1
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Kjer-Hansen P, Phan TG, Weatheritt RJ. Protein isoform-centric therapeutics: expanding targets and increasing specificity. Nat Rev Drug Discov 2024; 23:759-779. [PMID: 39232238 DOI: 10.1038/s41573-024-01025-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2024] [Indexed: 09/06/2024]
Abstract
Most protein-coding genes produce multiple protein isoforms; however, these isoforms are commonly neglected in drug discovery. The expression of protein isoforms can be specific to a disease, tissue and/or developmental stage, and this specific expression can be harnessed to achieve greater drug specificity than pan-targeting of all gene products and to enable improved treatments for diseases caused by aberrant protein isoform production. In recent years, several protein isoform-centric therapeutics have been developed. Here, we collate these studies and clinical trials to highlight three distinct but overlapping modes of action for protein isoform-centric drugs: isoform switching, isoform introduction or depletion, and modulation of isoform activity. In addition, we discuss how protein isoforms can be used clinically as targets for cell type-specific drug delivery and immunotherapy, diagnostic biomarkers and sources of cancer neoantigens. Collectively, we emphasize the value of a focus on isoforms as a route to discovering drugs with greater specificity and fewer adverse effects. This approach could enable the targeting of proteins for which pan-inhibition of all isoforms is toxic and poorly tolerated.
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Affiliation(s)
- Peter Kjer-Hansen
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- St. Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, New South Wales, Australia.
| | - Tri Giang Phan
- St. Vincent's Healthcare Clinical Campus, School of Clinical Medicine, Faculty of Medicine and Health, UNSW Sydney, Darlinghurst, New South Wales, Australia
- Precision Immunology Program, Garvan Institute of Medical Research, Sydney, New South Wales, Australia
| | - Robert J Weatheritt
- EMBL Australia, Garvan Institute of Medical Research, Darlinghurst, New South Wales, Australia.
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia.
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2
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Çakan E, Lara OD, Szymanowska A, Bayraktar E, Chavez-Reyes A, Lopez-Berestein G, Amero P, Rodriguez-Aguayo C. Therapeutic Antisense Oligonucleotides in Oncology: From Bench to Bedside. Cancers (Basel) 2024; 16:2940. [PMID: 39272802 PMCID: PMC11394571 DOI: 10.3390/cancers16172940] [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: 07/24/2024] [Revised: 08/16/2024] [Accepted: 08/17/2024] [Indexed: 09/15/2024] Open
Abstract
Advancements in our comprehension of tumor biology and chemoresistance have spurred the development of treatments that precisely target specific molecules within the body. Despite the expanding landscape of therapeutic options, there persists a demand for innovative approaches to address unmet clinical needs. RNA therapeutics have emerged as a promising frontier in this realm, offering novel avenues for intervention such as RNA interference and the utilization of antisense oligonucleotides (ASOs). ASOs represent a versatile class of therapeutics capable of selectively targeting messenger RNAs (mRNAs) and silencing disease-associated proteins, thereby disrupting pathogenic processes at the molecular level. Recent advancements in chemical modification and carrier molecule design have significantly enhanced the stability, biodistribution, and intracellular uptake of ASOs, thereby bolstering their therapeutic potential. While ASO therapy holds promise across various disease domains, including oncology, coronary angioplasty, neurological disorders, viral, and parasitic diseases, our review manuscript focuses specifically on the application of ASOs in targeted cancer therapies. Through a comprehensive examination of the latest research findings and clinical developments, we delve into the intricacies of ASO-based approaches to cancer treatment, shedding light on their mechanisms of action, therapeutic efficacy, and prospects.
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Affiliation(s)
- Elif Çakan
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Olivia D Lara
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
- Division of Gynecologic Oncology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Anna Szymanowska
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Emine Bayraktar
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Department of Medical Biology, Faculty of Medicine, University of Gaziantep, Gaziantep 27310, Turkey
| | | | - Gabriel Lopez-Berestein
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Paola Amero
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
| | - Cristian Rodriguez-Aguayo
- Department of Experimental Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, TX 77054, USA
- Center for RNA Interference and Non-Coding RNA, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Houston, TX 77030, USA
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3
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Fronk AD, Manzanares MA, Zheng P, Geier A, Anderson K, Stanton S, Zumrut H, Gera S, Munch R, Frederick V, Dhingra P, Arun G, Akerman M. Development and validation of AI/ML derived splice-switching oligonucleotides. Mol Syst Biol 2024; 20:676-701. [PMID: 38664594 PMCID: PMC11148135 DOI: 10.1038/s44320-024-00034-9] [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: 09/15/2023] [Revised: 04/03/2024] [Accepted: 04/09/2024] [Indexed: 06/05/2024] Open
Abstract
Splice-switching oligonucleotides (SSOs) are antisense compounds that act directly on pre-mRNA to modulate alternative splicing (AS). This study demonstrates the value that artificial intelligence/machine learning (AI/ML) provides for the identification of functional, verifiable, and therapeutic SSOs. We trained XGboost tree models using splicing factor (SF) pre-mRNA binding profiles and spliceosome assembly information to identify modulatory SSO binding sites on pre-mRNA. Using Shapley and out-of-bag analyses we also predicted the identity of specific SFs whose binding to pre-mRNA is blocked by SSOs. This step adds considerable transparency to AI/ML-driven drug discovery and informs biological insights useful in further validation steps. We applied this approach to previously established functional SSOs to retrospectively identify the SFs likely to regulate those events. We then took a prospective validation approach using a novel target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13). Targeting NEDD4Le13 with an AI/ML-designed SSO decreased the proliferative and migratory behavior of TNBC cells via downregulation of the TGFβ pathway. Overall, this study illustrates the ability of AI/ML to extract actionable insights from RNA-seq data.
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Affiliation(s)
| | | | - Paulina Zheng
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Adam Geier
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Hasan Zumrut
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Sakshi Gera
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | - Robin Munch
- Envisagenics, Inc., Long Island City, NY, 11101, USA
| | | | | | - Gayatri Arun
- Envisagenics, Inc., Long Island City, NY, 11101, USA
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4
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Le Sénéchal R, Keruzoré M, Quillévéré A, Loaëc N, Dinh VT, Reznichenko O, Guixens-Gallardo P, Corcos L, Teulade-Fichou MP, Granzhan A, Blondel M. Alternative splicing of BCL-x is controlled by RBM25 binding to a G-quadruplex in BCL-x pre-mRNA. Nucleic Acids Res 2023; 51:11239-11257. [PMID: 37811881 PMCID: PMC10639069 DOI: 10.1093/nar/gkad772] [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: 03/22/2023] [Revised: 08/05/2023] [Accepted: 09/09/2023] [Indexed: 10/10/2023] Open
Abstract
BCL-x is a master regulator of apoptosis whose pre-mRNA is alternatively spliced into either a long (canonical) anti-apoptotic Bcl-xL isoform, or a short (alternative) pro-apoptotic Bcl-xS isoform. The balance between these two antagonistic isoforms is tightly regulated and overexpression of Bcl-xL has been linked to resistance to chemotherapy in several cancers, whereas overexpression of Bcl-xS is associated to some forms of diabetes and cardiac disorders. The splicing factor RBM25 controls alternative splicing of BCL-x: its overexpression favours the production of Bcl-xS, whereas its downregulation has the opposite effect. Here we show that RBM25 directly and specifically binds to GQ-2, an RNA G-quadruplex (rG4) of BCL-x pre-mRNA that forms at the vicinity of the alternative 5' splice site leading to the alternative Bcl-xS isoform. This RBM25/rG4 interaction is crucial for the production of Bcl-xS and depends on the RE (arginine-glutamate-rich) motif of RBM25, thus defining a new type of rG4-interacting domain. PhenDC3, a benchmark G4 ligand, enhances the binding of RBM25 to the GQ-2 rG4 of BCL-x pre-mRNA, thereby promoting the alternative pro-apoptotic Bcl-xS isoform and triggering apoptosis. Furthermore, the screening of a combinatorial library of 90 putative G4 ligands led to the identification of two original compounds, PhenDH8 and PhenDH9, superior to PhenDC3 in promoting the Bcl-xS isoform and apoptosis. Thus, favouring the interaction between RBM25 and the GQ-2 rG4 of BCL-x pre-mRNA represents a relevant intervention point to re-sensitize cancer cells to chemotherapy.
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Affiliation(s)
- Ronan Le Sénéchal
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Marc Keruzoré
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Alicia Quillévéré
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Nadège Loaëc
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Van-Trang Dinh
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Oksana Reznichenko
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Pedro Guixens-Gallardo
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Laurent Corcos
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
| | - Marie-Paule Teulade-Fichou
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Anton Granzhan
- Chemistry and Modelling for the Biology of Cancer (CMBC), CNRS UMR9187, Inserm U1196, Institut Curie, Université Paris Saclay, F-91405 Orsay, France
| | - Marc Blondel
- Univ Brest; Inserm UMR1078; Etablissement Français du Sang (EFS) Bretagne; CHRU Brest, Hôpital Morvan, Laboratoire de Génétique Moléculaire, 22 avenue Camille Desmoulins, F-29200 Brest, France
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5
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Wang Y, Wang Y, Zhou J, Ying P, Wang Z, Wu Y, Hao M, Qiu S, Jin H, Wang X. A novel coiled-coil domain containing-related gene signature for predicting prognosis and treatment effect of breast cancer. J Cancer Res Clin Oncol 2023; 149:14205-14225. [PMID: 37558766 DOI: 10.1007/s00432-023-05222-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Accepted: 07/28/2023] [Indexed: 08/11/2023]
Abstract
PURPOSE Breast cancer (BRCA) is a prevalent tumor worldwide. The association between the coiled-coil domain-containing (CCDC) protein family and different tumors has been established. However, the prognostic significance of this protein family in breast cancer remains uncertain. METHODS Gene expression and clinical data were obtained from the TCGA, METABRIC, and GEO databases. Prognosis genes were identified using univariate Cox and LASSO Cox regression, leading to the establishment of a prognostic signature. Subsequently, the risk model was conducted based on survival and clinical feature analyses, and a nomogram for prognosis prediction was developed. Furthermore, analyses of biological function, immune characteristics, and drug sensitivity were performed. Finally, single-cell sequencing data were utilized to uncover the expression patterns of genes in the risk model. RESULTS Five genes were identified and utilized for risk modeling. The model demonstrated excellent prognostic value as indicated by ROC and Kaplan-Meier analysis. The high-risk group exhibited shorter survival time and higher likelihood of recurrence. Functional annotation indicated a correlation between the risk score and immune pathways. Conversely, the low-risk group displayed a greater enrichment in immune pathways and exhibited more active immune microenvironment characteristics. Additionally, drug sensitivity analysis using both public and our sequencing data revealed that the risk model possessed a broad range of predictive values. CONCLUSIONS We have developed a gene signature and have verified that patients with low-risk are more likely to have better prognosis and respond positively to therapy. This finding offers a valuable point of reference for BRCA individualized treatment.
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Affiliation(s)
- Yufei Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yanmei Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jia Zhou
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
| | - Pingting Ying
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Zhuo Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yan Wu
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Minyan Hao
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shuying Qiu
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hongchuan Jin
- Laboratory of Cancer Biology, Key Lab of Biotherapy in Zhejiang Province, Cancer Center of Zhejiang University, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xian Wang
- Department of Medical Oncology, Sir Run Run Shaw Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China.
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6
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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] [MESH Headings] [Grants] [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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7
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Abstract
Dysregulated RNA splicing is a molecular feature that characterizes almost all tumour types. Cancer-associated splicing alterations arise from both recurrent mutations and altered expression of trans-acting factors governing splicing catalysis and regulation. Cancer-associated splicing dysregulation can promote tumorigenesis via diverse mechanisms, contributing to increased cell proliferation, decreased apoptosis, enhanced migration and metastatic potential, resistance to chemotherapy and evasion of immune surveillance. Recent studies have identified specific cancer-associated isoforms that play critical roles in cancer cell transformation and growth and demonstrated the therapeutic benefits of correcting or otherwise antagonizing such cancer-associated mRNA isoforms. Clinical-grade small molecules that modulate or inhibit RNA splicing have similarly been developed as promising anticancer therapeutics. Here, we review splicing alterations characteristic of cancer cell transcriptomes, dysregulated splicing's contributions to tumour initiation and progression, and existing and emerging approaches for targeting splicing for cancer therapy. Finally, we discuss the outstanding questions and challenges that must be addressed to translate these findings into the clinic.
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Affiliation(s)
- Robert K Bradley
- Computational Biology Program, Public Health Sciences Division and Basic Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA.
| | - Olga Anczuków
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA.
- Department of Genetics and Genome Sciences, UConn Health, Farmington, CT, USA.
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8
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Corcos L, Le Scanf E, Quéré G, Arzur D, Cueff G, Jossic-Corcos CL, Le Maréchal C. Microsatellite Instability and Aberrant Pre-mRNA Splicing: How Intimate Is It? Genes (Basel) 2023; 14:genes14020311. [PMID: 36833239 PMCID: PMC9957390 DOI: 10.3390/genes14020311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/10/2023] [Accepted: 01/17/2023] [Indexed: 01/27/2023] Open
Abstract
Cancers that belong to the microsatellite instability (MSI) class can account for up to 15% of all cancers of the digestive tract. These cancers are characterized by inactivation, through the mutation or epigenetic silencing of one or several genes from the DNA MisMatch Repair (MMR) machinery, including MLH1, MLH3, MSH2, MSH3, MSH6, PMS1, PMS2 and Exo1. The unrepaired DNA replication errors turn into mutations at several thousand sites that contain repetitive sequences, mainly mono- or dinucleotides, and some of them are related to Lynch syndrome, a predisposition condition linked to a germline mutation in one of these genes. In addition, some mutations shortening the microsatellite (MS) stretch could occur in the 3'-intronic regions, i.e., in the ATM (ATM serine/threonine kinase), MRE11 (MRE11 homolog) or the HSP110 (Heat shock protein family H) genes. In these three cases, aberrant pre-mRNA splicing was observed, and it was characterized by the occurrence of selective exon skipping in mature mRNAs. Because both the ATM and MRE11 genes, which as act as players in the MNR (MRE11/NBS1 (Nibrin)/RAD50 (RAD50 double strand break repair protein) DNA damage repair system, participate in double strand breaks (DSB) repair, their frequent splicing alterations in MSI cancers lead to impaired activity. This reveals the existence of a functional link between the MMR/DSB repair systems and the pre-mRNA splicing machinery, the diverted function of which is the consequence of mutations in the MS sequences.
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Affiliation(s)
- Laurent Corcos
- Inserm U1078, Univ Brest, EFS, F-29200 Brest, France
- CHRU Brest, F-29200 Brest, France
- Correspondence:
| | | | - Gaël Quéré
- Inserm U1078, Univ Brest, EFS, F-29200 Brest, France
| | | | | | | | - Cédric Le Maréchal
- Inserm U1078, Univ Brest, EFS, F-29200 Brest, France
- CHRU Brest, F-29200 Brest, France
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9
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Rozza R, Janoš P, Spinello A, Magistrato A. Role of computational and structural biology in the development of small-molecule modulators of the spliceosome. Expert Opin Drug Discov 2022; 17:1095-1109. [PMID: 35983696 DOI: 10.1080/17460441.2022.2114452] [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] [Indexed: 12/29/2022]
Abstract
INTRODUCTION RNA splicing is a pivotal step of eukaryotic gene expression during which the introns are excised from the precursor (pre-)RNA and the exons are joined together to form mature RNA products (i.e a protein-coding mRNA or long non-coding (lnc)RNAs). The spliceosome, a complex ribonucleoprotein machine, performs pre-RNA splicing with extreme precision. Deregulated splicing is linked to cancer, genetic, and neurodegenerative diseases. Hence, the discovery of small-molecules targeting core spliceosome components represents an appealing therapeutic opportunity. AREA COVERED Several atomic-level structures of the spliceosome and distinct splicing-modulators bound to its protein/RNA components have been solved. Here, we review recent advances in the discovery of small-molecule splicing-modulators, discuss opportunities and challenges for their therapeutic applicability, and showcase how structural data and/or all-atom simulations can illuminate key facets of their mechanism, thus contributing to future drug-discovery campaigns. EXPERT OPINION This review highlights the potential of modulating pre-RNA splicing with small-molecules, and anticipates how the synergy of computer and wet-lab experiments will enrich our understanding of splicing regulation/deregulation mechanisms. This information will aid future structure-based drug-discovery efforts aimed to expand the currently limited portfolio of selective splicing-modulators.
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Affiliation(s)
- Riccardo Rozza
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Pavel Janoš
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
| | - Angelo Spinello
- Department of Biological, Chemical and Pharmaceutical Sciences, University of Palermo, Palermo, Italy
| | - Alessandra Magistrato
- National Research Council of Italy, Institute of Materials-foundry (CNR-IOM) C/o SISSA, Trieste, Italy
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10
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Bhogadia M, Stone B, Del Villar Guerra R, Muskett FW, Ghosh S, Taladriz-Sender A, Burley GA, Eperon IC, Hudson AJ, Dominguez C. Biophysical characterisation of the Bcl-x pre-mRNA and binding specificity of the ellipticine derivative GQC-05: Implication for alternative splicing regulation. Front Mol Biosci 2022; 9:943105. [PMID: 36060245 PMCID: PMC9428248 DOI: 10.3389/fmolb.2022.943105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/18/2022] [Indexed: 11/21/2022] Open
Abstract
The BCL2L1 gene expresses two isoforms of Bcl-x protein via the use of either of two alternative 5′ splice sites (5′ss) in exon 2. These proteins have antagonistic actions, Bcl-XL being anti-apoptotic and Bcl-XS pro-apoptotic. In a number of cancers the Bcl-XL isoform is over-expressed, resulting in cancer cell survival and growth, so switching splicing to the Xs isoform could have therapeutic benefits. We have previously proposed that a putative G-quadruplex (G4) exists downstream of the XS 5′ss and shown that the ellipticine derivative GQC-05, a previously identified DNA G4-specific ligand, induces an increase in the XS/XL ratio both in vitro and in cells. Here, we demonstrate that this G4 forms in vitro and that the structure is stabilised in the presence of GQC-05. We also show that GQC-05 binds RNA non-specifically in buffer conditions, but selectively to the Bcl-x G4 in the presence of nuclear extract, highlighting the limitations of biophysical measurements taken outside of a functional environment. We also demonstrate that GQC-05 is able to shift the equilibrium between competing G4 and duplex structures towards the G4 conformation, leading to an increase in accessibility of the XS 5′ss, supporting our previous model on the mechanism of action of GQC-05.
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Affiliation(s)
- Mohammed Bhogadia
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Beth Stone
- The Leicester Institute of Structural and Chemical Biology, Department of Chemistry, University of Leicester, Leicester, United Kingdom
| | - Rafael Del Villar Guerra
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Frederick W. Muskett
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Sudipta Ghosh
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
| | - Andrea Taladriz-Sender
- Department of Pure Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Glenn A. Burley
- Department of Pure Applied Chemistry, University of Strathclyde, Glasgow, United Kingdom
| | - Ian C. Eperon
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
- *Correspondence: Ian C. Eperon, ; Andrew J. Hudson, ; Cyril Dominguez,
| | - Andrew J. Hudson
- The Leicester Institute of Structural and Chemical Biology, Department of Chemistry, University of Leicester, Leicester, United Kingdom
- *Correspondence: Ian C. Eperon, ; Andrew J. Hudson, ; Cyril Dominguez,
| | - Cyril Dominguez
- The Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, United Kingdom
- *Correspondence: Ian C. Eperon, ; Andrew J. Hudson, ; Cyril Dominguez,
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11
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Pan YJ, Liu BW, Pei DS. The Role of Alternative Splicing in Cancer: Regulatory Mechanism, Therapeutic Strategy, and Bioinformatics Application. DNA Cell Biol 2022; 41:790-809. [PMID: 35947859 DOI: 10.1089/dna.2022.0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
[Formula: see text] Alternative splicing (AS) can generate distinct transcripts and subsequent isoforms that play differential functions from the same pre-mRNA. Recently, increasing numbers of studies have emerged, unmasking the association between AS and cancer. In this review, we arranged AS events that are closely related to cancer progression and presented promising treatments based on AS for cancer therapy. Obtaining proliferative capacity, acquiring invasive properties, gaining angiogenic features, shifting metabolic ability, and getting immune escape inclination are all splicing events involved in biological processes. Spliceosome-targeted and antisense oligonucleotide technologies are two novel strategies that are hopeful in tumor therapy. In addition, bioinformatics applications based on AS were summarized for better prediction and elucidation of regulatory routines mingled in. Together, we aimed to provide a better understanding of complicated AS events associated with cancer biology and reveal AS a promising target of cancer treatment in the future.
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Affiliation(s)
- Yao-Jie Pan
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
| | - Bo-Wen Liu
- Department of General Surgery, Xuzhou Medical University, Xuzhou, China
| | - Dong-Sheng Pei
- Department of Pathology, Laboratory of Clinical and Experimental Pathology, Xuzhou Medical University, Xuzhou, China
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12
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Athanasopoulou K, Adamopoulos PG, Daneva GN, Scorilas A. Decoding the concealed transcriptional signature of the apoptosis-related BCL2 antagonist/killer 1 (BAK1) gene in human malignancies. Apoptosis 2022; 27:869-882. [DOI: 10.1007/s10495-022-01753-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/11/2022] [Indexed: 11/29/2022]
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13
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Peng Q, Zhou Y, Oyang L, Wu N, Tang Y, Su M, Luo X, Wang Y, Sheng X, Ma J, Liao Q. Impacts and mechanisms of alternative mRNA splicing in cancer metabolism, immune response, and therapeutics. Mol Ther 2022; 30:1018-1035. [PMID: 34793975 PMCID: PMC8899522 DOI: 10.1016/j.ymthe.2021.11.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/29/2021] [Accepted: 11/11/2021] [Indexed: 02/08/2023] Open
Abstract
Alternative pre-mRNA splicing (AS) provides the potential to produce diversity at RNA and protein levels. Disruptions in the regulation of pre-mRNA splicing can lead to diseases. With the development of transcriptome and genome sequencing technology, increasing diseases have been identified to be associated with abnormal splicing of mRNAs. In tumors, abnormal alternative splicing frequently plays critical roles in cancer pathogenesis and may be considered as new biomarkers and therapeutic targets for cancer intervention. Metabolic abnormalities and immune disorders are important hallmarks of cancer. AS produces multiple different isoforms and diversifies protein expression, which is utilized by the immune and metabolic reprogramming systems to expand gene functions. The abnormal splicing events contributed to tumor progression, partially due to effects on immune response and metabolic reprogramming. Herein, we reviewed the vital role of alternative splicing in regulating cancer metabolism and immune response. We discussed how alternative splicing regulates metabolic reprogramming of cancer cells and antitumor immune response, and the possible strategies to targeting alternative splicing pathways or splicing-regulated metabolic pathway in the context of anticancer immunotherapy. Further, we highlighted the challenges and discuss the perspectives for RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms.
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Affiliation(s)
- Qiu Peng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China
| | - Yujuan Zhou
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China,Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China
| | - Linda Oyang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Nayiyuan Wu
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Yanyan Tang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Min Su
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xia Luo
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Ying Wang
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Xiaowu Sheng
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China
| | - Jian Ma
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Cancer Research Institute and School of Basic Medical Science, Central South University, Changsha, China.
| | - Qianjin Liao
- Hunan Key Laboratory of Cancer Metabolism, Hunan Cancer Hospital and the Affiliated Cancer Hospital of Xiangya School of Medicine, Central South University, Changsha, 410013 Hunan, China; Hunan Key Laboratory of Translational Radiation Oncology, 283 Tongzipo Road, Changsha 410013, Hunan, China.
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14
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Sahin I, George A, Seyhan AA. Therapeutic Targeting of Alternative RNA Splicing in Gastrointestinal Malignancies and Other Cancers. Int J Mol Sci 2021; 22:11790. [PMID: 34769221 PMCID: PMC8583749 DOI: 10.3390/ijms222111790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Revised: 10/27/2021] [Accepted: 10/28/2021] [Indexed: 12/22/2022] Open
Abstract
Recent comprehensive genomic studies including single-cell RNA sequencing and characterization have revealed multiple processes by which protein-coding and noncoding RNA processing are dysregulated in many cancers. More specifically, the abnormal regulation of mRNA and precursor mRNA (pre-mRNA) processing, which includes the removal of introns by splicing, is frequently altered in tumors, producing multiple different isoforms and diversifying protein expression. These alterations in RNA processing result in numerous cancer-specific mRNAs and pathogenically spliced events that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumor suppressor genes. Abnormally spliced pre-mRNAs are also associated with resistance to cancer treatment, and certain cancers are highly sensitive to the pharmacological inhibition of splicing. The discovery of these alterations in RNA processing has not only provided new insights into cancer pathogenesis but identified novel therapeutic vulnerabilities and therapeutic opportunities in targeting these aberrations in various ways (e.g., small molecules, splice-switching oligonucleotides (SSOs), and protein therapies) to modulate alternative RNA splicing or other RNA processing and modification mechanisms. Some of these strategies are currently progressing toward clinical development or are already in clinical trials. Additionally, tumor-specific neoantigens produced from these pathogenically spliced events and other abnormal RNA processes provide a potentially extensive source of tumor-specific therapeutic antigens (TAs) for targeted cancer immunotherapy. Moreover, a better understanding of the molecular mechanisms associated with aberrant RNA processes and the biological impact they play might provide insights into cancer initiation, progression, and metastasis. Our goal is to highlight key alternative RNA splicing and processing mechanisms and their roles in cancer pathophysiology as well as emerging therapeutic alternative splicing targets in cancer, particularly in gastrointestinal (GI) malignancies.
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Affiliation(s)
- Ilyas Sahin
- Division of Hematology Oncology, Department of Medicine, University of Florida Health Cancer Center, Gainesville, FL 32610, USA;
| | - Andrew George
- Department of Chemistry, Brown University, Providence, RI 02912, USA;
- Department of Molecular Biology, Cell Biology & Biochemistry, Division of Biology and Medicine, Brown University, Providence, RI 02912, USA
| | - Attila A. Seyhan
- Laboratory of Translational Oncology and Experimental Cancer Therapeutics, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- The Joint Program in Cancer Biology, Brown University and Lifespan Health System, Providence, RI 02912, USA
- Cancer Center at Brown University, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
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15
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Laliotis GI, Chavdoula E, Paraskevopoulou MD, Kaba A, La Ferlita A, Singh S, Anastas V, Nair KA, Orlacchio A, Taraslia V, Vlachos I, Capece M, Hatzigeorgiou A, Palmieri D, Tsatsanis C, Alaimo S, Sehgal L, Carbone DP, Coppola V, Tsichlis PN. AKT3-mediated IWS1 phosphorylation promotes the proliferation of EGFR-mutant lung adenocarcinomas through cell cycle-regulated U2AF2 RNA splicing. Nat Commun 2021; 12:4624. [PMID: 34330897 PMCID: PMC8324843 DOI: 10.1038/s41467-021-24795-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 03/05/2021] [Indexed: 02/06/2023] Open
Abstract
AKT-phosphorylated IWS1 regulates alternative RNA splicing via a pathway that is active in lung cancer. RNA-seq studies in lung adenocarcinoma cells lacking phosphorylated IWS1, identified a exon 2-deficient U2AF2 splice variant. Here, we show that exon 2 inclusion in the U2AF2 mRNA is a cell cycle-dependent process that is regulated by LEDGF/SRSF1 splicing complexes, whose assembly is controlled by the IWS1 phosphorylation-dependent deposition of histone H3K36me3 marks in the body of target genes. The exon 2-deficient U2AF2 mRNA encodes a Serine-Arginine-Rich (RS) domain-deficient U2AF65, which is defective in CDCA5 pre-mRNA processing. This results in downregulation of the CDCA5-encoded protein Sororin, a phosphorylation target and regulator of ERK, G2/M arrest and impaired cell proliferation and tumor growth. Analysis of human lung adenocarcinomas, confirmed activation of the pathway in EGFR-mutant tumors and showed that pathway activity correlates with tumor stage, histologic grade, metastasis, relapse after treatment, and poor prognosis.
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Affiliation(s)
- Georgios I Laliotis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA.
- School of Medicine, University of Crete, Heraklion, Crete, Greece.
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins School of Medicine, Baltimore, MD, USA.
| | - Evangelia Chavdoula
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | | | - Abdul Kaba
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Satishkumar Singh
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - Vollter Anastas
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, USA
| | - Keith A Nair
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Arturo Orlacchio
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Vasiliki Taraslia
- Molecular Oncology Research Institute, Tufts Medical Center, Boston, MA, USA
- Center of Basic Research, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Ioannis Vlachos
- DIANA-Lab, Hellenic Pasteur Institute, Athens, Greece
- Department Of Pathology, Beth Israel-Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Marina Capece
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | | | - Dario Palmieri
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Christos Tsatsanis
- School of Medicine, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Bioinformatics Unit, University of Catania, Catania, Italy
| | - Lalit Sehgal
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Medicine, Division of Hematology, The Ohio State University, Columbus, OH, USA
| | - David P Carbone
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
- Department of Internal Medicine, Division of Medical Oncology, The Ohio State University Medical Center, Columbus, OH, USA
| | - Vincenzo Coppola
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA
| | - Philip N Tsichlis
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, OH, USA.
- The Ohio State University Comprehensive Cancer Center-Arthur G. James Cancer Hospital and Richard J. Solove Research Institute, Columbus, OH, USA.
- Tufts Graduate School of Biomedical Sciences, Program in Genetics, Boston, MA, USA.
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16
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Palaz F, Kalkan AK, Can Ö, Demir AN, Tozluyurt A, Özcan A, Ozsoz M. CRISPR-Cas13 System as a Promising and Versatile Tool for Cancer Diagnosis, Therapy, and Research. ACS Synth Biol 2021; 10:1245-1267. [PMID: 34037380 DOI: 10.1021/acssynbio.1c00107] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Over the past decades, significant progress has been made in targeted cancer therapy. In precision oncology, molecular profiling of cancer patients enables the use of targeted cancer therapeutics. However, current diagnostic methods for molecular analysis of cancer are costly and require sophisticated equipment. Moreover, targeted cancer therapeutics such as monoclonal antibodies and small-molecule drugs may cause off-target effects and they are available for only a minority of cancer driver proteins. Therefore, there is still a need for versatile, efficient, and precise tools for cancer diagnostics and targeted cancer treatment. In recent years, the CRISPR-based genome and transcriptome engineering toolbox has expanded rapidly. Particularly, the RNA-targeting CRISPR-Cas13 system has unique biochemical properties, making Cas13 a promising tool for cancer diagnosis, therapy, and research. Cas13-based diagnostic methods allow early detection and monitoring of cancer markers from liquid biopsy samples without the need for complex instrumentation. In addition, Cas13 can be used for targeted cancer therapy through degrading and manipulating cancer-associated transcripts with high efficiency and specificity. Moreover, Cas13-mediated programmable RNA manipulation tools offer invaluable opportunities for cancer research, identification of drug-resistance mechanisms, and discovery of novel therapeutic targets. Here, we review and discuss the current use and potential applications of the CRISPR-Cas13 system in cancer diagnosis, therapy, and research. Thus, researchers will gain a deep understanding of CRISPR-Cas13 technologies, which have the potential to be used as next-generation cancer diagnostics and therapeutics.
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Affiliation(s)
- Fahreddin Palaz
- Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | | | - Özgür Can
- Department of Molecular Biology and Genetics, Koc University, Istanbul 34450, Turkey
| | - Ayça Nur Demir
- Faculty of Medicine, Afyonkarahisar Health Sciences University, Afyonkarahisar 03100, Turkey
| | - Abdullah Tozluyurt
- Department of Medical Microbiology, Faculty of Medicine, Hacettepe University, Ankara 06100, Turkey
| | - Ahsen Özcan
- Institute of Genetic Engineering and Biotechnology, TUBITAK Marmara Research Center, Kocaeli 41470, Turkey
| | - Mehmet Ozsoz
- Department of Biomedical Engineering, Near East University, 10 Mersin, Nicosia, Turkey
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17
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Dou Z, Zhao D, Chen X, Xu C, Jin X, Zhang X, Wang Y, Xie X, Li Q, Di C, Zhang H. Aberrant Bcl-x splicing in cancer: from molecular mechanism to therapeutic modulation. J Exp Clin Cancer Res 2021; 40:194. [PMID: 34118966 PMCID: PMC8196531 DOI: 10.1186/s13046-021-02001-w] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 05/30/2021] [Indexed: 12/13/2022] Open
Abstract
Bcl-x pre-mRNA splicing serves as a typical example to study the impact of alternative splicing in the modulation of cell death. Dysregulation of Bcl-x apoptotic isoforms caused by precarious equilibrium splicing is implicated in genesis and development of multiple human diseases, especially cancers. Exploring the mechanism of Bcl-x splicing and regulation has provided insight into the development of drugs that could contribute to sensitivity of cancer cells to death. On this basis, we review the multiple splicing patterns and structural characteristics of Bcl-x. Additionally, we outline the cis-regulatory elements, trans-acting factors as well as epigenetic modifications involved in the splicing regulation of Bcl-x. Furthermore, this review highlights aberrant splicing of Bcl-x involved in apoptosis evade, autophagy, metastasis, and therapy resistance of various cancer cells. Last, emphasis is given to the clinical role of targeting Bcl-x splicing correction in human cancer based on the splice-switching oligonucleotides, small molecular modulators and BH3 mimetics. Thus, it is highlighting significance of aberrant splicing isoforms of Bcl-x as targets for cancer therapy.
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Affiliation(s)
- Zhihui Dou
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Dapeng Zhao
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaohua Chen
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Caipeng Xu
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Xiaodong Jin
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
| | - Xuetian Zhang
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Yupei Wang
- Medical Genetics Center of Gansu Maternal and Child Health Care Center, Lanzhou, 730000, China
| | - Xiaodong Xie
- School of Basic Medical Sciences, Lanzhou University, Lanzhou, 730000, China
| | - Qiang Li
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China
| | - Cuixia Di
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China.
| | - Hong Zhang
- Department of Heavy Ion Radiation Medicine, Bio-Medical Research Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, 730000, China.
- Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, Lanzhou, 730000, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
- School of Nuclear Science and Technology, University of Chinese Academy of Sciences, Beijing, 101408, China.
- Advanced Energy Science and Technology Guangdong Laboratory, Huizhou, 516029, China.
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18
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Zhang Y, Qian J, Gu C, Yang Y. Alternative splicing and cancer: a systematic review. Signal Transduct Target Ther 2021; 6:78. [PMID: 33623018 PMCID: PMC7902610 DOI: 10.1038/s41392-021-00486-7] [Citation(s) in RCA: 174] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 09/24/2020] [Accepted: 09/28/2020] [Indexed: 01/31/2023] Open
Abstract
The abnormal regulation of alternative splicing is usually accompanied by the occurrence and development of tumors, which would produce multiple different isoforms and diversify protein expression. The aim of the present study was to conduct a systematic review in order to describe the regulatory mechanisms of alternative splicing, as well as its functions in tumor cells, from proliferation and apoptosis to invasion and metastasis, and from angiogenesis to metabolism. The abnormal splicing events contributed to tumor progression as oncogenic drivers and/or bystander factors. The alterations in splicing factors detected in tumors and other mis-splicing events (i.e., long non-coding and circular RNAs) in tumorigenesis were also included. The findings of recent therapeutic approaches targeting splicing catalysis and splicing regulatory proteins to modulate pathogenically spliced events (including tumor-specific neo-antigens for cancer immunotherapy) were introduced. The emerging RNA-based strategies for the treatment of cancer with abnormally alternative splicing isoforms were also discussed. However, further studies are still required to address the association between alternative splicing and cancer in more detail.
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Affiliation(s)
- Yuanjiao Zhang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Jinjun Qian
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chunyan Gu
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
| | - Ye Yang
- The Third Affiliated Hospital of Nanjing University of Chinese Medicine, Nanjing, China.
- School of Medicine & Holistic Integrative Medicine, Nanjing University of Chinese Medicine, Nanjing, China.
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19
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Bessa C, Matos P, Jordan P, Gonçalves V. Alternative Splicing: Expanding the Landscape of Cancer Biomarkers and Therapeutics. Int J Mol Sci 2020; 21:ijms21239032. [PMID: 33261131 PMCID: PMC7729450 DOI: 10.3390/ijms21239032] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 11/24/2020] [Accepted: 11/25/2020] [Indexed: 02/07/2023] Open
Abstract
Alternative splicing (AS) is a critical post-transcriptional regulatory mechanism used by more than 95% of transcribed human genes and responsible for structural transcript variation and proteome diversity. In the past decade, genome-wide transcriptome sequencing has revealed that AS is tightly regulated in a tissue- and developmental stage-specific manner, and also frequently dysregulated in multiple human cancer types. It is currently recognized that splicing defects, including genetic alterations in the spliced gene, altered expression of both core components or regulators of the precursor messenger RNA (pre-mRNA) splicing machinery, or both, are major drivers of tumorigenesis. Hence, in this review we provide an overview of our current understanding of splicing alterations in cancer, and emphasize the need to further explore the cancer-specific splicing programs in order to obtain new insights in oncology. Furthermore, we also discuss the recent advances in the identification of dysregulated splicing signatures on a genome-wide scale and their potential use as biomarkers. Finally, we highlight the therapeutic opportunities arising from dysregulated splicing and summarize the current approaches to therapeutically target AS in cancer.
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Affiliation(s)
- Cláudia Bessa
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Paulo Matos
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
| | - Peter Jordan
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: (P.J.); (V.G.); Tel.: +351-217-519-380 (P.J.)
| | - Vânia Gonçalves
- Department of Human Genetics, National Health Institute Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal; (C.B.); (P.M.)
- BioISI—Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisbon, 1749-016 Lisbon, Portugal
- Correspondence: (P.J.); (V.G.); Tel.: +351-217-519-380 (P.J.)
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20
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Dual genome-wide CRISPR knockout and CRISPR activation screens identify mechanisms that regulate the resistance to multiple ATR inhibitors. PLoS Genet 2020; 16:e1009176. [PMID: 33137164 PMCID: PMC7660927 DOI: 10.1371/journal.pgen.1009176] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/12/2020] [Accepted: 10/02/2020] [Indexed: 12/26/2022] Open
Abstract
The ataxia telangiectasia and Rad3-related (ATR) protein kinase is a key regulator of the cellular response to DNA damage. Due to increased amount of replication stress, cancer cells heavily rely on ATR to complete DNA replication and cell cycle progression. Thus, ATR inhibition is an emerging target in cancer therapy, with multiple ATR inhibitors currently undergoing clinical trials. Here, we describe dual genome-wide CRISPR knockout and CRISPR activation screens employed to comprehensively identify genes that regulate the cellular resistance to ATR inhibitors. Specifically, we investigated two different ATR inhibitors, namely VE822 and AZD6738, in both HeLa and MCF10A cells. We identified and validated multiple genes that alter the resistance to ATR inhibitors. Importantly, we show that the mechanisms of resistance employed by these genes are varied, and include restoring DNA replication fork progression, and prevention of ATR inhibitor-induced apoptosis. In particular, we describe a role for MED12-mediated inhibition of the TGFβ signaling pathway in regulating replication fork stability and cellular survival upon ATR inhibition. Our dual genome-wide screen findings pave the way for personalized medicine by identifying potential biomarkers for ATR inhibitor resistance.
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21
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Singh P, Singh A, Shah S, Vataliya J, Mittal A, Chitkara D. RNA Interference Nanotherapeutics for Treatment of Glioblastoma Multiforme. Mol Pharm 2020; 17:4040-4066. [PMID: 32902291 DOI: 10.1021/acs.molpharmaceut.0c00709] [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] [Indexed: 02/06/2023]
Abstract
Nucleic acid therapeutics for RNA interference (RNAi) are gaining attention in the treatment and management of several kinds of the so-called "undruggable" tumors via targeting specific molecular pathways or oncogenes. Synthetic ribonucleic acid (RNAs) oligonucleotides like siRNA, miRNA, shRNA, and lncRNA have shown potential as novel therapeutics. However, the delivery of such oligonucleotides is significantly hampered by their physiochemical (such as hydrophilicity, negative charge, and instability) and biopharmaceutical features (in vivo serum stability, fast renal clearance, interaction with extracellular proteins, and hindrance in cellular internalization) that markedly reduce their biological activity. Recently, several nanocarriers have evolved as suitable non-viral vectors for oligonucleotide delivery, which are known to either complex or conjugate with these oligonucleotides efficiently and also overcome the extracellular and intracellular barriers, thereby allowing access to the tumoral micro-environment for the better and desired outcome in glioblastoma multiforme (GBM). This Review focuses on the up-to-date advancements in the field of RNAi nanotherapeutics utilized for GBM treatment.
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Affiliation(s)
- Prabhjeet Singh
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Aditi Singh
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Shruti Shah
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Jalpa Vataliya
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Anupama Mittal
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
| | - Deepak Chitkara
- Department of Pharmacy, Birla Institute of Technology and Science (BITS) Pilani, Pilani Campus, Vidya Vihar, Pilani - 333 031, Rajasthan, India
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22
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Shahar N, Larisch S. Inhibiting the inhibitors: Targeting anti-apoptotic proteins in cancer and therapy resistance. Drug Resist Updat 2020; 52:100712. [DOI: 10.1016/j.drup.2020.100712] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 05/29/2020] [Accepted: 06/05/2020] [Indexed: 12/14/2022]
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23
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Technological advances and computational approaches for alternative splicing analysis in single cells. Comput Struct Biotechnol J 2020; 18:332-343. [PMID: 32099593 PMCID: PMC7033300 DOI: 10.1016/j.csbj.2020.01.009] [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: 08/31/2019] [Accepted: 01/26/2020] [Indexed: 12/15/2022] Open
Abstract
Alternative splicing of RNAs generates isoform diversity, resulting in different proteins that are necessary for maintaining cellular function and identity. The discovery of alternative splicing has been revolutionized by next-generation transcriptomic sequencing mainly using bulk RNA-sequencing, which has unravelled RNA splicing and mis-splicing of normal cells under steady-state and stress conditions. Single-cell RNA-sequencing studies have focused on gene-level expression analysis and revealed gene expression signatures distinguishable between different cellular types. Single-cell alternative splicing is an emerging area of research with the promise to reveal transcriptomic dynamics invisible to bulk- and gene-level analysis. In this review, we will discuss the technological advances for single-cell alternative splicing analysis, computational strategies for isoform detection and quantitation in single cells, and current applications of single-cell alternative splicing analysis and its potential future contributions to personalized medicine.
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Djuric U, Lam KHB, Kao J, Batruch I, Jevtic S, Papaioannou MD, Diamandis P. Defining Protein Pattern Differences Among Molecular Subtypes of Diffuse Gliomas Using Mass Spectrometry. Mol Cell Proteomics 2019; 18:2029-2043. [PMID: 31353322 PMCID: PMC6773564 DOI: 10.1074/mcp.ra119.001521] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 07/09/2019] [Indexed: 12/18/2022] Open
Abstract
Molecular characterization of diffuse gliomas has thus far largely focused on genomic and transcriptomic interrogations. Here, we utilized mass spectrometry and overlay protein-level information onto genomically defined cohorts of diffuse gliomas to improve our downstream molecular understanding of these lethal malignancies. Bulk and macrodissected tissues were utilized to quantitate 5,496 unique proteins over three glioma cohorts subclassified largely based on their IDH and 1p19q codeletion status (IDH wild type (IDHwt), n = 7; IDH mutated (IDHmt), 1p19q non-codeleted, n = 7; IDH mutated, 1p19q-codeleted, n = 10). Clustering analysis highlighted proteome and systems-level pathway differences in gliomas according to IDH and 1p19q-codeletion status, including 287 differentially abundant proteins in macrodissection-enriched tumor specimens. IDHwt tumors were enriched for proteins involved in invasiveness and epithelial to mesenchymal transition (EMT), while IDHmt gliomas had increased abundances of proteins involved in mRNA splicing. Finally, these abundance changes were compared with IDH-matched GBM stem-like cells (GSCs) to better pinpoint protein patterns enriched in putative cellular drivers of gliomas. Using this integrative approach, we outline specific proteins involved in chloride transport (e.g. chloride intracellular channel 1, CLIC1) and EMT (e.g. procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3, PLOD3, and serpin peptidase inhibitor clade H member 1, SERPINH1) that showed concordant IDH-status-dependent abundance differences in both primary tissue and purified GSC cultures. Given the downstream position proteins occupy in driving biology and phenotype, understanding the proteomic patterns operational in distinct glioma subtypes could help propose more specific, personalized, and effective targets for the management of patients with these aggressive malignancies.
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Affiliation(s)
- Ugljesa Djuric
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - K H Brian Lam
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jennifer Kao
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Ihor Batruch
- Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario, M5G 1X5, Canada
| | - Stefan Jevtic
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada
| | - Michail-Dimitrios Papaioannou
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada
| | - Phedias Diamandis
- Princess Margaret Cancer Centre, MacFeeters Hamilton Centre for Neuro-Oncology Research, College Street 101, Toronto, Ontario, M5G 1L7, Canada; Laboratory Medicine Program, University Health Network, 200 Elizabeth Street, Toronto, ON, Toronto, Ontario, M5G 2C4, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, M5S 1A8, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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Desterro J, Bak-Gordon P, Carmo-Fonseca M. Targeting mRNA processing as an anticancer strategy. Nat Rev Drug Discov 2019; 19:112-129. [PMID: 31554928 DOI: 10.1038/s41573-019-0042-3] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/08/2019] [Indexed: 12/19/2022]
Abstract
Discoveries in the past decade have highlighted the potential of mRNA as a therapeutic target for cancer. Specifically, RNA sequencing revealed that, in addition to gene mutations, alterations in mRNA can contribute to the initiation and progression of cancer. Indeed, precursor mRNA processing, which includes the removal of introns by splicing and the formation of 3' ends by cleavage and polyadenylation, is frequently altered in tumours. These alterations result in numerous cancer-specific mRNAs that generate altered levels of normal proteins or proteins with new functions, leading to the activation of oncogenes or the inactivation of tumour-suppressor genes. Abnormally spliced and polyadenylated mRNAs are also associated with resistance to cancer treatment and, unexpectedly, certain cancers are highly sensitive to the pharmacological inhibition of splicing. This Review summarizes recent progress in our understanding of how splicing and polyadenylation are altered in cancer and highlights how this knowledge has been translated for drug discovery, resulting in the production of small molecules and oligonucleotides that modulate the spliceosome and are in clinical trials for the treatment of cancer.
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Affiliation(s)
- Joana Desterro
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.,Instituto Português de Oncologia de Lisboa, Serviço de Hematologia, Lisboa, Portugal
| | - Pedro Bak-Gordon
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
| | - Maria Carmo-Fonseca
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal.
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26
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Stevens M, Oltean S. Modulation of the Apoptosis Gene Bcl-x Function Through Alternative Splicing. Front Genet 2019; 10:804. [PMID: 31552099 PMCID: PMC6743414 DOI: 10.3389/fgene.2019.00804] [Citation(s) in RCA: 81] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 07/31/2019] [Indexed: 01/09/2023] Open
Abstract
Apoptosis plays a vital role in cell homeostasis during development and disease. Bcl-x, a member of the Bcl-2 family of proteins, is a mitochondrial transmembrane protein that functions to regulate the intrinsic apoptosis pathway. An alternative splicing (AS) event in exon 2 of Bcl-x results in two isoforms of Bcl-x with antagonistic effects on cell survival: Bcl-xL (long isoform), which is anti-apoptotic, and Bcl-xS (short isoform), which is pro-apoptotic. Bcl-xL is the most abundant Bcl-x protein and functions to inhibit apoptosis by a number of different mechanisms including inhibition of Bax. In contrast, Bcl-xS can directly bind to and inhibit the anti-apoptotic Bcl-xL and Bcl-2 proteins, resulting in the release of the pro-apoptotic Bak. There are multiple splice factors and signaling pathways that influence the Bcl-xL/Bcl-xS splicing ratio, including serine/arginine-rich (SR) proteins, heterogeneous nuclear ribonucleoproteins (hnRNPs), transcription factors, and cytokines. Dysregulation of the AS of Bcl-x has been implicated in cancer and diabetes. In cancer, the upregulation of Bcl-xL expression in tumor cells can result in resistance to chemotherapeutic agents. On the other hand, dysregulation of Bcl-x AS to promote Bcl-xS expression has been shown to be detrimental to pancreatic β-cells in diabetes, resulting in β-cell apoptosis. Therefore, manipulation of the splice factor, transcription factor, and signaling pathways that modulate this splicing event is fast emerging as a therapeutic avenue in the treatment of cancer and diabetes.
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Affiliation(s)
- Megan Stevens
- Institute of Biomedical and Clinical Science, Medical School, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
| | - Sebastian Oltean
- Institute of Biomedical and Clinical Science, Medical School, College of Medicine and Health, University of Exeter, Exeter, United Kingdom
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27
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Pitout I, Flynn LL, Wilton SD, Fletcher S. Antisense-mediated splice intervention to treat human disease: the odyssey continues. F1000Res 2019; 8. [PMID: 31164976 PMCID: PMC6534073 DOI: 10.12688/f1000research.18466.1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/15/2019] [Indexed: 12/24/2022] Open
Abstract
Recent approvals of oligonucleotide analogue drugs to alter gene expression have been welcomed by patient communities but not universally supported. These compounds represent a class of drugs that are designed to target a specific gene transcript, and they include a number of chemical entities to evoke different antisense mechanisms, depending upon the disease aetiology. To date, oligonucleotide therapeutics that are in the clinic or at advanced stages of translation target rare diseases, posing challenges to clinical trial design, recruitment and evaluation and requiring new evaluation paradigms. This review discusses the currently available and emerging therapeutics that alter exon selection through an effect on pre-mRNA splicing and explores emerging concerns over safety and efficacy. Although modification of synthetic nucleic acids destined for therapeutic application is common practice to protect against nuclease degradation and to influence drug function, such modifications may also confer unexpected physicochemical and biological properties. Negatively charged oligonucleotides have a strong propensity to bind extra- and intra-cellular proteins, whereas those analogues with a neutral backbone show inefficient cellular uptake but excellent safety profiles. In addition, the potential for incorporation of chemically modified nucleic acid monomers, yielded by nuclease degradation of exogenous oligonucleotides, into biomolecules has been raised and the possibility not entirely discounted. We conclude with a commentary on the ongoing efforts to develop novel antisense compounds and enhance oligonucleotide delivery in order to further improve efficacy and accelerate implementation of antisense therapeutics for human disease.
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Affiliation(s)
| | - Loren L Flynn
- Murdoch University, Murdoch, WA, 6150, Australia.,The University of Western Australia, Nedlands, WA, 6009, Australia.,Perron Institute, Nedlands, WA, 6009, Australia
| | - Steve D Wilton
- Murdoch University, Murdoch, WA, 6150, Australia.,The University of Western Australia, Nedlands, WA, 6009, Australia.,Perron Institute, Nedlands, WA, 6009, Australia
| | - Sue Fletcher
- Murdoch University, Murdoch, WA, 6150, Australia.,The University of Western Australia, Nedlands, WA, 6009, Australia.,Perron Institute, Nedlands, WA, 6009, Australia
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28
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Krichevsky AM, Uhlmann EJ. Oligonucleotide Therapeutics as a New Class of Drugs for Malignant Brain Tumors: Targeting mRNAs, Regulatory RNAs, Mutations, Combinations, and Beyond. Neurotherapeutics 2019; 16:319-347. [PMID: 30644073 PMCID: PMC6554258 DOI: 10.1007/s13311-018-00702-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Malignant brain tumors are rapidly progressive and often fatal owing to resistance to therapies and based on their complex biology, heterogeneity, and isolation from systemic circulation. Glioblastoma is the most common and most aggressive primary brain tumor, has high mortality, and affects both children and adults. Despite significant advances in understanding the pathology, multiple clinical trials employing various treatment strategies have failed. With much expanded knowledge of the GBM genome, epigenome, and transcriptome, the field of neuro-oncology is getting closer to achieve breakthrough-targeted molecular therapies. Current developments of oligonucleotide chemistries for CNS applications make this new class of drugs very attractive for targeting molecular pathways dysregulated in brain tumors and are anticipated to vastly expand the spectrum of currently targetable molecules. In this chapter, we will overview the molecular landscape of malignant gliomas and explore the most prominent molecular targets (mRNAs, miRNAs, lncRNAs, and genomic mutations) that provide opportunities for the development of oligonucleotide therapeutics for this class of neurologic diseases. Because malignant brain tumors focally disrupt the blood-brain barrier, this class of diseases might be also more susceptible to systemic treatments with oligonucleotides than other neurologic disorders and, thus, present an entry point for the oligonucleotide therapeutics to the CNS. Nevertheless, delivery of oligonucleotides remains a crucial part of the treatment strategy. Finally, synthetic gRNAs guiding CRISPR-Cas9 editing technologies have a tremendous potential to further expand the applications of oligonucleotide therapeutics and take them beyond RNA targeting.
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Affiliation(s)
- Anna M Krichevsky
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Initiative for RNA Medicine, Boston, Massachusetts, 02115, USA.
| | - Erik J Uhlmann
- Ann Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, Initiative for RNA Medicine, Boston, Massachusetts, 02115, USA
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29
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Yosudjai J, Wongkham S, Jirawatnotai S, Kaewkong W. Aberrant mRNA splicing generates oncogenic RNA isoforms and contributes to the development and progression of cholangiocarcinoma. Biomed Rep 2019; 10:147-155. [PMID: 30906543 PMCID: PMC6403481 DOI: 10.3892/br.2019.1188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 01/04/2019] [Indexed: 12/13/2022] Open
Abstract
Cholangiocarcinoma is a lethal biliary cancer, with an unclear molecular pathogenesis. Alternative splicing is a post-transcriptional modification that generates mature mRNAs, which are subsequently translated into proteins. Aberrant alternative splicing has been reported to serve a role in tumor initiation, maintenance and metastasis in several types of human cancer, including cholangiocarcinoma. In this review, the aberrant splicing of genes and the functional contributions of the spliced genes, in the carcinogenesis, progression and aggressiveness of cholangiocarcinoma are summarized. In addition, factors that influence this aberrant splicing that may be relevant as therapeutic targets or prognosis markers for cholangiocarcinoma are discussed.
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Affiliation(s)
- Juthamas Yosudjai
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
| | - Sopit Wongkham
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Siwanon Jirawatnotai
- Siriraj Center for Research of Excellence (SiCORE) for System Pharmacology, Department of Pharmacology, Faculty of Medicine, Siriraj Medical School, Mahidol University, Bangkok 10700, Thailand
| | - Worasak Kaewkong
- Department of Biochemistry, Faculty of Medical Science, Naresuan University, Phitsanulok 65000, Thailand
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30
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Di C, Syafrizayanti, Zhang Q, Chen Y, Wang Y, Zhang X, Liu Y, Sun C, Zhang H, Hoheisel JD. Function, clinical application, and strategies of Pre-mRNA splicing in cancer. Cell Death Differ 2018; 26:1181-1194. [PMID: 30464224 PMCID: PMC6748147 DOI: 10.1038/s41418-018-0231-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Revised: 10/09/2018] [Accepted: 10/23/2018] [Indexed: 12/22/2022] Open
Abstract
Pre-mRNA splicing is a fundamental process that plays a considerable role in generating protein diversity. Pre-mRNA splicing is also the key to the pathology of numerous diseases, especially cancers. In this review, we discuss how aberrant splicing isoforms precisely regulate three basic functional aspects in cancer: proliferation, metastasis and apoptosis. Importantly, clinical function of aberrant splicing isoforms is also discussed, in particular concerning drug resistance and radiosensitivity. Furthermore, this review discusses emerging strategies how to modulate pathologic aberrant splicing isoforms, which are attractive, novel therapeutic agents in cancer. Last we outline current and future directions of isoforms diagnostic methodologies reported so far in cancer. Thus, it is highlighting significance of aberrant splicing isoforms as markers for cancer and as targets for cancer therapy.
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Affiliation(s)
- Cuixia Di
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Syafrizayanti
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.,Department of Chemistry, Faculty of Mathematics and Natural Sciences, Andalas University, Kampus Limau Manis, Padang, Indonesia
| | - Qianjing Zhang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yuhong Chen
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yupei Wang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Xuetian Zhang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China.,College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Yang Liu
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China
| | - Chao Sun
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China.,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China
| | - Hong Zhang
- Department of Radiation Medicine, Institute of Modern Physics, Chinese Academy of Sciences, 730000, Lanzhou, China. .,Key Laboratory of Heavy Ion Radiation Biology and Medicine of Chinese Academy of Sciences, 730000, Lanzhou, China.
| | - Jörg D Hoheisel
- Division of Functional Genome Analysis, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany.
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31
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Urbanski L, Leclair N, Anczuków O. Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9:e1476. [PMID: 29693319 PMCID: PMC6002934 DOI: 10.1002/wrna.1476] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Revised: 02/27/2018] [Accepted: 03/01/2018] [Indexed: 12/14/2022]
Abstract
Defects in alternative splicing are frequently found in human tumors and result either from mutations in splicing-regulatory elements of specific cancer genes or from changes in the regulatory splicing machinery. RNA splicing regulators have emerged as a new class of oncoproteins and tumor suppressors, and contribute to disease progression by modulating RNA isoforms involved in the hallmark cancer pathways. Thus, dysregulation of alternative RNA splicing is fundamental to cancer and provides a potentially rich source of novel therapeutic targets. Here, we review the alterations in splicing regulatory factors detected in human tumors, as well as the resulting alternatively spliced isoforms that impact cancer hallmarks, and discuss how they contribute to disease pathogenesis. RNA splicing is a highly regulated process and, as such, the regulators are themselves tightly regulated. Differential transcriptional and posttranscriptional regulation of splicing factors modulates their levels and activities in tumor cells. Furthermore, the composition of the tumor microenvironment can also influence which isoforms are expressed in a given cell type and impact drug responses. Finally, we summarize current efforts in targeting alternative splicing, including global splicing inhibition using small molecules blocking the spliceosome or splicing-factor-modifying enzymes, as well as splice-switching RNA-based therapeutics to modulate cancer-specific splicing isoforms. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Processing > Splicing Regulation/Alternative Splicing.
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32
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Therapeutic Applications of Targeted Alternative Splicing to Cancer Treatment. Int J Mol Sci 2017; 19:ijms19010075. [PMID: 29283381 PMCID: PMC5796025 DOI: 10.3390/ijms19010075] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 12/22/2017] [Accepted: 12/24/2017] [Indexed: 12/16/2022] Open
Abstract
A growing body of studies has documented the pathological influence of impaired alternative splicing (AS) events on numerous diseases, including cancer. In addition, the generation of alternatively spliced isoforms is frequently noted to result in drug resistance in many cancer therapies. To gain comprehensive insights into the impacts of AS events on cancer biology and therapeutic developments, this paper highlights recent findings regarding the therapeutic routes of targeting alternative-spliced isoforms and splicing regulators to treatment strategies for distinct cancers.
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33
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Soudah T, Mogilevsky M, Karni R, Yavin E. CLIP6-PNA-Peptide Conjugates: Non-Endosomal Delivery of Splice Switching Oligonucleotides. Bioconjug Chem 2017; 28:3036-3042. [PMID: 29211451 DOI: 10.1021/acs.bioconjchem.7b00638] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Efficient delivery of oligonucleotides still remains a challenge in the field of oligonucleotide based therapy. Peptide nucleic acid (PNA), a DNA analogue that is typically synthesized by solid phase peptide chemistry, has been conjugated to a variety of cell penetrating peptides (CPP) as a means of improving its cellular uptake. These CPPs typically deliver their cargoes into cells by an endosomal-dependent mechanism resulting in lower bioavailability of the cargo. Herein, we designed and synthesized PNA-peptide conjugates as splice switching oligonucleotides (SSO) targeting the Mnk2 gene, a therapeutic target in cancer. In humans, the MKNK2 gene, is alternatively spliced, generating isoforms with opposite biological activities: Mnk2a and Mnk2b. It was found that the Mnk2a isoform is down-regulated in breast, lung, brain, and colon tumors and is a tumor suppressor, whereas MnK2b is oncogenic. We have designed and synthesized PNAs that were conjugated to either of the following peptides: a nuclear localization sequence (NLS) or a cytosol localizing internalization peptide (CLIP6). CLIP6-PNA demonstrates effective cellular uptake and exclusively employs a nonendosomal mechanism to cross the cellular membranes of glioblastoma cells (U87). Simple incubation of PNA-peptide conjugates in human glioblastoma cells up-regulates the Mnk2a isoform leading to cancer cell death.
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Affiliation(s)
- Terese Soudah
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Maxim Mogilevsky
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Rotem Karni
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
| | - Eylon Yavin
- The Institute for Drug Research, The School of Pharmacy and ‡Department of Biochemistry and Molecular Biology, Institute for Medical Research Israel-Canada, The Faculty of Medicine, The Hebrew University of Jerusalem , Hadassah Ein-Kerem, Jerusalem 91120, Israel
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34
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Bates DO, Morris JC, Oltean S, Donaldson LF. Pharmacology of Modulators of Alternative Splicing. Pharmacol Rev 2017; 69:63-79. [PMID: 28034912 PMCID: PMC5226212 DOI: 10.1124/pr.115.011239] [Citation(s) in RCA: 64] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
More than 95% of genes in the human genome are alternatively spliced to form multiple transcripts, often encoding proteins with differing or opposing function. The control of alternative splicing is now being elucidated, and with this comes the opportunity to develop modulators of alternative splicing that can control cellular function. A number of approaches have been taken to develop compounds that can experimentally, and sometimes clinically, affect splicing control, resulting in potential novel therapeutics. Here we develop the concepts that targeting alternative splicing can result in relatively specific pathway inhibitors/activators that result in dampening down of physiologic or pathologic processes, from changes in muscle physiology to altering angiogenesis or pain. The targets and pharmacology of some of the current inhibitors/activators of alternative splicing are demonstrated and future directions discussed.
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Affiliation(s)
- David O Bates
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Jonathan C Morris
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Sebastian Oltean
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
| | - Lucy F Donaldson
- Cancer Biology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (D.O.B.); School of Chemistry, UNSW Australia, Sydney, Australia (J.C.M.); School of Physiology, Pharmacology and Neurosciences, School of Clinical Sciences/Bristol Renal, University of Bristol, Bristol, United Kingdom (S.O.); and School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham, United Kingdom (L.F.D.)
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Lin JC, Tsao MF, Lin YJ. Differential Impacts of Alternative Splicing Networks on Apoptosis. Int J Mol Sci 2016; 17:ijms17122097. [PMID: 27983653 PMCID: PMC5187897 DOI: 10.3390/ijms17122097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 11/26/2016] [Accepted: 12/02/2016] [Indexed: 12/16/2022] Open
Abstract
Apoptosis functions as a common mechanism to eliminate unnecessary or damaged cells during cell renewal and tissue development in multicellular organisms. More than 200 proteins constitute complex networks involved in apoptotic regulation. Imbalanced expressions of apoptosis-related factors frequently lead to malignant diseases. The biological functions of several apoptotic factors are manipulated through alternative splicing mechanisms which expand gene diversity by generating discrete variants from one messenger RNA precursor. It is widely observed that alternatively-spliced variants encoded from apoptosis-related genes exhibit differential effects on apoptotic regulation. Alternative splicing events are meticulously regulated by the interplay between trans-splicing factors and cis-responsive elements surrounding the regulated exons. The major focus of this review is to highlight recent studies that illustrate the influences of alternative splicing networks on apoptotic regulation which participates in diverse cellular processes and diseases.
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Affiliation(s)
- Jung-Chun Lin
- School of Medical Laboratory Science and Biotechnology, College of Medical Science and Technology, Taipei Medical University, Taipei 11031, Taiwan.
| | - Mei-Fen Tsao
- Department of Laboratory Medicine, Taipei Medical University Hospital, Taipei 11031, Taiwan.
| | - Ying-Ju Lin
- School of Chinese Medicine, China Medical University, Taichung 404, Taiwan.
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