry and Medical Genetics, Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, MB, Canada
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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5
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Spangsberg Petersen US, Dembic M, Martínez-Pizarro A, Richard E, Holm LL, Havelund JF, Doktor TK, Larsen MR, Færgeman NJ, Desviat LR, Andresen BS. Regulating PCCA gene expression by modulation of pseudoexon splicing patterns to rescue enzyme activity in propionic acidemia. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102101. [PMID: 38204914 PMCID: PMC10776996 DOI: 10.1016/j.omtn.2023.102101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 12/08/2023] [Indexed: 01/12/2024]
Abstract
Pseudoexons are nonfunctional intronic sequences that can be activated by deep-intronic sequence variation. Activation increases pseudoexon inclusion in mRNA and interferes with normal gene expression. The PCCA c.1285-1416A>G variation activates a pseudoexon and causes the severe metabolic disorder propionic acidemia by deficiency of the propionyl-CoA carboxylase enzyme encoded by PCCA and PCCB. We characterized this pathogenic pseudoexon activation event in detail and identified hnRNP A1 to be important for normal repression. The PCCA c.1285-1416A>G variation disrupts an hnRNP A1-binding splicing silencer and simultaneously creates a splicing enhancer. We demonstrate that blocking this region of regulation with splice-switching antisense oligonucleotides restores normal splicing and rescues enzyme activity in patient fibroblasts and in a cellular model created by CRISPR gene editing. Interestingly, the PCCA pseudoexon offers an unexploited potential to upregulate gene expression because healthy tissues show relatively high inclusion levels. By blocking inclusion of the nonactivated wild-type pseudoexon, we can increase both PCCA and PCCB protein levels, which increases the activity of the heterododecameric enzyme. Surprisingly, we can increase enzyme activity from residual levels in not only patient fibroblasts harboring PCCA missense variants but also those harboring PCCB missense variants. This is a potential treatment strategy for propionic acidemia.
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Affiliation(s)
- Ulrika Simone Spangsberg Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Maja Dembic
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
- Department of Clinical Genetics, Odense University Hospital, 5000 Odense C, Denmark
- Department of Mathematics and Computer Science, University of Southern Denmark, 5230 Odense M, Denmark
| | - Ainhoa Martínez-Pizarro
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Eva Richard
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lise Lolle Holm
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Jesper Foged Havelund
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Thomas Koed Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Martin Røssel Larsen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Nils J. Færgeman
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
| | - Lourdes Ruiz Desviat
- Centro de Biología Molecular Severo Ochoa, UAM-CSIC, CEDEM, CIBERER, IdiPaz, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Brage Storstein Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, 5230 Odense M, Denmark
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Chen W, Geng D, Chen J, Han X, Xie Q, Guo G, Chen X, Zhang W, Tang S, Zhong X. Roles and mechanisms of aberrant alternative splicing in melanoma - implications for targeted therapy and immunotherapy resistance. Cancer Cell Int 2024; 24:101. [PMID: 38462618 PMCID: PMC10926661 DOI: 10.1186/s12935-024-03280-x] [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: 10/29/2023] [Accepted: 02/22/2024] [Indexed: 03/12/2024] Open
Abstract
BACKGROUND Despite advances in therapeutic strategies, resistance to immunotherapy and the off-target effects of targeted therapy have significantly weakened the benefits for patients with melanoma. MAIN BODY Alternative splicing plays a crucial role in transcriptional reprogramming during melanoma development. In particular, aberrant alternative splicing is involved in the efficacy of immunotherapy, targeted therapy, and melanoma metastasis. Abnormal expression of splicing factors and variants may serve as biomarkers or therapeutic targets for the diagnosis and prognosis of melanoma. Therefore, comprehensively integrating their roles and related mechanisms is essential. This review provides the first detailed summary of the splicing process in melanoma and the changes occurring in this pathway. CONCLUSION The focus of this review is to provide strategies for developing novel diagnostic biomarkers and summarize their potential to alter resistance to targeted therapies and immunotherapy.
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Affiliation(s)
- Wanxian Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Deyi Geng
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Jiasheng Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaosha Han
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Qihu Xie
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Genghong Guo
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xuefen Chen
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Wancong Zhang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Shijie Tang
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China
| | - Xiaoping Zhong
- Department of Plastic and Burns Surgery, The Second Affiliated Hospital of Shantou University Medical College, Shantou, 515000, P. R. China.
- Plastic Surgery Research Institute, Ear Deformities Treatment Center and Cleft Lip and Palate Treatment Center, Shantou University Medical College, Shantou, China.
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7
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Mura-Escorche G, Perdomo-Ramírez A, Ramos-Trujillo E, Trujillo-Frías CJ, Claverie-Martín F. Characterization of pre-mRNA Splicing Defects Caused by CLCN5 and OCRL Mutations and Identification of Novel Variants Associated with Dent Disease. Biomedicines 2023; 11:3082. [PMID: 38002082 PMCID: PMC10669864 DOI: 10.3390/biomedicines11113082] [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: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
Dent disease (DD) is an X-linked renal tubulopathy characterized by low-molecular-weight proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis and progressive renal failure. Two-thirds of cases are associated with inactivating variants in the CLCN5 gene (Dent disease 1, DD1) and a few present variants in the OCRL gene (Dent disease 2, DD2). The aim of the present study was to test the effect on the pre-mRNA splicing process of DD variants, described here or in the literature, and describe the clinical and genotypic features of thirteen unrelated patients with suspected DD. All patients presented tubular proteinuria, ten presented hypercalciuria and five had nephrolithiasis or nephrocalcinosis. CLCN5 and OCRL genes were analyzed by Sanger sequencing. Nine patients showed variants in CLCN5 and four in OCRL; eight of these were new. Bioinformatics tools were used to select fifteen variants with a potential effect on pre-mRNA splicing from our patients' group and from the literature, and were experimentally tested using minigene assays. Results showed that three exonic missense mutations and two intronic variants affect the mRNA splicing process. Our findings widen the genotypic spectrum of DD and provide insight into the impact of variants causing DD.
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Affiliation(s)
- Glorián Mura-Escorche
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
- Departamento de Medicina Interna, Dermatología y Psiquiatría, Facultad de Medicina, Universidad de la Laguna, 38071 Santa Cruz de Tenerife, Spain
| | - Ana Perdomo-Ramírez
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
| | - Elena Ramos-Trujillo
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
- Departamento de Medicina Física y Farmacología, Facultad de Medicina, Universidad de la Laguna, 38071 Santa Cruz de Tenerife, Spain
| | - Carmen Jane Trujillo-Frías
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
| | - Félix Claverie-Martín
- Unidad de Investigación, Grupo RenalTube, Hospital Universitario Nuestra Señora de Candelaria, 38010 Santa Cruz de Tenerife, Spain; (G.M.-E.); (A.P.-R.); (C.J.T.-F.)
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8
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Gao R, Lu Y, Wu N, Liu H, Jin X. Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis. PeerJ 2023; 11:e16193. [PMID: 37849832 PMCID: PMC10578304 DOI: 10.7717/peerj.16193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/06/2023] [Indexed: 10/19/2023] Open
Abstract
As important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene family in rice. A total of 24 OsSR genes were phylogenetically classified into seven groups, corresponding to seven subfamilies. The OsSR genes' structures, distribution of conserved domains, and protein tertiary structure of OsSR were conserved within each subfamily. The synteny analysis revealed that segmental duplication events were critical for the expansion of OsSR gene family. Moreover, interspecific synteny revealed the distribution of orthologous SR gene pairs between rice and Arabidopsis, sorghum, wheat, and maize. Among all OsSR genes, 14 genes exhibited NAGNAG acceptors, and only four OsSR genes had AS events on the NAGNAG acceptors. Furthermore, the distinct tissue-specific expression patterns of OsSR genes showed that these genes may function in different developmental stages in rice. The AS patterns on the same OsSR gene were variable among the root, stem, leaf, and grains at different filling stages, and some isoforms could only be detected in one or a few of tested tissues. Meanwhile, our results showed that the expression of some OsSR genes changed dramatically under ABA, GA, salt, drought, cold or heat treatment, which were related to the wide distribution of corresponding cis-elements in their promoter regions, suggesting their specific roles in stress and hormone response. This research facilitates our understanding of SR gene family in rice and provides clues for further exploration of the function of OsSR genes.
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Affiliation(s)
- Rui Gao
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yingying Lu
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Nan Wu
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Hui Liu
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Xiaoli Jin
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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9
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Gotthardt M, Badillo-Lisakowski V, Parikh VN, Ashley E, Furtado M, Carmo-Fonseca M, Schudy S, Meder B, Grosch M, Steinmetz L, Crocini C, Leinwand L. Cardiac splicing as a diagnostic and therapeutic target. Nat Rev Cardiol 2023; 20:517-530. [PMID: 36653465 DOI: 10.1038/s41569-022-00828-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 12/09/2022] [Indexed: 01/19/2023]
Abstract
Despite advances in therapeutics for heart failure and arrhythmias, a substantial proportion of patients with cardiomyopathy do not respond to interventions, indicating a need to identify novel modifiable myocardial pathobiology. Human genetic variation associated with severe forms of cardiomyopathy and arrhythmias has highlighted the crucial role of alternative splicing in myocardial health and disease, given that it determines which mature RNA transcripts drive the mechanical, structural, signalling and metabolic properties of the heart. In this Review, we discuss how the analysis of cardiac isoform expression has been facilitated by technical advances in multiomics and long-read and single-cell sequencing technologies. The resulting insights into the regulation of alternative splicing - including the identification of cardiac splice regulators as therapeutic targets and the development of a translational pipeline to evaluate splice modulators in human engineered heart tissue, animal models and clinical trials - provide a basis for improved diagnosis and therapy. Finally, we consider how the medical and scientific communities can benefit from facilitated acquisition and interpretation of splicing data towards improved clinical decision-making and patient care.
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Affiliation(s)
- Michael Gotthardt
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany.
- DZHK (German Center for Cardiovascular Research Partner Site Berlin), Berlin, Germany.
- Department of Cardiology, Charité - Universitätsmedizin Berlin, Berlin, Germany.
| | - Victor Badillo-Lisakowski
- Neuromuscular and Cardiovascular Cell Biology, Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Berlin, Germany
- DZHK (German Center for Cardiovascular Research Partner Site Berlin), Berlin, Germany
| | - Victoria Nicole Parikh
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Euan Ashley
- Stanford Center for Inherited Cardiovascular Disease, Stanford University School of Medicine, Palo Alto, CA, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Marta Furtado
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Sarah Schudy
- Institute for Cardiomyopathies, Department of Medicine III, University of Heidelberg, Heidelberg, Germany
| | - Benjamin Meder
- Institute for Cardiomyopathies, Department of Medicine III, University of Heidelberg, Heidelberg, Germany
- DZHK (German Center for Cardiovascular Research Partner Site Heidelberg-Mannheim), Heidelberg, Germany
| | - Markus Grosch
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Lars Steinmetz
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
- European Molecular Biology Laboratory (EMBL), Genome Biology Unit, Heidelberg, Germany
| | - Claudia Crocini
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
| | - Leslie Leinwand
- Department of Molecular, Cellular, and Developmental Biology and BioFrontiers Institute, University of Colorado, Boulder, CO, USA
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10
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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: 7] [Impact Index Per Article: 7.0] [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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11
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Kumar K, Sinha SK, Maity U, Kirti PB, Kumar KRR. Insights into established and emerging roles of SR protein family in plants and animals. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1763. [PMID: 36131558 DOI: 10.1002/wrna.1763] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/11/2022] [Accepted: 08/22/2022] [Indexed: 05/13/2023]
Abstract
Splicing of pre-mRNA is an essential part of eukaryotic gene expression. Serine-/arginine-rich (SR) proteins are highly conserved RNA-binding proteins present in all metazoans and plants. SR proteins are involved in constitutive and alternative splicing, thereby regulating the transcriptome and proteome diversity in the organism. In addition to their role in splicing, SR proteins are also involved in mRNA export, nonsense-mediated mRNA decay, mRNA stability, and translation. Due to their pivotal roles in mRNA metabolism, SR proteins play essential roles in normal growth and development. Hence, any misregulation of this set of proteins causes developmental defects in both plants and animals. SR proteins from the animal kingdom are extensively studied for their canonical and noncanonical functions. Compared with the animal kingdom, plant genomes harbor more SR protein-encoding genes and greater diversity of SR proteins, which are probably evolved for plant-specific functions. Evidence from both plants and animals confirms the essential role of SR proteins as regulators of gene expression influencing cellular processes, developmental stages, and disease conditions. This article is categorized under: RNA Processing > Splicing Mechanisms RNA Processing > Splicing Regulation/Alternative Splicing.
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Affiliation(s)
- Kundan Kumar
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Shubham Kumar Sinha
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
| | - Upasana Maity
- Department of Biotechnology, Indira Gandhi National Tribal University (IGNTU), Amarkantak, India
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Suzuki Y, Yamada T, Suzuki MG. In Vitro Comparison of Sex-Specific Splicing Efficiencies of fem Pre-mRNA under Monoallelic and Heteroallelic Conditions of csd, a Master Sex-Determining Gene in the Honeybee. J Dev Biol 2023; 11:jdb11010010. [PMID: 36976099 PMCID: PMC10057164 DOI: 10.3390/jdb11010010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 03/05/2023] [Accepted: 03/08/2023] [Indexed: 03/12/2023] Open
Abstract
The sexual fate of honeybees is determined by the complementary sex determination (CSD) model: heterozygosity at a single locus (the CSD locus) determines femaleness, while hemizygosity or homozygosity at the CSD locus determines maleness. The csd gene encodes a splicing factor that regulates sex-specific splicing of the downstream target gene feminizer (fem), which is required for femaleness. The female mode of fem splicing occurs only when csd is present in the heteroallelic condition. To gain insights into how Csd proteins are only activated under the heterozygous allelic composition, we developed an in vitro assay system to evaluate the activity of Csd proteins. Consistent with the CSD model, the co-expression of two csd alleles, both of which lack splicing activity under the single-allele condition, restored the splicing activity that governs the female mode of fem splicing. RNA immunoprecipitation quantitative PCR analyses demonstrated that the CSD protein was specifically enriched in several exonic regions in the fem pre-mRNA, and enrichment in exons 3a and 5 was significantly greater under the heterozygous allelic composition than the single-allelic condition. However, in most cases csd expression under the monoallelic condition was capable of inducing the female mode of fem splicing contrary to the conventional CSD model. In contrast, repression of the male mode of fem splicing was predominant under heteroallelic conditions. These results were reproduced by real-time PCR of endogenous fem expression in female and male pupae. These findings strongly suggest that the heteroallelic composition of csd may be more important for the repression of the male splicing mode than for the induction of the female splicing mode of the fem gene.
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Affiliation(s)
- Yukihiro Suzuki
- INTERSTELLAR Inc., 301 Unico A, 3-4 Nisshin-cho, Kawasaki-ku, Kawasaki 210-0024, Kanagawa, Japan
| | - Takafumi Yamada
- YAMADA-KUN’S Bee Farm, 95 Ochino, Mugegawa, Seki 501-2602, Gifu, Japan
| | - Masataka G. Suzuki
- Division of Biological Sciences, Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, 302 Bioscience-Bldg, 5-1-5 Kashiwanoha, Kashiwa 277-8562, Chiba, Japan
- Correspondence: ; Tel.: +81-4-7136-3694
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13
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Sertznig H, Roesmann F, Wilhelm A, Heininger D, Bleekmann B, Elsner C, Santiago M, Schuhenn J, Karakoese Z, Benatzy Y, Snodgrass R, Esser S, Sutter K, Dittmer U, Widera M. SRSF1 acts as an IFN-I-regulated cellular dependency factor decisively affecting HIV-1 post-integration steps. Front Immunol 2022; 13:935800. [PMID: 36458014 PMCID: PMC9706209 DOI: 10.3389/fimmu.2022.935800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/19/2022] [Indexed: 08/24/2023] Open
Abstract
Efficient HIV-1 replication depends on balanced levels of host cell components including cellular splicing factors as the family of serine/arginine-rich splicing factors (SRSF, 1-10). Type I interferons (IFN-I) play a crucial role in the innate immunity against HIV-1 by inducing the expression of IFN-stimulated genes (ISGs) including potent host restriction factors. The less well known IFN-repressed genes (IRepGs) might additionally affect viral replication by downregulating host dependency factors that are essential for the viral life cycle; however, so far, the knowledge about IRepGs involved in HIV-1 infection is very limited. In this work, we could demonstrate that HIV-1 infection and the associated ISG induction correlated with low SRSF1 levels in intestinal lamina propria mononuclear cells (LPMCs) and peripheral blood mononuclear cells (PBMCs) during acute and chronic HIV-1 infection. In HIV-1-susceptible cell lines as well as primary monocyte-derived macrophages (MDMs), expression levels of SRSF1 were transiently repressed upon treatment with specific IFNα subtypes in vitro. Mechanically, 4sU labeling of newly transcribed mRNAs revealed that IFN-mediated SRSF1 repression is regulated on early RNA level. SRSF1 knockdown led to an increase in total viral RNA levels, but the relative proportion of the HIV-1 viral infectivity factor (Vif) coding transcripts, which is essential to counteract APOBEC3G-mediated host restriction, was significantly reduced. In the presence of high APOBEC3G levels, however, increased LTR activity upon SRSF1 knockdown facilitated the overall replication, despite decreased vif mRNA levels. In contrast, SRSF1 overexpression significantly impaired HIV-1 post-integration steps including LTR transcription, alternative splice site usage, and virus particle production. Since balanced SRSF1 levels are crucial for efficient viral replication, our data highlight the so far undescribed role of SRSF1 acting as an IFN-modulated cellular dependency factor decisively regulating HIV-1 post-integration steps.
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Affiliation(s)
- Helene Sertznig
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Fabian Roesmann
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Alexander Wilhelm
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Delia Heininger
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
| | - Barbara Bleekmann
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Carina Elsner
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Mario Santiago
- Department of Medicine, University of Colorado Denver, Aurora, CO, United States
| | - Jonas Schuhenn
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Zehra Karakoese
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Yvonne Benatzy
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Ryan Snodgrass
- Institute of Biochemistry I, Faculty of Medicine, Goethe-University Frankfurt am Main, Frankfurt, Germany
| | - Stefan Esser
- Clinic of Dermatology, University Hospital, University of Duisburg-Essen, Essen, Germany
| | - Kathrin Sutter
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Ulf Dittmer
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
| | - Marek Widera
- Institute for Virology, University Hospital Essen, University Duisburg-Essen, Essen, Germany
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt am Main, Frankfurt am Main, Germany
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14
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Feng J, Zhou J, Lin Y, Huang W. hnRNP A1 in RNA metabolism regulation and as a potential therapeutic target. Front Pharmacol 2022; 13:986409. [PMID: 36339596 PMCID: PMC9634572 DOI: 10.3389/fphar.2022.986409] [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: 07/05/2022] [Accepted: 10/10/2022] [Indexed: 11/22/2022] Open
Abstract
Abnormal RNA metabolism, regulated by various RNA binding proteins, can have functional consequences for multiple diseases. Heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1) is an important RNA binding protein, that regulates various RNA metabolic processes, including transcription, alternative splicing of pre-mRNA, translation, miRNA processing and mRNA stability. As a potent splicing factor, hnRNP A1 can regulate multiple splicing events, including itself, collaborating with other cooperative or antagonistical splicing factors by binding to splicing sites and regulatory elements in exons or introns. hnRNP A1 can modulate gene transcription by directly interacting with promoters or indirectly impacting Pol II activities. Moreover, by interacting with the internal ribosome entry site (IRES) or 3′-UTR of mRNAs, hnRNP A1 can affect mRNA translation. hnRNP A1 can alter the stability of mRNAs by binding to specific locations of 3′-UTR, miRNAs biogenesis and Nonsense-mediated mRNA decay (NMD) pathway. In this review, we conclude the selective sites where hnRNP A1 binds to RNA and DNA, and the co-regulatory factors that interact with hnRNP A1. Given the dysregulation of hnRNP A1 in diverse diseases, especially in cancers and neurodegeneration diseases, targeting hnRNP A1 for therapeutic treatment is extremely promising. Therefore, this review also provides the small-molecule drugs, biomedicines and novel strategies targeting hnRNP A1 for therapeutic purposes.
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Feng X, Rahman MM, Hu Q, Wang B, Karim H, Guzmán C, Harwood W, Xu Q, Zhang Y, Tang H, Jiang Y, Qi P, Deng M, Ma J, Lan J, Wang J, Chen G, Lan X, Wei Y, Zheng Y, Jiang Q. HvGBSSI mutation at the splicing receptor site affected RNA splicing and decreased amylose content in barley. FRONTIERS IN PLANT SCIENCE 2022; 13:1003333. [PMID: 36212333 PMCID: PMC9538149 DOI: 10.3389/fpls.2022.1003333] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/24/2022] [Indexed: 06/16/2023]
Abstract
Granule-bound starch synthase I (HvGBSSI) is encoded by the barley waxy (Wx-1) gene and is the sole enzyme in the synthesis of amylose. Here, a Wx-1 mutant was identified from an ethyl methane sulfonate (EMS)-mutagenized barley population. There were two single-base mutations G1086A and A2424G in Wx-1 in the mutant (M2-1105). The G1086A mutation is located at the 3' splicing receptor (AG) site of the fourth intron, resulting in an abnormal RNA splicing. The A2424G mutation was a synonymous mutation in the ninth intron. The pre-mRNA of Wx-1 was incorrectly spliced and transcribed into two abnormal transcripts. The type I transcript had a 6 bp deletion in the 5' of fifth exon, leading to a translated HvGBSSI protein lacking two amino acids with a decreased starch-binding capacity. In the type II transcript, the fourth intron was incorrectly cleaved and retained, resulting in the premature termination of the barley Wx-1 gene. The mutations in the Wx-1 decreased the enzymatic activity of the HvGBSSI enzyme and resulted in a decreased level in amylose content. This work sheds light on a new Wx-1 gene inaction mechanism.
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Affiliation(s)
- Xiuqin Feng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Md. Mostafijur Rahman
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qian Hu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Bang Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Hassan Karim
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Carlos Guzmán
- Departamento de Genética, Escuela Técnica Superior de Ingeniería Agronómica y de Montes, Universidad de Córdoba, Cordoba, Spain
| | - Wendy Harwood
- John Innes Center, Norwich Research Park, Norwich, United Kingdom
| | - Qiang Xu
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yazhou Zhang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Huaping Tang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yunfeng Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Pengfei Qi
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Mei Deng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jian Ma
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jingyu Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Jirui Wang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Guoyue Chen
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Xiujin Lan
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yuming Wei
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Youliang Zheng
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qiantao Jiang
- State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China, Sichuan Agricultural University, Chengdu, SichuanChina
- Triticeae Research Institute, Sichuan Agricultural University, Chengdu, Sichuan, China
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16
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Goyal S, Vanita V. A missense mutation in TTC8/BBS8 affecting mRNA splicing in patients with non-syndromic retinitis pigmentosa. Mol Genet Genomics 2022; 297:1439-1449. [PMID: 35939099 DOI: 10.1007/s00438-022-01933-y] [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: 12/28/2021] [Accepted: 07/19/2022] [Indexed: 11/27/2022]
Abstract
Splicing disruption is one type of mutation mechanism for disease-predisposing alleles. To date, less than 30 mutations in TTC8/BBS8 have been reported; however, mutations affecting the splice site are rare. Generally missense mutations are assumed to alter protein function; however, reports have shown that mutations in protein coding exons can disrupt splicing by altering exonic splicing silencer or enhancer motifs. Hence, a missense mutation c.1347G > C (p.Q449H) involving final base of the exon 13 in the TTC8, previously identified by us to be linked with non-syndromic autosomal recessive retinitis pigmentosa (arRP), in an Indian family, that might deleteriously affect splicing has been functionally characterized. RNA was isolated, cDNA prepared and amplified using region-specific primers. PCR products were purified and sequenced bi-directionally by Sanger sequencing. Effect of mutation (c.1347G > C) on mRNA splicing has been predicted using bioinformatics tools. We reported that missense mutation (c.1347G > C) at the last base of exon 13 of TTC8 disrupted the canonical donor splice-site resulting in aberrant RNA splicing. A cryptic donor splice-site got activated 77 bases downstream of the authentic splice donor site in intron 13, resulting in the retention of 77 bases of intron 13, and a frameshift leading to pre-mature termination codon in exon 14 at codon 486. Further, duplication of exon 15 and fusion of its duplicated copy occurred with exon 13. The binding site for SC35 protein, normally involved in splicing, also got disrupted (as predicted by SpliceAid2 software), hence, leading to alternative splicing. Our findings strongly suggest that a missense mutation c.1347G > C in TTC8 disrupted the splice donor site causing retention of 77 bases of intron 13, resulting in a frameshift and subsequently introduced a pre-mature termination codon into exon 14, hence creating an altered mRNA transcript. These findings emphasize the significance of examining missense mutations especially in TTC8, to determine their pathogenic role through alternative splicing. Present findings also reiterate the notion that mutations in the TTC8/BBS8 cause phenotypic heterogeneity and does not always follow Mendelian genetics in this ciliopathy.
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Affiliation(s)
- Shiwali Goyal
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, 143005, India
| | - Vanita Vanita
- Department of Human Genetics, Guru Nanak Dev University, Amritsar, Punjab, 143005, India.
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Samadi M, Beigi L, Yadegari F, Ansari AM, Majidzadeh-A K, Eskordi M, Farahmand L. Recognition of functional genetic polymorphism using ESE motif definition: a conservative evolutionary approach to CYP2D6/CYP2C19 gene variants. Genetica 2022; 150:289-297. [PMID: 35913522 DOI: 10.1007/s10709-022-00161-x] [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: 07/27/2021] [Accepted: 03/24/2022] [Indexed: 11/04/2022]
Abstract
Although predicting the effects of variants near intron-exon boundaries is relatively straightforward, predicting the functional Exon Splicing Enhancers (ESEs) and the possible effects of variants within ESEs remains a challenge. Considering the essential role of CYP2D6/CYP2C19 genes in drug metabolism, we attempted to identify variants that are most likely to disrupt splicing through their effect on these ESEs. ESEs were predicted in these two genes using ESEfinder 3.0, incorporating a series of filters (increased threshold and evolutionary conservation). Finally, reported mutations were evaluated for their potential to disrupt splicing by affecting these ESEs. Initially, 169 and 243 ESEs were predicted for CYP2C19/CYP2D6, respectively. However, applying the filters, the number of predicted ESEs was reduced to 26 and 19 in CYP2C19/CYP2D6, respectively. Comparing prioritized predicted ESEs with known sequence variants in CYP2C19/CYP2D6 genes highlights 18 variations within conserved ESEs for each gene. We found good agreement in cases where such predictions could be compared to experimental evidence. In total, we prioritized a subset of mutational changes in CYP2C19/CYP2D6 genes that may affect the function of these genes and lead to altered drug responses. Clinical studies and functional analysis for investigating detailed functional consequences of the mentioned mutations and their phenotypic outcomes is mostly recommended.
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Affiliation(s)
- Mitra Samadi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Laleh Beigi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Fatemeh Yadegari
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Alireza Madjid Ansari
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Keivan Majidzadeh-A
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Maryam Eskordi
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Leila Farahmand
- Recombinant Proteins Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran.
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Eusebi PG, Cortés Ó, Contreras E, Cañón J, Dunner S, Sevane N. A novel missense variant in endothelin-2 (EDN2) causes a growth and respiratory lethal syndrome in bovine. Anim Genet 2022; 53:583-591. [PMID: 35912509 PMCID: PMC9544818 DOI: 10.1111/age.13246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Revised: 07/12/2022] [Accepted: 07/20/2022] [Indexed: 11/29/2022]
Abstract
The high level of fragmentation of the Spanish Lidia cattle breed, divided into lineages called ‘castas’ and into herds within lineages based on reproductive isolation, increases the risk of homozygosity and the outbreak of recessive genetic defects. Since 2004, an increasing number of calves have been identified in a Lidia herd with signs of severe growth retardation, respiratory alterations and juvenile lethality, which constitutes a novel inherited syndrome in cattle and was subsequently termed growth and respiratory lethal syndrome. We performed a genome‐wide association study on a cohort of 13 affected calves and 24 putative non‐carrier parents, mapping the disease to a wide 6 cM region on bovine chromosome 3 (p < 10−7). Whole genome re‐sequencing of three affected calves and three putative non‐carrier parents identified a novel missense variant (c.149G>A|p.Cys50Tyr) in exon 2 of the endothelin 2 (EDN2) gene. Bioinformatic analyses of p.Cys50Tyr effects predicted them to be damaging for both the structure and the function of the edn2 protein, and to create a new site of splicing that may also affect the pattern of pre‐mRNA splicing and exon definition. Sanger sequencing of this variant on the rest of the sample set confirmed the segregation pattern obtained with whole genome re‐sequencing. The identification of the causative variant and the development of a diagnostic genetic test enable the efficient design of matings to keep the effective population size as high as possible, as well as providing insights into the first EDN2‐associated hereditary disease in cattle or other species.
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Affiliation(s)
- Paulina G Eusebi
- Departmento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Óscar Cortés
- Departmento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Elisabeth Contreras
- Departmento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Javier Cañón
- Departmento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Susana Dunner
- Departmento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Natalia Sevane
- Departmento de Producción Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
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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: 0] [Impact Index Per Article: 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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Crespo R, Rao S, Mahmoudi T. HibeRNAtion: HIV-1 RNA Metabolism and Viral Latency. Front Cell Infect Microbiol 2022; 12:855092. [PMID: 35774399 PMCID: PMC9237370 DOI: 10.3389/fcimb.2022.855092] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 05/10/2022] [Indexed: 01/12/2023] Open
Abstract
HIV-1 infection remains non-curative due to the latent reservoir, primarily a small pool of resting memory CD4+ T cells bearing replication-competent provirus. Pharmacological reversal of HIV-1 latency followed by intrinsic or extrinsic cell killing has been proposed as a promising strategy to target and eliminate HIV-1 viral reservoirs. Latency reversing agents have been extensively studied for their role in reactivating HIV-1 transcription in vivo, although no permanent reduction of the viral reservoir has been observed thus far. This is partly due to the complex nature of latency, which involves strict intrinsic regulation at multiple levels at transcription and RNA processing. Still, the molecular mechanisms that control HIV-1 latency establishment and maintenance have been almost exclusively studied in the context of chromatin remodeling, transcription initiation and elongation and most known LRAs target LTR-driven transcription by manipulating these. RNA metabolism is a largely understudies but critical mechanistic step in HIV-1 gene expression and latency. In this review we provide an update on current knowledge on the role of RNA processing mechanisms in viral gene expression and latency and speculate on the possible manipulation of these pathways as a therapeutic target for future cure studies.
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Affiliation(s)
- Raquel Crespo
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Shringar Rao
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Tokameh Mahmoudi
- Department of Biochemistry, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Pathology, Erasmus University Medical Center, Rotterdam, Netherlands
- Department of Urology, Erasmus University Medical Center, Rotterdam, Netherlands
- *Correspondence: Tokameh Mahmoudi,
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21
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Bhat GR, Sethi I, Rah B, Kumar R, Afroze D. Innovative in Silico Approaches for Characterization of Genes and Proteins. Front Genet 2022; 13:865182. [PMID: 35664302 PMCID: PMC9159363 DOI: 10.3389/fgene.2022.865182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Accepted: 04/11/2022] [Indexed: 11/13/2022] Open
Abstract
Bioinformatics is an amalgamation of biology, mathematics and computer science. It is a science which gathers the information from biology in terms of molecules and applies the informatic techniques to the gathered information for understanding and organizing the data in a useful manner. With the help of bioinformatics, the experimental data generated is stored in several databases available online like nucleotide database, protein databases, GENBANK and others. The data stored in these databases is used as reference for experimental evaluation and validation. Till now several online tools have been developed to analyze the genomic, transcriptomic, proteomics, epigenomics and metabolomics data. Some of them include Human Splicing Finder (HSF), Exonic Splicing Enhancer Mutation taster, and others. A number of SNPs are observed in the non-coding, intronic regions and play a role in the regulation of genes, which may or may not directly impose an effect on the protein expression. Many mutations are thought to influence the splicing mechanism by affecting the existing splice sites or creating a new sites. To predict the effect of mutation (SNP) on splicing mechanism/signal, HSF was developed. Thus, the tool is helpful in predicting the effect of mutations on splicing signals and can provide data even for better understanding of the intronic mutations that can be further validated experimentally. Additionally, rapid advancement in proteomics have steered researchers to organize the study of protein structure, function, relationships, and dynamics in space and time. Thus the effective integration of all of these technological interventions will eventually lead to steering up of next-generation systems biology, which will provide valuable biological insights in the field of research, diagnostic, therapeutic and development of personalized medicine.
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Affiliation(s)
- Gh. Rasool Bhat
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Soura, India
| | - Itty Sethi
- Institute of Human Genetics, University of Jammu, Jammu, India
| | - Bilal Rah
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Soura, India
| | - Rakesh Kumar
- School of Biotechnology, Shri Mata Vaishno Devi University, Katra, India
| | - Dil Afroze
- Advanced Centre for Human Genetics, Sher-I- Kashmir Institute of Medical Sciences, Soura, India
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22
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RNPS1 inhibits excessive tumor necrosis factor/tumor necrosis factor receptor signaling to support hematopoiesis in mice. Proc Natl Acad Sci U S A 2022; 119:e2200128119. [PMID: 35482923 DOI: 10.1073/pnas.2200128119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceMessenger RNA (mRNA) splicing is fundamental to protein expression in mammals. Homozygous deletion of single protein components of the splicing machinery or its regulatory factors is embryonic lethal. However, through forward genetic screening in mice, we identified a viable hypomorphic missense mutation of the splicing regulator RNPS1. Homozygous mutant mice displayed altered immune cell development due to excessive tumor necrosis factor (TNF)-dependent immune cell apoptosis. Splicing was impaired in CD8+ T cells and hematopoietic stem cells from RNPS1 mutant mice. TNF knockout rescued hematopoiesis and dramatically reduced splicing defects in RNPS1 hematopoietic cells, demonstrating a surprising link between elevated TNF and defects in splicing caused by RNPS1 deficiency.
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23
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SRSF6 Regulates the Alternative Splicing of the Apoptotic Fas Gene by Targeting a Novel RNA Sequence. Cancers (Basel) 2022; 14:cancers14081990. [PMID: 35454897 PMCID: PMC9025165 DOI: 10.3390/cancers14081990] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/20/2022] Open
Abstract
Simple Summary Alternative splicing (AS) produces multiple mRNA isoforms from a gene to make a large number of proteins. Fas (Apo-1/CD95) pre-mRNA, a member of TNF receptor family that mediates apoptosis, can generate pro-apoptotic and anti-apoptotic proteins through AS. Here, we identified SRSF6 as an essential regulator protein in Fas AS. We further located a new functional target sequence of SRSF6 in Fas splicing. In addition, our large-scale RNA-seq analysis using GTEX and TCGA indicated that while SRSF6 expression was correlated with Fas expression in normal tissues, the correlation was disrupted in tumors. Our results suggest a novel regulatory mechanisms of Fas AS. Abstract Alternative splicing (AS) is a procedure during gene expression that allows the production of multiple mRNAs from a single gene, leading to a larger number of proteins with various functions. The alternative splicing (AS) of Fas (Apo-1/CD95) pre-mRNA can generate membrane-bound or soluble isoforms with pro-apoptotic and anti-apoptotic functions. SRSF6, a member of the Serine/Arginine-rich protein family, plays essential roles in both constitutive and alternative splicing. Here, we identified SRSF6 as an important regulatory protein in Fas AS. The cassette exon inclusion of Fas was decreased by SRSF6-targeting shRNA treatment, but increased by SRSF6 overexpression. The deletion and substitution mutagenesis of the Fas minigene demonstrated that the UGCCAA sequence in the cassette exon of the Fas gene causes the functional disruption of SRSF6, indicating that these sequences are essential for SRSF6 function in Fas splicing. In addition, biotin-labeled RNA-pulldown and immunoblotting analysis showed that SRSF6 interacted with these RNA sequences. Mutagenesis in the splice-site strength alteration demonstrated that the 5′ splice-site, but not the 3′ splice-site, was required for the SRSF6 regulation of Fas pre-mRNA. In addition, a large-scale RNA-seq analysis using GTEX and TCGA indicated that while SRSF6 expression was correlated with Fas expression in normal tissues, the correlation was disrupted in tumors. Furthermore, high SRSF6 expression was linked to the high expression of pro-apoptotic and immune activation genes. Therefore, we identified a novel RNA target with 5′ splice-site dependence of SRSF6 in Fas pre-mRNA splicing, and a correlation between SRSF6 and Fas expression.
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24
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A Novel, Apparently Silent Variant in MFSD8 Causes Neuronal Ceroid Lipofuscinosis with Marked Intrafamilial Variability. Int J Mol Sci 2022; 23:ijms23042271. [PMID: 35216386 PMCID: PMC8877174 DOI: 10.3390/ijms23042271] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/09/2022] [Accepted: 02/16/2022] [Indexed: 02/06/2023] Open
Abstract
Variants in MFSD8 can cause neuronal ceroid lipofuscinoses (NCLs) as well as nonsyndromic retinopathy. The mutation spectrum includes mainly missense and stop variants, but splice sites and frameshift variants have also been reported. To date, apparently synonymous substitutions have not been shown to cause MFSD8-associated diseases. We report two closely related subjects from a consanguineous Turkish family who presented classical features of NCLs but demonstrated marked intrafamilial variability in age at the onset and severity of symptoms. In fact, the difference in the onset of first neurologic symptoms was 15 years and that of ophthalmologic symptoms was 12 years. One subject presented an intellectual disability and a considerable cerebellar ataxia syndrome, while the other subject showed no intellectual disability and only a mild atactic syndrome. The diagnostic genetic testing of both subjects based on genome sequencing prioritized a novel, apparently synonymous variant in MFSD8, which was found in homozygosity in both subjects. The variant was not located within an integral part of the splice site consensus sequences. However, the bioinformatic analyses suggested that the mutant allele is more likely to cause exon skipping due to an altered ratio of exonic splice enhancer and silencer motifs. Exon skipping was confirmed in vitro by minigene assays and in vivo by RNA analysis from patient lymphocytes. The mutant transcript is predicted to result in a frameshift and, if translated, in a truncated protein. Synonymous variants are often given a low priority in genetic diagnostics because of their expected lack of functional impact. This study highlights the importance of investigating the impact of synonymous variants on splicing.
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25
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Gao Y, Lin KT, Jiang T, Yang Y, Rahman MA, Gong S, Bai J, Wang L, Sun J, Sheng L, Krainer AR, Hua Y. Systematic characterization of short intronic splicing-regulatory elements in SMN2 pre-mRNA. Nucleic Acids Res 2022; 50:731-749. [PMID: 35018432 PMCID: PMC8789036 DOI: 10.1093/nar/gkab1280] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Revised: 12/01/2021] [Accepted: 12/14/2021] [Indexed: 12/23/2022] Open
Abstract
Intronic splicing enhancers and silencers (ISEs and ISSs) are two groups of splicing-regulatory elements (SREs) that play critical roles in determining splice-site selection, particularly for alternatively spliced introns or exons. SREs are often short motifs; their mutation or dysregulation of their cognate proteins frequently causes aberrant splicing and results in disease. To date, however, knowledge about SRE sequences and how they regulate splicing remains limited. Here, using an SMN2 minigene, we generated a complete pentamer-sequence library that comprises all possible combinations of 5 nucleotides in intron 7, at a fixed site downstream of the 5′ splice site. We systematically analyzed the effects of all 1023 mutant pentamers on exon 7 splicing, in comparison to the wild-type minigene, in HEK293 cells. Our data show that the majority of pentamers significantly affect exon 7 splicing: 584 of them are stimulatory and 230 are inhibitory. To identify actual SREs, we utilized a motif set enrichment analysis (MSEA), from which we identified groups of stimulatory and inhibitory SRE motifs. We experimentally validated several strong SREs in SMN1/2 and other minigene settings. Our results provide a valuable resource for understanding how short RNA sequences regulate splicing. Many novel SREs can be explored further to elucidate their mechanism of action.
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Affiliation(s)
- Yuan Gao
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Tao Jiang
- Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Yang Yang
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Mohammad A Rahman
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Shuaishuai Gong
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Jialin Bai
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Li Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Junjie Sun
- Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Lei Sheng
- Department of Neurology and Suzhou Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou 215004, China.,Institute of Neuroscience, Soochow University, 199 Renai Road, Suzhou, Jiangsu 215123, China
| | - Adrian R Krainer
- Cold Spring Harbor Laboratory, PO Box 100, Cold Spring Harbor, NY 11724, USA
| | - Yimin Hua
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
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26
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Chen Y, Weng X, Zhou X, Gu J, Hu Q, Luo Q, Wen M, Li C, Wang ZY. Overexpression of cassava RSZ21b enhances drought tolerance in Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2022; 268:153574. [PMID: 34890846 DOI: 10.1016/j.jplph.2021.153574] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 06/13/2023]
Abstract
Drought is one of the major environmental constraints affecting crop productivity. Plants have to adjust their developmental and physiological processes to cope with drought. We previously identified 18 cassava serine/arginine-rich (SR) proteins that had a pivotal role in alternative splicing in response to environmental stress. However, functional characterization of SR proteins is rarely explored. Here, we characterized the RSZ subfamily gene MeRSZ21b in cassava. The RSZ21b belongs to the RSZ subfamily, which was widely distributed in major crops and was highly conserved. Quantitative RT-PCR assay showed that the expression of MeRSZ21b was significantly induced by drought. Moreover, overexpression of MeRSZ21b in Arabidopsis was hypersensitive to abscisic acid (ABA) in the phases of seed germination and post-germination seedling growth. Meantime, MeRSZ21b overexpression lines were resistant to sorbitol treatment, and quickly closed the stomata when compared with Col-0 under drought condition. Importantly, overexpression of MeRSZ21b resulted in improved drought tolerance through modulating ABA-dependent signaling. Therefore, our findings refine our knowledge of the SR protein-coding genes and provide novel insights for enhancing plant resistance to environmental stress.
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Affiliation(s)
- Yanhang Chen
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Xun Weng
- College of Life Sciences, South China Agricultural University, Guangdong, 510642, China
| | - Xiaoxia Zhou
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Jinbao Gu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qing Hu
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China
| | - Qingwen Luo
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Mingfu Wen
- Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China
| | - Cong Li
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China.
| | - Zhen-Yu Wang
- Institute of Nanfan&Seed Industry, Guangdong Academy of Sciences, Guangdong, 510316, China; Zhanjiang Sugarcane Research Center, Guangzhou Sugarcane Industry Research Institute, Zhanjiang, Guangdong, 524300, China.
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27
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Impact of Alternative Splicing Variants on Liver Cancer Biology. Cancers (Basel) 2021; 14:cancers14010018. [PMID: 35008179 PMCID: PMC8750444 DOI: 10.3390/cancers14010018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/15/2021] [Accepted: 12/16/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Among the top ten deadly solid tumors are the two most frequent liver cancers, hepatocellular carcinoma, and intrahepatic cholangiocarcinoma, whose development and malignancy are favored by multifactorial conditions, which include aberrant maturation of pre-mRNA due to abnormalities in either the machinery involved in the splicing, i.e., the spliceosome and associated factors, or the nucleotide sequences of essential sites for the exon recognition process. As a consequence of cancer-associated aberrant splicing in hepatocytes- and cholangiocytes-derived cancer cells, abnormal proteins are synthesized. They contribute to the dysregulated proliferation and eventually transformation of these cells to phenotypes with enhanced invasiveness, migration, and multidrug resistance, which contributes to the poor prognosis that characterizes these liver cancers. Abstract The two most frequent primary cancers affecting the liver, whose incidence is growing worldwide, are hepatocellular carcinoma (HCC) and intrahepatic cholangiocarcinoma (iCCA), which are among the five most lethal solid tumors with meager 5-year survival rates. The common difficulty in most cases to reach an early diagnosis, the aggressive invasiveness of both tumors, and the lack of favorable response to pharmacotherapy, either classical chemotherapy or modern targeted therapy, account for the poor outcome of these patients. Alternative splicing (AS) during pre-mRNA maturation results in changes that might affect proteins involved in different aspects of cancer biology, such as cell cycle dysregulation, cytoskeleton disorganization, migration, and adhesion, which favors carcinogenesis, tumor promotion, and progression, allowing cancer cells to escape from pharmacological treatments. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the available information regarding the impact of AS on liver carcinogenesis and the development of malignant characteristics of HCC and iCCA, whose understanding is required to develop novel therapeutical approaches aimed at manipulating the phenotype of cancer cells.
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28
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Baralle M, Baralle FE. Alternative splicing and liver disease. Ann Hepatol 2021; 26:100534. [PMID: 34547477 DOI: 10.1016/j.aohep.2021.100534] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 07/27/2021] [Accepted: 07/30/2021] [Indexed: 02/04/2023]
Abstract
Alternative splicing produces complex and dynamic changes in the protein isoforms that are necessary for the proper biological functioning of the metabolic pathways involved in liver development and hepatocyte homeostasis. Changes in the physiological state of alternatively spliced forms are increasingly linked to liver pathologies. This may occur when the expression or function of the set of proteins controlling the alternative splicing processes are altered by external effectors such as oxidative stress and other environmental variations. Studies addressing these modifications reveal a complex interplay between the expression levels of different proteins that regulate the alternative splicing process as well as the changes in alternative splicing. This interplay results in a cascade of different protein isoforms that correlate with the progression of non-alcoholic fatty liver disease, hepatocellular carcinoma, and alcoholic liver disease. However, research on the detailed molecular mechanism underlying the production of these isoforms is needed. It is imperative to identify the physiological processes affected by the differentially spliced isoforms and confirm their role on the onset and maintenance of the pathology. This is required to design potential therapeutic approaches targeting the key splicing changes to revert the pathological condition as well as identify prognostic markers. In this review, we describe the complexity of the splicing process through an example to encourage researchers to go down this path. Subsequently, rather than a catalog of splicing events we have hand-picked and discuss a few selected studies of specific liver pathologies and suggested ways to focus research on these areas.
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Affiliation(s)
- Marco Baralle
- International Centre for Genetic Engineering and Biotechnology (ICGEB), Padriciano 99, Italy
| | - Francisco E Baralle
- Fondazione Italiana Fegato-Onlus, Bldg. Q, AREA Science Park, ss14, Km 163.5, Basovizza, 34149 Trieste, Italy.
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29
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Petersen USS, Doktor TK, Andresen BS. Pseudoexon activation in disease by non-splice site deep intronic sequence variation - wild type pseudoexons constitute high-risk sites in the human genome. Hum Mutat 2021; 43:103-127. [PMID: 34837434 DOI: 10.1002/humu.24306] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Revised: 11/02/2021] [Accepted: 11/06/2021] [Indexed: 12/27/2022]
Abstract
Accuracy of pre-messenger RNA (pre-mRNA) splicing is crucial for normal gene expression. Complex regulation supports the spliceosomal distinction between authentic exons and the many seemingly functional splice sites delimiting pseudoexons. Pseudoexons are nonfunctional intronic sequences that can be activated for aberrant inclusion in mRNA, which may cause disease. Pseudoexon activation is very challenging to predict, in particular when activation occurs by sequence variants that alter the splicing regulatory environment without directly affecting splice sites. As pseudoexon inclusion often evades detection due to activation of nonsense-mediated mRNA decay, and because conventional diagnostic procedures miss deep intronic sequence variation, pseudoexon activation is a heavily underreported disease mechanism. Pseudoexon characteristics have mainly been studied based on in silico predicted sequences. Moreover, because recognition of sequence variants that create or strengthen splice sites is possible by comparison with well-established consensus sequences, this type of pseudoexon activation is by far the most frequently reported. Here we review all known human disease-associated pseudoexons that carry functional splice sites and are activated by deep intronic sequence variants located outside splice site sequences. We delineate common characteristics that make this type of wild type pseudoexons distinct high-risk sites in the human genome.
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Affiliation(s)
- Ulrika S S Petersen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Thomas K Doktor
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
| | - Brage S Andresen
- Department of Biochemistry and Molecular Biology and the Villum Center for Bioanalytical Sciences, University of Southern Denmark, Odense M, Denmark
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30
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Gachet-Castro C, Freitas-Castro F, Gonzáles-Córdova RA, da Fonseca CK, Gomes MD, Ishikawa-Ankerhold HC, Baqui MMA. Modulation of the Host Nuclear Compartment by Trypanosoma cruzi Uncovers Effects on Host Transcription and Splicing Machinery. Front Cell Infect Microbiol 2021; 11:718028. [PMID: 34737973 PMCID: PMC8560699 DOI: 10.3389/fcimb.2021.718028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 09/24/2021] [Indexed: 11/22/2022] Open
Abstract
Host manipulation is a common strategy for invading pathogens. Trypanosoma cruzi, the causative agent of Chagas Disease, lives intracellularly within host cells. During infection, parasite-associated modifications occur to the host cell metabolism and morphology. However, little is known about the effect of T. cruzi infection on the host cell nucleus and nuclear functionality. Here, we show that T. cruzi can modulate host transcription and splicing machinery in non-professional phagocytic cells during infection. We found that T. cruzi regulates host RNA polymerase II (RNAPII) in a time-dependent manner, resulting in a drastic decrease in RNAPII activity. Furthermore, host cell ribonucleoproteins associated with mRNA transcription (hnRNPA1 and AB2) are downregulated concurrently. We reasoned that T. cruzi may hijack the host U2AF35 auxiliary factor, a key regulator for RNA processing, as a strategy to affect the splicing machinery activities directly. In support of our hypothesis, we carried out in vivo splicing assays using an adenovirus E1A pre-mRNA splicing reporter, showing that intracellular T. cruzi directly modulates the host cells by appropriating U2AF35. For the first time, our results provide evidence of a complex and intimate molecular relationship between T. cruzi and the host cell nucleus during infection.
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Affiliation(s)
- Camila Gachet-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Felipe Freitas-Castro
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Raul Alexander Gonzáles-Córdova
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Carol Kobori da Fonseca
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | - Marcelo Damário Gomes
- Department of Biochemistry and Immunology, Ribeirão Preto Medical School, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
| | | | - Munira Muhammad Abdel Baqui
- Department of Cellular and Molecular Biology and Pathogenic Bioagents, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto, Brazil
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31
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Schorr AL, Mangone M. miRNA-Based Regulation of Alternative RNA Splicing in Metazoans. Int J Mol Sci 2021; 22:ijms222111618. [PMID: 34769047 PMCID: PMC8584187 DOI: 10.3390/ijms222111618] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 10/21/2021] [Accepted: 10/22/2021] [Indexed: 12/15/2022] Open
Abstract
Alternative RNA splicing is an important regulatory process used by genes to increase their diversity. This process is mainly executed by specific classes of RNA binding proteins that act in a dosage-dependent manner to include or exclude selected exons in the final transcripts. While these processes are tightly regulated in cells and tissues, little is known on how the dosage of these factors is achieved and maintained. Several recent studies have suggested that alternative RNA splicing may be in part modulated by microRNAs (miRNAs), which are short, non-coding RNAs (~22 nt in length) that inhibit translation of specific mRNA transcripts. As evidenced in tissues and in diseases, such as cancer and neurological disorders, the dysregulation of miRNA pathways disrupts downstream alternative RNA splicing events by altering the dosage of splicing factors involved in RNA splicing. This attractive model suggests that miRNAs can not only influence the dosage of gene expression at the post-transcriptional level but also indirectly interfere in pre-mRNA splicing at the co-transcriptional level. The purpose of this review is to compile and analyze recent studies on miRNAs modulating alternative RNA splicing factors, and how these events contribute to transcript rearrangements in tissue development and disease.
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Affiliation(s)
- Anna L. Schorr
- Molecular and Cellular Biology Graduate Program, School of Life Sciences, 427 East Tyler Mall, Tempe, AZ 85287, USA;
| | - Marco Mangone
- Virginia G. Piper Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University, 1001 S McAllister Ave., Tempe, AZ 85287, USA
- Correspondence: ; Tel.: +1-480-965-7957
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32
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Impact of alternative splicing on mechanisms of resistance to anticancer drugs. Biochem Pharmacol 2021; 193:114810. [PMID: 34673012 DOI: 10.1016/j.bcp.2021.114810] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 12/15/2022]
Abstract
A shared characteristic of many tumors is the lack of response to anticancer drugs. Multiple mechanisms of pharmacoresistance (MPRs) are involved in permitting cancer cells to overcome the effect of these agents. Pharmacoresistance can be primary (intrinsic) or secondary (acquired), i.e., triggered or enhanced in response to the treatment. Moreover, MPRs usually result in the lack of sensitivity to several agents, which accounts for diverse multidrug-resistant (MDR) phenotypes. MPRs are based on the dynamic expression of more than one hundred genes, constituting the so-called resistome. Alternative splicing (AS) during pre-mRNA maturation results in changes affecting proteins involved in the resistome. The resulting splicing variants (SVs) reduce the efficacy of anticancer drugs by lowering the intracellular levels of active agents, altering molecular targets, enhancing both DNA repair ability and defensive mechanism of tumors, inducing changes in the balance between pro-survival and pro-apoptosis signals, modifying interactions with the tumor microenvironment, and favoring malignant phenotypic transitions. Reasons accounting for cancer-associated aberrant splicing include mutations that create or disrupt splicing sites or splicing enhancers or silencers, abnormal expression of splicing factors, and impaired signaling pathways affecting the activity of the splicing machinery. Here we have reviewed the impact of AS on MPR in cancer cells.
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33
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Liu S, Kang WJ, Abrimian A, Xu J, Cartegni L, Majumdar S, Hesketh P, Bekker A, Pan YX. Alternative Pre-mRNA Splicing of the Mu Opioid Receptor Gene, OPRM1: Insight into Complex Mu Opioid Actions. Biomolecules 2021; 11:biom11101525. [PMID: 34680158 PMCID: PMC8534031 DOI: 10.3390/biom11101525] [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: 08/30/2021] [Revised: 10/11/2021] [Accepted: 10/11/2021] [Indexed: 12/03/2022] Open
Abstract
Most opioid analgesics used clinically, including morphine and fentanyl, as well as the recreational drug heroin, act primarily through the mu opioid receptor, a class A Rhodopsin-like G protein-coupled receptor (GPCR). The single-copy mu opioid receptor gene, OPRM1, undergoes extensive alternative splicing, creating multiple splice variants or isoforms via a variety of alternative splicing events. These OPRM1 splice variants can be categorized into three major types based on the receptor structure: (1) full-length 7 transmembrane (TM) C-terminal variants; (2) truncated 6TM variants; and (3) single TM variants. Increasing evidence suggests that these OPRM1 splice variants are pharmacologically important in mediating the distinct actions of various mu opioids. More importantly, the OPRM1 variants can be targeted for development of novel opioid analgesics that are potent against multiple types of pain, but devoid of many side-effects associated with traditional opiates. In this review, we provide an overview of OPRM1 alternative splicing and its functional relevance in opioid pharmacology.
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Affiliation(s)
- Shan Liu
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
| | - Wen-Jia Kang
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
| | - Anna Abrimian
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
| | - Jin Xu
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
| | - Luca Cartegni
- Department of Chemical Biology, Ernest Mario School of Pharmacy Rutgers University, Piscataway, NJ 08854, USA;
| | - Susruta Majumdar
- Center for Clinical Pharmacology, University of Health Sciences & Pharmacy and Washington University School of Medicine, St. Louis, MO 63110, USA;
| | - Patrick Hesketh
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
| | - Alex Bekker
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
| | - Ying-Xian Pan
- Department of Anesthesiology, Rutgers New Jersey Medical School, Newark, NJ 07103, USA; (S.L.); (W.-J.K.); (A.A.); (J.X.); (P.H.); (A.B.)
- Correspondence: ; Tel.: +1-973-972-3213
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Cyclophilins and Their Functions in Abiotic Stress and Plant-Microbe Interactions. Biomolecules 2021; 11:biom11091390. [PMID: 34572603 PMCID: PMC8464771 DOI: 10.3390/biom11091390] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/15/2021] [Accepted: 09/17/2021] [Indexed: 01/12/2023] Open
Abstract
Plants have developed a variety of mechanisms and regulatory pathways to change their gene expression profiles in response to abiotic stress conditions and plant–microbe interactions. The plant–microbe interaction can be pathogenic or beneficial. Stress conditions, both abiotic and pathogenic, negatively affect the growth, development, yield and quality of plants, which is very important for crops. In contrast, the plant–microbe interaction could be growth-promoting. One of the proteins involved in plant response to stress conditions and plant–microbe interactions is cyclophilin. Cyclophilins (CyPs), together with FK506-binding proteins (FKBPs) and parvulins, belong to a big family of proteins with peptidyl-prolyl cis-trans isomerase activity (Enzyme Commission (EC) number 5.2.1.8). Genes coding for proteins with the CyP domain are widely expressed in all organisms examined, including bacteria, fungi, animals, and plants. Their different forms can be found in the cytoplasm, endoplasmic reticulum, nucleus, chloroplast, mitochondrion and in the phloem space. They are involved in numerous processes, such as protein folding, cellular signaling, mRNA processing, protein degradation and apoptosis. In the past few years, many new functions, and molecular mechanisms for cyclophilins have been discovered. In this review, we aim to summarize recent advances in cyclophilin research to improve our understanding of their biological functions in plant defense and symbiotic plant–microbe interactions.
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Han S, Na Y, Koh I, Nho K, Lee Y. Alternative Splicing Regulation of Low-Frequency Genetic Variants in Exon 2 of TREM2 in Alzheimer's Disease by Splicing-Based Aggregation. Int J Mol Sci 2021; 22:ijms22189865. [PMID: 34576031 PMCID: PMC8471326 DOI: 10.3390/ijms22189865] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 08/26/2021] [Accepted: 09/08/2021] [Indexed: 01/02/2023] Open
Abstract
TREM2 is among the most well-known Alzheimer’s disease (AD) risk genes; however, the functional roles of its AD-associated variants remain to be elucidated, and most known risk alleles are low-frequency variants whose investigation is challenging. Here, we utilized a splicing-guided aggregation method in which multiple low-frequency TREM2 variants were bundled together to investigate the functional impact of those variants on alternative splicing in AD. We analyzed whole genome sequencing (WGS) and RNA-seq data generated from cognitively normal elderly controls (CN) and AD patients in two independent cohorts, representing three regions in the frontal lobe of the human brain: the dorsolateral prefrontal cortex (CN = 213 and AD = 376), frontal pole (CN = 72 and AD = 175), and inferior frontal (CN = 63 and AD = 157). We observed an exon skipping event in the second exon of TREM2, with that exon tending to be more frequently skipped (p = 0.0012) in individuals having at least one low-frequency variant that caused loss-of-function for a splicing regulatory element. In addition, genes differentially expressed between AD patients with high vs. low skipping of the second exon (i.e., loss of a TREM2 functional domain) were significantly enriched in immune-related pathways. Our splicing-guided aggregation method thus provides new insight into the regulation of alternative splicing of the second exon of TREM2 by low-frequency variants and could be a useful tool for further exploring the potential molecular mechanisms of multiple, disease-associated, low-frequency variants.
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Affiliation(s)
- Seonggyun Han
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA;
| | - Yirang Na
- Transdisciplinary Department of Medicine and Advanced Technology, Seoul National University Hospital, Seoul 03080, Korea;
| | - Insong Koh
- Department of Physiology, Hanyang University, Seoul 04763, Korea
- Correspondence: (I.K.); (K.N.); (Y.L.)
| | - Kwangsik Nho
- Department of Radiology and Imaging Sciences, Indiana Alzheimer’s Disease Research Center, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN 46202, USA
- Correspondence: (I.K.); (K.N.); (Y.L.)
| | - Younghee Lee
- Department of Biomedical Informatics, University of Utah School of Medicine, Salt Lake City, UT 84108, USA;
- Correspondence: (I.K.); (K.N.); (Y.L.)
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Zhou X, Xu H, Cai X, Tang B, Liu X, Shi Y, Zheng J, Liao W, Yu L. Differences in SCN1A intronic variants result in diverse aberrant splicing patterns and are related to the phenotypes of epilepsy with febrile seizures. Epilepsy Res 2021; 176:106711. [PMID: 34293681 DOI: 10.1016/j.eplepsyres.2021.106711] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 06/05/2021] [Accepted: 07/05/2021] [Indexed: 10/20/2022]
Abstract
OBJECTIVE Intronic variants of the SCN1A gene are detected in patients with epilepsy with febrile seizures (EFS), which includes a series of phenotypes with different severities. However, the pathogenicity of intronic variants and their genotype-phenotype correlation remain under characterized. The purpose of this study was to determine the changes in mRNA splicing caused by SCN1A intronic variants associated with EFS and their association with phenotypes. METHODS Five SCN1A intronic variants detected in patients with focal epilepsy with antecedent febrile seizures plus (FEFS+) and Dravet syndrome (DS) were molecularly cloned. Through an in vitro minigene splicing assay, their influence on mRNA splicing was qualitatively and quantitatively compared and analyzed using reverse-transcription polymerase chain reaction (RT-PCR) and fluorescence quantitative PCR (Q-PCR). RESULTS The severe phenotype of DS-associated variants c.602 + 1G > A and c.4853-1G > C, which occurred in canonical splice sites of introns, caused exon skipping and little retention of full-length mRNA, while the milder phenotype of FEFS+-associated variants c.473 + 5G > A, c.473 + 5G > C and c.4853-25T > A, which occurred in potential splice sites or in deep intronic regions, presented partial exon skipping or intronic insertion and significantly higher retention of full-length mRNA at different levels. Full-length mRNA retention was negatively correlated with the location of intronic variants and phenotype severity. CONCLUSION The different aberrant splicing patterns resulting from SCN1A intronic variants with different positions represent a potential molecular mechanism for phenotypic differences in EFS. This research provides valuable clues for functional studies on the pathogenicity of intronic variants and for the evaluation of genotype-phenotype correlations.
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Affiliation(s)
- Xijing Zhou
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Haiqing Xu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Xiuqu Cai
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Bin Tang
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Xiaorong Liu
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Yiwu Shi
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China
| | - Jinou Zheng
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, GX, China
| | - Weiping Liao
- Institute of Neuroscience and the Second Affiliated Hospital of Guangzhou Medical University, Guangzhou, GD, China.
| | - Lu Yu
- Department of Neurology, The First Affiliated Hospital of Guangxi Medical University, Nanning, GX, China.
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Chen S, Wu P, Wu B, Lin C, Chen J, Chen L, Lv G. A Missense Mutation rs781536408 (c.2395G>A) of TYK2 Affects Splicing and Causes Skipping of Exon18 in vivo. Front Genet 2021; 12:679678. [PMID: 34234812 PMCID: PMC8255812 DOI: 10.3389/fgene.2021.679678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
TYK2 variants can impact disease onset or progression. In our previous study, we identified abnormal splicing that happened near rs781536408 in the TYK2 gene. The purpose of this research was to examine the effect of the mutation on alternative splicing in vivo and in vitro. Whole exome sequencing was performed to identify the mutations followed by bidirectional Sanger sequencing. Then the minigene analysis was carried out based on HeLa and HEK293T cell lines. The results showed that rs781536408 (c.2395G>A, p.G799R) was homozygous in the patient, but heterozygous in parents. PCR amplification confirmed the abnormal splicing in the somatic cells of the patients, but not in the parents. Sanger sequencing results showed that there was a skipping of exon18 near the mutation. For minigene analysis, there was no difference between the wild-type and the mutant type in the two minigene construction strategies, indicating that mutation c.2395G>A had no effect on splicing in vitro. Combining the results of in vivo, we speculated that the effect of the mutation on splicing was not absolute, but rather in degree.
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Affiliation(s)
- Suqing Chen
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Peilin Wu
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Bin Wu
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Chenye Lin
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Junhong Chen
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Lishengdan Chen
- Department of Pediatrics, The First Affiliated Hospital of Fujian Medical University, Fuzhou, China
| | - Ge Lv
- Chongqing Key Laboratory of Child Infectious and Immunity, Children's Hospital of Chongqing Medical University, Chongqing, China
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Li Z, Tang J, Bassham DC, Howell SH. Daily temperature cycles promote alternative splicing of RNAs encoding SR45a, a splicing regulator in maize. PLANT PHYSIOLOGY 2021; 186:1318-1335. [PMID: 33705553 PMCID: PMC8195531 DOI: 10.1093/plphys/kiab110] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 02/18/2021] [Indexed: 05/04/2023]
Abstract
Elevated temperatures enhance alternative RNA splicing in maize (Zea mays) with the potential to expand the repertoire of plant responses to heat stress. Alternative RNA splicing generates multiple RNA isoforms for many maize genes, and here we observed changes in the pattern of RNA isoforms with temperature changes. Increases in maximum daily temperature elevated the frequency of the major modes of alternative splices (AS), in particular retained introns and skipped exons. The genes most frequently targeted by increased AS with temperature encode factors involved in RNA processing and plant development. Genes encoding regulators of alternative RNA splicing were themselves among the principal AS targets in maize. Under controlled environmental conditions, daily changes in temperature comparable to field conditions altered the abundance of different RNA isoforms, including the RNAs encoding the splicing regulator SR45a, a member of the SR45 gene family. We established an "in protoplast" RNA splicing assay to show that during the afternoon on simulated hot summer days, SR45a RNA isoforms were produced with the potential to encode proteins efficient in splicing model substrates. With the RNA splicing assay, we also defined the exonic splicing enhancers that the splicing-efficient SR45a forms utilize to aid in the splicing of model substrates. Hence, with rising temperatures on hot summer days, SR45a RNA isoforms in maize are produced with the capability to encode proteins with greater RNA splicing potential.
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Affiliation(s)
- Zhaoxia Li
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
| | - Jie Tang
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Diane C Bassham
- Genetics, Development and Cell Biology Department, Iowa State University, Ames, Iowa 50011, USA
| | - Stephen H. Howell
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011, USA
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Li Q, Zeng C, Liu H, Yung KWY, Chen C, Xie Q, Zhang Y, Wan SWC, Mak BSW, Xia J, Xiong S, Ngo JCK. Protein-Protein Interaction Inhibitor of SRPKs Alters the Splicing Isoforms of VEGF and Inhibits Angiogenesis. iScience 2021; 24:102423. [PMID: 33997701 PMCID: PMC8102418 DOI: 10.1016/j.isci.2021.102423] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Revised: 03/13/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022] Open
Abstract
Serine-arginine (SR) protein kinases (SRPKs) regulate the functions of the SR-rich splicing factors by phosphorylating multiple serines within their C-terminal arginine-serine-rich domains. Dysregulation of these phosphorylation events has been implicated in many diseases, suggesting SRPKs are potential therapeutic targets. In particular, aberrant SRPK1 expression alters the balances of proangiogenic (VEGF165) and antiangiogenic (VEGF165b) splicing isoforms of the key angiogenesis factor, vascular endothelial growth factor (VEGF), through the phosphorylation of prototypic SR protein SRSF1. Here, we report a protein-protein interaction (PPI) inhibitor of SRPKs, docking blocker of SRPK1 (DBS1), that specifically blocks a conserved substrate docking groove unique to SRPKs. DBS1 is a cell-permeable inhibitor that effectively inhibits the binding and phosphorylation of SRSF1 and subsequently switches VEGF splicing from the proangiogenic to the antiangiogenic isoform. Our findings thus provide a new direction for the development of SRPK inhibitors through targeting a unique PPI site to combat angiogenic diseases.
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Affiliation(s)
- Qingyun Li
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
- Hong Kong Branch of National Engineering Research Center of Genetic Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Chuyue Zeng
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Haizhen Liu
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Kristen Wing Yu Yung
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Chun Chen
- Department of Cellular Biology, Jinan University, Guangzhou, China
| | - Qiuling Xie
- Department of Cellular Biology, Jinan University, Guangzhou, China
| | - Yu Zhang
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Stephanie Winn Chee Wan
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Bertha Sze Wing Mak
- School of Life Sciences, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Jiang Xia
- Department of Chemistry, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Sheng Xiong
- Department of Cellular Biology, Jinan University, Guangzhou, China
- Hong Kong Branch of National Engineering Research Center of Genetic Medicine, 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
- Hong Kong Branch of National Engineering Research Center of Genetic Medicine, 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
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Lei S, Zhang B, Huang L, Zheng Z, Xie S, Shen L, Breitzig M, Czachor A, Liu H, Luo H, Chen Y, Liu K, Sun H, Zheng Q, Li Q, Wang F. SRSF1 promotes the inclusion of exon 3 of SRA1 and the invasion of hepatocellular carcinoma cells by interacting with exon 3 of SRA1pre-mRNA. Cell Death Discov 2021; 7:117. [PMID: 34011971 PMCID: PMC8134443 DOI: 10.1038/s41420-021-00498-w] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 04/04/2021] [Accepted: 04/24/2021] [Indexed: 12/27/2022] Open
Abstract
Steroid receptor RNA activator 1 (SRA1) has been described as a novel transcriptional co-activator that affects the migration of cancer cells. Through RT-PCR, we identified that skipping exon 3 of SRA1 produces two isoforms, including the truncated short isoform, SRA1-S, and the long isoform, SRA1-L. However, the effect of these two isomers on the migration of HCC cells, as well as the specific mechanism of exon 3 skipping remain unclear. In this study, we found up regulated expression of SRSF1 and SRA1-L in highly metastatic HCCLM3, as well as in HCCs with SRSF1 demonstrating the strongest correlation with SRA1-L. In contrast, we observed a constitutively low expression of SRA1-S and SRSF1 in lowly metastatic HepG2 cells. Overexpression of SRSF1 or SRA1-L promoted migration and invasion by increasing the expression of CD44, while SRA1-S reversed the effect of SRSF1 and SRA1-L in vitro. In addition, lung metastasis in mice revealed that, knockdown of SRSF1 or SRA1-L inhibited the migration of HCC cells, while SRA1-L overexpression abolished the effect of SRSF1 knockout and instead promoted HCC cells migration in vivo. More importantly, RNA immunoprecipitation and Cross-link immunoprecipitation analyses showed that SRSF1 interacts with exon 3 of SRA1 to up regulate the expression of SRA1-L in HCC cells. RNA pull-down results indicated that SRSF1 could also bind to exon 3 of SRA1 in vitro. Finally, minigene -MS2 mutation experiments showed that mutation of the SRA1 exon 3 binding site for SRSF1 prevented the binding of SRA1 pre-mRNA. In summary, our results provide experimental evidence that SRA1 exon 3 inclusion is up regulated by SRSF1 to promote tumor invasion and metastasis in hepatocellular carcinoma.
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Affiliation(s)
- Sijia Lei
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Bin Zhang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Luyuan Huang
- University of Chinese Academy of Science, Beijing, China
| | - Ziyou Zheng
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Shaohan Xie
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Lianghua Shen
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Mason Breitzig
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
- Brown School of Social Work, Washington University in St. Louis, St. Louis, MO, USA
| | - Alexander Czachor
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Hongtao Liu
- College of Life Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Huiru Luo
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Yanxia Chen
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China
| | - Kangshou Liu
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, China
| | - Hanxiao Sun
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Qing Zheng
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China
| | - Qiang Li
- Department of General Surgery, The First Affiliated Hospital, Jinan University, Guangzhou, China.
| | - Feng Wang
- Institute of Genomic Medicine, College of Pharmacy, Jinan University, Guangzhou, China.
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of Pharmacy, Jinan University, Guangzhou, China.
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
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El Marabti E, Abdel-Wahab O. Therapeutic Modulation of RNA Splicing in Malignant and Non-Malignant Disease. Trends Mol Med 2021; 27:643-659. [PMID: 33994320 DOI: 10.1016/j.molmed.2021.04.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/11/2021] [Accepted: 04/13/2021] [Indexed: 01/24/2023]
Abstract
RNA splicing is the enzymatic process by which non-protein coding sequences are removed from RNA to produce mature protein-coding mRNA. Splicing is thereby a major mediator of proteome diversity as well as a dynamic regulator of gene expression. Genetic alterations disrupting splicing of individual genes or altering the function of splicing factors contribute to a wide range of human genetic diseases as well as cancer. These observations have resulted in the development of therapies based on oligonucleotides that bind to RNA sequences and modulate splicing for therapeutic benefit. In parallel, small molecules that bind to splicing factors to alter their function or modify RNA processing of individual transcripts are being pursued for monogenic disorders as well as for cancer.
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Affiliation(s)
- Ettaib El Marabti
- Clinical Transplant Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Omar Abdel-Wahab
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Leukemia Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA.
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Bedi K, Magnuson BR, Narayanan I, Paulsen M, Wilson TE, Ljungman M. Co-transcriptional splicing efficiencies differ within genes and between cell types. RNA (NEW YORK, N.Y.) 2021; 27:rna.078662.120. [PMID: 33975916 PMCID: PMC8208053 DOI: 10.1261/rna.078662.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Accepted: 05/05/2021] [Indexed: 06/01/2023]
Abstract
Pre-mRNA splicing is carried out by the spliceosome and involves splice site recognition, removal of introns, and ligation of exons. Components of the spliceosome have been shown to interact with the elongating RNA polymerase II (RNAPII) which is thought to allow splicing to occur concurrently with transcription. However, little is known about the regulation and efficiency of co-transcriptional splicing in human cells. In this study, we used Bru-seq and BruChase-seq to determine the co-transcriptional splicing efficiencies of 17,000 introns expressed across 6 human cell lines. We found that less than half of all introns across these 6 cell lines were co-transcriptionally spliced. Splicing efficiencies for individual introns showed variations across cell lines, suggesting that splicing may be regulated in a cell-type specific manner. Moreover, the splicing efficiency of introns varied within genes. The efficiency of co-transcriptional splicing did not correlate with gene length, intron position, splice site strengths, or the intron/neighboring exons GC content. However, we identified binding signals from multiple RNA binding proteins (RBPs) that correlated with splicing efficiency, including core spliceosomal machinery components-such as SF3B4, U2AF1 and U2AF2 showing higher binding signals in poorly spliced introns. In addition, multiple RBPs, such as BUD13, PUM1 and SND1, showed preferential binding in exons that flank introns with high splicing efficiencies. The nascent RNA splicing patterns presented here across multiple cell types add to our understanding of the complexity in RNA splicing, wherein RNA-binding proteins may play important roles in determining splicing outcomes in a cell type- and intron-specific manner.
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Nogueira G, Fernandes R, García-Moreno JF, Romão L. Nonsense-mediated RNA decay and its bipolar function in cancer. Mol Cancer 2021; 20:72. [PMID: 33926465 PMCID: PMC8082775 DOI: 10.1186/s12943-021-01364-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/19/2021] [Indexed: 12/17/2022] Open
Abstract
Nonsense-mediated decay (NMD) was first described as a quality-control mechanism that targets and rapidly degrades aberrant mRNAs carrying premature termination codons (PTCs). However, it was found that NMD also degrades a significant number of normal transcripts, thus arising as a mechanism of gene expression regulation. Based on these important functions, NMD regulates several biological processes and is involved in the pathophysiology of a plethora of human genetic diseases, including cancer. The present review aims to discuss the paradoxical, pro- and anti-tumorigenic roles of NMD, and how cancer cells have exploited both functions to potentiate the disease. Considering recent genetic and bioinformatic studies, we also provide a comprehensive overview of the present knowledge of the advantages and disadvantages of different NMD modulation-based approaches in cancer therapy, reflecting on the challenges imposed by the complexity of this disease. Furthermore, we discuss significant advances in the recent years providing new perspectives on the implications of aberrant NMD-escaping frameshifted transcripts in personalized immunotherapy design and predictive biomarker optimization. A better understanding of how NMD differentially impacts tumor cells according to their own genetic identity will certainly allow for the application of novel and more effective personalized treatments in the near future.
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Affiliation(s)
- Gonçalo Nogueira
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Rafael Fernandes
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Juan F García-Moreno
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal.,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal
| | - Luísa Romão
- Departamento de Genética Humana, Instituto Nacional de Saúde Doutor Ricardo Jorge, 1649-016, Lisbon, Portugal. .,BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisbon, Portugal.
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44
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Wang H, Jiang Y. SRp20: A potential therapeutic target for human tumors. Pathol Res Pract 2021; 224:153444. [PMID: 34126370 DOI: 10.1016/j.prp.2021.153444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 04/11/2021] [Accepted: 04/11/2021] [Indexed: 12/12/2022]
Abstract
As an important member of SR protein family, SRp20 plays a crucial role in alternative splicing. It not only participates in cell cycle regulation, export of mRNA, cleaving of primary microRNAs, homologous recombination-mediated DNA repair, cellular senescence and apoptosis, but also gets involved in the integrity and pluripotency of genome. Alternative splicing maintains a strict balance in the body to ensure the normal physiological function of cells. Once the balance is broken, diseases, even tumors, will follow. Through the analysis of SRp20-related articles, we found that Alzheimer's disease, glaucoma, bipolar disorder and other diseases have a certain relationship with SRp20. More importantly, SRp20 is closely related to the occurrence, proliferation, invasion and metastasis of various tumors, as well as chemotherapy resistance. Some SRp20 inhibitors have shown significant anticancer efficacy, suggesting a potential therapeutic strategy for tumors.
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Affiliation(s)
- Han Wang
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen, China
| | - Yanxia Jiang
- Department of Pathology, The Affiliated Hospital of Qingdao University, Qingdao, China.
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45
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Choi N, Liu Y, Oh J, Ha J, Ghigna C, Zheng X, Shen H. Relative strength of 5’ splice-site strength defines functions of SRSF2 and SRSF6 in alternative splicing of Bcl-x pre-mRNA. BMB Rep 2021. [PMID: 33050987 PMCID: PMC8016662 DOI: 10.5483/bmbrep.2021.54.3.170] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Bcl-x, a member of the Bcl-2 family, plays a key role in apoptosis. Alternative splicing of Bcl-x pre-mRNA through alternative 5’ splice-site selection produces an anti-apoptotic mRNA isoform that includes exon 2b and a pro-apoptotic Bcl-x mRNA isoform that excludes exon 2b. Here we used Bcl-x minigene and identified SRSF2 and SRSF6 as two regulatory factors of 5’ splice-site selection of Bcl-x pre-mRNA. We selected binding clusters closer to 5’ splice-sites from multiple potential binding sites of SRSF2 and SRSF6 to perform loss of functions analysis through site-directed mutagenesis. Our results demonstrated that these mutations did not abolish regulatory functions of SRSF2 or SRSF6, indicating that a single binding motif or a cluster was not a functional target of these proteins in Bcl-x pre-mRNA splicing. Random deletion mutagenesis did not disrupt the role of SRSF2 and SRSF6. Importantly, mutagenesis of 5’ splice-site to a conserved or a weaker score demonstrated that the weaker strength of the target 5’ splice-site or higher strength of the other 5’ splice-site strength limited the role of SRSF2 and SRSF6 in 5’ splice-site activation.
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Affiliation(s)
- Namjeong Choi
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Yongchao Liu
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jagyeong Oh
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Jiyeon Ha
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Claudia Ghigna
- Institute of Molecular Genetics “Luigi Luca Cavalli-Sforza”, National Research Council, Pavia 27100, Italy
| | - Xuexiu Zheng
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
| | - Haihong Shen
- School of Life Sciences, Gwangju Institute of Science and Technology, Gwangju 61005, Korea
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46
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SRSF9 Regulates Cassette Exon Splicing of Caspase-2 by Interacting with Its Downstream Exon. Cells 2021; 10:cells10030679. [PMID: 33808656 PMCID: PMC8003524 DOI: 10.3390/cells10030679] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Revised: 03/01/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Alternative splicing (AS) is an important posttranscriptional regulatory process. Damaged or unnecessary cells need to be removed though apoptosis to maintain physiological processes. Caspase-2 pre-mRNA produces pro-apoptotic long mRNA and anti-apoptotic short mRNA isoforms through AS. How AS of Caspase-2 is regulated remains unclear. In the present study, we identified a novel regulatory protein SRSF9 for AS of Caspase-2 cassette exon 9. Knock-down (KD) of SRSF9 increased inclusion of cassette exon and on the other hand, overexpression of SRSF9 decreased inclusion of this exon. Deletion mutagenesis demonstrated that exon 9, parts of intron 9, exon 8 and exon 10 were not required for the role of SRSF9 in Caspase-2 AS. However, deletion and substitution mutation analysis revealed that AGGAG sequence located at exon 10 provided functional target for SRSF9. In addition, RNA-pulldown mediated immunoblotting analysis showed that SRSF9 interacted with this sequence. Gene ontology analysis of RNA-seq from SRSF9 KD cells demonstrates that SRSF9 could regulate AS of a subset of apoptosis related genes. Collectively, our results reveal a basis for regulation of Caspase-2 AS.
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47
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Alvelos MI, Brüggemann M, Sutandy FXR, Juan-Mateu J, Colli ML, Busch A, Lopes M, Castela Â, Aartsma-Rus A, König J, Zarnack K, Eizirik DL. The RNA-binding profile of the splicing factor SRSF6 in immortalized human pancreatic β-cells. Life Sci Alliance 2021; 4:e202000825. [PMID: 33376132 PMCID: PMC7772782 DOI: 10.26508/lsa.202000825] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Revised: 12/15/2020] [Accepted: 12/15/2020] [Indexed: 12/16/2022] Open
Abstract
In pancreatic β-cells, the expression of the splicing factor SRSF6 is regulated by GLIS3, a transcription factor encoded by a diabetes susceptibility gene. SRSF6 down-regulation promotes β-cell demise through splicing dysregulation of central genes for β-cells function and survival, but how RNAs are targeted by SRSF6 remains poorly understood. Here, we define the SRSF6 binding landscape in the human pancreatic β-cell line EndoC-βH1 by integrating individual-nucleotide resolution UV cross-linking and immunoprecipitation (iCLIP) under basal conditions with RNA sequencing after SRSF6 knockdown. We detect thousands of SRSF6 bindings sites in coding sequences. Motif analyses suggest that SRSF6 specifically recognizes a purine-rich consensus motif consisting of GAA triplets and that the number of contiguous GAA triplets correlates with increasing binding site strength. The SRSF6 positioning determines the splicing fate. In line with its role in β-cell function, we identify SRSF6 binding sites on regulated exons in several diabetes susceptibility genes. In a proof-of-principle, the splicing of the susceptibility gene LMO7 is modulated by antisense oligonucleotides. Our present study unveils the splicing regulatory landscape of SRSF6 in immortalized human pancreatic β-cells.
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Affiliation(s)
- Maria Inês Alvelos
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Mirko Brüggemann
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | | | - Jonàs Juan-Mateu
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Maikel Luis Colli
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Anke Busch
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Miguel Lopes
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Ângela Castela
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | | | - Julian König
- Institute of Molecular Biology gGmbH, Mainz, Germany
| | - Kathi Zarnack
- Buchman Institute for Molecular Life Sciences (BMLS), Goethe University Frankfurt, Frankfurt am Main, Germany
- Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Décio L Eizirik
- ULB Center for Diabetes Research, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Welbio, Medical Faculty, Université Libre de Bruxelles (ULB), Brussels, Belgium
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
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48
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Wu P, Zhang M, Webster NJG. Alternative RNA Splicing in Fatty Liver Disease. Front Endocrinol (Lausanne) 2021; 12:613213. [PMID: 33716968 PMCID: PMC7953061 DOI: 10.3389/fendo.2021.613213] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 01/13/2021] [Indexed: 12/12/2022] Open
Abstract
Alternative RNA splicing is a process by which introns are removed and exons are assembled to construct different RNA transcript isoforms from a single pre-mRNA. Previous studies have demonstrated an association between dysregulation of RNA splicing and a number of clinical syndromes, but the generality to common disease has not been established. Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease affecting one-third of adults worldwide, increasing the risk of cirrhosis and hepatocellular carcinoma (HCC). In this review we focus on the change in alternative RNA splicing in fatty liver disease and the role for splicing regulation in disease progression.
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Affiliation(s)
- Panyisha Wu
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
| | - Moya Zhang
- University of California Los Angeles, Los Angeles, CA, United States
| | - Nicholas J. G. Webster
- VA San Diego Healthcare System, San Diego, CA, United States
- Department of Medicine, Division of Endocrinology and Metabolism, University of California San Diego, La Jolla, CA, United States
- Moores Cancer Center, University of California, San Diego, La Jolla, CA, United States
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49
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Vona B, Mazaheri N, Lin SJ, Dunbar LA, Maroofian R, Azaiez H, Booth KT, Vitry S, Rad A, Rüschendorf F, Varshney P, Fowler B, Beetz C, Alagramam KN, Murphy D, Shariati G, Sedaghat A, Houlden H, Petree C, VijayKumar S, Smith RJH, Haaf T, El-Amraoui A, Bowl MR, Varshney GK, Galehdari H. A biallelic variant in CLRN2 causes non-syndromic hearing loss in humans. Hum Genet 2021; 140:915-931. [PMID: 33496845 PMCID: PMC8099798 DOI: 10.1007/s00439-020-02254-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 12/31/2020] [Indexed: 01/10/2023]
Abstract
Deafness, the most frequent sensory deficit in humans, is extremely heterogeneous with hundreds of genes involved. Clinical and genetic analyses of an extended consanguineous family with pre-lingual, moderate-to-profound autosomal recessive sensorineural hearing loss, allowed us to identify CLRN2, encoding a tetraspan protein, as a new deafness gene. Homozygosity mapping followed by exome sequencing identified a 14.96 Mb locus on chromosome 4p15.32p15.1 containing a likely pathogenic missense variant in CLRN2 (c.494C > A, NM_001079827.2) segregating with the disease. Using in vitro RNA splicing analysis, we show that the CLRN2 c.494C > A variant leads to two events: (1) the substitution of a highly conserved threonine (uncharged amino acid) to lysine (charged amino acid) at position 165, p.(Thr165Lys), and (2) aberrant splicing, with the retention of intron 2 resulting in a stop codon after 26 additional amino acids, p.(Gly146Lysfs*26). Expression studies and phenotyping of newly produced zebrafish and mouse models deficient for clarin 2 further confirm that clarin 2, expressed in the inner ear hair cells, is essential for normal organization and maintenance of the auditory hair bundles, and for hearing function. Together, our findings identify CLRN2 as a new deafness gene, which will impact future diagnosis and treatment for deaf patients.
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Affiliation(s)
- Barbara Vona
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany. .,Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany.
| | - Neda Mazaheri
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Sheng-Jia Lin
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Lucy A Dunbar
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK
| | - Reza Maroofian
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Hela Azaiez
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology and Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Kevin T Booth
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology and Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA.,Department of Neurobiology, Harvard Medical School, Boston, MA, USA
| | - Sandrine Vitry
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy Institut Pasteur, Institut de L'Audition, INSERM-UMRS1120, Sorbonne Université, 63 rue de Charenton, 75012, Paris, France
| | - Aboulfazl Rad
- Department of Otolaryngology-Head and Neck Surgery, Tübingen Hearing Research Centre, Eberhard Karls University Tübingen, Tübingen, Germany
| | - Franz Rüschendorf
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, 13125, Berlin, Germany
| | - Pratishtha Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Ben Fowler
- Imaging & Histology Core, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | | | - Kumar N Alagramam
- Department of Otolaryngology, School of Medicine, University Hospitals Cleveland Medical Center, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, 44106, USA.,Department of Neurosciences, Case Western Reserve University, 11100 Euclid Avenue, Cleveland, OH, 44106, USA.,Department of Genetics and Genomic Sciences, Case Western Reserve University, Cleveland, OH, 44106, USA
| | - David Murphy
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Gholamreza Shariati
- Department of Medical Genetics, Faculty of Medicine, Ahvaz Jundishapur, University of Medical Sciences, Ahvaz, Iran.,Narges Medical Genetics and Prenatal Diagnostics Laboratory, East Mihan Ave, Kianpars, Ahvaz, Iran
| | - Alireza Sedaghat
- Diabetes Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Henry Houlden
- Department of Neuromuscular Disorders, UCL Queen Square Institute of Neurology, London, WC1N 3BG, UK
| | - Cassidy Petree
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Shruthi VijayKumar
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Richard J H Smith
- Molecular Otolaryngology and Renal Research Laboratories, Department of Otolaryngology and Interdisciplinary Graduate Program in Molecular Medicine, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University Würzburg, Würzburg, Germany
| | - Aziz El-Amraoui
- Unit Progressive Sensory Disorders, Pathophysiology and Therapy Institut Pasteur, Institut de L'Audition, INSERM-UMRS1120, Sorbonne Université, 63 rue de Charenton, 75012, Paris, France
| | - Michael R Bowl
- Mammalian Genetics Unit, MRC Harwell Institute, Harwell Campus, Didcot, OX11 0RD, UK. .,UCL Ear Institute, University College London, 332 Gray's Inn Road, London, WC1X 8EE, UK.
| | - Gaurav K Varshney
- Genes & Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Hamid Galehdari
- Department of Genetics, Faculty of Science, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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50
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Vilys L, Peciuliene I, Jakubauskiene E, Zinkeviciute R, Makino Y, Kanopka A. U2AF - Hypoxia-induced fas alternative splicing regulator. Exp Cell Res 2020; 399:112444. [PMID: 33347855 DOI: 10.1016/j.yexcr.2020.112444] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Revised: 12/01/2020] [Accepted: 12/15/2020] [Indexed: 01/21/2023]
Abstract
The splicing machinery heavily contributes to biological complexity and especially to the ability of cells to adapt to altered cellular conditions. Hypoxia also plays a key role in the pathophysiology of many disease states. Recent studies have revealed that tumorigenesis and hypoxia are involved in large-scale alterations in alternative pre-mRNA splicing. Fas pre-mRNA is alternatively spliced by excluding exon 6 to produce soluble Fas (sFas) protein that lacks a transmembrane domain and acts by inhibiting Fas mediated apoptosis. In the present study we show that U2AF is involved in hypoxia dependent anti-apoptotic Fas mRNA isoform formation. Our performed studies show that U2AF-RNA interaction is reduced in hypoxic cells, leading to reduction of Fas and increased sFas mRNAs formation. Efficient U2AF-RNA interactions of both subunits are important for Fas exon 6 inclusion into forming mRNA in normoxic and hypoxic cells.
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Affiliation(s)
- Laurynas Vilys
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Inga Peciuliene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Egle Jakubauskiene
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Ruta Zinkeviciute
- Department of Eukaryote Gene Engineering, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Yuichi Makino
- Division of Metabolism and Biosystemic Science, Department of Medicine, Asahikawa Medical College, Asahikawa, Hokkaido, Japan
| | - Arvydas Kanopka
- Department of Immunology and Cell Biology, Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania.
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