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Gonzalez-Salinas F, Martinez-Amador C, Trevino V. Characterizing genes associated with cancer using the CRISPR/Cas9 system: A systematic review of genes and methodological approaches. Gene 2022; 833:146595. [PMID: 35598687 DOI: 10.1016/j.gene.2022.146595] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 04/22/2022] [Accepted: 05/16/2022] [Indexed: 12/24/2022]
Abstract
The CRISPR/Cas9 system enables a versatile set of genomes editing and genetic-based disease modeling tools due to its high specificity, efficiency, and accessible design and implementation. In cancer, the CRISPR/Cas9 system has been used to characterize genes and explore different mechanisms implicated in tumorigenesis. Different experimental strategies have been proposed in recent years, showing dependency on various intrinsic factors such as cancer type, gene function, mutation type, and technical approaches such as cell line, Cas9 expression, and transfection options. However, the successful methodological approaches, genes, and other experimental factors have not been analyzed. We, therefore, initially considered more than 1,300 research articles related to CRISPR/Cas9 in cancer to finally examine more than 400 full-text research publications. We summarize findings regarding target genes, RNA guide designs, cloning, Cas9 delivery systems, cell enrichment, and experimental validations. This analysis provides valuable information and guidance for future cancer gene validation experiments.
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Affiliation(s)
- Fernando Gonzalez-Salinas
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Claudia Martinez-Amador
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico
| | - Victor Trevino
- Tecnologico de Monterrey, School of Medicine and Health Sciences, Morones Prieto avenue 3000, Monterrey, Nuevo Leon 64710, Mexico; Tecnologico de Monterrey, The Institute for Obesity Research, Eugenio Garza Sada avenue 2501, Monterrey, Nuevo Leon 64849, México.
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Koganti P, Kadali VN, Manikoth Ayyathan D, Emanuelli A, Paolini B, Levy-Cohen G, Blank M. The E3 ubiquitin ligase SMURF2 stabilizes RNA editase ADAR1p110 and promotes its adenosine-to-inosine (A-to-I) editing function. Cell Mol Life Sci 2022; 79:237. [PMID: 35403872 PMCID: PMC11072456 DOI: 10.1007/s00018-022-04272-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 11/03/2022]
Abstract
Epitranscriptomic changes in RNA catalyzed by the RNA-editing enzyme ADAR1 play an essential role in the regulation of diverse molecular and cellular processes, both under physiological conditions and in disease states, including cancer. Yet, despite a growing body of evidence pointing to ADAR1 as a potential therapeutic target, the mechanisms regulating its cellular abundance and activity, particularly of its constitutively expressed and ubiquitous form, ADAR1p110, are poorly understood. Here, we report the HECT-type E3 ubiquitin ligase SMURF2 as a pivotal regulator of ADAR1p110. We show that SMURF2, which is primarily known to promote the ubiquitin-mediated degradation of its protein substrates, protects ADAR1p110 from proteolysis and promotes its A-to-I editase activity in human and mouse cells and tissues. ADAR1p110's interactome analysis performed in human cells also showed a positive influence of SMURF2 on the stability and function of ADAR1p110. Mechanistically, we found that SMURF2 directly binds, ubiquitinates and stabilizes ADAR1p110 in an E3 ubiquitin ligase-dependent manner, through ADAR1p110 ubiquitination at lysine-744 (K744). Mutation of this residue to arginine (K744R), which is also associated with several human disorders, including dyschromatosis symmetrica hereditaria (DSH) and some types of cancer, abolished SMURF2-mediated protection of ADAR1p110 from both proteasomal and lysosomal degradation and inactivated ADAR1p110-mediated RNA editing. Our findings reveal a novel mechanism underlying the regulation of ADAR1 in mammalian cells and suggest SMURF2 as a key cellular factor influencing the protein abundance, interactions and functions of ADAR1p110.
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Affiliation(s)
- Praveen Koganti
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502, Safed, Israel
| | - Venkata Narasimha Kadali
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502, Safed, Israel
| | - Dhanoop Manikoth Ayyathan
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502, Safed, Israel
| | - Andrea Emanuelli
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502, Safed, Israel
| | - Biagio Paolini
- Department of Pathology and Laboratory Medicine, IRCCS Fondazione, Istituto Nazionale dei Tumori, Milan, Italy
| | - Gal Levy-Cohen
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502, Safed, Israel
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, 1311502, Safed, Israel.
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Shah PA, Boutros-Suleiman S, Emanuelli A, Paolini B, Levy-Cohen G, Blank M. The Emerging Role of E3 Ubiquitin Ligase SMURF2 in the Regulation of Transcriptional Co-Repressor KAP1 in Untransformed and Cancer Cells and Tissues. Cancers (Basel) 2022; 14:cancers14071607. [PMID: 35406379 PMCID: PMC8997158 DOI: 10.3390/cancers14071607] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 03/18/2022] [Indexed: 02/04/2023] Open
Abstract
Simple Summary KAP1 plays an essential role in different molecular and cellular processes central to carcinogenesis, disease progression, and treatment response, revealing both tumor promoting and anticancer functions. The mechanisms that control the steady-state levels of KAP1 and its protein abundance are not well known. Our findings show that SMURF2, a ubiquitously-expressed HECT-type E3 ubiquitin ligase with suggested anticancer activities, is capable to directly bind, ubiquitinate, and regulate KAP1 expression levels in non-cancerous and tumor cells and tissues. The data further show that SMURF2 has a significant influence on KAP1 interactome, regulating its protein–protein interactions and functions in a catalytically-dependent manner. These findings reveal SMURF2 as a pivotal regulator of KAP1, laying a foundation for the investigation of the role of the SMURF2–KAP1 axis in carcinogenic processes and therapeutic responses to anticancer treatment. Abstract KAP1 is an essential nuclear factor acting as a scaffold for protein complexes repressing transcription. KAP1 plays fundamental role in normal and cancer cell biology, affecting cell proliferation, DNA damage response, genome integrity maintenance, migration and invasion, as well as anti-viral and immune response. Despite the foregoing, the mechanisms regulating KAP1 cellular abundance are poorly understood. In this study, we identified the E3 ubiquitin ligase SMURF2 as an important regulator of KAP1. We show that SMURF2 directly interacts with KAP1 and ubiquitinates it in vitro and in the cellular environment in a catalytically-dependent manner. Interestingly, while in the examined untransformed cells, SMURF2 mostly exerted a negative impact on KAP1 expression, a phenomenon that was also monitored in certain Smurf2-ablated mouse tissues, in tumor cells SMURF2 stabilized KAP1. This stabilization relied on the unaltered E3 ubiquitin ligase function of SMURF2. Further investigations showed that SMURF2 regulates KAP1 post-translationally, interfering with its proteasomal degradation. The conducted immunohistochemical studies showed that the reciprocal relationship between the expression of SMURF2 and KAP1 also exists in human normal and breast cancer tissues and suggested that this relationship may be disrupted by the carcinogenic process. Finally, through stratifying KAP1 interactome in cells expressing either SMURF2 wild-type or its E3 ligase-dead form, we demonstrate that SMURF2 has a profound impact on KAP1 protein–protein interactions and the associated functions, adding an additional layer in the SMURF2-mediated regulation of KAP1. Cumulatively, these findings uncover SMURF2 as a novel regulator of KAP1, governing its protein expression, interactions, and functions.
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Affiliation(s)
- Pooja Anil Shah
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (P.A.S.); (S.B.-S.); (A.E.); (G.L.-C.)
| | - Sandy Boutros-Suleiman
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (P.A.S.); (S.B.-S.); (A.E.); (G.L.-C.)
| | - Andrea Emanuelli
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (P.A.S.); (S.B.-S.); (A.E.); (G.L.-C.)
| | - Biagio Paolini
- Department of Pathology and Laboratory Medicine, IRCCS Fondazione, Istituto Nazionale dei Tumori, 20133 Milan, Italy;
| | - Gal Levy-Cohen
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (P.A.S.); (S.B.-S.); (A.E.); (G.L.-C.)
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed 1311502, Israel; (P.A.S.); (S.B.-S.); (A.E.); (G.L.-C.)
- Correspondence:
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Manikoth Ayyathan D, Levy-Cohen G, Shubely M, Boutros-Suleiman S, Lepechkin-Zilbermintz V, Shokhen M, Albeck A, Gruzman A, Blank M. Development and characterisation of SMURF2-targeting modifiers. J Enzyme Inhib Med Chem 2021; 36:401-409. [PMID: 33430646 PMCID: PMC7808752 DOI: 10.1080/14756366.2020.1871337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
The C2-WW-HECT-domain E3 ubiquitin ligase SMURF2 emerges as an important regulator of diverse cellular processes. To date, SMURF2-specific modulators were not developed. Here, we generated and investigated a set of SMURF2-targeting synthetic peptides and peptidomimetics designed to stimulate SMURF2’s autoubiquitination and turnover via a disruption of the inhibitory intramolecular interaction between its C2 and HECT domains. The results revealed the effects of these molecules both in vitro and in cellulo at the nanomolar concentration range. Moreover, the data showed that targeting of SMURF2 with either these modifiers or SMURF2-specific shRNAs could accelerate cell growth in a cell-context-dependent manner. Intriguingly, a concomitant cell treatment with a selected SMURF2-targeting compound and the DNA-damaging drug etoposide markedly increased the cytotoxicity produced by this drug in growing cells. Altogether, these findings demonstrate that SMURF2 can be druggable through its self-destructive autoubiquitination, and inactivation of SMURF2 might be used to affect cell sensitivity to certain anticancer drugs.
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Affiliation(s)
- Dhanoop Manikoth Ayyathan
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Gal Levy-Cohen
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Moran Shubely
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Sandy Boutros-Suleiman
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | | | - Michael Shokhen
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Amnon Albeck
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Arie Gruzman
- Department of Chemistry, Bar-Ilan University, Ramat Gan, Israel
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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SMURF2 prevents detrimental changes to chromatin, protecting human dermal fibroblasts from chromosomal instability and tumorigenesis. Oncogene 2020; 39:3396-3410. [PMID: 32103168 DOI: 10.1038/s41388-020-1226-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 02/13/2020] [Accepted: 02/17/2020] [Indexed: 01/17/2023]
Abstract
E3 ubiquitin ligases (E3s) play essential roles in the maintenance of tissue homeostasis under normal and stress conditions, as well as in disease states, particularly in cancer. However, the role of E3s in the initiation of human tumors is poorly understood. Previously, we reported that genetic ablation of the HECT-type E3 ubiquitin ligase Smurf2 induces carcinogenesis in mice; but whether and how these findings are pertinent to the inception of human cancer remain unknown. Here we show that SMURF2 is essential to protect human dermal fibroblasts (HDFs) from malignant transformation, and its depletion converts HDFs into tumorigenic entity. This phenomenon was associated with the radical changes in chromatin structural and epigenetic landscape, dysregulated gene expression and cell-cycle control, mesenchymal-to-epithelial transition and impaired DNA damage response. Furthermore, we show that SMURF2-mediated tumor suppression is interlinked with SMURF2's ability to regulate the expression of two central chromatin modifiers-an E3 ubiquitin ligase RNF20 and histone methyltransferase EZH2. Silencing these factors significantly reduced the growth and transformation capabilities of SMURF2-depleted cells. Finally, we demonstrate that SMURF2-compromised HDFs are highly tumorigenic in nude mice. These findings suggest the critical role that SMURF2 plays in preventing malignant alterations, chromosomal instability and cancer.
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Koganti P, Levy-Cohen G, Blank M. Smurfs in Protein Homeostasis, Signaling, and Cancer. Front Oncol 2018; 8:295. [PMID: 30116722 PMCID: PMC6082930 DOI: 10.3389/fonc.2018.00295] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 07/16/2018] [Indexed: 12/13/2022] Open
Abstract
Protein ubiquitination is an evolutionary conserved highly-orchestrated enzymatic cascade essential for normal cellular functions and homeostasis maintenance. This pathway relies on a defined set of cellular enzymes, among them, substrate-specific E3 ubiquitin ligases (E3s). These ligases are the most critical players, as they define the spatiotemporal nature of ubiquitination and confer specificity to this cascade. Smurf1 and Smurf2 (Smurfs) are the C2-WW-HECT-domain E3 ubiquitin ligases, which recently emerged as important determinants of pivotal cellular processes. These processes include cell proliferation and differentiation, chromatin organization and dynamics, DNA damage response and genomic integrity maintenance, gene expression, cell stemness, migration, and invasion. All these processes are intimately connected and profoundly altered in cancer. Initially, Smurf proteins were identified as negative regulators of the bone morphogenetic protein (BMP) and the transforming growth factor beta (TGF-β) signaling pathways. However, recent studies have extended the scope of Smurfs' biological functions beyond the BMP/TGF-β signaling regulation. Here, we provide a critical literature overview and updates on the regulatory roles of Smurfs in molecular and cell biology, with an emphasis on cancer. We also highlight the studies demonstrating the impact of Smurf proteins on tumor cell sensitivity to anticancer therapies. Further in-depth analyses of Smurfs' biological functions and influences on molecular pathways could provide novel therapeutic targets and paradigms for cancer diagnosis and treatment.
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Affiliation(s)
- Praveen Koganti
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Gal Levy-Cohen
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
| | - Michael Blank
- Laboratory of Molecular and Cellular Cancer Biology, Azrieli Faculty of Medicine, Bar-Ilan University, Safed, Israel
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Zhang Y, Tang N, Sadigh Y, Baigent S, Shen Z, Nair V, Yao Y. Application of CRISPR/Cas9 Gene Editing System on MDV-1 Genome for the Study of Gene Function. Viruses 2018; 10:v10060279. [PMID: 29794970 PMCID: PMC6024840 DOI: 10.3390/v10060279] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 05/17/2018] [Accepted: 05/22/2018] [Indexed: 12/14/2022] Open
Abstract
Marek’s disease virus (MDV) is a member of alphaherpesviruses associated with Marek’s disease, a highly contagious neoplastic disease in chickens. Complete sequencing of the viral genome and recombineering techniques using infectious bacterial artificial chromosome (BAC) clones of Marek’s disease virus genome have identified major genes that are associated with pathogenicity. Recent advances in CRISPR/Cas9-based gene editing have given opportunities for precise editing of the viral genome for identifying pathogenic determinants. Here we describe the application of CRISPR/Cas9 gene editing approaches to delete the Meq and pp38 genes from the CVI988 vaccine strain of MDV. This powerful technology will speed up the MDV gene function studies significantly, leading to a better understanding of the molecular mechanisms of MDV pathogenesis.
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Affiliation(s)
- Yaoyao Zhang
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
| | - Na Tang
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
- Binzhou Animal Science and Veterinary Medicine Academy & UK-China Centre of Excellence for Research on Avian Diseases, Binzhou 256600, Shandong, China.
| | - Yashar Sadigh
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
| | - Susan Baigent
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
| | - Zhiqiang Shen
- Binzhou Animal Science and Veterinary Medicine Academy & UK-China Centre of Excellence for Research on Avian Diseases, Binzhou 256600, Shandong, China.
| | - Venugopal Nair
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
| | - Yongxiu Yao
- The Pirbright Institute & UK-China Centre of Excellence for Research on Avian Diseases, Pirbright, Ash Road, Guildford, Surrey GU24 0NF, UK.
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