1
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Rosemann J, Pyko J, Jacob R, Macho J, Kappler M, Eckert AW, Haemmerle M, Gutschner T. NANOS1 restricts oral cancer cell motility and TGF-ß signaling. Eur J Cell Biol 2024; 103:151400. [PMID: 38401491 DOI: 10.1016/j.ejcb.2024.151400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 02/04/2024] [Accepted: 02/20/2024] [Indexed: 02/26/2024] Open
Abstract
Oral squamous cell carcinoma (OSCC) is the most frequent type of cancer of the head and neck area accounting for approx. 377,000 new cancer cases every year. The epithelial-to-mesenchymal transition (EMT) program plays an important role in OSCC progression and metastasis therefore contributing to a poor prognosis in patients with advanced disease. Transforming growth factor beta (TGF-ß) is a powerful inducer of EMT thereby increasing cancer cell aggressiveness. Here, we aimed at identifying RNA-binding proteins (RBPs) that affect TGF-ß-induced EMT. To this end we treated oral cancer cells with TGF-ß and identified a total of 643 significantly deregulated protein-coding genes in response to TGF-ß. Of note, 19 genes encoded RBPs with NANOS1 being the most downregulated RBP. Subsequent cellular studies demonstrated a strong inhibitory effect of NANOS1 on migration and invasion of SAS oral cancer cells. Further mechanistic studies revealed an interaction of NANOS1 with the TGF-ß receptor 1 (TGFBR1) mRNA, leading to increased decay of this transcript and a reduced TGFBR1 protein expression, thereby preventing downstream TGF-ß/SMAD signaling. In summary, we identified NANOS1 as negative regulator of TGF-ß signaling in oral cancer cells.
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Affiliation(s)
- Julia Rosemann
- Institute of Molecular Medicine, Section for RNA biology and pathogenesis, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Jonas Pyko
- Institute of Molecular Medicine, Section for RNA biology and pathogenesis, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Roland Jacob
- Institute of Molecular Medicine, Section for RNA biology and pathogenesis, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Jana Macho
- Institute of Molecular Medicine, Section for RNA biology and pathogenesis, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Matthias Kappler
- Department of Oral and Maxillofacial Plastic Surgery, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Alexander W Eckert
- Department of Cranio Maxillofacial Surgery, Paracelsus Medical University, Nuremberg 90471, Germany
| | - Monika Haemmerle
- Institute of Pathology, Section for Experimental Pathology, Martin Luther University Halle-Wittenberg, Halle 06120, Germany
| | - Tony Gutschner
- Institute of Molecular Medicine, Section for RNA biology and pathogenesis, Martin Luther University Halle-Wittenberg, Halle 06120, Germany.
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2
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Zhang YE, Stuelten CH. Alternative splicing in EMT and TGF-β signaling during cancer progression. Semin Cancer Biol 2024; 101:1-11. [PMID: 38614376 PMCID: PMC11180579 DOI: 10.1016/j.semcancer.2024.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 11/20/2023] [Accepted: 04/04/2024] [Indexed: 04/15/2024]
Abstract
Epithelial to mesenchymal transition (EMT) is a physiological process during development where epithelial cells transform to acquire mesenchymal characteristics, which allows them to migrate and colonize secondary tissues. Many cellular signaling pathways and master transcriptional factors exert a myriad of controls to fine tune this vital process to meet various developmental and physiological needs. Adding to the complexity of this network are post-transcriptional and post-translational regulations. Among them, alternative splicing has been shown to play important roles to drive EMT-associated phenotypic changes, including actin cytoskeleton remodeling, cell-cell junction changes, cell motility and invasiveness. In advanced cancers, transforming growth factor-β (TGF-β) is a major inducer of EMT and is associated with tumor cell metastasis, cancer stem cell self-renewal, and drug resistance. This review aims to provide an overview of recent discoveries regarding alternative splicing events and the involvement of splicing factors in the EMT and TGF-β signaling. It will emphasize the importance of various splicing factors involved in EMT and explore their regulatory mechanisms.
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Affiliation(s)
- Ying E Zhang
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA.
| | - Christina H Stuelten
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA
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3
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Tao Y, Zhang Q, Wang H, Yang X, Mu H. Alternative splicing and related RNA binding proteins in human health and disease. Signal Transduct Target Ther 2024; 9:26. [PMID: 38302461 PMCID: PMC10835012 DOI: 10.1038/s41392-024-01734-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 12/18/2023] [Accepted: 12/27/2023] [Indexed: 02/03/2024] Open
Abstract
Alternative splicing (AS) serves as a pivotal mechanism in transcriptional regulation, engendering transcript diversity, and modifications in protein structure and functionality. Across varying tissues, developmental stages, or under specific conditions, AS gives rise to distinct splice isoforms. This implies that these isoforms possess unique temporal and spatial roles, thereby associating AS with standard biological activities and diseases. Among these, AS-related RNA-binding proteins (RBPs) play an instrumental role in regulating alternative splicing events. Under physiological conditions, the diversity of proteins mediated by AS influences the structure, function, interaction, and localization of proteins, thereby participating in the differentiation and development of an array of tissues and organs. Under pathological conditions, alterations in AS are linked with various diseases, particularly cancer. These changes can lead to modifications in gene splicing patterns, culminating in changes or loss of protein functionality. For instance, in cancer, abnormalities in AS and RBPs may result in aberrant expression of cancer-associated genes, thereby promoting the onset and progression of tumors. AS and RBPs are also associated with numerous neurodegenerative diseases and autoimmune diseases. Consequently, the study of AS across different tissues holds significant value. This review provides a detailed account of the recent advancements in the study of alternative splicing and AS-related RNA-binding proteins in tissue development and diseases, which aids in deepening the understanding of gene expression complexity and offers new insights and methodologies for precision medicine.
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Affiliation(s)
- Yining Tao
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Qi Zhang
- Department of Biochemistry and Molecular Cell Biology, Shanghai Key Laboratory for Tumor Microenvironment and Inflammation, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
| | - Haoyu Wang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Xiyu Yang
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China
- Shanghai Bone Tumor Institution, 200000, Shanghai, China
| | - Haoran Mu
- Department of Orthopedics, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, 200000, Shanghai, China.
- Shanghai Bone Tumor Institution, 200000, Shanghai, China.
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4
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Maurin M, Ranjouri M, Megino-Luque C, Newberg JY, Du D, Martin K, Miner RE, Prater MS, Wee DKB, Centeno B, Pruett-Miller SM, Stewart P, Fleming JB, Yu X, Bravo-Cordero JJ, Guccione E, Black MA, Mann KM. RBFOX2 deregulation promotes pancreatic cancer progression and metastasis through alternative splicing. Nat Commun 2023; 14:8444. [PMID: 38114498 PMCID: PMC10730836 DOI: 10.1038/s41467-023-44126-w] [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: 08/02/2022] [Accepted: 11/30/2023] [Indexed: 12/21/2023] Open
Abstract
RNA splicing is an important biological process associated with cancer initiation and progression. However, the contribution of alternative splicing to pancreatic cancer (PDAC) development is not well understood. Here, we identify an enrichment of RNA binding proteins (RBPs) involved in splicing regulation linked to PDAC progression from a forward genetic screen using Sleeping Beauty insertional mutagenesis in a mouse model of pancreatic cancer. We demonstrate downregulation of RBFOX2, an RBP of the FOX family, promotes pancreatic cancer progression and liver metastasis. Specifically, we show RBFOX2 regulates exon splicing events in transcripts encoding proteins involved in cytoskeletal remodeling programs. These exons are differentially spliced in PDAC patients, with enhanced exon skipping in the classical subtype for several RBFOX2 targets. RBFOX2 mediated splicing of ABI1, encoding the Abelson-interactor 1 adapter protein, controls the abundance and localization of ABI1 protein isoforms in pancreatic cancer cells and promotes the relocalization of ABI1 from the cytoplasm to the periphery of migrating cells. Using splice-switching antisense oligonucleotides (AONs) we demonstrate the ABI1 ∆Ex9 isoform enhances cell migration. Together, our data identify a role for RBFOX2 in promoting PDAC progression through alternative splicing regulation.
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Affiliation(s)
- Michelle Maurin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | | | - Cristina Megino-Luque
- Division of Hematology and Oncology, Department of Medicine, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Justin Y Newberg
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Dongliang Du
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Katelyn Martin
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Robert E Miner
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Mollie S Prater
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Dave Keng Boon Wee
- Institute for Molecular and Cell Biology (IMCB), Agency for Science, Technology and Research (A*STAR), Singapore, 138673, Republic of Singapore
| | - Barbara Centeno
- Department of Anatomic Pathology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology and Center for Advanced Genome Engineering (CAGE), St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Paul Stewart
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Jason B Fleming
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Xiaoqing Yu
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, 33612, USA
| | - Jose Javier Bravo-Cordero
- Division of Hematology and Oncology, Department of Medicine, The Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Ernesto Guccione
- Center for OncoGenomics and Innovative Therapeutics (COGIT), Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Center for Therapeutics Discovery, Department of Oncological Sciences and Pharmacological Sciences, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Michael A Black
- Department of Biochemistry, University of Otago, Dunedin, 9054, New Zealand
| | - Karen M Mann
- Department of Molecular Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA.
- Department of Gastrointestinal Oncology, Moffitt Cancer Center, Tampa, FL, 33612, USA.
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5
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Kwon MJ. Role of epithelial splicing regulatory protein 1 in cancer progression. Cancer Cell Int 2023; 23:331. [PMID: 38110955 PMCID: PMC10729575 DOI: 10.1186/s12935-023-03180-6] [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: 12/12/2023] [Indexed: 12/20/2023] Open
Abstract
As aberrant alternative splicing by either dysregulation or mutations of splicing factors contributes to cancer initiation and progression, splicing factors are emerging as potential therapeutic targets for cancer therapy. Therefore, pharmacological modulators targeting splicing factors have been under development. Epithelial splicing regulatory protein 1 (ESRP1) is an epithelial cell-specific splicing factor, whose downregulation is associated with epithelial-mesenchymal transition (EMT) by regulating alternative splicing of multiple genes, such as CD44, CTNND1, ENAH, and FGFR2. Consistent with the downregulation of ESRP1 during EMT, it has been initially revealed that high ESRP1 expression is associated with favorable prognosis and ESRP1 plays a tumor-suppressive role in cancer progression. However, ESRP1 has been found to promote cancer progression in some cancers, such as breast and ovarian cancers, indicating that it plays a dual role in cancer progression depending on the type of cancer. Furthermore, recent studies have reported that ESRP1 affects tumor growth by regulating the metabolism of tumor cells or immune cell infiltration in the tumor microenvironment, suggesting the novel roles of ESRP1 in addition to EMT. ESRP1 expression was also associated with response to anticancer drugs. This review describes current understanding of the roles and mechanisms of ESRP1 in cancer progression, and further discusses the emerging novel roles of ESRP1 in cancer and recent attempts to target splicing factors for cancer therapy.
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Affiliation(s)
- Mi Jeong Kwon
- Vessel-Organ Interaction Research Center (MRC), College of Pharmacy, Kyungpook National University, Daegu, Republic of Korea.
- BK21 FOUR KNU Community-Based Intelligent Novel Drug Discovery Education Unit, College of Pharmacy and Research Institute of Pharmaceutical Sciences, Kyungpook National University, 80 Daehak-ro, Buk-gu, Daegu, 41566, Republic of Korea.
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6
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Maltseva D, Tonevitsky A. RNA-binding proteins regulating the CD44 alternative splicing. Front Mol Biosci 2023; 10:1326148. [PMID: 38106992 PMCID: PMC10722200 DOI: 10.3389/fmolb.2023.1326148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Accepted: 11/15/2023] [Indexed: 12/19/2023] Open
Abstract
Alternative splicing is often deregulated in cancer, and cancer-specific isoform switches are part of the oncogenic transformation of cells. Accumulating evidence indicates that isoforms of the multifunctional cell-surface glycoprotein CD44 play different roles in cancer cells as compared to normal cells. In particular, the shift of CD44 isoforms is required for epithelial to mesenchymal transition (EMT) and is crucial for the maintenance of pluripotency in normal human cells and the acquisition of cancer stem cells phenotype for malignant cells. The growing and seemingly promising use of splicing inhibitors for treating cancer and other pathologies gives hope for the prospect of using such an approach to regulate CD44 alternative splicing. This review integrates current knowledge about regulating CD44 alternative splicing by RNA-binding proteins.
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Affiliation(s)
- Diana Maltseva
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
| | - Alexander Tonevitsky
- Faculty of Biology and Biotechnology, HSE University, Moscow, Russia
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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7
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Li L, Zheng J, Oltean S. Regulation of Epithelial-Mesenchymal Transitions by Alternative Splicing: Potential New Area for Cancer Therapeutics. Genes (Basel) 2023; 14:2001. [PMID: 38002944 PMCID: PMC10671305 DOI: 10.3390/genes14112001] [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: 09/14/2023] [Revised: 10/23/2023] [Accepted: 10/25/2023] [Indexed: 11/26/2023] Open
Abstract
The epithelial-mesenchymal transition (EMT) is a complicated biological process in which cells with epithelial phenotype are transformed into mesenchymal cells with loss of cell polarity and cell-cell adhesion and gain of the ability to migrate. EMT and the reverse mesenchymal-epithelial transitions (METs) are present during cancer progression and metastasis. Using the dynamic switch between EMT and MET, tumour cells can migrate to neighbouring organs or metastasize in the distance and develop resistance to traditional chemotherapy and targeted drug treatments. Growing evidence shows that reversing or inhibiting EMT may be an advantageous approach for suppressing the migration of tumour cells or distant metastasis. Among different levels of modulation of EMT, alternative splicing (AS) plays an important role. An in-depth understanding of the role of AS and EMT in cancer is not only helpful to better understand the occurrence and regulation of EMT in cancer progression, but also may provide new therapeutic strategies. This review will present and discuss various splice variants and splicing factors that have been shown to play a crucial role in EMT.
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Affiliation(s)
| | | | - Sebastian Oltean
- Department of Clinical and Biomedical Sciences, Faculty of Health and Life Sciences, University of Exeter Medical School, Exeter EX1 2LU, UK; (L.L.)
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8
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Datta S, Cao W, Skillman M, Wu M. Hypoplastic Left Heart Syndrome: Signaling & Molecular Perspectives, and the Road Ahead. Int J Mol Sci 2023; 24:15249. [PMID: 37894928 PMCID: PMC10607600 DOI: 10.3390/ijms242015249] [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: 09/13/2023] [Revised: 10/07/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Hypoplastic left heart syndrome (HLHS) is a lethal congenital heart disease (CHD) affecting 8-25 per 100,000 neonates globally. Clinical interventions, primarily surgical, have improved the life expectancy of the affected subjects substantially over the years. However, the etiological basis of HLHS remains fundamentally unclear to this day. Based upon the existing paradigm of studies, HLHS exhibits a multifactorial mode of etiology mediated by a complicated course of genetic and signaling cascade. This review presents a detailed outline of the HLHS phenotype, the prenatal and postnatal risks, and the signaling and molecular mechanisms driving HLHS pathogenesis. The review discusses the potential limitations and future perspectives of studies that can be undertaken to address the existing scientific gap. Mechanistic studies to explain HLHS etiology will potentially elucidate novel druggable targets and empower the development of therapeutic regimens against HLHS in the future.
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Affiliation(s)
| | | | | | - Mingfu Wu
- Department of Pharmacological and Pharmaceutical Sciences, College of Pharmacy, University of Houston, Houston, TX 77204, USA; (S.D.); (W.C.); (M.S.)
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9
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Yang Y, Lee GC, Nakagaki-Silva E, Huang Y, Peacey M, Partridge R, Gooding C, Smith CJ. Cell-type specific regulator RBPMS switches alternative splicing via higher-order oligomerization and heterotypic interactions with other splicing regulators. Nucleic Acids Res 2023; 51:9961-9982. [PMID: 37548402 PMCID: PMC10570038 DOI: 10.1093/nar/gkad652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 06/28/2023] [Accepted: 07/26/2023] [Indexed: 08/08/2023] Open
Abstract
Alternative pre-mRNA splicing decisions are regulated by RNA binding proteins (RBPs) that can activate or repress regulated splice sites. Repressive RBPs typically harness multivalent interactions to bind stably to target RNAs. Multivalency can be achieved by homomeric oligomerization and heteromeric interactions with other RBPs, often mediated by intrinsically disordered regions (IDRs), and by possessing multiple RNA binding domains. Cell-specific splicing decisions often involve the action of widely expressed RBPs, which are able to bind multivalently around target exons, but without effect in the absence of a cell-specific regulator. To address how cell-specific regulators can collaborate with constitutive RBPs in alternative splicing regulation, we used the smooth-muscle specific regulator RBPMS. Recombinant RBPMS is sufficient to confer smooth muscle cell specific alternative splicing of Tpm1 exon 3 in cell-free assays by preventing assembly of ATP-dependent splicing complexes. This activity depends upon a C-terminal IDR that facilitates dynamic higher-order self-assembly, cooperative binding to multivalent RNA and interactions with widely expressed splicing co-regulators, including MBNL1 and RBFOX2, allowing cooperative assembly of stable cell-specific regulatory complexes.
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Affiliation(s)
- Yi Yang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Giselle C Lee
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | | | - Yuling Huang
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Matthew Peacey
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Ruth Partridge
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
| | - Clare Gooding
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK
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10
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Bonner EA, Lee SC. Therapeutic Targeting of RNA Splicing in Cancer. Genes (Basel) 2023; 14:1378. [PMID: 37510283 PMCID: PMC10379351 DOI: 10.3390/genes14071378] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 06/25/2023] [Accepted: 06/27/2023] [Indexed: 07/30/2023] Open
Abstract
RNA splicing is a key regulatory step in the proper control of gene expression. It is a highly dynamic process orchestrated by the spliceosome, a macro-molecular machinery that consists of protein and RNA components. The dysregulation of RNA splicing has been observed in many human pathologies ranging from neurodegenerative diseases to cancer. The recent identification of recurrent mutations in the core components of the spliceosome in hematologic malignancies has advanced our knowledge of how splicing alterations contribute to disease pathogenesis. This review article will discuss our current understanding of how aberrant RNA splicing regulation drives tumor initiation and progression. We will also review current therapeutic modalities and highlight emerging technologies designed to target RNA splicing for cancer treatment.
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Affiliation(s)
- Elizabeth A Bonner
- Molecular and Cellular Biology Graduate Program, University of Washington, Seattle, WA 98195, USA
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
| | - Stanley C Lee
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, WA 98109, USA
- Department of Laboratory Medicine and Pathology, University of Washington School of Medicine, Seattle, WA 98195, USA
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11
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Novosad VO, Maltseva DV. The RNA-Binding Proteins OAS1, ZFP36L2, and DHX58 Are Involved in the Regulation of CD44 mRNA Splicing in Colorectal Cancer Cells. Bull Exp Biol Med 2023:10.1007/s10517-023-05826-x. [PMID: 37336810 DOI: 10.1007/s10517-023-05826-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Indexed: 06/21/2023]
Abstract
Regulation of alternative splicing is carried out by RNA-binding proteins. Each alternative splicing event is controlled by several RNA-binding proteins, which in combination create the distribution of alternative splicing products in a given cell type. Transmembrane protein CD44 plays an important role at various stages of the metastatic cascade and is considered as a promising molecule for the therapy of tumor diseases and the construction of prognostic classifiers. However, the functions of specific isoforms of this protein may differ significantly. In this work, we performed a bioinformatic search of RNA-binding proteins that can determine the expression of clinically significant isoforms 3 and 4 of CD44 protein. The analysis revealed five RNA-binding proteins, three of which (OAS1, ZFP36L2, and DHX58) are shown for the first time as potential regulators of the studied process.
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Affiliation(s)
- V O Novosad
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - D V Maltseva
- Faculty of Biology and Biotechnologies, National Research University Higher School of Economics (HSE University), Moscow, Russia.
- M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.
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12
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Ellis JA, Hale MA, Cleary JD, Wang E, Andrew Berglund J. Alternative splicing outcomes across an RNA-binding protein concentration gradient. J Mol Biol 2023:168156. [PMID: 37230319 DOI: 10.1016/j.jmb.2023.168156] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 04/18/2023] [Accepted: 05/17/2023] [Indexed: 05/27/2023]
Abstract
Alternative splicing (AS) is a dynamic RNA processing step that produces multiple RNA isoforms from a single pre-mRNA transcript and contributes to the complexity of the cellular transcriptome and proteome. This process is regulated through a network of cis-regulatory sequence elements and trans-acting factors, most-notably RNA binding proteins (RBPs). The muscleblind-like (MBNL) and RNA binding fox-1 homolog (RBFOX) are two well characterized families of RBPs that regulate fetal to adult AS transitions critical for proper muscle, heart, and central nervous system development. To better understand how the concentration of these RBPs influences AS transcriptome wide, we engineered a MBNL1 and RBFOX1 inducible HEK-293 cell line. Modest induction of exogenous RBFOX1 in this cell line modulated MBNL1-dependent AS outcomes in 3 skipped exon events, despite significant levels of endogenous RBFOX1 and RBFOX2. Due to background RBFOX levels, we conducted a focused analysis of dose-dependent MBNL1 skipped exon AS outcomes and generated transcriptome wide dose-response curves. Analysis of this data demonstrates that MBNL1-regulated exclusion events may require higher concentrations of MBNL1 protein to properly regulate AS outcomes compared to inclusion events and that multiple arrangements of YGCY motifs can produce similar splicing outcomes. These results suggest that rather than a simple relationship between the organization of RBP binding sites and a specific splicing outcome, that complex interaction networks govern both AS inclusion and exclusion events across a RBP gradient.
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Affiliation(s)
- Joseph A Ellis
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Melissa A Hale
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; Department of Neurology, School of Medicine, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - John D Cleary
- The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States
| | - Eric Wang
- Department of Microbiology and Molecular Genetics & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States
| | - J Andrew Berglund
- Department of Biochemistry & Molecular Biology & Center for NeuroGenetics, College of Medicine, University of Florida, Gainesville, Florida 32610, United States; The RNA Institute, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; Department of Biological Sciences, College of Arts and Sciences, University at Albany, SUNY, Albany, NY 12222, United States; RNA Institute, State University of New York at Albany, LSRB-2033, 1400 Washington Avenue, Albany, New York, 12222.
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13
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Jbara A, Lin KT, Stossel C, Siegfried Z, Shqerat H, Amar-Schwartz A, Elyada E, Mogilevsky M, Raitses-Gurevich M, Johnson JL, Yaron TM, Ovadia O, Jang GH, Danan-Gotthold M, Cantley LC, Levanon EY, Gallinger S, Krainer AR, Golan T, Karni R. RBFOX2 modulates a metastatic signature of alternative splicing in pancreatic cancer. Nature 2023; 617:147-153. [PMID: 36949200 PMCID: PMC10156590 DOI: 10.1038/s41586-023-05820-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/10/2023] [Indexed: 03/24/2023]
Abstract
Pancreatic ductal adenocarcinoma (PDA) is characterized by aggressive local invasion and metastatic spread, leading to high lethality. Although driver gene mutations during PDA progression are conserved, no specific mutation is correlated with the dissemination of metastases1-3. Here we analysed RNA splicing data of a large cohort of primary and metastatic PDA tumours to identify differentially spliced events that correlate with PDA progression. De novo motif analysis of these events detected enrichment of motifs with high similarity to the RBFOX2 motif. Overexpression of RBFOX2 in a patient-derived xenograft (PDX) metastatic PDA cell line drastically reduced the metastatic potential of these cells in vitro and in vivo, whereas depletion of RBFOX2 in primary pancreatic tumour cell lines increased the metastatic potential of these cells. These findings support the role of RBFOX2 as a potent metastatic suppressor in PDA. RNA-sequencing and splicing analysis of RBFOX2 target genes revealed enrichment of genes in the RHO GTPase pathways, suggesting a role of RBFOX2 splicing activity in cytoskeletal organization and focal adhesion formation. Modulation of RBFOX2-regulated splicing events, such as via myosin phosphatase RHO-interacting protein (MPRIP), is associated with PDA metastases, altered cytoskeletal organization and the induction of focal adhesion formation. Our results implicate the splicing-regulatory function of RBFOX2 as a tumour suppressor in PDA and suggest a therapeutic approach for metastatic PDA.
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Affiliation(s)
- Amina Jbara
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Kuan-Ting Lin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Chani Stossel
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Zahava Siegfried
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Haya Shqerat
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Adi Amar-Schwartz
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Ela Elyada
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Maxim Mogilevsky
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | | | - Jared L Johnson
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Tomer M Yaron
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Englander Institute for Precision Medicine, Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY, USA
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY, USA
| | - Ofek Ovadia
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel
| | - Gun Ho Jang
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Miri Danan-Gotthold
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Lewis C Cantley
- Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Erez Y Levanon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Steven Gallinger
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | | | - Talia Golan
- Division of Oncology, Sheba Medical Center Tel Hashomer, Ramat-Gan, Israel
| | - Rotem Karni
- Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, Hebrew University-Hadassah Medical School, Jerusalem, Israel.
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14
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Londero M, Gallo A, Cattaneo C, Ghilardi A, Ronzio M, Del Giacco L, Mantovani R, Dolfini D. NF-YAl drives EMT in Claudin low tumours. Cell Death Dis 2023; 14:65. [PMID: 36707502 PMCID: PMC9883497 DOI: 10.1038/s41419-023-05591-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 01/11/2023] [Accepted: 01/13/2023] [Indexed: 01/29/2023]
Abstract
NF-Y is a trimeric transcription factor whose binding site -the CCAAT box- is enriched in cancer-promoting genes. The regulatory subunit, the sequence-specificity conferring NF-YA, comes in two major isoforms, NF-YA long (NF-YAl) and short (NF-YAs). Extensive expression analysis in epithelial cancers determined two features: widespread overexpression and changes in NF-YAl/NF-YAs ratios (NF-YAr) in tumours with EMT features. We performed wet and in silico experiments to explore the role of the isoforms in breast -BRCA- and gastric -STAD- cancers. We generated clones of two Claudinlow BRCA lines SUM159PT and BT549 ablated of exon-3, thus shifting expression from NF-YAl to NF-YAs. Edited clones show normal growth but reduced migratory capacities in vitro and ability to metastatize in vivo. Using TCGA, including upon deconvolution of scRNA-seq data, we formalize the clinical importance of high NF-YAr, associated to EMT genes and cell populations. We derive a novel, prognostic 158 genes signature common to BRCA and STAD Claudinlow tumours. Finally, we identify splicing factors associated to high NF-YAr, validating RBFOX2 as promoting expression of NF-YAl. These data bring three relevant results: (i) the definition and clinical implications of NF-YAr and the 158 genes signature in Claudinlow tumours; (ii) genetic evidence of 28 amino acids in NF-YAl with EMT-promoting capacity; (iii) the definition of selected splicing factors associated to NF-YA isoforms.
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Affiliation(s)
- Michela Londero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Alberto Gallo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Camilla Cattaneo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Anna Ghilardi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Mirko Ronzio
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Luca Del Giacco
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Roberto Mantovani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy
| | - Diletta Dolfini
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133, Milano, Italy.
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15
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Functional roles of long noncoding RNA MALAT1 in gynecologic cancers. CLINICAL & TRANSLATIONAL ONCOLOGY : OFFICIAL PUBLICATION OF THE FEDERATION OF SPANISH ONCOLOGY SOCIETIES AND OF THE NATIONAL CANCER INSTITUTE OF MEXICO 2023; 25:48-65. [PMID: 36042115 DOI: 10.1007/s12094-022-02914-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 07/25/2022] [Indexed: 02/06/2023]
Abstract
Gynecologic cancers are reproductive disorders characterized by pelvic pain and infertility. The identification of new predictive markers and therapeutic targets for the treatment of gynecologic cancers is urgently necessary. One of the recent successes in gynecologic cancers research is identifying the role of signaling pathways in the pathogenesis of the disease. Recent experiments showed long noncoding RNAs (lncRNA) can be novel therapeutic approaches for the diagnosis and treatment of gynecologic cancers. LncRNA are transcribed RNA molecules that play pivotal roles in multiple biological processes by regulating the different steps of gene expression. Metastasis-associated lung adenocarcinoma transcript-1 (MALAT1) is a well-known lncRNA that plays functional roles in gene expression, RNA processing, and epigenetic regulation. High expression of MALAT1 is closely related to numerous human diseases. It is generally believed that MALAT1 expression is associated with cancer cell growth, autophagy, invasion, and metastasis. MALAT1 by targeting multiple signaling pathways and microRNAs (miRNAs) could contribute to the pathogenesis of gynecologic cancers. In this review, we will summarize functional roles of MALAT1 in the most common gynecologic cancers, including endometrium, breast, ovary, and cervix.
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16
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Lemaitre F, Chakrama F, O’Grady T, Peulen O, Rademaker G, Deward A, Chabot B, Piette J, Colige A, Lambert C, Dequiedt F, Habraken Y. The transcription factor c-Jun inhibits RBM39 to reprogram pre-mRNA splicing during genotoxic stress. Nucleic Acids Res 2022; 50:12768-12789. [PMID: 36477312 PMCID: PMC9825188 DOI: 10.1093/nar/gkac1130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 10/31/2022] [Accepted: 11/10/2022] [Indexed: 12/13/2022] Open
Abstract
Genotoxic agents, that are used in cancer therapy, elicit the reprogramming of the transcriptome of cancer cells. These changes reflect the cellular response to stress and underlie some of the mechanisms leading to drug resistance. Here, we profiled genome-wide changes in pre-mRNA splicing induced by cisplatin in breast cancer cells. Among the set of cisplatin-induced alternative splicing events we focused on COASY, a gene encoding a mitochondrial enzyme involved in coenzyme A biosynthesis. Treatment with cisplatin induces the production of a short isoform of COASY lacking exons 4 and 5, whose depletion impedes mitochondrial function and decreases sensitivity to cisplatin. We identified RBM39 as a major effector of the cisplatin-induced effect on COASY splicing. RBM39 also controls a genome-wide set of alternative splicing events partially overlapping with the cisplatin-mediated ones. Unexpectedly, inactivation of RBM39 in response to cisplatin involves its interaction with the AP-1 family transcription factor c-Jun that prevents RBM39 binding to pre-mRNA. Our findings therefore uncover a novel cisplatin-induced interaction between a splicing regulator and a transcription factor that has a global impact on alternative splicing and contributes to drug resistance.
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Affiliation(s)
| | | | - Tina O’Grady
- Laboratory of Gene Expression and Cancer, GIGA-Molecular Biology of Diseases, B34, University of Liège, Liège 4000, Belgium
| | - Olivier Peulen
- Metastasis Research Laboratory, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Gilles Rademaker
- Metastasis Research Laboratory, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Adeline Deward
- Laboratory of Virology and Immunology, GIGA-Molecular Biology of Diseases, B34, University of Liège, Liège 4000, Belgium
| | - Benoit Chabot
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences. Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Jacques Piette
- Laboratory of Virology and Immunology, GIGA-Molecular Biology of Diseases, B34, University of Liège, Liège 4000, Belgium
| | - Alain Colige
- Laboratory of Connective Tissues Biology, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Charles Lambert
- Laboratory of Connective Tissues Biology, GIGA-Cancer, B23, University of Liège, Liège 4000, Belgium
| | - Franck Dequiedt
- Correspondence may also be addressed to Franck Dequiedt. Tel: +32 366 9028;
| | - Yvette Habraken
- To whom correspondence should be addressed. Tel: +32 4 366 2447; Fax: +32 4 366 4198;
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17
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Mehta M, Raguraman R, Ramesh R, Munshi A. RNA binding proteins (RBPs) and their role in DNA damage and radiation response in cancer. Adv Drug Deliv Rev 2022; 191:114569. [PMID: 36252617 PMCID: PMC10411638 DOI: 10.1016/j.addr.2022.114569] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 09/27/2022] [Accepted: 09/29/2022] [Indexed: 01/24/2023]
Abstract
Traditionally majority of eukaryotic gene expression is influenced by transcriptional and post-transcriptional events. Alterations in the expression of proteins that act post-transcriptionally can affect cellular signaling and homeostasis. RNA binding proteins (RBPs) are a family of proteins that specifically bind to RNAs and are involved in post-transcriptional regulation of gene expression and important cellular processes such as cell differentiation and metabolism. Deregulation of RNA-RBP interactions and any changes in RBP expression or function can lead to various diseases including cancer. In cancer cells, RBPs play an important role in regulating the expression of tumor suppressors and oncoproteins involved in various cell-signaling pathways. Several RBPs such as HuR, AUF1, RBM38, LIN28, RBM24, tristetrapolin family and Musashi play critical roles in various types of cancers and their aberrant expression in cancer cells makes them an attractive therapeutic target for cancer treatment. In this review we provide an overview of i). RBPs involved in cancer progression and their mechanism of action ii). the role of RBPs, including HuR, in breast cancer progression and DNA damage response and iii). explore RBPs with emphasis on HuR as therapeutic target for breast cancer therapy.
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Affiliation(s)
- Meghna Mehta
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajeswari Raguraman
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Rajagopal Ramesh
- Department of Pathology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA
| | - Anupama Munshi
- Department of Radiation Oncology, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA; Stephenson Cancer Center, The University of Oklahoma Health Sciences Center, Oklahoma City, OK 73013, USA.
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18
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Bareche Y, Kelly D, Abbas-Aghababazadeh F, Nakano M, Esfahani PN, Tkachuk D, Mohammad H, Samstein R, Lee CH, Morris LGT, Bedard PL, Haibe-Kains B, Stagg J. Leveraging big data of immune checkpoint blockade response identifies novel potential targets. Ann Oncol 2022; 33:1304-1317. [PMID: 36055464 DOI: 10.1016/j.annonc.2022.08.084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 08/03/2022] [Accepted: 08/22/2022] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The development of immune checkpoint blockade (ICB) has changed the way we treat various cancers. While ICB produces durable survival benefits in a number of malignancies, a large proportion of treated patients do not derive clinical benefit. Recent clinical profiling studies have shed light on molecular features and mechanisms that modulate response to ICB. Nevertheless, none of these identified molecular features were investigated in large enough cohorts to be of clinical value. MATERIALS AND METHODS Literature review was carried out to identify relevant studies including clinical dataset of patients treated with ICB [anti-programmed cell death protein 1 (PD-1)/programmed death-ligand 1 (PD-L1), anti-cytotoxic T-lymphocyte antigen 4 (CTLA-4) or the combination] and available sequencing data. Tumor mutational burden (TMB) and 37 previously reported gene expression (GE) signatures were computed with respect to the original publication. Biomarker association with ICB response (IR) and survival (progression-free survival/overall survival) was investigated separately within each study and combined together for meta-analysis. RESULTS We carried out a comparative meta-analysis of genomic and transcriptomic biomarkers of IRs in over 3600 patients across 12 tumor types and implemented an open-source web application (predictIO.ca) for exploration. TMB and 21/37 gene signatures were predictive of IRs across tumor types. We next developed a de novo GE signature (PredictIO) from our pan-cancer analysis and demonstrated its superior predictive value over other biomarkers. To identify novel targets, we computed the T-cell dysfunction score for each gene within PredictIO and their ability to predict dual PD-1/CTLA-4 blockade in mice. Two genes, F2RL1 (encoding protease-activated receptor-2) and RBFOX2 (encoding RNA-binding motif protein 9), were concurrently associated with worse ICB clinical outcomes, T-cell dysfunction in ICB-naive patients and resistance to dual PD-1/CTLA-4 blockade in preclinical models. CONCLUSION Our study highlights the potential of large-scale meta-analyses in identifying novel biomarkers and potential therapeutic targets for cancer immunotherapy.
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Affiliation(s)
- Y Bareche
- Faculty of Pharmacy, Université de Montréal, Montreal, Canada; Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Institut du Cancer de Montréal, Montreal, Canada
| | - D Kelly
- Princess Margaret Cancer Centre, University Health Network, Division of Medical Oncology and Hematology, Toronto, Canada
| | - F Abbas-Aghababazadeh
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - M Nakano
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - P N Esfahani
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - D Tkachuk
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - H Mohammad
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada
| | - R Samstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, USA
| | - C-H Lee
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, USA
| | - L G T Morris
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA
| | - P L Bedard
- Princess Margaret Cancer Centre, University Health Network, Division of Medical Oncology and Hematology, Toronto, Canada
| | - B Haibe-Kains
- Princess Margaret Bioinformatics and Computational Genomics Laboratory, University Health Network, Toronto, Canada; Princess Margaret Cancer Centre, University Health Network, Toronto, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Canada; Department ofComputer Science, University of Toronto, Toronto, Canada; Department ofOntario Institute for Cancer Research, Toronto, Canada; Department ofVector Institute for Artificial Intelligence, Toronto, Canada; Department ofBiostatistics Division, Dalla Lana School of Public Health, Toronto, Canada.
| | - J Stagg
- Faculty of Pharmacy, Université de Montréal, Montreal, Canada; Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Institut du Cancer de Montréal, Montreal, Canada.
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19
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Zhang S, Mao M, Lv Y, Yang Y, He W, Song Y, Wang Y, Yang Y, Al Abo M, Freedman JA, Patierno SR, Wang Y, Wang Z. A widespread length-dependent splicing dysregulation in cancer. SCIENCE ADVANCES 2022; 8:eabn9232. [PMID: 35977015 PMCID: PMC9385142 DOI: 10.1126/sciadv.abn9232] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 07/01/2022] [Indexed: 06/15/2023]
Abstract
Dysregulation of alternative splicing is a key molecular hallmark of cancer. However, the common features and underlying mechanisms remain unclear. Here, we report an intriguing length-dependent splicing regulation in cancers. By systematically analyzing the transcriptome of thousands of cancer patients, we found that short exons are more likely to be mis-spliced and preferentially excluded in cancers. Compared to other exons, cancer-associated short exons (CASEs) are more conserved and likely to encode in-frame low-complexity peptides, with functional enrichment in GTPase regulators and cell adhesion. We developed a CASE-based panel as reliable cancer stratification markers and strong predictors for survival, which is clinically useful because the detection of short exon splicing is practical. Mechanistically, mis-splicing of CASEs is regulated by elevated transcription and alteration of certain RNA binding proteins in cancers. Our findings uncover a common feature of cancer-specific splicing dysregulation with important clinical implications in cancer diagnosis and therapies.
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Affiliation(s)
- Sirui Zhang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Miaowei Mao
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Yuesheng Lv
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Yingqun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
- Shanghai Tech University, Shanghai 200031, China
| | - Weijing He
- Department of Colorectal Surgery, Fudan University Shanghai Cancer Center, Shanghai 200032, China
- Department of Oncology, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yongmei Song
- State Key Laboratory of Molecular Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100021, China
| | - Yongbo Wang
- Department of Cellular and Genetic Medicine, School of Basic Medical Sciences, Fudan University, Shanghai 200032, China
| | - Yun Yang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
| | - Muthana Al Abo
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
| | - Jennifer A. Freedman
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Steven R. Patierno
- Duke Cancer Institute, Duke University School of Medicine, Durham, NC 27710, USA
- Division of Medical Oncology, Department of Medicine, Duke University Medical Center, Durham, NC 27710, USA
| | - Yang Wang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian 116044, China
| | - Zefeng Wang
- CAS Key Laboratory of Computational Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai 200031, China
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20
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Secchi M, Lodola C, Garbelli A, Bione S, Maga G. DEAD-Box RNA Helicases DDX3X and DDX5 as Oncogenes or Oncosuppressors: A Network Perspective. Cancers (Basel) 2022; 14:cancers14153820. [PMID: 35954483 PMCID: PMC9367324 DOI: 10.3390/cancers14153820] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/01/2022] [Accepted: 08/04/2022] [Indexed: 11/16/2022] Open
Abstract
Simple Summary The transformation of a normal cell into a cancerous one is caused by the deregulation of different metabolic pathways, involving a complex network of protein–protein interactions. The cellular enzymes DDX3X and DDX5 play important roles in the maintenance of normal cell metabolism, but their deregulation can accelerate tumor transformation. Both DDX3X and DDX5 interact with hundreds of different cellular proteins, and depending on the specific pathways in which they are involved, both proteins can either act as suppressors of cancer or as oncogenes. In this review, we summarize the current knowledge about the roles of DDX3X and DDX5 in different tumors. In addition, we present a list of interacting proteins and discuss the possible contribution of some of these protein–protein interactions in determining the roles of DDX3X and DDX5 in the process of cancer proliferation, also suggesting novel hypotheses for future studies. Abstract RNA helicases of the DEAD-box family are involved in several metabolic pathways, from transcription and translation to cell proliferation, innate immunity and stress response. Given their multiple roles, it is not surprising that their deregulation or mutation is linked to different pathological conditions, including cancer. However, while in some cases the loss of function of a given DEAD-box helicase promotes tumor transformation, indicating an oncosuppressive role, in other contexts the overexpression of the same enzyme favors cancer progression, thus acting as a typical oncogene. The roles of two well-characterized members of this family, DDX3X and DDX5, as both oncogenes and oncosuppressors have been documented in several cancer types. Understanding the interplay of the different cellular contexts, as defined by the molecular interaction networks of DDX3X and DDX5 in different tumors, with the cancer-specific roles played by these proteins could help to explain their apparently conflicting roles as cancer drivers or suppressors.
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21
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Alternative Splicing of the Aryl Hydrocarbon Receptor Nuclear Translocator (ARNT) Is Regulated by RBFOX2 in Lymphoid Malignancies. Mol Cell Biol 2022; 42:e0050321. [PMID: 35404107 PMCID: PMC9119065 DOI: 10.1128/mcb.00503-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aberrant alternative splicing (AS) of pre-mRNAs promotes the development and proliferation of cancerous cells. Accordingly, we had previously observed higher levels of the aryl hydrocarbon receptor nuclear translocator (ARNT) spliced variant isoform 1 in human lymphoid malignancies compared to that in normal lymphoid cells, which is a consequence of increased inclusion of alternative exon 5. ARNT is a transcription factor that has been implicated in the survival of various cancers. Notably, we found that ARNT isoform 1 promoted the growth and survival of lymphoid malignancies, but the regulatory mechanism controlling ARNT AS is unclear. Here, we report cis- and trans-regulatory elements which are important for the inclusion of ARNT exon 5. Specifically, we identified recognition motifs for the RNA-binding protein RBFOX2, which are required for RBFOX2-mediated exon 5 inclusion. RBFOX2 upregulation was observed in lymphoid malignancies, correlating with the observed increase in ARNT exon 5 inclusion. Moreover, suppression of RBFOX2 significantly reduced ARNT isoform 1 levels and cell growth. These observations reveal RBFOX2 as a critical regulator of ARNT AS in lymphoid malignancies and suggest that blocking the ARNT-specific RBFOX2 motifs to decrease ARNT isoform 1 levels is a viable option for targeting the growth of lymphoid malignancies.
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22
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Alanazi IO, Alamery SF, Ebrahimie E, Mohammadi-Dehcheshmeh M. Splice-disrupt genomic variants in prostate cancer. Mol Biol Rep 2022; 49:4237-4246. [PMID: 35286517 PMCID: PMC9262760 DOI: 10.1007/s11033-022-07257-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Background Splice-disrupt genomic variants are one of the causes of cancer-causing errors in gene expression. Little is known about splice-disrupt genomic variants. Methods and results Here, pattern of splice-disrupt variants was investigated using 21,842,764 genomic variants in different types of prostate cancer. A particular attention was paid to genomic locations of splice-disrupt variants on target genes. HLA-A in prostate cancer, MSR1 in familial prostate cancer, and EGFR in both castration-resistant prostate cancer and metastatic castration-resistant had the highest allele frequencies of splice-disrupt variations. Some splice-disrupt variants, located on coding sequences of NCOR2, PTPRC, and CRP, were solely present in the advanced metastatic castration-resistant prostate cancer. High-risk splice-disrupt variants were identified based on computationally calculated Polymorphism Phenotyping (PolyPhen), Sorting Intolerant From Tolerant (SIFT), and Genomic Evolutionary Rate Profiling (GERP) + + scores as well as the recorded clinical significance in dbSNP database of NCBI. Functional annotation of damaging splice-disrupt variants highlighted important cancer-associated functions, including endocrine resistance, lipid metabolic process, steroid metabolic process, regulation of mitotic cell cycle, and regulation of metabolic process. This is the first study that profiles the splice-disrupt genomic variants and their target genes in prostate cancer. Literature mining based variant analysis highlighted the importance of rs1800716 variant, located on the CYP2D6 gene, involved in a range of important functions, such as RNA spicing, drug interaction, death, and urotoxicity. Conclusions This is the first study that profiles the splice-disrupt genomic variants and their target genes in different types of prostate cancer. Unravelling alternative splicing opens a new avenue towards the establishment of new diagnostic and prognostic markers for prostate cancer progression and metastasis. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07257-9.
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Affiliation(s)
- Ibrahim O. Alanazi
- National Center for Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Salman F. Alamery
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, VIC 3086 Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, 5371 Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Manijeh Mohammadi-Dehcheshmeh
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, VIC 3086 Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, 5371 Australia
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23
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Transcriptional and post-transcriptional control of epithelial-mesenchymal plasticity: why so many regulators? Cell Mol Life Sci 2022; 79:182. [PMID: 35278142 PMCID: PMC8918127 DOI: 10.1007/s00018-022-04199-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 01/18/2022] [Accepted: 02/07/2022] [Indexed: 12/12/2022]
Abstract
The dynamic transition between epithelial-like and mesenchymal-like cell states has been a focus for extensive investigation for decades, reflective of the importance of Epithelial-Mesenchymal Transition (EMT) through development, in the adult, and the contributing role EMT has to pathologies including metastasis and fibrosis. Not surprisingly, regulation of the complex genetic networks that underlie EMT have been attributed to multiple transcription factors and microRNAs. What is surprising, however, are the sheer number of different regulators (hundreds of transcription factors and microRNAs) for which critical roles have been described. This review seeks not to collate these studies, but to provide a perspective on the fundamental question of whether it is really feasible that so many regulators play important roles and if so, what does this tell us about EMT and more generally, the genetic machinery that controls complex biological processes.
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24
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Verma SK, Deshmukh V, Thatcher K, Belanger KK, Rhyner A, Meng S, Holcomb R, Bressan M, Martin J, Cooke J, Wythe J, Widen S, Lincoln J, Kuyumcu-Martinez M. RBFOX2 is required for establishing RNA regulatory networks essential for heart development. Nucleic Acids Res 2022; 50:2270-2286. [PMID: 35137168 PMCID: PMC8881802 DOI: 10.1093/nar/gkac055] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/25/2022] [Indexed: 12/14/2022] Open
Abstract
Human genetic studies identified a strong association between loss of function mutations in RBFOX2 and hypoplastic left heart syndrome (HLHS). There are currently no Rbfox2 mouse models that recapitulate HLHS. Therefore, it is still unknown how RBFOX2 as an RNA binding protein contributes to heart development. To address this, we conditionally deleted Rbfox2 in embryonic mouse hearts and found profound defects in cardiac chamber and yolk sac vasculature formation. Importantly, our Rbfox2 conditional knockout mouse model recapitulated several molecular and phenotypic features of HLHS. To determine the molecular drivers of these cardiac defects, we performed RNA-sequencing in Rbfox2 mutant hearts and identified dysregulated alternative splicing (AS) networks that affect cell adhesion to extracellular matrix (ECM) mediated by Rho GTPases. We identified two Rho GTPase cycling genes as targets of RBFOX2. Modulating AS of these two genes using antisense oligos led to cell cycle and cell-ECM adhesion defects. Consistently, Rbfox2 mutant hearts displayed cell cycle defects and inability to undergo endocardial-mesenchymal transition, processes dependent on cell-ECM adhesion and that are seen in HLHS. Overall, our work not only revealed that loss of Rbfox2 leads to heart development defects resembling HLHS, but also identified RBFOX2-regulated AS networks that influence cell-ECM communication vital for heart development.
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Affiliation(s)
- Sunil K Verma
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Vaibhav Deshmukh
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Kaitlyn Thatcher
- Department of Pediatrics, Medical College of Wisconsin, Division of Pediatric Cardiology, The Herma Heart Institute, Children's WI, Milwaukee, WI 53226, USA
| | - KarryAnne K Belanger
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Alexander M Rhyner
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shu Meng
- Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX 77030, USA
| | - Richard Joshua Holcomb
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Michael Bressan
- Department of Cell Biology and Physiology, McAllister Heart Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC27599, USA
| | - James F Martin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030, USA
- Cardiomyocyte Renewal Lab;Texas Heart Institute, Houston, TX77030, USA
| | - John P Cooke
- Houston Methodist Research Institute, Department of Cardiovascular Sciences, Houston, TX 77030, USA
| | - Joshua D Wythe
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
- Center for Organ Repair and Renewal, Baylor College of Medicine, Houston, TX 77030, USA
- Cardiomyocyte Renewal Lab;Texas Heart Institute, Houston, TX77030, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
| | - Joy Lincoln
- Department of Pediatrics, Medical College of Wisconsin, Division of Pediatric Cardiology, The Herma Heart Institute, Children's WI, Milwaukee, WI 53226, USA
| | - Muge N Kuyumcu-Martinez
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX 77555, USA
- Department of Neuroscience, Cell Biology and Anatomy, Institute for Translational Sciences, University of Texas Medical Branch, 301 University Blvd. Galveston, TX 77555, USA
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25
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Ou X, Zhou X, Li J, Ye J, Liu H, Fang D, Cai Q, Cai S, He Y, Xu J. p53-Induced LINC00893 Regulates RBFOX2 Stability to Suppress Gastric Cancer Progression. Front Cell Dev Biol 2022; 9:796451. [PMID: 35127712 PMCID: PMC8807521 DOI: 10.3389/fcell.2021.796451] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/29/2021] [Indexed: 01/07/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) have been reported to regulate diverse tumorigenic processes. However, little is known about long intergenic non-protein coding RNA 00893 (LINC00893) and its role in gastric cancer (GC). Herein we investigated its biological functions and molecular mechanism in GC. LINC00893 was decreased in GC tissues but significantly elevated in AGS cells after treatment with Nutlin-3. In GC patients, it was found that low expression of LINC00893 was correlated with tumor growth, metastasis and poor survival. Functionally, overexpression of LINC00893 suppressed the proliferation, migration and invasion of GC cells. Mechanistically, LINC00893 regulated the expression of epithelial-mesenchymal transition (EMT)-related proteins by binding to RNA binding fox-1 homolog 2 (RBFOX2) and promoting its ubiquitin-mediated degradation, thus suppressing the EMT and related functions of GC. In addition, the transcription factor p53 can regulate the expression of LINC00893 in an indirect way. Taken together, these results suggested that LINC00893 regulated by p53 repressed GC proliferation, migration and invasion by functioning as a binding site for RBFOX2 to regulate its stability and the expression of EMT-related proteins. LINC00893 acts as a tumor-inhibiting lncRNA that is induced by p53 in GC and regulates EMT by binding to RBFOX2, thus providing a novel experimental basis for the clinical treatment of GC.
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Affiliation(s)
- Xinde Ou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Xingyu Zhou
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jin Li
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
| | - Jinning Ye
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Haohan Liu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Deliang Fang
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Qinbo Cai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Laboratory of General Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Shirong Cai
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yulong He
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- Digestive Disease Center, The Seventh Affiliated Hospital, Sun Yat-sen University, Shenzhen, China
- *Correspondence: Yulong He, ; Jianbo Xu,
| | - Jianbo Xu
- Department of Gastrointestinal Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
- *Correspondence: Yulong He, ; Jianbo Xu,
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26
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Öther-Gee Pohl S, Myant KB. Alternative RNA splicing in tumour heterogeneity, plasticity and therapy. Dis Model Mech 2022; 15:dmm049233. [PMID: 35014671 PMCID: PMC8764416 DOI: 10.1242/dmm.049233] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Alternative splicing is a process by which a single gene is able to encode multiple different protein isoforms. It is regulated by the inclusion or exclusion of introns and exons that are joined in different patterns prior to protein translation, thus enabling transcriptomic and proteomic diversity. It is now widely accepted that alternative splicing is dysregulated across nearly all cancer types. This widespread dysregulation means that nearly all cellular processes are affected - these include processes synonymous with the hallmarks of cancer - evasion of apoptosis, tissue invasion and metastasis, altered cellular metabolism, genome instability and drug resistance. Emerging evidence indicates that the dysregulation of alternative splicing also promotes a permissive environment for increased tumour heterogeneity and cellular plasticity. These are fundamental regulators of a patient's response to therapy. In this Review, we introduce the mechanisms of alternative splicing and the role of aberrant splicing in cancer, with particular focus on newfound evidence of alternative splicing promoting tumour heterogeneity, cellular plasticity and altered metabolism. We discuss recent in vivo models generated to study alternative splicing and the importance of these for understanding complex tumourigenic processes. Finally, we review the effects of alternative splicing on immune evasion, cell death and genome instability, and how targeting these might enhance therapeutic efficacy.
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Affiliation(s)
| | - Kevin B. Myant
- Cancer Research UK Edinburgh Centre, Institute of Genetics of Cancer, The University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
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27
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Lyu J, Cheng C. Regulation of Alternative Splicing during Epithelial-Mesenchymal Transition. Cells Tissues Organs 2022; 211:238-251. [PMID: 34348273 PMCID: PMC8741878 DOI: 10.1159/000518249] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/28/2021] [Indexed: 01/03/2023] Open
Abstract
Alternative splicing is an essential mechanism of gene regulation, giving rise to remarkable protein diversity in higher eukaryotes. Epithelial-mesenchymal transition (EMT) is a developmental process that plays an essential role in metazoan embryogenesis. Recent studies have revealed that alternative splicing serves as a fundamental layer of regulation that governs cells to undergo EMT. In this review, we summarize recent findings on the functional impact of alternative splicing in EMT and EMT-associated activities. We then discuss the regulatory mechanisms that control alternative splicing changes during EMT.
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Affiliation(s)
- Jingyi Lyu
- Lester and Sue Smith Breast Center, Department of Molecular
& Human Genetics, Department of Molecular & Cellular Biology, Baylor College
of Medicine, Houston, TX 77030, USA,Integrative Molecular and Biomedical Sciences Graduate
Program, Baylor College of Medicine, Houston, TX 77030, USA
| | - Chonghui Cheng
- Lester and Sue Smith Breast Center, Department of Molecular
& Human Genetics, Department of Molecular & Cellular Biology, Baylor College
of Medicine, Houston, TX 77030, USA,Integrative Molecular and Biomedical Sciences Graduate
Program, Baylor College of Medicine, Houston, TX 77030, USA.,To whom correspondence should be addressed:
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28
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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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29
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Naro C, De Musso M, Delle Monache F, Panzeri V, de la Grange P, Sette C. The oncogenic kinase NEK2 regulates an RBFOX2-dependent pro-mesenchymal splicing program in triple-negative breast cancer cells. J Exp Clin Cancer Res 2021; 40:397. [PMID: 34930366 PMCID: PMC8686545 DOI: 10.1186/s13046-021-02210-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 12/06/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Triple-negative breast cancer (TNBC) is the most heterogeneous and malignant subtype of breast cancer (BC). TNBC is defined by the absence of expression of estrogen, progesterone and HER2 receptors and lacks efficacious targeted therapies. NEK2 is an oncogenic kinase that is significantly upregulated in TNBC, thereby representing a promising therapeutic target. NEK2 localizes in the nucleus and promotes oncogenic splice variants in different cancer cells. Notably, alternative splicing (AS) dysregulation has recently emerged as a featuring trait of TNBC that contributes to its aggressive phenotype. METHODS To investigate whether NEK2 modulates TNBC transcriptome we performed RNA-sequencing analyses in a representative TNBC cell line (MDA-MB-231) and results were validated in multiple TNBC cell lines. Bioinformatics and functional analyses were carried out to elucidate the mechanism of splicing regulation by NEK2. Data from The Cancer Genome Atlas were mined to evaluate the potential of NEK2-sensitive exons as markers to identify the TNBC subtype and to assess their prognostic value. RESULTS Transcriptome analysis revealed a widespread impact of NEK2 on the transcriptome of TNBC cells, with 1830 AS events that are susceptible to its expression. NEK2 regulates the inclusion of cassette exons in splice variants that discriminate TNBC from other BC and that correlate with poor prognosis, suggesting that this kinase contributes to the TNBC-specific splicing program. NEK2 elicits its effects by modulating the expression of the splicing factor RBFOX2, a well-known regulator of epithelial to mesenchymal transition (EMT). Accordingly, NEK2 splicing-regulated genes are enriched in functional terms related to cell adhesion and contractile cytoskeleton and NEK2 depletion in mesenchymal TNBC cells induces phenotypic and molecular traits typical of epithelial cells. Remarkably, depletion of select NEK2-sensitive splice-variants that are prognostic in TNBC patients is sufficient to interfere with TNBC cell morphology and motility, suggesting that NEK2 orchestrates a pro-mesenchymal splicing program that modulates migratory and invasive properties of TNBC cells. CONCLUSIONS Our study uncovers an extensive splicing program modulated by NEK2 involving splice variants that confer an invasive phenotype to TNBCs and that might represent, together with NEK2 itself, valuable therapeutic targets for this disease.
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Affiliation(s)
- Chiara Naro
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy.
| | - Monica De Musso
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Francesca Delle Monache
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | - Valentina Panzeri
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli, IRCCS, Rome, Italy
| | | | - Claudio Sette
- Department of Neuroscience, Section of Human Anatomy, Catholic University of the Sacred Heart, 00168, Rome, Italy.
- Fondazione Santa Lucia, IRCCS, Rome, Italy.
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30
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Kim JH, Jeong K, Li J, Murphy JM, Vukadin L, Stone JK, Richard A, Tran J, Gillespie GY, Flemington EK, Sobol RW, Lim STS, Ahn EYE. SON drives oncogenic RNA splicing in glioblastoma by regulating PTBP1/PTBP2 switching and RBFOX2 activity. Nat Commun 2021; 12:5551. [PMID: 34548489 PMCID: PMC8455679 DOI: 10.1038/s41467-021-25892-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 09/01/2021] [Indexed: 12/15/2022] Open
Abstract
While dysregulation of RNA splicing has been recognized as an emerging target for cancer therapy, the functional significance of RNA splicing and individual splicing factors in brain tumors is poorly understood. Here, we identify SON as a master regulator that activates PTBP1-mediated oncogenic splicing while suppressing RBFOX2-mediated non-oncogenic neuronal splicing in glioblastoma multiforme (GBM). SON is overexpressed in GBM patients and SON knockdown causes failure in intron removal from the PTBP1 transcript, resulting in PTBP1 downregulation and inhibition of its downstream oncogenic splicing. Furthermore, SON forms a complex with hnRNP A2B1 and antagonizes RBFOX2, which leads to skipping of RBFOX2-targeted cassette exons, including the PTBP2 neuronal exon. SON knockdown inhibits proliferation and clonogenicity of GBM cells in vitro and significantly suppresses tumor growth in orthotopic xenografts in vivo. Collectively, our study reveals that SON-mediated RNA splicing is a GBM vulnerability, implicating SON as a potential therapeutic target in brain tumors.
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Affiliation(s)
- Jung-Hyun Kim
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kyuho Jeong
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jianfeng Li
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - James M Murphy
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Lana Vukadin
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Joshua K Stone
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Alexander Richard
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - Johnny Tran
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Erik K Flemington
- Department of Pathology, Tulane University School of Medicine, Tulane Cancer Center, New Orleans, LA, USA
| | - Robert W Sobol
- Mitchell Cancer Institute, University of South Alabama, Mobile, AL, USA.
- Department of Pharmacology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Ssang-Teak Steve Lim
- Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.
| | - Eun-Young Erin Ahn
- Department of Pathology, Division of Molecular and Cellular Pathology, University of Alabama at Birmingham, Birmingham, AL, USA.
- O'Neal Comprehensive Cancer Center, University of Alabama at Birmingham, Birmingham, AL, USA.
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31
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Freitag N, Xie Y, Adam LM, Borowski S, Blois SM, Barrientos G. Expression of the alternative splicing regulator Rbfox2 during placental development is differentially regulated in preeclampsia mouse models. Am J Reprod Immunol 2021; 86:e13491. [PMID: 34363260 DOI: 10.1111/aji.13491] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 07/21/2021] [Accepted: 08/03/2021] [Indexed: 12/14/2022] Open
Abstract
PROBLEM Proper placental development is pivotal to ensure healthy pregnancy outcomes. Among the multiple cellular mechanisms involved in the orchestration of this process, little is known on the role of alternative splicing events in the modulation of trophoblast cell biology. Here, we evaluated the expression of the alternative splicing regulator Rbfox2 in the pre- and post-placentation period in mouse pregnancies in both healthy and pathological settings. METHOD OF STUDY Immunofluorescence analysis of Rbfox2 expression in mouse implantation sites collected during the pre-placentation period (E5-E7) and post-placentation (E13). RESULTS We identified a progressive increase of Rbfox2 levels throughout the peri-implantation period with a shift from a cytoplasmatic expression on E5-E6 to a predominantly nuclear expression on E7, together with a prominent expression of this factor in both subcellular compartments of the primitive placenta. Our results further showed that in contrast to healthy gestations, Rbfox2 expression decreased in preeclamptic models during the post-placentation period. Finally, we further demonstrated enhanced expression of Rbfox2 proteins in allogeneic pregnancy compared to syngeneic models. CONCLUSIONS Our findings uncover a novel role for Rbfox2-controlled splicing events in the modulation of trophoblast function, with potential implications for the pathogenesis of preeclampsia and other pregnancy complications originated from defective placentation.
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Affiliation(s)
- Nancy Freitag
- Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, AG GlycoImmunology, and the Charité - Universitätsmedizin Berlin, Berlin, Germany.,Department for Psychosomatic Medicine, Charité - Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Yiran Xie
- Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Reproductive Medicine Center, Taihe Hospital, Hubei Medical University, Shiyan, China
| | - Lisa-Marie Adam
- Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Sophia Borowski
- Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Experimental and Clinical Research Center, a Cooperation between the Max Delbrück Center for Molecular Medicine in the Helmholtz Association, AG GlycoImmunology, and the Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Sandra M Blois
- Department of Obstetrics and Fetal Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Gabriela Barrientos
- Laboratorio de Medicina Experimental, Hospital Alemán, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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32
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Ashok C, Ahuja N, Natua S, Mishra J, Samaiya A, Shukla S. E2F1 and epigenetic modifiers orchestrate breast cancer progression by regulating oxygen-dependent ESRP1 expression. Oncogenesis 2021; 10:58. [PMID: 34362878 PMCID: PMC8346533 DOI: 10.1038/s41389-021-00347-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 07/16/2021] [Accepted: 07/26/2021] [Indexed: 02/07/2023] Open
Abstract
Epithelial splicing regulatory protein 1 (ESRP1) is an RNA binding protein that governs the alternative splicing events related to epithelial phenotypes. ESRP1 contributes significantly at different stages of cancer progression. ESRP1 expression is substantially elevated in carcinoma in situ compared to the normal epithelium, whereas it is drastically ablated in cancer cells within hypoxic niches, which promotes epithelial to mesenchymal transition (EMT). Although a considerable body of research sought to understand the EMT-associated ESRP1 downregulation, the regulatory mechanisms underlying ESRP1 upregulation in primary tumors remained largely uncharted. This study seeks to unveil the regulatory mechanisms that spatiotemporally fine-tune the ESRP1 expression during breast carcinogenesis. Our results reveal that an elevated expression of transcription factor E2F1 and increased CpG hydroxymethylation of the E2F1 binding motif conjointly induce ESRP1 expression in breast carcinoma. However, E2F1 fails to upregulate ESRP1 despite its abundance in oxygen-deprived breast cancer cells. Mechanistically, impelled by the hypoxia-driven reduction of tet methylcytosine dioxygenase 3 (TET3) activity, CpG sites across the E2F1 binding motif lose the hydroxymethylation marks while gaining the de novo methyltransferase-elicited methylation marks. These two oxygen-sensitive epigenetic events work in concert to repel E2F1 from the ESRP1 promoter, thereby diminishing ESRP1 expression under hypoxia. Furthermore, E2F1 skews the cancer spliceome by upregulating splicing factor SRSF7 in hypoxic breast cancer cells. Our findings provide previously unreported mechanistic insights into the plastic nature of ESRP1 expression and insinuate important implications in therapeutics targeting breast cancer progression.
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Affiliation(s)
- Cheemala Ashok
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
| | - Neha Ahuja
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
| | - Subhashis Natua
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
| | - Jharna Mishra
- Department of Pathology, Bansal Hospital, Bhopal, Madhya Pradesh India
| | - Atul Samaiya
- Department of Surgical Oncology, Bansal Hospital, Bhopal, Madhya Pradesh India
| | - Sanjeev Shukla
- grid.462376.20000 0004 1763 8131Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Bhopal, Madhya Pradesh India
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33
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Mochizuki Y, Funayama R, Shirota M, Kikukawa Y, Ohira M, Karasawa H, Kobayashi M, Ohnuma S, Unno M, Nakayama K. Alternative microexon splicing by RBFOX2 and PTBP1 is associated with metastasis in colorectal cancer. Int J Cancer 2021; 149:1787-1800. [PMID: 34346508 DOI: 10.1002/ijc.33758] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Revised: 07/28/2021] [Accepted: 07/30/2021] [Indexed: 11/09/2022]
Abstract
The splicing of microexons (very small exons) is frequently dysregulated in the brain of individuals with autism spectrum disorder. However, little is known of the patterns, regulatory mechanisms and roles of microexon splicing in cancer. We here examined the transcriptome-wide profile of microexon splicing in matched colorectal cancer (CRC) and normal tissue specimens. Out of 1492 microexons comprising 3 to 15 nucleotides, 21 (1%) manifested differential splicing between CRC and normal tissue. The 21 genes harboring the differentially spliced microexons were enriched in gene ontology terms related to cell adhesion and migration. RNA interference-mediated knockdown experiments identified two splicing factors, RBFOX2 and PTBP1, as regulators of microexon splicing in CRC cells. RBFOX2 and PTBP1 were found to directly bind to microexon-containing pre-mRNAs and to control their splicing in such cells. Differential microexon splicing was shown to be due, at least in part, to altered expression of RBFOX2 and PTBP1 in CRC tissue compared to matched normal tissue. Finally, we found that changes in the pattern of microexon splicing were associated with CRC metastasis. Our data thus suggest that altered expression of RBFOX2 and PTBP1 might influence CRC metastasis through the regulation of microexon splicing.
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Affiliation(s)
- Yasushi Mochizuki
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Ryo Funayama
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Matsuyuki Shirota
- Division of Interdisciplinary Medical Science, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Yuna Kikukawa
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Masahiro Ohira
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Hideaki Karasawa
- Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Minoru Kobayashi
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan.,Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Shinobu Ohnuma
- Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Michiaki Unno
- Department of Surgery, Graduate School of Medicine, Tohoku University, Sendai, Japan
| | - Keiko Nakayama
- Department of Cell Proliferation, ART, Graduate School of Medicine, Tohoku University, Sendai, Japan
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34
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Luo C, Xu X, Liu C, He S, Chen J, Feng Y, Liu S, Peng W, Zhou Y, Liu Y, Wei P, Li B, Mai H, Xia X, Bei J. RBFOX2/GOLIM4 Splicing Axis Activates Vesicular Transport Pathway to Promote Nasopharyngeal Carcinogenesis. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2021; 8:e2004852. [PMID: 34180133 PMCID: PMC8373120 DOI: 10.1002/advs.202004852] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/29/2021] [Indexed: 05/05/2023]
Abstract
20-30% of patients with nasopharyngeal carcinoma (NPC) develop distant metastasis or recurrence leading to poor survival, of which the underlying key molecular events have yet to be addressed. Here alternative splicing events in 85 NPC samples are profiled using transcriptome analysis and it is revealed that the long isoform of GOLIM4 (-L) with exon-7 is highly expressed in NPC and associated with poor prognosis. Lines of evidence demonstrate the pro-tumorigenic function of GOLIM4-L in NPC cells. It is further revealed that RBFOX2 binds to a GGAA motif in exon-7 and promotes its inclusion forming GOLIM4-L. RBFOX2 knockdown suppresses the tumorigenesis of NPC cells, phenocopying GOLIM4-L knockdown, which is significantly rescued by GOLIM4-L overexpression. High expression of RBFOX2 is correlated with the exon-7 inclusion of GOLIM4 in NPC biopsies and associated with worse prognosis. It is observed that RBFOX2 and GOLIM4 can influence vesicle-mediated transport through maintaining the organization of Golgi apparatus. Finally, it is revealed that RAB26 interacts with GOLIM4 and mediates its tumorigenic potentials in NPC cells. Taken together, the findings provide insights into how alternative splicing contributes to NPC development, by highlighting a functional link between GOLIM4-L and its splicing regulator RBFOX2 activating vesicle-mediated transport involving RAB26.
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Affiliation(s)
- Chun‐Ling Luo
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Xiao‐Chen Xu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Chu‐Jun Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Shuai He
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Jie‐Rong Chen
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Yan‐Chun Feng
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Shu‐Qiang Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Wan Peng
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Ya‐Qing Zhou
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Yu‐Xiang Liu
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Pan‐Pan Wei
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Bo Li
- Department of Biochemistry and Molecular BiologyZhongshan School of MedicineSun Yat‐sen UniversityGuangzhou510080P. R. China
- RNA Biomedical InstituteSun Yat‐sen Memorial HospitalSun Yat‐sen UniversityGuangzhou510120P. R. China
| | - Hai‐Qiang Mai
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
| | - Xiao‐Jun Xia
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
| | - Jin‐Xin Bei
- Sun Yat‐sen University Cancer CenterState Key Laboratory of Oncology in South ChinaCollaborative Innovation Center for Cancer MedicineGuangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and TherapyGuangzhou510060P. R. China
- Department of Experimental ResearchSun Yat‐sen University Cancer CenterGuangzhou510060P. R. China
- Department of Medical OncologyNational Cancer Centre of SingaporeSingapore169610Singapore
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35
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Zhou D, Couture S, Scott MS, Abou Elela S. RBFOX2 alters splicing outcome in distinct binding modes with multiple protein partners. Nucleic Acids Res 2021; 49:8370-8383. [PMID: 34244793 PMCID: PMC8373071 DOI: 10.1093/nar/gkab595] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/22/2021] [Accepted: 06/28/2021] [Indexed: 11/12/2022] Open
Abstract
RBFOX2 controls the splicing of a large number of transcripts implicated in cell differentiation and development. Parsing RNA-binding protein datasets, we uncover that RBFOX2 can interact with hnRNPC, hnRNPM and SRSF1 to regulate splicing of a broad range of splicing events using different sequence motifs and binding modes. Using immunoprecipitation, specific RBP knockdown, RNA-seq and splice-sensitive PCR, we show that RBFOX2 can target splice sites using three binding configurations: single, multiple or secondary modes. In the single binding mode RBFOX2 is recruited to its target splice sites through a single canonical binding motif, while in the multiple binding mode RBFOX2 binding sites include the adjacent binding of at least one other RNA binding protein partner. Finally, in the secondary binding mode RBFOX2 likely does not bind the RNA directly but is recruited to splice sites lacking its canonical binding motif through the binding of one of its protein partners. These dynamic modes bind distinct sets of transcripts at different positions and distances relative to alternative splice sites explaining the heterogeneity of RBFOX2 targets and splicing outcomes.
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Affiliation(s)
- Delong Zhou
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sonia Couture
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Michelle S Scott
- Département de biochimie et génomique fonctionnelle, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Sherif Abou Elela
- Département de microbiologie et d'infectiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
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36
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Saulnier O, Guedri-Idjouadiene K, Aynaud MM, Chakraborty A, Bruyr J, Pineau J, O'Grady T, Mirabeau O, Grossetête S, Galvan B, Claes M, Al Oula Hassoun Z, Sadacca B, Laud K, Zaïdi S, Surdez D, Baulande S, Rambout X, Tirode F, Dutertre M, Delattre O, Dequiedt F. ERG transcription factors have a splicing regulatory function involving RBFOX2 that is altered in the EWS-FLI1 oncogenic fusion. Nucleic Acids Res 2021; 49:5038-5056. [PMID: 34009296 PMCID: PMC8136815 DOI: 10.1093/nar/gkab305] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 04/12/2021] [Accepted: 04/14/2021] [Indexed: 01/30/2023] Open
Abstract
ERG family proteins (ERG, FLI1 and FEV) are a subfamily of ETS transcription factors with key roles in physiology and development. In Ewing sarcoma, the oncogenic fusion protein EWS-FLI1 regulates both transcription and alternative splicing of pre-messenger RNAs. However, whether wild-type ERG family proteins might regulate splicing is unknown. Here, we show that wild-type ERG proteins associate with spliceosomal components, are found on nascent RNAs, and induce alternative splicing when recruited onto a reporter minigene. Transcriptomic analysis revealed that ERG and FLI1 regulate large numbers of alternative spliced exons (ASEs) enriched with RBFOX2 motifs and co-regulated by this splicing factor. ERG and FLI1 are associated with RBFOX2 via their conserved carboxy-terminal domain, which is present in EWS-FLI1. Accordingly, EWS-FLI1 is also associated with RBFOX2 and regulates ASEs enriched in RBFOX2 motifs. However, in contrast to wild-type ERG and FLI1, EWS-FLI1 often antagonizes RBFOX2 effects on exon inclusion. In particular, EWS-FLI1 reduces RBFOX2 binding to the ADD3 pre-mRNA, thus increasing its long isoform, which represses the mesenchymal phenotype of Ewing sarcoma cells. Our findings reveal a RBFOX2-mediated splicing regulatory function of wild-type ERG family proteins, that is altered in EWS-FLI1 and contributes to the Ewing sarcoma cell phenotype.
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Affiliation(s)
- Olivier Saulnier
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, F-75013 Paris, France
| | - Katia Guedri-Idjouadiene
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Marie-Ming Aynaud
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Alina Chakraborty
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, F-91405 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, INSERM U1278, F-91405 Orsay, France.,Équipe Labellisée Ligue Nationale Contre le Cancer, F-91405 Orsay, France
| | - Jonathan Bruyr
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Joséphine Pineau
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Tina O'Grady
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Olivier Mirabeau
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sandrine Grossetête
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Bartimée Galvan
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Margaux Claes
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Zahra Al Oula Hassoun
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Benjamin Sadacca
- INSERM U932, RT2Lab Team, Translational Research Department, PSL Research University, Institut Curie, F-75005 Paris, France.,CNRS UMR5219, Institut de Mathématiques de Toulouse; Université de Toulouse; F-31062 Toulouse, France
| | - Karine Laud
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sakina Zaïdi
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Didier Surdez
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Sylvain Baulande
- Institut Curie, PSL Research University, NGS Platform, 26 rue d'Ulm, F-75005 Paris, France
| | - Xavier Rambout
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
| | - Franck Tirode
- Claude Bernard University Lyon 1, INSERM 1052, CNRS 5286, Cancer Research Center of Lyon (CRCL), Lyon University, Lyon, France
| | - Martin Dutertre
- Institut Curie, PSL Research University, CNRS UMR3348, INSERM U1278, F-91405 Orsay, France.,Université Paris-Saclay, CNRS UMR3348, INSERM U1278, F-91405 Orsay, France.,Équipe Labellisée Ligue Nationale Contre le Cancer, F-91405 Orsay, France
| | - Olivier Delattre
- INSERM U830, Équipe Labellisée LNCC, PSL Research University, SIREDO Oncology Centre, Institut Curie, 75005 Paris, France
| | - Franck Dequiedt
- University of Liège, Interdisciplinary Cluster for Applied Genoproteomics (GIGA), Liège, Belgium.,University of Liège, GIGA-Molecular Biology of Diseases, Liège, Belgium
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37
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Yang H, Beutler B, Zhang D. Emerging roles of spliceosome in cancer and immunity. Protein Cell 2021; 13:559-579. [PMID: 34196950 PMCID: PMC9232692 DOI: 10.1007/s13238-021-00856-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 05/08/2021] [Indexed: 12/19/2022] Open
Abstract
Precursor messenger RNA (pre-mRNA) splicing is catalyzed by an intricate ribonucleoprotein complex called the spliceosome. Although the spliceosome is considered to be general cell “housekeeping” machinery, mutations in core components of the spliceosome frequently correlate with cell- or tissue-specific phenotypes and diseases. In this review, we expound the links between spliceosome mutations, aberrant splicing, and human cancers. Remarkably, spliceosome-targeted therapies (STTs) have become efficient anti-cancer strategies for cancer patients with splicing defects. We also highlight the links between spliceosome and immune signaling. Recent studies have shown that some spliceosome gene mutations can result in immune dysregulation and notable phenotypes due to mis-splicing of immune-related genes. Furthermore, several core spliceosome components harbor splicing-independent immune functions within the cell, expanding the functional repertoire of these diverse proteins.
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Affiliation(s)
- Hui Yang
- Department of Neurosurgery, Huashan Hospital, Shanghai Key laboratory of Brain Function Restoration and Neural Regeneration, MOE Frontiers Center for Brain Science, Institute for Translational Brain Research, Shanghai Medical College, Fudan University, Shanghai, 200032, China
| | - Bruce Beutler
- Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA.
| | - Duanwu Zhang
- Children's Hospital of Fudan University, and Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism, Ministry of Science and Technology, Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, China.
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38
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Batsché E, Yi J, Mauger O, Kornobis E, Hopkins B, Hanmer-Lloyd C, Muchardt C. CD44 alternative splicing senses intragenic DNA methylation in tumors via direct and indirect mechanisms. Nucleic Acids Res 2021; 49:6213-6237. [PMID: 34086943 PMCID: PMC8216461 DOI: 10.1093/nar/gkab437] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 02/07/2023] Open
Abstract
DNA methylation (meDNA) is a modulator of alternative splicing, and splicing perturbations are involved in tumorigenesis nearly as frequently as DNA mutations. However, the impact of meDNA on tumorigenesis via splicing-mediated mechanisms has not been thoroughly explored. Here, we found that HCT116 colon carcinoma cells inactivated for the DNA methylases DNMT1/3b undergo a partial epithelial to mesenchymal transition associated with increased CD44 variant exon skipping. These skipping events are directly mediated by the loss of intragenic meDNA and the chromatin factors MBD1/2/3 and HP1γ and are also linked to phosphorylation changes in elongating RNA polymerase II. The role of meDNA in alternative splicing was confirmed by using the dCas9/DNMT3b tool. We further tested whether the meDNA level could have predictive value in the MCF10A model for breast cancer progression and in patients with acute lymphoblastic leukemia (B ALL). We found that a small number of differentially spliced genes, mostly involved in splicing and signal transduction, are correlated with the local modulation of meDNA. Our observations suggest that, although DNA methylation has multiple avenues to affect alternative splicing, its indirect effect may also be mediated through alternative splicing isoforms of these meDNA sensors.
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Affiliation(s)
- Eric Batsché
- Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7–9 Quai Saint Bernard, 75005 Paris, France
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
| | - Jia Yi
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Ecole Doctorale Complexite du Vivant (ED515), Sorbonne Université, Paris, France
| | - Oriane Mauger
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Ecole Doctorale Complexite du Vivant (ED515), Sorbonne Université, Paris, France
| | - Etienne Kornobis
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
| | - Benjamin Hopkins
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Keele University, Keele, Staffordshire ST5 5BG UK
| | - Charlotte Hanmer-Lloyd
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
- Keele University, Keele, Staffordshire ST5 5BG UK
| | - Christian Muchardt
- Epigenetics and RNA metabolism in human diseases. CNRS UMR8256 - Biological Adaptation and Ageing. Institut de Biologie Paris-Seine. Sciences Sorbonne Université. 7–9 Quai Saint Bernard, 75005 Paris, France
- Unité de Régulation Epigénétique, Institut Pasteur, Paris, France
- UMR3738, CNRS, Paris, France
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39
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Differential Splicing of Skipped-exons Predicts Drug Response in Cancer Cell Lines. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:901-912. [PMID: 33662622 PMCID: PMC9402787 DOI: 10.1016/j.gpb.2019.08.003] [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: 10/23/2018] [Revised: 03/07/2019] [Accepted: 08/23/2019] [Indexed: 12/02/2022]
Abstract
Alternative splicing of pre-mRNA transcripts is an important regulatory mechanism that increases the diversity of gene products in eukaryotes. Various studies have linked specific transcript isoforms to altered drug response in cancer; however, few algorithms have incorporated splicing information into drug response prediction. In this study, we evaluated whether basal-level splicing information could be used to predict drug sensitivity by constructing doxorubicin-sensitivity classification models with splicing and expression data. We detailed splicing differences between sensitive and resistant cell lines by implementing quasi-binomial generalized linear modeling (QBGLM) and found altered inclusion of 277 skipped exons. We additionally conducted RNA-binding protein (RBP) binding motif enrichment and differential expression analysis to characterize cis- and trans-acting elements that potentially influence doxorubicin response-mediating splicing alterations. Our results showed that a classification model built with skipped exon data exhibited strong predictive power. We discovered an association between differentially spliced events and epithelial-mesenchymal transition (EMT) and observed motif enrichment, as well as differential expression of RBFOX and ELAVL RBP family members. Our work demonstrates the potential of incorporating splicing data into drug response algorithms and the utility of a QBGLM approach for fast, scalable identification of relevant splicing differences between large groups of samples.
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40
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Alternative splicing modulates cancer aggressiveness: role in EMT/metastasis and chemoresistance. Mol Biol Rep 2021; 48:897-914. [PMID: 33400075 DOI: 10.1007/s11033-020-06094-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Accepted: 12/15/2020] [Indexed: 12/11/2022]
Abstract
Enhanced metastasis and disease recurrence accounts for the high mortality rates associated with cancer. The process of Epithelial-Mesenchymal Transition (EMT) contributes towards the augmentation of cancer invasiveness along with the gain of stem-like and the subsequent drug-resistant behavior. Apart from the well-established transcriptional regulation, EMT is also controlled post-transcriptionally by virtue of alternative splicing (AS). Numerous genes including Fibroblast Growth Factor receptor (FGFR) as well as CD44 are differentially spliced during this trans-differentiation process which, in turn, governs cancer progression. These splicing alterations are controlled by various splicing factors including ESRP, RBFOX2 as well as hnRNPs. Here, we have depicted the mechanisms governing the splice isoform switching of FGFR and CD44. Moreover, the role of the splice variants generated by AS of these gene transcripts in modulating the metastatic potential and stem-like/chemoresistant behavior of cancer cells has also been highlighted. Additionally, the involvement of splicing factors in regulating EMT/invasiveness along with drug-resistance as well as the metabolic properties of the cells has been emphasized. Tumorigenesis is accompanied by a remodeling of the cellular splicing profile generating diverse protein isoforms which, in turn, control the cancer-associated hallmarks. Therefore, we have also briefly discussed about a wide variety of genes which are differentially spliced in the tumor cells and promote cancer progression. We have also outlined different strategies for targeting the tumor-associated splicing events which have shown promising results and therefore this approach might be useful in developing therapies to reduce cancer aggressiveness in a more specific manner.
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Wu HY, Li QQ, Liang L, Qiu LL, Wei HW, Huang BY, Gang- C, He RQ, Huang ZG, Hou W, Hu QP, Pan SL. Prognostic alternative splicing signature in cervical squamous cell carcinoma. IET Syst Biol 2020; 14:314-322. [PMID: 33399095 DOI: 10.1049/iet-syb.2019.0095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Basing on alternative splicing events (ASEs) databases, the authors herein aim to explore potential prognostic biomarkers for cervical squamous cell carcinoma (CESC). mRNA expression profiles and relevant clinical data of 223 patients with CESC were obtained from The Cancer Genome Atlas (TCGA). Correlated genes, ASEs and percent-splice-in (PSI) were downloaded from SpliceSeq, respectively. The PSI values of survival-associated alternative splicing events (SASEs) were used to construct the basis of a prognostic index (PI). A protein-protein interaction (PPI) network of genes related to SASEs was generated by STRING and analysed with Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Consequently, 41,776 ASEs were discovered in 19,724 genes, 2596 of which linked with 3669 SASEs. The PPI network of SASEs related genes revealed that TP53 and UBA52 were core genes. The low-risk group had a longer survival period than high-risk counterparts, both groups being defined according to PI constructed upon the top 20 splicing events or PI on the overall splicing events. The AUC value of ROC reached up to 0.88, demonstrating the prognostic potential of PI in CESC. These findings suggested that ASEs involve in the pathogenesis of CESC and may serve as promising prognostic biomarkers for this female malignancy.
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Affiliation(s)
- Hua-Yu Wu
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Qi-Qi Li
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Liang Liang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi Zhuang Autonomous Region 530021, People's Republic of China
| | - Lan-Lan Qiu
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Hong-Wei Wei
- Department of Obstetrics and Gynecology, Women and Children Hospital of Guangxi Zhuang Autonomous Region, Nanning 530003, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Bing-Ying Huang
- Department of Nephrology, Second Affiliated Hospital of Guangxi Medical University, Nanning, 530007, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Chen Gang-
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Rong-Quan He
- Department of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Zhi-Guang Huang
- Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Wei Hou
- Department of Pediatrics, Guangxi Key Laboratory of Thalassemia Research, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Qi-Ping Hu
- Department of Cell Biology and Genetics, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China
| | - Shang-Ling Pan
- Department of Pathophysiology, School of Pre-clinical Medicine, Guangxi Medical University, Nanning 530021, Guangxi Zhuang Autonomous Region, People's Republic of China.
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Ahuja N, Ashok C, Natua S, Pant D, Cherian A, Pandkar MR, Yadav P, Vishnu NSS, Mishra J, Samaiya A, Shukla S. Hypoxia-induced TGF-β-RBFOX2-ESRP1 axis regulates human MENA alternative splicing and promotes EMT in breast cancer. NAR Cancer 2020; 2:zcaa021. [PMID: 33089214 PMCID: PMC7116222 DOI: 10.1093/narcan/zcaa021] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Hypoxic microenvironment heralds epithelial-mesenchymal transition (EMT), invasion and metastasis in solid tumors. Deregulation of alternative splicing (AS) of several cancer-associated genes has been instrumental in hypoxia-induced EMT. Our study in breast cancer unveils a previously unreported mechanism underlying hypoxia-mediated AS of hMENA, a crucial cytoskeleton remodeler during EMT. We report that the hypoxia-driven depletion of splicing regulator ESRP1 leads to skipping of hMENA exon 11a producing a pro-metastatic isoform, hMENAΔ11a. The transcriptional repression of ESRP1 is mediated by SLUG, which gets stimulated via hypoxia-driven TGF-β signaling. Interestingly, RBFOX2, an otherwise RNA-binding protein, is also found to transcriptionally repress ESRP1 while interacting with SLUG. Similar to SLUG, RBFOX2 gets upregulated under hypoxia via TGF-β signaling. Notably, we found that the exosomal delivery of TGF-β contributes to the elevation of TGF-β signaling under hypoxia. Moreover, our results show that in addition to hMENA, hypoxia-induced TGF-β signaling contributes to global changes in AS of genes associated with EMT. Overall, our findings reveal a new paradigm of hypoxia-driven AS regulation of hMENA and insinuate important implications in therapeutics targeting EMT.
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Affiliation(s)
- Neha Ahuja
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Cheemala Ashok
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Subhashis Natua
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Deepak Pant
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Anna Cherian
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Madhura R Pandkar
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Pooja Yadav
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Narayanan S S Vishnu
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - Jharna Mishra
- Department of Pathology, Bansal Hospital, Bhopal, Madhya Pradesh 462016, India
| | - Atul Samaiya
- Department of Surgical Oncology, Bansal Hospital, Bhopal, Madhya Pradesh 462016, India
| | - Sanjeev Shukla
- Department of Biological Sciences, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
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Wineberg Y, Bar-Lev TH, Futorian A, Ben-Haim N, Armon L, Ickowicz D, Oriel S, Bucris E, Yehuda Y, Pode-Shakked N, Gilad S, Benjamin S, Hohenstein P, Dekel B, Urbach A, Kalisky T. Single-Cell RNA Sequencing Reveals mRNA Splice Isoform Switching during Kidney Development. J Am Soc Nephrol 2020; 31:2278-2291. [PMID: 32651222 DOI: 10.1681/asn.2019080770] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 05/23/2020] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND During mammalian kidney development, nephron progenitors undergo a mesenchymal-to-epithelial transition and eventually differentiate into the various tubular segments of the nephron. Recently, Drop-seq single-cell RNA sequencing technology for measuring gene expression from thousands of individual cells identified the different cell types in the developing kidney. However, that analysis did not include the additional layer of heterogeneity that alternative mRNA splicing creates. METHODS Full transcript length single-cell RNA sequencing characterized the transcriptomes of 544 individual cells from mouse embryonic kidneys. RESULTS Gene expression levels measured with full transcript length single-cell RNA sequencing identified each cell type. Further analysis comprehensively characterized splice isoform switching during the transition between mesenchymal and epithelial cellular states, which is a key transitional process in kidney development. The study also identified several putative splicing regulators, including the genes Esrp1/2 and Rbfox1/2. CONCLUSIONS Discovery of the sets of genes that are alternatively spliced as the fetal kidney mesenchyme differentiates into tubular epithelium will improve our understanding of the molecular mechanisms that drive kidney development.
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Affiliation(s)
- Yishay Wineberg
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Tali Hana Bar-Lev
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Anna Futorian
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Nissim Ben-Haim
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Leah Armon
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Debby Ickowicz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Sarit Oriel
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Efrat Bucris
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Yishai Yehuda
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
| | - Naomi Pode-Shakked
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Division of Pediatric Nephrology, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Shlomit Gilad
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Sima Benjamin
- The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | - Peter Hohenstein
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Benjamin Dekel
- Pediatric Stem Cell Research Institute, Edmond and Lily Safra Children's Hospital, Sheba Medical Center, Tel-Hashomer, Israel.,Division of Pediatric Nephrology, Sheba Medical Center, Tel-Hashomer, Israel.,Sackler Faculty of Medicine, Tel-Aviv University, Tel-Aviv, Israel
| | - Achia Urbach
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel
| | - Tomer Kalisky
- Department of Bioengineering and Bar-Ilan Institute of Nanotechnology and Advanced Materials, Bar-Ilan University, Ramat Gan, Israel
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Goldman-Wohl D, Greenfield C, Eisenberg-Loebl I, Denichenko P, Jbara A, Karni R, Ariel I, Yagel S. Trophoblast lineage specific expression of the alternative splicing factor RBFOX2 suggests a role in placental development. Placenta 2020; 100:142-149. [PMID: 32762877 DOI: 10.1016/j.placenta.2020.07.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 06/30/2020] [Accepted: 07/06/2020] [Indexed: 12/17/2022]
Abstract
INTRODUCTION RBFOX2, an RNA-binding protein, controls tissue-specific alternative splicing of exons in diverse processes of development. The progenitor cytotrophoblast of the human placenta differentiates into either the syncytiotrophoblast, formed via cell fusion, or the invasive extravillous trophoblast lineage. The placenta affords a singular system where a role for RBFOX2 in both cell invasion and cell fusion may be studied. We investigated a role for RBFOX2 in trophoblast cell differentiation, as a foundation for investigations of RBFOX2 in embryo implantation and placental development. METHODS Immunohistochemistry of RBFOX2 was performed on placental tissue sections from three trimesters of pregnancy and from pathological pregnancies. Primary trophoblast cell culture and immunofluorescence were employed to determine RBFOX2 expression upon cell fusion. Knockdown of RBFOX2 expression was performed with βhCG and syncytin-1 as molecular indicators of fusion. RESULTS In both normal and pathological placentas, RBFOX2 expression was confined to the cytotrophoblast and the extravillous trophoblast, but absent from the syncytiotrophoblast. Additionally, we showed that primary trophoblasts that spontaneously fused in cell culture downregulated RBFOX2 expression. In functional experiments, knockdown expression of RBFOX2 significantly upregulated βhCG, while the upregulation of syncytin-1 did not reach statistical significance. DISCUSSION RBFOX2, by conferring mRNA diversity, may act as a regulator switch in trophoblast differentiation to either the fusion or invasive pathways. By studying alternative splicing we further our understanding of placental development, yielding possible insights into preeclampsia, where expression of antiangiogenic isoforms produced through alternative splicing play a critical role in disease development and severity.
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Affiliation(s)
- Debra Goldman-Wohl
- The Magda and Richard Hoffman Center for Human Placenta Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Caryn Greenfield
- The Magda and Richard Hoffman Center for Human Placenta Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Iris Eisenberg-Loebl
- The Magda and Richard Hoffman Center for Human Placenta Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Polina Denichenko
- IMRIC Hadassah-Hebrew University School of Medicine, Jerusalem, Israel
| | - Amina Jbara
- IMRIC Hadassah-Hebrew University School of Medicine, Jerusalem, Israel
| | - Rotem Karni
- IMRIC Hadassah-Hebrew University School of Medicine, Jerusalem, Israel
| | - Ilana Ariel
- Department of Pathology Hadassah-Hebrew University Medical Center, Jerusalem, Israel
| | - Simcha Yagel
- The Magda and Richard Hoffman Center for Human Placenta Research, Department of Obstetrics and Gynecology, Hadassah-Hebrew University Medical Center, Jerusalem, Israel.
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Lee S, Sears MJ, Zhang Z, Li H, Salhab I, Krebs P, Xing Y, Nah HD, Williams T, Carstens RP. Cleft lip and cleft palate in Esrp1 knockout mice is associated with alterations in epithelial-mesenchymal crosstalk. Development 2020; 147:dev.187369. [PMID: 32253237 DOI: 10.1242/dev.187369] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 03/24/2020] [Indexed: 12/17/2022]
Abstract
Cleft lip is one of the most common human birth defects. However, there remain a limited number of mouse models of cleft lip that can be leveraged to characterize the genes and mechanisms that cause this disorder. Crosstalk between epithelial and mesenchymal cells underlies formation of the face and palate, but the basic molecular events mediating this crosstalk remain poorly understood. We previously demonstrated that mice lacking the epithelial-specific splicing factor Esrp1 have fully penetrant bilateral cleft lip and palate. In this study, we further investigated the mechanisms leading to cleft lip as well as cleft palate in both existing and new Esrp1 mutant mouse models. These studies included a detailed transcriptomic analysis of changes in ectoderm and mesenchyme in Esrp1-/- embryos during face formation. We identified altered expression of genes previously implicated in cleft lip and/or palate, including components of multiple signaling pathways. These findings provide the foundation for detailed investigations using Esrp1 mutant disease models to examine gene regulatory networks and pathways that are essential for normal face and palate development - the disruption of which leads to orofacial clefting in human patients.
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Affiliation(s)
- SungKyoung Lee
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Matthew J Sears
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Zijun Zhang
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hong Li
- Department of Craniofacial Biology, University of Colorado School of Dental, Medicine, Aurora, CO 80045, USA
| | - Imad Salhab
- Division of Plastic and Reconstructive Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Philippe Krebs
- Institute of Pathology, University of Bern, Bern, Switzerland
| | - Yi Xing
- Center for Computational and Genomic Medicine, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA.,Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Hyun-Duck Nah
- Division of Plastic and Reconstructive Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Trevor Williams
- Department of Craniofacial Biology, University of Colorado School of Dental, Medicine, Aurora, CO 80045, USA
| | - Russ P Carstens
- Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA .,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
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Wang Y, Chen SX, Rao X, Liu Y. Modulator-Dependent RBPs Changes Alternative Splicing Outcomes in Kidney Cancer. Front Genet 2020; 11:265. [PMID: 32273884 PMCID: PMC7113372 DOI: 10.3389/fgene.2020.00265] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022] Open
Abstract
Alternative splicing alterations can contribute to human disease. The ability of an RNA-binding protein to regulate alternative splicing outcomes can be modulated by a variety of genetic and epigenetic mechanisms. In this study, we use a computational framework to investigate the roles of certain genes, termed modulators, on changing RBPs' effect on splicing regulation. A total of 1,040,254 modulator-mediated RBP-splicing interactions were identified, including 137 RBPs, 4,309 splicing events and 2,905 modulator candidates from TCGA-KIRC RNA sequencing data. Modulators function categories were defined according to the correlation changes between RBPs expression and their targets splicing outcomes. QKI, as one of the RBPs influencing the most splicing events, attracted our attention in this study: 2,014 changing triplets were identified, including 1,101 modulators and 187 splicing events. Pathway enrichment analysis showed that QKI splicing targets were enriched in tight junction pathway, endocytosis and MAPK signaling pathways, all of which are highly associated with cancer development and progression. This is the first instance of a comprehensive study on how alternative splicing outcomes changes are associated with different expression level of certain proteins, even though they were regulated by the same RBP. Our work may provide a novel view on understanding alternative splicing mechanisms in kidney cancer.
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Affiliation(s)
- Yang Wang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,State Key Laboratory of Biocatalysts and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
| | - Steven X Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xi Rao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States
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47
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Mohibi S, Chen X, Zhang J. Cancer the'RBP'eutics-RNA-binding proteins as therapeutic targets for cancer. Pharmacol Ther 2019; 203:107390. [PMID: 31302171 DOI: 10.1016/j.pharmthera.2019.07.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 07/02/2019] [Indexed: 12/11/2022]
Abstract
RNA-binding proteins (RBPs) play a critical role in the regulation of various RNA processes, including splicing, cleavage and polyadenylation, transport, translation and degradation of coding RNAs, non-coding RNAs and microRNAs. Recent studies indicate that RBPs not only play an instrumental role in normal cellular processes but have also emerged as major players in the development and spread of cancer. Herein, we review the current knowledge about RNA binding proteins and their role in tumorigenesis as well as the potential to target RBPs for cancer therapeutics.
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Affiliation(s)
- Shakur Mohibi
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Xinbin Chen
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States
| | - Jin Zhang
- Comparative Oncology Laboratory, Schools of Veterinary Medicine and Medicine, University of California at Davis, United States.
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48
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Metabolic Plasticity and Epithelial-Mesenchymal Transition. J Clin Med 2019; 8:jcm8070967. [PMID: 31277295 PMCID: PMC6678349 DOI: 10.3390/jcm8070967] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/26/2019] [Accepted: 06/28/2019] [Indexed: 01/13/2023] Open
Abstract
A major transcriptional and phenotypic reprogramming event during development is the establishment of the mesodermal layer from the ectoderm through epithelial-mesenchymal transition (EMT). EMT is employed in subsequent developmental events, and also in many physiological and pathological processes, such as the dissemination of cancer cells through metastasis, as a reversible transition between epithelial and mesenchymal states. The remarkable phenotypic remodeling accompanying these transitions is driven by characteristic transcription factors whose activities and/or activation depend upon signaling cues and co-factors, including intermediary metabolites. In this review, we summarize salient metabolic features that enable or instigate these transitions, as well as adaptations undergone by cells to meet the metabolic requirements of their new states, with an emphasis on the roles played by the metabolic regulation of epigenetic modifications, notably methylation and acetylation.
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49
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Aiello NM, Kang Y. Context-dependent EMT programs in cancer metastasis. J Exp Med 2019; 216:1016-1026. [PMID: 30975895 PMCID: PMC6504222 DOI: 10.1084/jem.20181827] [Citation(s) in RCA: 365] [Impact Index Per Article: 73.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2019] [Revised: 03/22/2019] [Accepted: 03/22/2019] [Indexed: 12/12/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) is a developmental process whereby stationary, adherent cells acquire the ability to migrate. EMT is critical for dramatic cellular movements during embryogenesis; however, tumor cells can reactivate EMT programs, which increases their aggressiveness. In addition to motility, EMT is associated with enhanced stem cell properties and drug resistance; thus it can drive metastasis, tumor recurrence, and therapy resistance in the context of cancer. However, the precise requirements for EMT in metastasis have not been fully delineated, with different tumor types relying on discrete EMT effectors. Most tumor cells do not undergo a full EMT, but rather adopt some qualities of mesenchymal cells and maintain some epithelial characteristics. Emerging evidence suggests that partial EMT can drive distinct migratory properties and enhance the epithelial-mesenchymal plasticity of cancer cells as well as cell fate plasticity. This review discusses the diverse regulatory mechanisms and functional consequences of EMT, with an emphasis on the importance of partial EMT.
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Affiliation(s)
- Nicole M Aiello
- Department of Molecular Biology, Princeton University, Princeton, NJ
| | - Yibin Kang
- Department of Molecular Biology, Princeton University, Princeton, NJ
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50
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Choi S, Sa M, Cho N, Kim KK, Park SH. Rbfox2 dissociation from stress granules suppresses cancer progression. Exp Mol Med 2019; 51:1-12. [PMID: 31028247 PMCID: PMC6486603 DOI: 10.1038/s12276-019-0246-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 01/23/2019] [Indexed: 01/11/2023] Open
Abstract
Stress granules (SGs) are stalled translation initiation complexes comprising untranslated mRNAs and RNA-binding proteins (RBPs). RBP fox-1 homolog 2 (Rbfox2), a component of SGs, binds to retinoblastoma 1 (RB1) mRNA, which is closely related to cancer progression; however, the role of Rbfox2 in cancer progression remains largely unknown. In this study, we confirmed that Rbfox2, which is present in the nucleus as a splicing regulator, localizes to the cytoplasm of human colon cancer tissues and that induction of Rbfox2 dissociation from SGs by resveratrol treatment inhibits cancer progression. We also observed that Rbfox2 in SGs inhibited RB1 protein expression and promoted cell cycle progression. Additionally, resveratrol treatment inhibited SG-mediated Rbfox2 localization, further inhibiting RB1 protein expression, and inhibited specific Rbfox2 localization to the cytoplasm in melanoma B16-F10 cells, thereby effectively inhibiting metastasis and tumor growth ability. These results indicate that Rbfox2 dissociation from SGs attenuates cancer progression and offer insight into the mechanism associated with Rbfox2 dissociation, thereby marking Rbfox2 as a potential candidate target for cancer therapy. Resveratrol, an antioxidant found in red grapes, slows cancer progression by interfering with the localization and function of the RNA-binding protein Rbfox2. A study led by Kee Kim at Chungnam National University and Su-Hyung Park at Korea Advanced Institute of Science and Technology, Daejeon, Republic of Korea, showed that in human colon cancer cells Rbfox2 is located in the cytoplasm where it promotes cell proliferation by blocking the assembly of the tumor suppressor protein RB1. Treatment with resveratrol prevented the migration of Rbfox2 from the nucleus to the cytoplasm and significantly reduced tumor growth in a mouse model of melanoma. This study not only sheds light on the protective effects of resveratrol but also suggests that Rbfox2 could be a potential target for the development of new anticancer drugs.
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Affiliation(s)
- Sunkyung Choi
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Moa Sa
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Namjoon Cho
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - Kee K Kim
- Department of Biochemistry, College of Natural Sciences, Chungnam National University, Daejeon, 34134, Republic of Korea.
| | - Su-Hyung Park
- Biomedical Science and Engineering Interdisciplinary Program, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea. .,Graduate School of Medical Science and Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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