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Wei L, Li Y, Chen J, Wang Y, Wu J, Yang H, Zhang Y. Alternative splicing in ovarian cancer. Cell Commun Signal 2024; 22:507. [PMID: 39425166 PMCID: PMC11488268 DOI: 10.1186/s12964-024-01880-8] [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: 07/29/2024] [Accepted: 10/06/2024] [Indexed: 10/21/2024] Open
Abstract
Ovarian cancer is the second leading cause of gynecologic cancer death worldwide, with only 20% of cases detected early due to its elusive nature, limiting successful treatment. Most deaths occur from the disease progressing to advanced stages. Despite advances in chemo- and immunotherapy, the 5-year survival remains below 50% due to high recurrence and chemoresistance. Therefore, leveraging new research perspectives to understand molecular signatures and identify novel therapeutic targets is crucial for improving the clinical outcomes of ovarian cancer. Alternative splicing, a fundamental mechanism of post-transcriptional gene regulation, significantly contributes to heightened genomic complexity and protein diversity. Increased awareness has emerged about the multifaceted roles of alternative splicing in ovarian cancer, including cell proliferation, metastasis, apoptosis, immune evasion, and chemoresistance. We begin with an overview of altered splicing machinery, highlighting increased expression of spliceosome components and associated splicing factors like BUD31, SF3B4, and CTNNBL1, and their relationships to ovarian cancer. Next, we summarize the impact of specific variants of CD44, ECM1, and KAI1 on tumorigenesis and drug resistance through diverse mechanisms. Recent genomic and bioinformatics advances have enhanced our understanding. By incorporating data from The Cancer Genome Atlas RNA-seq, along with clinical information, a series of prognostic models have been developed, which provided deeper insights into how the splicing influences prognosis, overall survival, the immune microenvironment, and drug sensitivity and resistance in ovarian cancer patients. Notably, novel splicing events, such as PIGV|1299|AP and FLT3LG|50,941|AP, have been identified in multiple prognostic models and are associated with poorer and improved prognosis, respectively. These novel splicing variants warrant further functional characterization to unlock the underlying molecular mechanisms. Additionally, experimental evidence has underscored the potential therapeutic utility of targeting alternative splicing events, exemplified by the observation that knockdown of splicing factor BUD31 or antisense oligonucleotide-induced BCL2L12 exon skipping promotes apoptosis of ovarian cancer cells. In clinical settings, bevacizumab, a humanized monoclonal antibody that specifically targets the VEGF-A isoform, has demonstrated beneficial effects in the treatment of patients with advanced epithelial ovarian cancer. In conclusion, this review constitutes the first comprehensive and detailed exposition of the intricate interplay between alternative splicing and ovarian cancer, underscoring the significance of alternative splicing events as pivotal determinants in cancer biology and as promising avenues for future diagnostic and therapeutic intervention.
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Affiliation(s)
- Liwei Wei
- Medical School, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310030, China
| | - Yisheng Li
- College of Pharmacy, Zhejiang University of Technology, Hangzhou, Zhejiang, 310014, China
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310030, China
| | - Jiawang Chen
- Oujiang Laboratory, Zhejiang Lab for Regenerative Medicine, Vision and Brain Health, Wenzhou, Zhejiang, 325101, China
| | - Yuanmei Wang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310030, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianmin Wu
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310030, China
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China
| | - Huanming Yang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310030, China.
| | - Yi Zhang
- HIM-BGI Omics Center, Hangzhou Institute of Medicine (HIM), Chinese Academy of Sciences, Hangzhou, Zhejiang, 310030, China.
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou, Zhejiang, 325035, China.
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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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3
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Yu D, Huang CJ, Tucker HO. Established and Evolving Roles of the Multifunctional Non-POU Domain-Containing Octamer-Binding Protein (NonO) and Splicing Factor Proline- and Glutamine-Rich (SFPQ). J Dev Biol 2024; 12:3. [PMID: 38248868 PMCID: PMC10801543 DOI: 10.3390/jdb12010003] [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: 10/16/2023] [Revised: 12/25/2023] [Accepted: 12/28/2023] [Indexed: 01/23/2024] Open
Abstract
It has been more than three decades since the discovery of multifunctional factors, the Non-POU-Domain-Containing Octamer-Binding Protein, NonO, and the Splicing Factor Proline- and Glutamine-Rich, SFPQ. Some of their functions, including their participation in transcriptional and posttranscriptional regulation as well as their contribution to paraspeckle subnuclear body organization, have been well documented. In this review, we focus on several other established roles of NonO and SFPQ, including their participation in the cell cycle, nonhomologous end-joining (NHEJ), homologous recombination (HR), telomere stability, childhood birth defects and cancer. In each of these contexts, the absence or malfunction of either or both NonO and SFPQ leads to either genome instability, tumor development or mental impairment.
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Affiliation(s)
- Danyang Yu
- Department of Biology, New York University in Shanghai, Shanghai 200122, China;
| | - Ching-Jung Huang
- Department of Biology, New York University in Shanghai, Shanghai 200122, China;
| | - Haley O. Tucker
- Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas at Austin, 1 University Station A5000, Austin, TX 78712, USA
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Wu K, Sun Q, Liu D, Lu J, Wen D, Zang X, Gao L. Alternative Splicing Landscape of Head and Neck Squamous Cell Carcinoma. Technol Cancer Res Treat 2024; 23:15330338241272051. [PMID: 39113534 PMCID: PMC11307358 DOI: 10.1177/15330338241272051] [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: 11/17/2023] [Revised: 06/16/2024] [Accepted: 06/24/2024] [Indexed: 08/10/2024] Open
Abstract
Head and neck malignancies are a significant global health concern, with head and neck squamous cell carcinoma (HNSCC) being the sixth most common cancer worldwide accounting for > 90% of cases. In recent years, there has been growing recognition of the potential role of alternative splicing (AS) in the etiology of cancer. Increasing evidence suggests that AS is associated with various aspects of cancer progression, including tumor occurrence, invasion, metastasis, and drug resistance. Additionally, AS is involved in shaping the tumor microenvironment, which plays a crucial role in tumor development and response to therapy. AS can influence the expression of factors involved in angiogenesis, immune response, and extracellular matrix remodeling, all of which contribute to the formation of a supportive microenvironment for tumor growth. Exploring the mechanism of AS events in HNSCC could provide insights into the development and progression of this cancer, as well as its interaction with the tumor microenvironment. Understanding how AS contributes to the molecular changes in HNSCC cells and influences the tumor microenvironment could lead to the identification of new therapeutic targets. Targeted chemotherapy and immunotherapy strategies tailored to the specific AS patterns in HNSCC could potentially improve treatment outcomes and reduce side effects. This review explores the concept, types, processes, and technological advancements of AS, focusing on its role in the initiation, progression, treatment, and prognosis of HNSCC.
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Affiliation(s)
- Kehan Wu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Qianhui Sun
- Department of Cardiology, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Dongxu Liu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Jiayi Lu
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Deyu Wen
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Xiyan Zang
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
| | - Li Gao
- Department of Oral and Maxillofacial Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang, PR China
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5
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Takeiwa T, Ikeda K, Horie K, Inoue S. Role of RNA binding proteins of the Drosophila behavior and human splicing (DBHS) family in health and cancer. RNA Biol 2024; 21:1-17. [PMID: 38551131 PMCID: PMC10984136 DOI: 10.1080/15476286.2024.2332855] [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] [Revised: 02/19/2024] [Accepted: 03/15/2024] [Indexed: 04/02/2024] Open
Abstract
RNA-binding proteins (RBPs) play crucial roles in the functions and homoeostasis of various tissues by regulating multiple events of RNA processing including RNA splicing, intracellular RNA transport, and mRNA translation. The Drosophila behavior and human splicing (DBHS) family proteins including PSF/SFPQ, NONO, and PSPC1 are ubiquitously expressed RBPs that contribute to the physiology of several tissues. In mammals, DBHS proteins have been reported to contribute to neurological diseases and play crucial roles in cancers, such as prostate, breast, and liver cancers, by regulating cancer-specific gene expression. Notably, in recent years, multiple small molecules targeting DBHS family proteins have been developed for application as cancer therapeutics. This review provides a recent overview of the functions of DBHS family in physiology and pathophysiology, and discusses the application of DBHS family proteins as promising diagnostic and therapeutic targets for cancers.
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Affiliation(s)
- Toshihiko Takeiwa
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo, Japan
| | - Kazuhiro Ikeda
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Kuniko Horie
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
| | - Satoshi Inoue
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute for Geriatrics and Gerontology, Itabashi-ku, Tokyo, Japan
- Division of Systems Medicine & Gene Therapy, Faculty of Medicine, Saitama Medical University, Hidaka, Saitama, Japan
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6
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Montero-Hidalgo AJ, Pérez-Gómez JM, Martínez-Fuentes AJ, Gómez-Gómez E, Gahete MD, Jiménez-Vacas JM, Luque RM. Alternative splicing in bladder cancer: potential strategies for cancer diagnosis, prognosis, and treatment. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1760. [PMID: 36063028 DOI: 10.1002/wrna.1760] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/25/2022] [Accepted: 08/05/2022] [Indexed: 05/13/2023]
Abstract
Bladder cancer is the most common malignancy of the urinary tract worldwide. The therapeutic options to tackle this disease comprise surgery, intravesical or systemic chemotherapy, and immunotherapy. Unfortunately, a wide number of patients ultimately become resistant to these treatments and develop aggressive metastatic disease, presenting a poor prognosis. Therefore, the identification of novel therapeutic approaches to tackle this devastating pathology is urgently needed. However, a significant limitation is that the progression and drug response of bladder cancer is strongly associated with its intrinsic molecular heterogeneity. In this sense, RNA splicing is recently gaining importance as a critical hallmark of cancer since can have a significant clinical value. In fact, a profound dysregulation of the splicing process has been reported in bladder cancer, especially in the expression of certain key splicing variants and circular RNAs with a potential clinical value as diagnostic/prognostic biomarkers or therapeutic targets in this pathology. Indeed, some authors have already evidenced a profound antitumor effect by targeting some splicing factors (e.g., PTBP1), mRNA splicing variants (e.g., PKM2, HYAL4-v1), and circular RNAs (e.g., circITCH, circMYLK), which illustrates new possibilities to significantly improve the management of this pathology. This review represents the first detailed overview of the splicing process and its alterations in bladder cancer, and highlights opportunities for the development of novel diagnostic/prognostic biomarkers and their clinical potential for the treatment of this devastating cancer type. This article is categorized under: RNA Processing > Splicing Regulation/Alternative Splicing RNA in Disease and Development > RNA in Disease.
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Affiliation(s)
- Antonio J Montero-Hidalgo
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Jesús M Pérez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Antonio J Martínez-Fuentes
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Enrique Gómez-Gómez
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- Urology Service, HURS/IMIBIC, Cordoba, 14004, Spain
| | - Manuel D Gahete
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Juan M Jiménez-Vacas
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
| | - Raúl M Luque
- Maimonides Biomedical Research Institute of Cordoba (IMIBIC), Cordoba, 14004, Spain
- Department of Cell Biology, Physiology and Immunology, University of Cordoba, Cordoba, 14004, Spain
- Reina Sofia University Hospital (HURS), Cordoba, 14004, Spain
- CIBER Physiopathology of Obesity and Nutrition (CIBERobn), Cordoba, 14004, Spain
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Love SL, Emerson JD, Koide K, Hoskins AA. Pre-mRNA splicing-associated diseases and therapies. RNA Biol 2023; 20:525-538. [PMID: 37528617 PMCID: PMC10399480 DOI: 10.1080/15476286.2023.2239601] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/18/2023] [Indexed: 08/03/2023] Open
Abstract
Precursor mRNA (pre-mRNA) splicing is an essential step in human gene expression and is carried out by a large macromolecular machine called the spliceosome. Given the spliceosome's role in shaping the cellular transcriptome, it is not surprising that mutations in the splicing machinery can result in a range of human diseases and disorders (spliceosomopathies). This review serves as an introduction into the main features of the pre-mRNA splicing machinery in humans and how changes in the function of its components can lead to diseases ranging from blindness to cancers. Recently, several drugs have been developed that interact directly with this machinery to change splicing outcomes at either the single gene or transcriptome-scale. We discuss the mechanism of action of several drugs that perturb splicing in unique ways. Finally, we speculate on what the future may hold in the emerging area of spliceosomopathies and spliceosome-targeted treatments.
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Affiliation(s)
- Sierra L. Love
- Genetics Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Joseph D. Emerson
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kazunori Koide
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, USA
| | - Aaron A. Hoskins
- Department of Biochemistry, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
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8
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Li Y, Zhao Q, Song X, Song J. [Construction of an adenovirus vector expressing engineered splicing factor for regulating alternative splicing of YAP1 in neonatal rat cardiomyocytes]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2022; 42:1013-1018. [PMID: 35869763 DOI: 10.12122/j.issn.1673-4254.2022.07.07] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
OBJECTIVE To construct an adenovirus vector expressing artificial splicing factor capable of regulating alternative splicing of Yap1 in cardiomyocytes. METHODS The splicing factors with different sequences were constructed against Exon6 of YAP1 based on the sequence specificity of Pumilio1. The PCR fragment of the artificially synthesized PUF-SR or wild-type PUFSR was cloned into pAd-Track plasmid, and the recombinant plasmids were transformed into E. coli DH5α for plasmid amplification. The amplified plasmids were digested with Pac I and transfected into 293A cells for packaging to obtain the adenovirus vectors. Cultured neonatal rat cardiomyocytes were transfected with the adenoviral vectors, and alternative splicing of YAP1 was detected using quantitative and semi-quantitative PCR; Western blotting was performed to detect the signal of the fusion protein Flag. RESULTS The transfection efficiency of the adenovirus vectors was close to 100% in rat cardiomyocytes, and no fluorescent protein was detected in the cells with plasmid transfection. The results of Western blotting showed that both the negative control and Flag-SR-NLS-PUF targeting the YAPExon6XULIE sequence were capable of detecting the expression of the protein fused to Flag. The results of reverse transcription-PCR and PCR demonstrated that the artificial splicing factor constructed based on the 4th target sequence of YAP1 effectively regulated the splicing of YAP1 Exon6 in the cardiomyocytes (P < 0.05). CONCLUSION We successfully constructed adenovirus vectors capable of regulating YAP1 alternative splicing rat cardiomyocytes.
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Affiliation(s)
- Y Li
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200082, China.,Department of Anesthesiology, Shidong Hospital Affiliated to University of Shanghai for Science and Technology, Shanghai 200082, China
| | - Q Zhao
- School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai 200082, China
| | - X Song
- Department of Heart Medicine, Changhai Hospital, Naval Medical University, Shanghai 200082, China
| | - J Song
- Department of Anesthesiology, Shidong Hospital Affiliated to University of Shanghai for Science and Technology, Shanghai 200082, China
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A critical update on the strategies towards small molecule inhibitors targeting Serine/arginine-rich (SR) proteins and Serine/arginine-rich proteins related kinases in alternative splicing. Bioorg Med Chem 2022; 70:116921. [PMID: 35863237 DOI: 10.1016/j.bmc.2022.116921] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 07/01/2022] [Accepted: 07/06/2022] [Indexed: 11/02/2022]
Abstract
>90% of genes in the human body undergo alternative splicing (AS) after transcription, which enriches protein species and regulates protein levels. However, there is growing evidence that various genetic isoforms resulting from dysregulated alternative splicing are prevalent in various types of cancers. Dysregulated alternative splicing leads to cancer generation and maintenance of cancer properties such as proliferation differentiation, apoptosis inhibition, invasion metastasis, and angiogenesis. Serine/arginine-rich proteins and SR protein-associated kinases mediate splice site recognition and splice complex assembly during variable splicing. Based on the impact of dysregulated alternative splicing on disease onset and progression, the search for small molecule inhibitors targeting alternative splicing is imminent. In this review, we discuss the structure and specific biological functions of SR proteins and describe the regulation of SR protein function by SR protein related kinases meticulously, which are closely related to the occurrence and development of various types of cancers. On this basis, we summarize the reported small molecule inhibitors targeting SR proteins and SR protein related kinases from the perspective of medicinal chemistry. We mainly categorize small molecule inhibitors from four aspects, including targeting SR proteins, targeting Serine/arginine-rich protein-specific kinases (SRPKs), targeting Cdc2-like kinases (CLKs) and targeting dual-specificity tyrosine-regulated kinases (DYRKs), in terms of structure, inhibition target, specific mechanism of action, biological activity, and applicable diseases. With this review, we are expected to provide a timely summary of recent advances in alternative splicing regulated by kinases and a preliminary introduction to relevant small molecule inhibitors.
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Ye F, Liang Y, Cheng Z, Liu Y, Hu J, Li W, Chen X, Gao J, Jiang H. Immunological Characteristics of Alternative Splicing Profiles Related to Prognosis in Bladder Cancer. Front Immunol 2022; 13:911902. [PMID: 35769470 PMCID: PMC9234272 DOI: 10.3389/fimmu.2022.911902] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 05/20/2022] [Indexed: 11/20/2022] Open
Abstract
Several studies have found that pathological imbalance of alterative splicing (AS) events is associated with cancer susceptibility. carcinogenicity. Nevertheless, the relationship between heritable variation in AS events and carcinogenicity has not been extensively explored. Here, we downloaded AS event signatures, transcriptome profiles, and matched clinical information from The Cancer Genome Atlas (TCGA) database, identified the prognostic AS-related events via conducting the univariate Cox regression algorism. Subsequently, the prognostic AS-related events were further reduced by the least absolute shrinkage and selection operator (LASSO) logistic regression model, and employed for constructing the risk model. Single-sample (ssGSEA), ESTIMATE, and the CIBERSORT algorithms were conducted to evaluate tumor microenvironment status. CCK8, cell culture scratch, transwell invasion assays and flow cytometry were conducted to confirm the reliability of the model. We found 2751 prognostic-related AS events, and constructed a risk model with seven prognostic-related AS events. Compared with high-risk score patients, the overall survival rate of the patients with low-risk score was remarkably longer. Besides, we further found that risk score was also closely related to alterations in immune cell infiltration and immunotherapeutic molecules, indicating its potential as an observation of immune infiltration and clinical response to immunotherapy. In addition, the downstream target gene (DYM) could be a promising prognostic factor for bladder cancer. Our investigation provided an indispensable reference for ulteriorly exploring the role of AS events in the tumor microenvironment and immunotherapy efficiency, and rendered personalized prognosis monitoring for bladder cancer.
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Affiliation(s)
- Fangdie Ye
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yingchun Liang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Zhang Cheng
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Yufei Liu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jimeng Hu
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Weijian Li
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Xinan Chen
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
| | - Jiahao Gao
- Department of Radiology, Huashan Hospital, Fudan University, Shanghai, China
| | - Haowen Jiang
- Department of Urology, Huashan Hospital, Fudan University, Shanghai, China
- Fudan Institute of Urology, Huashan Hospital, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
- *Correspondence: Haowen Jiang,
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11
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Takeiwa T, Ikeda K, Suzuki T, Sato W, Iino K, Mitobe Y, Kawabata H, Horie K, Inoue S. PSPC1 is a potential prognostic marker for hormone-dependent breast cancer patients and modulates RNA processing of ESR1 and SCFD2. Sci Rep 2022; 12:9495. [PMID: 35681031 PMCID: PMC9184599 DOI: 10.1038/s41598-022-13601-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 05/16/2022] [Indexed: 11/08/2022] Open
Abstract
Breast cancer is the most common cancer type among women worldwide. The majority of breast cancer expresses estrogen receptor (ER) and endocrine therapy is a standard treatment of ER-positive breast cancer. However, development of the therapy resistance is still a major challenge and thus new therapeutic approaches are needed. Here we show that an RNA-binding protein, PSPC1, play a crucial role in ER-positive breast cancer growth through post-transcriptional gene regulation. We showed that siRNA-mediated PSPC1 silencing suppressed the proliferation of ER-positive breast cancer cells. Strong immunoreactivity (IR) of PSPC1 was correlated with poor prognosis for ER-positive breast cancer patients. Using immunoprecipitation, RNA-immunoprecipitation (RIP) and quantitative PCR (qPCR) experiments, we showed that PSPC1 interacted with PSF and was involved in post-transcriptional regulation of PSF target genes, ESR1 and SCFD2. Strong SCFD2 IR was correlated with poor prognosis for ER-positive breast cancer patients and combinations of PSPC1, PSF, and SCFD2 IRs were potent prognostic factors. Moreover, we identified DDIAS and MYBL1 as SCFD2 downstream target genes using microarray analysis, and finally showed that SCFD2 silencing suppressed tamoxifen-resistant breast tumor growth in vivo. These results indicated that PSPC1 and SCFD2 axis could be a promising target in the clinical management of the disease.
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Affiliation(s)
- Toshihiko Takeiwa
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
| | - Kazuhiro Ikeda
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Takashi Suzuki
- Department of Anatomic Pathology, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Wataru Sato
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Kaori Iino
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Yuichi Mitobe
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan
| | - Hidetaka Kawabata
- Department of Breast and Endocrine Surgery, Toranomon Hospital, Tokyo, Japan
| | - Kuniko Horie
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
| | - Satoshi Inoue
- Division of Systems Medicine and Gene Therapy, Saitama Medical University, 1397-1 Yamane, Hidaka, Saitama, 350-1241, Japan.
- Department of Systems Aging Science and Medicine, Tokyo Metropolitan Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan.
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12
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Multiple Phosphorylations of SR Protein SRSF3 and Its Binding to m6A Reader YTHDC1 in Human Cells. Cells 2022; 11:cells11091461. [PMID: 35563766 PMCID: PMC9100204 DOI: 10.3390/cells11091461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 12/04/2022] Open
Abstract
N6-methyladenosine (m6A) is a well-known RNA modification and has various functions with its binding proteins. Nuclear m6A reader protein YTHDC1 plays a significant role in RNA metabolism including some non-coding RNA such as LINE or circRNA. It is also known to regulate mRNA splicing through recruiting SRSF3 to the targeted mRNAs, which then mediates export of YTHDC1-bound RNA to the cytoplasm. Additionally, it has been indicated that SRSF3 binding to YHTDC1 may be mediated by its dephosphorylated status. However, their binding mechanism, including the positions of dephosphorylated residues of SRSF3, has not been sufficiently investigated. Thus, we explored the mechanism of interaction between SRSF3 and YTHDC1 in human cells. We used co-immunoprecipitation to examine the binding of YTHDC1/SRSF3 through their N- and C-terminal amino-acid residues. Furthermore, dephosphorylation-mimic serine to alanine mutants of SRSF3 indicated the position of phosphorylated residues. Cumulatively, our results demonstrate that YTHDC1 binding to SRSF3 is regulated by not only hypo-phosphorylated residues of arginine/serine-rich (RS) domain of SRSF3 but also other parts of SRSF3 via YTHDC1 N- or C-terminal residues. Our results contribute to the understanding of the complex mechanism of binding between SR protein SRSF3 and the m6A reader YTHDC1 to regulate the expression of mRNA and non-coding RNAs.
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Li J, Sang M, Zheng Y, Meng L, Gu L, Li Z, Liu F, Wu Y, Li W, Shan B. HNRNPUL1 inhibits cisplatin sensitivity of esophageal squamous cell carcinoma through regulating the formation of circMAN1A2. Exp Cell Res 2021; 409:112891. [PMID: 34688610 DOI: 10.1016/j.yexcr.2021.112891] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 10/10/2021] [Accepted: 10/20/2021] [Indexed: 10/20/2022]
Abstract
Cisplatin (CDDP) is widely used for chemotherapy of esophageal squamous cell carcinoma (ESCC) but the drug resistance limits its therapeutic benefit. Heterogeneous nuclear ribonucleoprotein U-like 1 (HNRNPUL1) belongs to the family of RNA-binding proteins (RBPs) and is involved in DNA damage repair. To investigate whether and how HNRNPUL1 affects CDDP resistance of ESCC, we evaluated the expression of HNRNPUL1 and found that it was associated with recurrence in ESCC patients receiving postoperative platinum-based chemotherapy and was an independent prognostic factor for disease-free survival (DFS). Besides, we showed that the reduced expression of HNRNPUL1 enhanced the CDDP sensitivity of ESCC cells. Furthermore, RNA immunoprecipitation coupled with high-throughput sequencing (RIP-seq) were performed and a range of HNRNPUL1-binding RNAs influenced by CDDP treatment were identified followed by bioinformatics analysis. In terms of mechanism, we found that HNRNPUL1 inhibited CDDP sensitivity of ESCC cells by regulating the CDDP sensitivity-inhibited circular RNA (circRNA) MAN1A2 formation. Taken together, our results first demonstrated the role of HNRNPUL1 in CDDP resistance of ESCC and suggested that HNRNPUL1 may be a potential target of ESCC chemotherapy.
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Affiliation(s)
- Juan Li
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Meixiang Sang
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China; Tumor Research Institute, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Yang Zheng
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Lingjiao Meng
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Lina Gu
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Ziyi Li
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Fei Liu
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Yunyan Wu
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Weijing Li
- Department of Anesthesiology, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China
| | - Baoen Shan
- Research Center, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China; Tumor Research Institute, The Fourth Affiliated Hospital of Hebei Medical University, Shijiazhuang, Hebei, 050017, People's Republic of China.
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14
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Comprehensive analysis of aberrant alternative splicing related to carcinogenesis and prognosis of papillary thyroid cancer. Aging (Albany NY) 2021; 13:23149-23168. [PMID: 34628367 PMCID: PMC8544310 DOI: 10.18632/aging.203608] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/13/2021] [Indexed: 02/05/2023]
Abstract
As a key mechanism, alternative splicing (AS) plays a role in the cancer initiation and development. However, in papillary thyroid cancer (PTC), data for the comprehensive AS event profile and its clinical implications are lacking. Herein, a genome-wide AS event profiling using RNA-Seq data and its correlation with matched clinical information was performed using a 389 PTC patient cohort from the project of The Cancer Genome Atlas (TCGA). We identified 1,925 cancer-associated AS events (CASEs) by comparing paired tumors and neighboring healthy tissues. Parent genes with CASEs remarkably enriched in the pathways were linked with carcinogenesis, such as P53, KRAS, IL6-JAK-STAT3, apoptosis, and MYC signaling. The regulatory networks of AS implied an obvious correlation between the expression of splicing factor and CASE. We identified eight CASEs as predictors for overall survival (OS) and disease-free survival (DFS). The established risk score model based on DFS-associated CASEs successfully predicted the prognosis of PTC patients. From the unsupervised clustering analysis results, it is found that different clusters based on AS correlated with prognosis, molecular features, and immune characteristics. Taken together, the comprehensive genome-wide AS landscape analysis in PTC showed new AS events linked with tumorigenesis and prognosis, which provide new insights for clinical monitoring and therapy for PTC.
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15
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Identification of Prognostic alternative splicing signatures and their clinical significance in uveal melanoma. Exp Eye Res 2021; 209:108666. [PMID: 34129849 DOI: 10.1016/j.exer.2021.108666] [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: 02/27/2021] [Revised: 05/07/2021] [Accepted: 06/07/2021] [Indexed: 12/30/2022]
Abstract
As a posttranscriptional regulatory mechanism, alternative splicing (AS) has the potential to generate a large amount of protein diversity from limited genes. The purpose of our study was to assess the usefulness of prognostic splicing events as novel diagnostic and therapeutic signatures for uveal melanoma (UM). The datasets, clinical traits and AS data of UM were obtained from The Cancer Genome Atlas (TCGA) database and TCGA SpliceSeq database. Using bioinformatics analysis, we identified 1047 AS events as candidate AS events closely related to prognosis from 920 parent genes. The gene enrichment analysis indicated that these genes were mainly enriched in cellular components (CC) including cytosol, nucleoplasm, cytoplasm and ribosome, and in molecular functions (MF), including protein binding and poly(A) RNA binding. Furthermore, we selected all survival-associated splicing events to generate prognostic signatures, which included 4 exon skip (ES) events (DNASE1L1-90581-ES, NUDT1-78611-ES, BIN1-55198-ES, SEPN1-1195-ES) and 1 alternate promoter (AP) event (DPYSL2-83132-AP). The AS prognostic model was confirmed as independent overall survival (OS)-related factors (p = 0.014). A total of 17 splicing factors (SFs) involved in the regulation of AS were identified as related to the OS of UM patients. Our pooled data highlighted the usefulness and importance of AS biomarkers, which provided a potential strategy for the diagnosis and treatment of UM.
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16
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Scalia P, Giordano A, Martini C, Williams SJ. Isoform- and Paralog-Switching in IR-Signaling: When Diabetes Opens the Gates to Cancer. Biomolecules 2020; 10:biom10121617. [PMID: 33266015 PMCID: PMC7761347 DOI: 10.3390/biom10121617] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Revised: 11/21/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022] Open
Abstract
Insulin receptor (IR) and IR-related signaling defects have been shown to trigger insulin-resistance in insulin-dependent cells and ultimately to give rise to type 2 diabetes in mammalian organisms. IR expression is ubiquitous in mammalian tissues, and its over-expression is also a common finding in cancerous cells. This latter finding has been shown to associate with both a relative and absolute increase in IR isoform-A (IR-A) expression, missing 12 aa in its EC subunit corresponding to exon 11. Since IR-A is a high-affinity transducer of Insulin-like Growth Factor-II (IGF-II) signals, a growth factor is often secreted by cancer cells; such event offers a direct molecular link between IR-A/IR-B increased ratio in insulin resistance states (obesity and type 2 diabetes) and the malignant advantage provided by IGF-II to solid tumors. Nonetheless, recent findings on the biological role of isoforms for cellular signaling components suggest that the preferential expression of IR isoform-A may be part of a wider contextual isoform-expression switch in downstream regulatory factors, potentially enhancing IR-dependent oncogenic effects. The present review focuses on the role of isoform- and paralog-dependent variability in the IR and downstream cellular components playing a potential role in the modulation of the IR-A signaling related to the changes induced by insulin-resistance-linked conditions as well as to their relationship with the benign versus malignant transition in underlying solid tumors.
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Affiliation(s)
- Pierluigi Scalia
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- ISOPROG-Somatolink EPFP Network, Functional Research Unit, Philadelphia, PA 19104, USA and 93100 Caltanissetta, Italy
- Correspondence:
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- Department of Medical Biotechnologies, University of Siena, 52100 Siena, Italy
| | - Caroline Martini
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
| | - Stephen J. Williams
- Sbarro Institute for Cancer Research and Molecular Medicine, Temple University, Philadelphia, PA 19122, USA; (A.G.); (C.M.); (S.J.W.)
- ISOPROG-Somatolink EPFP Network, Functional Research Unit, Philadelphia, PA 19104, USA and 93100 Caltanissetta, Italy
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17
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Taniguchi-Ponciano K, Peña-Martínez E, Silva-Román G, Vela-Patiño S, Guzman-Ortiz AL, Quezada H, Gomez-Apo E, Chavez-Macias L, Mercado-Medrez S, Vargas-Ortega G, Espinosa-de-los-Monteros AL, Gonzales-Virla B, Ferreira-Hermosillo A, Espinosa-Cardenas E, Ramirez-Renteria C, Sosa E, Lopez-Felix B, Guinto G, Marrero-Rodríguez D, Mercado M. Proteomic and Transcriptomic Analysis Identify Spliceosome as a Significant Component of the Molecular Machinery in the Pituitary Tumors Derived from POU1F1- and NR5A1-Cell Lineages. Genes (Basel) 2020; 11:genes11121422. [PMID: 33261069 PMCID: PMC7760979 DOI: 10.3390/genes11121422] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/20/2022] Open
Abstract
Background: Pituitary adenomas (PA) are the second most common tumor in the central nervous system and have low counts of mutated genes. Splicing occurs in 95% of the coding RNA. There is scarce information about the spliceosome and mRNA-isoforms in PA, and therefore we carried out proteomic and transcriptomic analysis to identify spliceosome components and mRNA isoforms in PA. Methods: Proteomic profile analysis was carried out by nano-HPLC and mass spectrometry with a quadrupole time-of-flight mass spectrometer. The mRNA isoforms and transcriptomic profiles were carried out by microarray technology. With proteins and mRNA information we carried out Gene Ontology and exon level analysis to identify splicing-related events. Results: Approximately 2000 proteins were identified in pituitary tumors. Spliceosome proteins such as SRSF1, U2AF1 and RBM42 among others were found in PA. These results were validated at mRNA level, which showed up-regulation of spliceosome genes in PA. Spliceosome-related genes segregate and categorize PA tumor subtypes. The PA showed alterations in CDK18 and THY1 mRNA isoforms which could be tumor specific. Conclusions: Spliceosome components are significant constituents of the PA molecular machinery and could be used as molecular markers and therapeutic targets. Splicing-related genes and mRNA-isoforms profiles characterize tumor subtypes.
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Affiliation(s)
- Keiko Taniguchi-Ponciano
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Eduardo Peña-Martínez
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Gloria Silva-Román
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Sandra Vela-Patiño
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Ana Laura Guzman-Ortiz
- Laboratorio de Investigacion en Inmunologia y Proteomica, Hospital Infantil de Mexico “Federico Gomez”, Mexico City 06720, Mexico; (A.L.G.-O.); (H.Q.)
| | - Hector Quezada
- Laboratorio de Investigacion en Inmunologia y Proteomica, Hospital Infantil de Mexico “Federico Gomez”, Mexico City 06720, Mexico; (A.L.G.-O.); (H.Q.)
| | - Erick Gomez-Apo
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de México 06720, Mexico; (E.G.-A.); (L.C.-M.)
| | - Laura Chavez-Macias
- Área de Neuropatología, Servicio de Anatomía Patológica, Hospital General de México “Dr. Eduardo Liceaga”, Ciudad de México 06720, Mexico; (E.G.-A.); (L.C.-M.)
- Facultad de Medicina, Universidad Nacional Autonoma de México, Mexico City 04510, Mexico
| | - Sophia Mercado-Medrez
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
| | - Guadalupe Vargas-Ortega
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Ana Laura Espinosa-de-los-Monteros
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Baldomero Gonzales-Virla
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Aldo Ferreira-Hermosillo
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Etual Espinosa-Cardenas
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Claudia Ramirez-Renteria
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Ernesto Sosa
- Servicio de Endocrinologia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (G.V.-O.); (A.L.E.-d.-l.-M.); (B.G.-V.); (E.E.-C.); (E.S.)
| | - Blas Lopez-Felix
- Servicio de Neurocirugia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (B.L.-F.); (G.G.)
| | - Gerardo Guinto
- Servicio de Neurocirugia, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Ciudad de México 06720, Mexico; (B.L.-F.); (G.G.)
| | - Daniel Marrero-Rodríguez
- Catedra CONACyT-Laboratorio de Endocrinologia Experimental, Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico
- Correspondence: (D.M.-R.); (M.M.); Tel.: +54-401-021 (D.M.-R. & M.M.)
| | - Moises Mercado
- Unidad de Investigación Medica en Enfermedades Endocrinas, Hospital de Especialidades, Centro Medico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Av. Cuauhtémoc 330, Col. Doctores, Mexico D.F. 06720, Mexico; (K.T.-P.); (E.P.-M.); (G.S.-R.); (S.V.-P.); (S.M.-M.); (A.F.-H.); (C.R.-R.)
- Correspondence: (D.M.-R.); (M.M.); Tel.: +54-401-021 (D.M.-R. & M.M.)
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Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals. Int J Mol Sci 2020; 21:ijms21207599. [PMID: 33066638 PMCID: PMC7590145 DOI: 10.3390/ijms21207599] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/12/2020] [Accepted: 10/13/2020] [Indexed: 01/18/2023] Open
Abstract
Multiple mRNA isoforms are often generated during processing such as alternative splicing of precursor mRNAs (pre-mRNA), resulting in a diversity of generated proteins. Alternative splicing is an essential mechanism for the functional complexity of eukaryotes. Temperature, which is involved in all life activities at various levels, is one of regulatory factors for controlling patterns of alternative splicing. Temperature-dependent alternative splicing is associated with various phenotypes such as flowering and circadian clock in plants and sex determination in poikilothermic animals. In some specific situations, temperature-dependent alternative splicing can be evoked even in homothermal animals. For example, the splicing pattern of mRNA for a cold shock protein, cold-inducible RNA-binding protein (CIRP or CIRBP), is changed in response to a marked drop in body temperature during hibernation of hamsters. In this review, we describe the current knowledge about mechanisms and functions of temperature-dependent alternative splicing in plants and animals. Then we discuss the physiological significance of hypothermia-induced alternative splicing of a cold shock protein gene in hibernating and non-hibernating animals.
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Francies FZ, Hull R, Khanyile R, Dlamini Z. Breast cancer in low-middle income countries: abnormality in splicing and lack of targeted treatment options. Am J Cancer Res 2020; 10:1568-1591. [PMID: 32509398 PMCID: PMC7269781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 04/30/2020] [Indexed: 06/11/2023] Open
Abstract
Breast cancer is a common malignancy among women worldwide. Regardless of the economic status of a country, breast cancer poses a burden in prevention, diagnosis and treatment. Developed countries such as the U.S. have high incidence and mortality rates of breast cancer. Although low incidence rates are observed in developing countries, the mortality rate is on the rise implying that low- to middle-income countries lack the resources for preventative screening for early detection and adequate treatment resources. The differences in incidence between countries can be attributed to changes in exposure to environmental risk factors, behaviour and lifestyle factors of the different population groups. Genomic modifications are an important factor that significantly alters the risk profile of breast tumourigenesis. The incidence of early-onset breast cancer is increasing and evidence shows that early onset of breast cancer is far more aggressive than late onset of the disease; possibly due to the difference in genetic alterations or tumour biology. Alternative splicing is a pivotal factor in the progressions of breast cancer. It plays a significant role in tumour prognosis, survival and drug resistance; hence, it offers a valuable option as a therapeutic target. In this review, the differences in breast cancer incidence and mortality rates in developed countries will be compared to low- to middle-income countries. The review will also discuss environmental and lifestyle risk factors, and the underlying molecular mechanisms, genetic variations or mutations and alternative splicing that may contribute to the development and novel drug targets for breast cancer.
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Affiliation(s)
- Flavia Zita Francies
- SA-MRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences Hatfield, 0028, South Africa
| | - Rodney Hull
- SA-MRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences Hatfield, 0028, South Africa
| | - Richard Khanyile
- SA-MRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences Hatfield, 0028, South Africa
| | - Zodwa Dlamini
- SA-MRC/UP Precision Prevention & Novel Drug Targets for HIV-Associated Cancers (PPNDTHAC) Extramural Unit, Pan African Cancer Research Institute (PACRI), University of Pretoria, Faculty of Health Sciences Hatfield, 0028, South Africa
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