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MacAuley MJ, Abuhussein O, Vizeacoumar FS. Identification of Synthetic Lethal Interactions Using High-Throughput, Arrayed CRISPR/Cas9-Based Platforms. Methods Mol Biol 2021; 2381:135-149. [PMID: 34590274 DOI: 10.1007/978-1-0716-1740-3_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Over the past two decades, the concept of synthetic lethality (SL) that queries genetic relationships between gene pairs has gradually emerged as one of the best strategies to selectively eliminate cancer cells. Some of the most successful approaches to identify synthetic lethal interactions (SLIs) were largely dependent on pooled screening formats that require heavy validation in order to mitigate false positives. Here, we describe a high-throughput method to identify SLIs using CRISPR-based strategy that covers, high-throughput production of plasmid DNA preparations, lentiviral production, and subsequent cellular transduction using single guide RNAs (sgRNAs). This method could be adopted to query hundreds of SLIs. As an example, we describe the methods associated with building an interaction map for DNA damage and repair (DDR) genes. The use of multiwell plates and image-based quantification allows a comparative measurement of SLIs at a high-resolution on a one-by-one basis. Furthermore, this scalable, arrayed CRISPR screening method can be applied to multiple cancer cell types, and genes of interest, resulting in new functional discoveries that can be exploited therapeutically.
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Affiliation(s)
- MacKenzie J MacAuley
- Department of Health Sciences, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
| | - Omar Abuhussein
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Frederick S Vizeacoumar
- Department of Health Sciences, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada.
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Cunningham CE, MacAuley MJ, Vizeacoumar FS, Abuhussein O, Freywald A, Vizeacoumar FJ. The CINs of Polo-Like Kinase 1 in Cancer. Cancers (Basel) 2020; 12:cancers12102953. [PMID: 33066048 PMCID: PMC7599805 DOI: 10.3390/cancers12102953] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Many alterations specific to cancer cells have been investigated as targets for targeted therapies. Chromosomal instability is a characteristic of nearly all cancers that can limit response to targeted therapies by ensuring the tumor population is not genetically homogenous. Polo-like Kinase 1 (PLK1) is often up regulated in cancers and it regulates chromosomal instability extensively. PLK1 has been the subject of much pre-clinical and clinical studies, but thus far, PLK1 inhibitors have not shown significant improvement in cancer patients. We discuss the numerous roles and interactions of PLK1 in regulating chromosomal instability, and how these may provide an avenue for identifying targets for targeted therapies. As selective inhibitors of PLK1 showed limited clinical success, we also highlight how genetic interactions of PLK1 may be exploited to tackle these challenges. Abstract Polo-like kinase 1 (PLK1) is overexpressed near ubiquitously across all cancer types and dysregulation of this enzyme is closely tied to increased chromosomal instability and tumor heterogeneity. PLK1 is a mitotic kinase with a critical role in maintaining chromosomal integrity through its function in processes ranging from the mitotic checkpoint, centrosome biogenesis, bipolar spindle formation, chromosome segregation, DNA replication licensing, DNA damage repair, and cytokinesis. The relation between dysregulated PLK1 and chromosomal instability (CIN) makes it an attractive target for cancer therapy. However, clinical trials with PLK1 inhibitors as cancer drugs have generally displayed poor responses or adverse side-effects. This is in part because targeting CIN regulators, including PLK1, can elevate CIN to lethal levels in normal cells, affecting normal physiology. Nevertheless, aiming at related genetic interactions, such as synthetic dosage lethal (SDL) interactions of PLK1 instead of PLK1 itself, can help to avoid the detrimental side effects associated with increased levels of CIN. Since PLK1 overexpression contributes to tumor heterogeneity, targeting SDL interactions may also provide an effective strategy to suppressing this malignant phenotype in a personalized fashion.
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Affiliation(s)
- Chelsea E. Cunningham
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
- Correspondence: (C.E.C.); (A.F.); (F.J.V.); Tel.: +1-(306)-327-7864 (C.E.C.); +1-(306)-966-5248 (A.F.); +1-(306)-966-7010 (F.J.V.)
| | - Mackenzie J. MacAuley
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
| | - Frederick S. Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
| | - Omar Abuhussein
- College of Pharmacy, University of Saskatchewan, 104 Clinic Place, Saskatoon, SK S7N 2Z4, Canada;
| | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
- Correspondence: (C.E.C.); (A.F.); (F.J.V.); Tel.: +1-(306)-327-7864 (C.E.C.); +1-(306)-966-5248 (A.F.); +1-(306)-966-7010 (F.J.V.)
| | - Franco J. Vizeacoumar
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada; (M.J.M.); (F.S.V.)
- College of Pharmacy, University of Saskatchewan, 104 Clinic Place, Saskatoon, SK S7N 2Z4, Canada;
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada
- Correspondence: (C.E.C.); (A.F.); (F.J.V.); Tel.: +1-(306)-327-7864 (C.E.C.); +1-(306)-966-5248 (A.F.); +1-(306)-966-7010 (F.J.V.)
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Islam MF, Watanabe A, Wong L, Lazarou C, Vizeacoumar FS, Abuhussein O, Hill W, Uppalapati M, Geyer CR, Vizeacoumar FJ. Enhancing the throughput and multiplexing capabilities of next generation sequencing for efficient implementation of pooled shRNA and CRISPR screens. Sci Rep 2017; 7:1040. [PMID: 28432350 PMCID: PMC5430825 DOI: 10.1038/s41598-017-01170-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 03/20/2017] [Indexed: 11/11/2022] Open
Abstract
Next generation sequencing is becoming the method of choice for functional genomic studies that use pooled shRNA or CRISPR libraries. A key challenge in sequencing these mixed-oligo libraries is that they are highly susceptible to hairpin and/or heteroduplex formation. This results in polyclonal, low quality, and incomplete reads and reduces sequencing throughput. Unfortunately, this challenge is significantly magnified in low-to-medium throughput bench-top sequencers as failed reads significantly perturb the maximization of sequence coverage and multiplexing capabilities. Here, we report a methodology that can be adapted to maximize the coverage on a bench-top, Ion PGM System for smaller shRNA libraries with high efficiency. This ligation-based, half-shRNA sequencing strategy minimizes failed sequences and is also equally amenable to high-throughput sequencers for increased multiplexing. Towards this, we also demonstrate that our strategy to reduce heteroduplex formation improves multiplexing capabilities of pooled CRISPR screens using Illumina NextSeq 500. Overall, our method will facilitate sequencing of pooled shRNA or CRISPR libraries from genomic DNA and maximize sequence coverage.
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Affiliation(s)
- Md Fahmid Islam
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Atsushi Watanabe
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.,Department of Hematology, Nephrology and Rheumatology, Graduate School of Medicine, Akita University, Akita, Japan
| | - Lai Wong
- Department of Biochemistry, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Conor Lazarou
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | | | - Omar Abuhussein
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada
| | - Wayne Hill
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | - Maruti Uppalapati
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada
| | - C Ronald Geyer
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology, University of Saskatchewan, Saskatoon, S7N 0W8, Canada. .,College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, S7N 5C9, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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Cunningham CE, Li S, Vizeacoumar FS, Bhanumathy KK, Lee JS, Parameswaran S, Furber L, Abuhussein O, Paul JM, McDonald M, Templeton SD, Shukla H, El Zawily AM, Boyd F, Alli N, Mousseau DD, Geyer R, Bonham K, Anderson DH, Yan J, Yu-Lee LY, Weaver BA, Uppalapati M, Ruppin E, Sablina A, Freywald A, Vizeacoumar FJ. Therapeutic relevance of the protein phosphatase 2A in cancer. Oncotarget 2016; 7:61544-61561. [PMID: 27557495 PMCID: PMC5308671 DOI: 10.18632/oncotarget.11399] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 08/10/2016] [Indexed: 11/25/2022] Open
Abstract
Chromosomal Instability (CIN) is regarded as a unifying feature of heterogeneous tumor populations, driving intratumoral heterogeneity. Polo-Like Kinase 1 (PLK1), a serine-threonine kinase that is often overexpressed across multiple tumor types, is one of the key regulators of CIN and is considered as a potential therapeutic target. However, targeting PLK1 has remained a challenge due to the off-target effects caused by the inhibition of other members of the polo-like family. Here we use synthetic dosage lethality (SDL), where the overexpression of PLK1 is lethal only when another, normally non-lethal, mutation or deletion is present. Rather than directly inhibiting PLK1, we found that inhibition of PP2A causes selective lethality to PLK1-overexpressing breast, pancreatic, ovarian, glioblastoma, and prostate cancer cells. As PP2A is widely regarded as a tumor suppressor, we resorted to gene expression datasets from cancer patients to functionally dissect its therapeutic relevance. We identified two major classes of PP2A subunits that negatively correlated with each other. Interestingly, most mitotic regulators, including PLK1, exhibited SDL interactions with only one class of PP2A subunits (PPP2R1A, PPP2R2D, PPP2R3B, PPP2R5B and PPP2R5D). Validation studies and other functional cell-based assays showed that inhibition of PPP2R5D affects both levels of phospho-Rb as well as sister chromatid cohesion in PLK1-overexpressing cells. Finally, analysis of clinical data revealed that patients with high expression of mitotic regulators and low expression of Class I subunits of PP2A improved survival. Overall, these observations point to a context-dependent role of PP2A that warrants further exploration for therapeutic benefits.
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Affiliation(s)
- Chelsea E. Cunningham
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Shuangshuang Li
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Frederick S. Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | | | - Joo Sang Lee
- Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, Maryland, MD 20742, USA
| | - Sreejit Parameswaran
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Levi Furber
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Omar Abuhussein
- College of Pharmacy, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 2Z4, Canada
| | - James M. Paul
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Megan McDonald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Shaina D. Templeton
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Hersh Shukla
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Amr M. El Zawily
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Frederick Boyd
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Nezeka Alli
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Darrell D. Mousseau
- Cell Signaling Laboratory, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Ron Geyer
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Keith Bonham
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Deborah H. Anderson
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Jiong Yan
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Li-Yuan Yu-Lee
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Beth A. Weaver
- Department of Cell and Regenerative Biology and Carbone Cancer Center, University of Wisconsin-Madison, Madison, WI 53705-2275, USA
| | - Maruti Uppalapati
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Eytan Ruppin
- Center for Bioinformatics and Computational Biology, Department of Computer Science, University of Maryland, Maryland, MD 20742, USA
| | - Anna Sablina
- VIB Center for the Biology of Disease, VIB, 3000 Leuven, Belgium
| | - Andrew Freywald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
| | - Franco J. Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 5E5 Canada
- College of Pharmacy, University of Saskatchewan, Saskatoon, Saskatchewan, S7N 2Z4, Canada
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, Saskatchewan, S7N 5E5, Canada
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