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Chen Q, Pang M, Chen P, Zhou Z, Lei J, He B, Sun Z, Paek C, Jing B, Wu Y, Liu S, Chen Y, Yin L. High-fidelity CRISPR/Cas12a dual-crRNA screening reveals novel synergistic interactions in hepatocellular carcinoma. Clin Transl Med 2024; 14:e1758. [PMID: 39073026 PMCID: PMC11283585 DOI: 10.1002/ctm2.1758] [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: 01/08/2024] [Revised: 06/20/2024] [Accepted: 06/24/2024] [Indexed: 07/30/2024] Open
Abstract
: CRISPR/Cas12a-based combinational screening has shown remarkable potential for identifying genetic interactions. Here, we describe an innovative method for combinational genetic screening with rapid construction of a dual-CRISPR RNA (crRNA) library using gene splicing through overlap extension PCR (SOE PCR) and the adoption of CeCas12a, which we previously identified with strict PAM recognition and low off-targeting to guarantee fidelity and efficiency. The custom-pooled SOE crRNA array (SOCA) library for double-knockout screening could be conveniently constructed in the laboratory for widespread use, and the CeCas12a-mediated high-fidelity screen displayed good performance even under a negative selection screen. By designing a SOCA dual-crRNA library that covered most of the kinase and metabolism-associated gene targets of FDA-approved drugs implicated in hepatocellular carcinoma (HCC) tumourigenesis, novel cross-talk between the two gene sets was negatively selected to inhibit HCC cell growth in vitro and in vivo and was validated using virtual double-knockdown screening based on TCGA databases. Thus, this rapid, efficient and high-fidelity double-knockout screening system is promising for systemically identifying potential genetic interactions between multiple gene sets or combinations of FDA- approved drugs for clinical translational medicine in the future.
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Affiliation(s)
- Qian Chen
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Minhui Pang
- Department of Case StatisticsThe Sixth Hospital of WuhanAffiliated Hospital of Jianghan UniversityWuhanChina
| | - Peng Chen
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Zihao Zhou
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Jun Lei
- Department of Clinical OncologyRenmin Hospital of Wuhan UniversityWuhan UniversityWuhanChina
| | - Boxiao He
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Zaiqiao Sun
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Chonil Paek
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Baowei Jing
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Yankang Wu
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Shiqi Liu
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
| | - Yongshun Chen
- Department of Clinical OncologyRenmin Hospital of Wuhan UniversityWuhan UniversityWuhanChina
| | - Lei Yin
- State Key Laboratory of VirologyHubei Key Laboratory of Cell HomeostasisDepartment of Biochemistry and Molecular BiologyCollege of Life SciencesWuhan UniversityWuhanChina
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El Zawily A, Vizeacoumar FS, Dahiya R, Banerjee SL, Bhanumathy KK, Elhasasna H, Hanover G, Sharpe JC, Sanchez MG, Greidanus P, Stacey RG, Moon KM, Alexandrov I, Himanen JP, Nikolov DB, Fonge H, White AP, Foster LJ, Wang B, Toosi BM, Bisson N, Mirzabekov TA, Vizeacoumar FJ, Freywald A. A Multipronged Unbiased Strategy Guides the Development of an Anti-EGFR/EPHA2-Bispecific Antibody for Combination Cancer Therapy. Clin Cancer Res 2023; 29:2686-2701. [PMID: 36976175 PMCID: PMC10345963 DOI: 10.1158/1078-0432.ccr-22-2535] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/26/2022] [Accepted: 03/01/2023] [Indexed: 03/29/2023]
Abstract
PURPOSE Accumulating analyses of pro-oncogenic molecular mechanisms triggered a rapid development of targeted cancer therapies. Although many of these treatments produce impressive initial responses, eventual resistance onset is practically unavoidable. One of the main approaches for preventing this refractory condition relies on the implementation of combination therapies. This includes dual-specificity reagents that affect both of their targets with a high level of selectivity. Unfortunately, selection of target combinations for these treatments is often confounded by limitations in our understanding of tumor biology. Here, we describe and validate a multipronged unbiased strategy for predicting optimal co-targets for bispecific therapeutics. EXPERIMENTAL DESIGN Our strategy integrates ex vivo genome-wide loss-of-function screening, BioID interactome profiling, and gene expression analysis of patient data to identify the best fit co-targets. Final validation of selected target combinations is done in tumorsphere cultures and xenograft models. RESULTS Integration of our experimental approaches unambiguously pointed toward EGFR and EPHA2 tyrosine kinase receptors as molecules of choice for co-targeting in multiple tumor types. Following this lead, we generated a human bispecific anti-EGFR/EPHA2 antibody that, as predicted, very effectively suppresses tumor growth compared with its prototype anti-EGFR therapeutic antibody, cetuximab. CONCLUSIONS Our work not only presents a new bispecific antibody with a high potential for being developed into clinically relevant biologics, but more importantly, successfully validates a novel unbiased strategy for selecting biologically optimal target combinations. This is of a significant translational relevance, as such multifaceted unbiased approaches are likely to augment the development of effective combination therapies for cancer treatment. See related commentary by Kumar, p. 2570.
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Affiliation(s)
- Amr El Zawily
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biology, College of Liberal Arts and Sciences, University of Iowa, Iowa City, Iowa
| | - Frederick S. Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Renuka Dahiya
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Sara L. Banerjee
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, Canada
| | - Kalpana K. Bhanumathy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Hussain Elhasasna
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Glinton Hanover
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
| | - Jessica C. Sharpe
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Malkon G. Sanchez
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
| | - Paul Greidanus
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
| | - R. Greg Stacey
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kyung-Mee Moon
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Juha P. Himanen
- Department of Biochemistry, University of Turku, Turku, Finland
| | - Dimitar B. Nikolov
- Structural Biology Program, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Humphrey Fonge
- Department of Medical Imaging, College of Medicine, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
- Department of Medical Imaging, Royal University Hospital, Saskatoon, Saskatchewan, Canada
| | - Aaron P. White
- Department of Biochemistry, Microbiology and Immunology, University of Saskatchewan, Health Sciences, Saskatoon, Saskatchewan, Canada
- Vaccine and Infectious Disease Organization-International Vaccine Centre, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Leonard J. Foster
- Michael Smith Laboratories and Department of Biochemistry and Molecular Biology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Bingcheng Wang
- Division of Cancer Biology, Department of Medicine, MetroHealth Medical Center, and Case Western Reserve University School of Medicine, Case Comprehensive Cancer Center, Cleveland, Ohio
| | - Behzad M. Toosi
- Department of Small Animal Clinical Sciences, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Nicolas Bisson
- Department of Molecular Biology, Medical Biochemistry and Pathology, PROTEO and Centre de recherche du Centre Hospitalier Universitaire (CHU) de Quebec-Université Laval, Division Oncologie, Québec, Canada
| | | | - Franco J. Vizeacoumar
- Cancer Research, Saskatchewan Cancer Agency and Division of Oncology, University of Saskatchewan, Saskatoon, Saskatchewan, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, Saskatchewan, Canada
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Maranda V, Zhang Y, Vizeacoumar FS, Freywald A, Vizeacoumar FJ. A CRISPR Platform for Targeted In Vivo Screens. Methods Mol Biol 2023; 2614:397-409. [PMID: 36587138 DOI: 10.1007/978-1-0716-2914-7_24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Large-scale genetic screens are becoming increasingly used as powerful tools to query the genome to identify therapeutic targets in cancer. The advent of the CRISPR technology has revolutionized the effectiveness of these screens and has made it possible to carry out loss-of-function screens to identify cancer-specific genetic interactions. Such loss-of-function screens can be performed in silico, in vitro, and in vivo, depending on the scale of the screen, as well as research questions to be answered. Performing screens in vivo has its challenges but also advantages, providing opportunities to study the tumor microenvironment and cancer immunity. In this chapter, we present a procedural framework and associated notes for conducting in vivo CRISPR knockout screens in cancer models to study cancer biology, anti-tumor immune responses, tumor microenvironment, and predicting treatment responses.
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Affiliation(s)
- Vincent Maranda
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Yue Zhang
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada
| | | | - Andrew Freywald
- Department of Pathology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
| | - Franco J Vizeacoumar
- Division of Oncology, College of Medicine, University of Saskatchewan, Saskatoon, Canada.
- Cancer Research Department, Saskatchewan Cancer Agency, Saskatoon, Canada.
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Inhibition of Scavenger Receptor Class B Type 1 (SR-B1) Expression and Activity as a Potential Novel Target to Disrupt Cholesterol Availability in Castration-Resistant Prostate Cancer. Pharmaceutics 2021; 13:pharmaceutics13091509. [PMID: 34575583 PMCID: PMC8467449 DOI: 10.3390/pharmaceutics13091509] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 02/07/2023] Open
Abstract
There have been several studies that have linked elevated scavenger receptor class b type 1 (SR-B1) expression and activity to the development and progression of castration-resistant prostate cancer (CRPC). SR-B1 facilitates the influx of cholesterol to the cell from lipoproteins in systemic circulation. This influx of cholesterol may be important for many cellular functions, including the synthesis of androgens. Castration-resistant prostate cancer tumors can synthesize androgens de novo to supplement the loss of exogenous sources often induced by androgen deprivation therapy. Silencing of SR-B1 may impact the ability of prostate cancer cells, particularly those of the castration-resistant state, to maintain the intracellular supply of androgens by removing a supply of cholesterol. SR-B1 expression is elevated in CRPC models and has been linked to poor survival of patients. The overarching belief has been that cholesterol modulation, through either synthesis or uptake inhibition, will impact essential signaling processes, impeding the proliferation of prostate cancer. The reduction in cellular cholesterol availability can impede prostate cancer proliferation through both decreased steroid synthesis and steroid-independent mechanisms, providing a potential therapeutic target for the treatment of prostate cancer. In this article, we discuss and highlight the work on SR-B1 as a potential novel drug target for CRPC management.
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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] [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] [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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Wang R, Han Y, Zhao Z, Yang F, Chen T, Zhou W, Wang X, Qi L, Zhao W, Guo Z, Gu Y. Link synthetic lethality to drug sensitivity of cancer cells. Brief Bioinform 2020; 20:1295-1307. [PMID: 29300844 DOI: 10.1093/bib/bbx172] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Revised: 11/22/2017] [Indexed: 12/16/2022] Open
Abstract
Synthetic lethal (SL) interactions occur when alterations in two genes lead to cell death but alteration in only one of them is not lethal. SL interactions provide a new strategy for molecular-targeted cancer therapy. Currently, there are few drugs targeting SL interactions that entered into clinical trials. Therefore, it is necessary to investigate the link between SL interactions and drug sensitivity of cancer cells systematically for drug development purpose. We identified SL interactions by integrating the high-throughput data from The Cancer Genome Atlas, small hairpin RNA data and genetic interactions of yeast. By integrating SL interactions from other studies, we tested whether the SL pairs that consist of drug target genes and the genes with genomic alterations are related with drug sensitivity of cancer cells. We found that only 6.26%∼34.61% of SL interactions showed the expected significant drug sensitivity using the pooled cancer cell line data from different tissues, but the proportion increased significantly to approximately 90% using the cancer cell line data for each specific tissue. From an independent pharmacogenomics data of 41 breast cancer cell lines, we found three SL interactions (ABL1-IFI16, ABL1-SLC50A1 and ABL1-SYT11) showed significantly better prognosis for the patients with both genes being altered than the patients with only one gene being altered, which partially supports the SL effect between the gene pairs. Our study not only provides a new way for unraveling the complex mechanisms of drug sensitivity but also suggests numerous potentially important drug targets for cancer therapy.
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Ramón y Cajal S, Sesé M, Capdevila C, Aasen T, De Mattos-Arruda L, Diaz-Cano SJ, Hernández-Losa J, Castellví J. Clinical implications of intratumor heterogeneity: challenges and opportunities. J Mol Med (Berl) 2020; 98:161-177. [PMID: 31970428 PMCID: PMC7007907 DOI: 10.1007/s00109-020-01874-2] [Citation(s) in RCA: 223] [Impact Index Per Article: 55.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 11/05/2019] [Accepted: 01/07/2020] [Indexed: 02/06/2023]
Abstract
In this review, we highlight the role of intratumoral heterogeneity, focusing on the clinical and biological ramifications this phenomenon poses. Intratumoral heterogeneity arises through complex genetic, epigenetic, and protein modifications that drive phenotypic selection in response to environmental pressures. Functionally, heterogeneity provides tumors with significant adaptability. This ranges from mutual beneficial cooperation between cells, which nurture features such as growth and metastasis, to the narrow escape and survival of clonal cell populations that have adapted to thrive under specific conditions such as hypoxia or chemotherapy. These dynamic intercellular interplays are guided by a Darwinian selection landscape between clonal tumor cell populations and the tumor microenvironment. Understanding the involved drivers and functional consequences of such tumor heterogeneity is challenging but also promises to provide novel insight needed to confront the problem of therapeutic resistance in tumors.
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Affiliation(s)
- Santiago Ramón y Cajal
- Translational Molecular Pathology, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Pathology Department, Vall d’Hebron Hospital, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
- Department of Pathology, Vall d’Hebron University Hospital, Autonomous University of Barcelona, Pg. Vall d’Hebron, 119-129, 08035 Barcelona, Spain
| | - Marta Sesé
- Translational Molecular Pathology, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Claudia Capdevila
- Translational Molecular Pathology, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Department of Genetics and Development, Columbia University Medical Center, New York, NY 10032 USA
| | - Trond Aasen
- Translational Molecular Pathology, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Leticia De Mattos-Arruda
- Vall d’Hebron Institute of Oncology, Vall d’Hebron University Hospital, c/Natzaret, 115-117, 08035 Barcelona, Spain
| | - Salvador J. Diaz-Cano
- Department of Histopathology, King’s College Hospital and King’s Health Partners, London, UK
| | - Javier Hernández-Losa
- Translational Molecular Pathology, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Pathology Department, Vall d’Hebron Hospital, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Josep Castellví
- Translational Molecular Pathology, Vall d’Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Pathology Department, Vall d’Hebron Hospital, Passeig Vall d’Hebron 119-129, 08035 Barcelona, Spain
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
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Kirzinger MWB, Vizeacoumar FS, Haave B, Gonzalez-Lopez C, Bonham K, Kusalik A, Vizeacoumar FJ. Humanized yeast genetic interaction mapping predicts synthetic lethal interactions of FBXW7 in breast cancer. BMC Med Genomics 2019; 12:112. [PMID: 31351478 PMCID: PMC6660958 DOI: 10.1186/s12920-019-0554-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 06/27/2019] [Indexed: 02/08/2023] Open
Abstract
Background Synthetic lethal interactions (SLIs) that occur between gene pairs are exploited for cancer therapeutics. Studies in the model eukaryote yeast have identified ~ 550,000 negative genetic interactions that have been extensively studied, leading to characterization of novel pathways and gene functions. This resource can be used to predict SLIs that can be relevant to cancer therapeutics. Methods We used patient data to identify genes that are down-regulated in breast cancer. InParanoid orthology mapping was performed to identify yeast orthologs of the down-regulated genes and predict their corresponding SLIs in humans. The predicted network graphs were drawn with Cytoscape. CancerRXgene database was used to predict drug response. Results Harnessing the vast available knowledge of yeast genetics, we generated a Humanized Yeast Genetic Interaction Network (HYGIN) for 1009 human genes with 10,419 interactions. Through the addition of patient-data from The Cancer Genome Atlas (TCGA), we generated a breast cancer specific subnetwork. Specifically, by comparing 1009 genes in HYGIN to genes that were down-regulated in breast cancer, we identified 15 breast cancer genes with 130 potential SLIs. Interestingly, 32 of the 130 predicted SLIs occurred with FBXW7, a well-known tumor suppressor that functions as a substrate-recognition protein within a SKP/CUL1/F-Box ubiquitin ligase complex for proteasome degradation. Efforts to validate these SLIs using chemical genetic data predicted that patients with loss of FBXW7 may respond to treatment with drugs like Selumitinib or Cabozantinib. Conclusions This study provides a patient-data driven interpretation of yeast SLI data. HYGIN represents a novel strategy to uncover therapeutically relevant cancer drug targets and the yeast SLI data offers a major opportunity to mine these interactions. Electronic supplementary material The online version of this article (10.1186/s12920-019-0554-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Morgan W B Kirzinger
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, 176 Thorvaldson Bldg, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Bjorn Haave
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Cristina Gonzalez-Lopez
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Keith Bonham
- Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada.,Division of Oncology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada
| | - Anthony Kusalik
- Department of Computer Science, College of Arts and Science, University of Saskatchewan, 176 Thorvaldson Bldg, 110 Science Place, Saskatoon, Saskatchewan, S7N 5C9, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Division of Oncology, College of Medicine, University of Saskatchewan, 107 Wiggins Road, Saskatoon, Saskatchewan, S7N 5E5, Canada. .,Cancer Cluster, Rm 4D01.5 Health Science Bldg, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK, S7N 5E5, Canada.
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10
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Ramón Y Cajal S, Hümmer S, Peg V, Guiu XM, De Torres I, Castellvi J, Martinez-Saez E, Hernandez-Losa J. Integrating clinical, molecular, proteomic and histopathological data within the tissue context: tissunomics. Histopathology 2019; 75:4-19. [PMID: 30667539 PMCID: PMC6851567 DOI: 10.1111/his.13828] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Accepted: 01/19/2019] [Indexed: 12/14/2022]
Abstract
Malignant tumours show a marked degree of morphological, molecular and proteomic heterogeneity. This variability is closely related to microenvironmental factors and the location of the tumour. The activation of genetic alterations is very tissue‐dependent and only few tumours have distinct genetic alterations. Importantly, the activation state of proteins and signaling factors is heterogeneous in the primary tumour and in metastases and recurrences. The molecular diagnosis based only on genetic alterations can lead to treatments with unpredictable responses, depending on the tumour location, such as the tumour response in melanomas versus colon carcinomas with BRAF mutations. Therefore, we understand that the correct evaluation of tumours requires a system that integrates both morphological, molecular and protein information in a clinical and pathological context, where intratumoral heterogeneity can be assessed. Thus, we propose the term ‘tissunomics’, where the diagnosis will be contextualised in each tumour based on the complementation of the pathological, molecular, protein expression, environmental cells and clinical data.
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Affiliation(s)
- Santiago Ramón Y Cajal
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Stefan Hümmer
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Vicente Peg
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Xavier M Guiu
- Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain.,Department of Pathology, Bellvitge University Hospital, Barcelona, Spain
| | - Inés De Torres
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Josep Castellvi
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
| | - Elena Martinez-Saez
- Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Javier Hernandez-Losa
- Translational Molecular Pathology, Vall d'Hebron Institute of Research (VHIR), Universitat Autònoma de Barcelona, Barcelona, Spain.,Department of Pathology, Vall d'Hebron University Hospital, Barcelona, Spain.,Spanish Biomedical Research Network Centre in Oncology (CIBERONC), Barcelona, Spain
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11
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Gu Y, Wang R, Han Y, Zhou W, Zhao Z, Chen T, Zhang Y, Peng F, Liang H, Qi L, Zhao W, Yang D, Guo Z. A landscape of synthetic viable interactions in cancer. Brief Bioinform 2019; 19:644-655. [PMID: 28096076 DOI: 10.1093/bib/bbw142] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Indexed: 01/25/2023] Open
Abstract
Synthetic viability, which is defined as the combination of gene alterations that can rescue the lethal effects of a single gene alteration, may represent a mechanism by which cancer cells resist targeted drugs. Approaches to detect synthetic viable (SV) interactions in cancer genome to investigate drug resistance are still scarce. Here, we present a computational method to detect synthetic viability-induced drug resistance (SVDR) by integrating the multidimensional data sets, including copy number alteration, whole-exome mutation, expression profile and clinical data. SVDR comprehensively characterized the landscape of SV interactions across 8580 tumors in 32 cancer types by integrating The Cancer Genome Atlas data, small hairpin RNA-based functional experimental data and yeast genetic interaction data. We revealed that the SV interactions are favorable to cells and can predict clinical prognosis for cancer patients, which were robustly observed in an independent data set. By integrating the cancer pharmacogenomics data sets from Cancer Cell Line Encyclopedia (CCLE) and Broad Cancer Therapeutics Response Portal, we have demonstrated that SVDR enables drug resistance prediction and exhibits high reliability between two databases. To our knowledge, SVDR is the first genome-scale data-driven approach for the identification of SV interactions related to drug resistance in cancer cells. This data-driven approach lays the foundation for identifying the genomic markers to predict drug resistance and successfully infers the potential drug combination for anti-cancer therapy.
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Affiliation(s)
- Yunyan Gu
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Ruiping Wang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yue Han
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenbin Zhou
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Zhangxiang Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Tingting Chen
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Yuanyuan Zhang
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Fuduan Peng
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Haihai Liang
- Department of Pharmacology, Harbin Medical University, Harbin, China
| | - Lishuang Qi
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Wenyuan Zhao
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Da Yang
- Department of Pharmaceutical Sciences and Department of Computational & Systems Biology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Zheng Guo
- Department of Systems Biology, College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China.,Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Department of Bioinformatics, Fujian Medical University, Fuzhou, China
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12
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Cunningham CE, MacAuley MJ, Yadav G, Vizeacoumar FS, Freywald A, Vizeacoumar FJ. Targeting the CINful genome: Strategies to overcome tumor heterogeneity. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2019; 147:77-91. [PMID: 30817936 DOI: 10.1016/j.pbiomolbio.2019.02.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 02/14/2019] [Accepted: 02/17/2019] [Indexed: 01/21/2023]
Abstract
Genomic instability, and more specifically chromosomal instability (CIN), arises from a number of processes that are defective in cancer, such as aberrant mitotic cell division, replication stress, defective DNA damage repair, and ineffective telomere maintenance. CIN is an emerging hallmark of cancer that contributes to tumor heterogeneity through increased rates of genetic alterations. As genetic heterogeneity within a single tumor and between tumors is a key challenge leading to treatment failures, this brings to question, whether therapeutic approaches should aim at the genetic diversity or a specific mutation present within these tumors. Answering this question will determine the future of personalized targeted therapies. Here we discuss, how the genetic diversity associated with CIN in tumor cells can be used as a therapeutic advantage and targeted by exploiting the genetic concepts of synthetic lethality and synthetic dosage lethality. Given that a number of CIN-related pathways work together to fix the DNA damage within our genome and ensure proper segregation of chromosomes, we specifically focus on the genetic interactions amongst these pathways and their potential therapeutic applicability in cancer. We also discuss, how tumor genetic heterogeneity can be targeted in emerging immunotherapeutic approaches.
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Affiliation(s)
- Chelsea E Cunningham
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Mackenzie J MacAuley
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Garima Yadav
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Frederick S Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada
| | - Andrew Freywald
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada.
| | - Franco J Vizeacoumar
- Department of Pathology, Cancer Cluster, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5 Canada; Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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13
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Parameswaran S, Kundapur D, Vizeacoumar FS, Freywald A, Uppalapati M, Vizeacoumar FJ. A Road Map to Personalizing Targeted Cancer Therapies Using Synthetic Lethality. Trends Cancer 2018; 5:11-29. [PMID: 30616753 DOI: 10.1016/j.trecan.2018.11.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 10/28/2018] [Accepted: 11/08/2018] [Indexed: 12/12/2022]
Abstract
Targeted therapies rely on the genetic and epigenetic status of the tumor cells and are seen as the most promising approach to treat cancer today. However, current targeted therapies focus on directly inhibiting those molecules that are altered in tumor cells. Unfortunately, targeting these molecules, even with specific inhibitors, is challenging as tumor cells rewire their genetic circuitry to eliminate genetic dependency on these targets. Here, we describe how synthetic lethality approaches can be used to identify genetic dependencies and develop personalized targeted therapies. We also discuss strategies to specifically target these genetic dependencies, using small molecule and biologic drugs.
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Affiliation(s)
- Sreejit Parameswaran
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada; These authors contributed equally
| | - Deeksha Kundapur
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada; These authors contributed equally
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada.
| | - Maruti Uppalapati
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada.
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Saskatoon, S7N 5E5, Canada; Cancer Research, Saskatchewan Cancer Agency, 107 Wiggins Road, Saskatoon, S7N 5E5, Canada.
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14
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Synthetic lethal combinations of low-toxicity drugs for breast cancer identified in silico by genetic screens in yeast. Oncotarget 2018; 9:36379-36391. [PMID: 30555636 PMCID: PMC6284748 DOI: 10.18632/oncotarget.26372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 10/21/2018] [Indexed: 12/20/2022] Open
Abstract
In recent years, the concept of synthetic lethality, describing a cellular state where loss of two genes leads to a non-viable phenotype while loss of one gene can be compensated, has emerged as a novel strategy for cancer therapy. Various compounds targeting synthetic lethal pathways are either under clinical investigation or are already routinely used in multiple cancer entities such as breast cancer. Most of them target the well-described synthetic lethal interplay between PARP1 and BRCA1/2. In our study, we investigated, using an in silico methodological approach, clinically utilized drug combinations for breast cancer treatment, by correlating their known molecular targets with known homologous interaction partners that cause synthetic lethality in yeast. Further, by creating a machine-learning algorithm, we were able to suggest novel synthetic lethal drug combinations of low-toxicity drugs in breast cancer and showed their negative effects on cancer cell viability in vitro. Our findings foster the understanding of evolutionarily conserved synthetic lethality in breast cancer cells and might lead to new drug combinations with favorable toxicity profile in this entity.
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15
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Tang YC, Ho SC, Tan E, Ng AWT, McPherson JR, Goh GYL, Teh BT, Bard F, Rozen SG. Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer. Breast Cancer Res 2018; 20:22. [PMID: 29566768 PMCID: PMC5863852 DOI: 10.1186/s13058-018-0949-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 03/02/2018] [Indexed: 12/29/2022] Open
Abstract
Background Phosphatase and tensin homolog (PTEN) is one of the most frequently inactivated tumor suppressors in breast cancer. While PTEN itself is not considered a druggable target, PTEN synthetic-sick or synthetic-lethal (PTEN-SSL) genes are potential drug targets in PTEN-deficient breast cancers. Therefore, with the aim of identifying potential targets for precision breast cancer therapy, we sought to discover PTEN-SSL genes present in a broad spectrum of breast cancers. Methods To discover broad-spectrum PTEN-SSL genes in breast cancer, we used a multi-step approach that started with (1) a genome-wide short interfering RNA (siRNA) screen of ~ 21,000 genes in a pair of isogenic human mammary epithelial cell lines, followed by (2) a short hairpin RNA (shRNA) screen of ~ 1200 genes focused on hits from the first screen in a panel of 11 breast cancer cell lines; we then determined reproducibility of hits by (3) identification of overlaps between our results and reanalyzed data from 3 independent gene-essentiality screens, and finally, for selected candidate PTEN-SSL genes we (4) confirmed PTEN-SSL activity using either drug sensitivity experiments in a panel of 19 cell lines or mutual exclusivity analysis of publicly available pan-cancer somatic mutation data. Results The screens (steps 1 and 2) and the reproducibility analysis (step 3) identified six candidate broad-spectrum PTEN-SSL genes (PIK3CB, ADAMTS20, AP1M2, HMMR, STK11, and NUAK1). PIK3CB was previously identified as PTEN-SSL, while the other five genes represent novel PTEN-SSL candidates. Confirmation studies (step 4) provided additional evidence that NUAK1 and STK11 have PTEN-SSL patterns of activity. Consistent with PTEN-SSL status, inhibition of the NUAK1 protein kinase by the small molecule drug HTH-01-015 selectively impaired viability in multiple PTEN-deficient breast cancer cell lines, while mutations affecting STK11 and PTEN were largely mutually exclusive across large pan-cancer data sets. Conclusions Six genes showed PTEN-SSL patterns of activity in a large proportion of PTEN-deficient breast cancer cell lines and are potential specific vulnerabilities in PTEN-deficient breast cancer. Furthermore, the NUAK1 PTEN-SSL vulnerability identified by RNA interference techniques can be recapitulated and exploited using the small molecule kinase inhibitor HTH-01-015. Thus, NUAK1 inhibition may be an effective strategy for precision treatment of PTEN-deficient breast tumors. Electronic supplementary material The online version of this article (10.1186/s13058-018-0949-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yew Chung Tang
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Szu-Chi Ho
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Elisabeth Tan
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Alvin Wei Tian Ng
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,NUS Graduate School for Integrative Sciences and Engineering, National University of Singapore, 5 Lower Kent Ridge Road, Singapore, 119074, Singapore
| | - John R McPherson
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Germaine Yen Lin Goh
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Bin Tean Teh
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.,Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore.,National Cancer Centre Singapore, 11 Hospital Drive, Singapore, 169610, Singapore
| | - Frederic Bard
- Institute of Molecular and Cell Biology, 61 Biopolis Drive, Singapore, 138673, Singapore
| | - Steven G Rozen
- Programme in Cancer and Stem Cell Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore. .,Centre for Computational Biology, Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore.
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16
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Paul JM, Toosi B, Vizeacoumar FS, Bhanumathy KK, Li Y, Gerger C, El Zawily A, Freywald T, Anderson DH, Mousseau D, Kanthan R, Zhang Z, Vizeacoumar FJ, Freywald A. Targeting synthetic lethality between the SRC kinase and the EPHB6 receptor may benefit cancer treatment. Oncotarget 2018; 7:50027-50042. [PMID: 27418135 PMCID: PMC5226566 DOI: 10.18632/oncotarget.10569] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022] Open
Abstract
Application of tumor genome sequencing has identified numerous loss-of-function alterations in cancer cells. While these alterations are difficult to target using direct interventions, they may be attacked with the help of the synthetic lethality (SL) approach. In this approach, inhibition of one gene causes lethality only when another gene is also completely or partially inactivated. The EPHB6 receptor tyrosine kinase has been shown to have anti-malignant properties and to be downregulated in multiple cancers, which makes it a very attractive target for SL applications. In our work, we used a genome-wide SL screen combined with expression and interaction network analyses, and identified the SRC kinase as a SL partner of EPHB6 in triple-negative breast cancer (TNBC) cells. Our experiments also reveal that this SL interaction can be targeted by small molecule SRC inhibitors, SU6656 and KX2-391, and can be used to improve elimination of human TNBC tumors in a xenograft model. Our observations are of potential practical importance, since TNBC is an aggressive heterogeneous malignancy with a very high rate of patient mortality due to the lack of targeted therapies, and our work indicates that FDA-approved SRC inhibitors may potentially be used in a personalized manner for treating patients with EPHB6-deficient TNBC. Our findings are also of a general interest, as EPHB6 is downregulated in multiple malignancies and our data serve as a proof of principle that EPHB6 deficiency may be targeted by small molecule inhibitors in the SL approach.
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Affiliation(s)
- James M Paul
- Department of Biochemistry, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Behzad Toosi
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Frederick S Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Kalpana Kalyanasundaram Bhanumathy
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Yue Li
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada.,Present address: Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Courtney Gerger
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Amr El Zawily
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada.,Faculty of Science, Damanhour University, Damanhour, 22516, Egypt
| | - Tanya Freywald
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, S7N 5E5, Canada
| | - Deborah H Anderson
- Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, S7N 5E5, Canada
| | - Darrell Mousseau
- Cell Signaling Laboratory, Neuroscience Cluster, University of Saskatchewan, Saskatoon, SK, S7N 5E5, Canada
| | - Rani Kanthan
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
| | - Zhaolei Zhang
- Department of Computer Science, University of Toronto, Toronto, ON, M5S 3G4, Canada.,The Donnelly Centre, University of Toronto, Toronto, ON, M5S 3E1, Canada
| | - Franco J Vizeacoumar
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada.,Cancer Research, Saskatchewan Cancer Agency, Saskatoon, SK, S7N 5E5, Canada
| | - Andrew Freywald
- Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Royal University Hospital, Saskatoon, SK, S7N 0W8, Canada
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17
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Thompson LL, Jeusset LMP, Lepage CC, McManus KJ. Evolving Therapeutic Strategies to Exploit Chromosome Instability in Cancer. Cancers (Basel) 2017; 9:cancers9110151. [PMID: 29104272 PMCID: PMC5704169 DOI: 10.3390/cancers9110151] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2017] [Revised: 10/27/2017] [Accepted: 10/31/2017] [Indexed: 12/12/2022] Open
Abstract
Cancer is a devastating disease that claims over 8 million lives each year. Understanding the molecular etiology of the disease is critical to identify and develop new therapeutic strategies and targets. Chromosome instability (CIN) is an abnormal phenotype, characterized by progressive numerical and/or structural chromosomal changes, which is observed in virtually all cancer types. CIN generates intratumoral heterogeneity, drives cancer development, and promotes metastatic progression, and thus, it is associated with highly aggressive, drug-resistant tumors and poor patient prognosis. As CIN is observed in both primary and metastatic lesions, innovative strategies that exploit CIN may offer therapeutic benefits and better outcomes for cancer patients. Unfortunately, exploiting CIN remains a significant challenge, as the aberrant mechanisms driving CIN and their causative roles in cancer have yet to be fully elucidated. The development and utilization of CIN-exploiting therapies is further complicated by the associated risks for off-target effects and secondary cancers. Accordingly, this review will assess the strengths and limitations of current CIN-exploiting therapies, and discuss emerging strategies designed to overcome these challenges to improve outcomes and survival for patients diagnosed with cancer.
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Affiliation(s)
- Laura L Thompson
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Lucile M-P Jeusset
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Chloe C Lepage
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada.
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18
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Wang S, Peng J. Network-assisted target identification for haploinsufficiency and homozygous profiling screens. PLoS Comput Biol 2017; 13:e1005553. [PMID: 28574983 PMCID: PMC5482495 DOI: 10.1371/journal.pcbi.1005553] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 06/23/2017] [Accepted: 05/05/2017] [Indexed: 12/20/2022] Open
Abstract
Chemical genomic screens have recently emerged as a systematic approach to drug discovery on a genome-wide scale. Drug target identification and elucidation of the mechanism of action (MoA) of hits from these noisy high-throughput screens remain difficult. Here, we present GIT (Genetic Interaction Network-Assisted Target Identification), a network analysis method for drug target identification in haploinsufficiency profiling (HIP) and homozygous profiling (HOP) screens. With the drug-induced phenotypic fitness defect of the deletion of a gene, GIT also incorporates the fitness defects of the gene's neighbors in the genetic interaction network. On three genome-scale yeast chemical genomic screens, GIT substantially outperforms previous scoring methods on target identification on HIP and HOP assays, respectively. Finally, we showed that by combining HIP and HOP assays, GIT further boosts target identification and reveals potential drug's mechanism of action.
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Affiliation(s)
- Sheng Wang
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
| | - Jian Peng
- Department of Computer Science, University of Illinois at Urbana-Champaign, Urbana, Illinois, United States of America
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19
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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] [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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20
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Mammalian SWI/SNF complexes in cancer: emerging therapeutic opportunities. Curr Opin Genet Dev 2017; 42:56-67. [PMID: 28391084 DOI: 10.1016/j.gde.2017.02.004] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/23/2017] [Accepted: 02/07/2017] [Indexed: 02/08/2023]
Abstract
Mammalian SWI/SNF (BAF) chromatin remodeling complexes orchestrate a diverse set of chromatin alterations which impact transcriptional output. Recent whole-exome sequencing efforts have revealed that the genes encoding subunits of mSWI/SNF complexes are mutated in over 20% of cancers, spanning a wide range of tissue types. The majority of mutations result in loss of subunit protein expression, implicating mSWI/SNF subunits as tumor suppressors. mSWI/SNF-deficient cancers remain a therapeutic challenge, owing to a lack of potent and selective agents which target complexes or unique pathway dependencies generated by mSWI/SNF subunit perturbations. Here, we review the current landscape of mechanistic insights and emerging therapeutic opportunities for human malignancies driven by mSWI/SNF complex perturbation.
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21
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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] [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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22
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Jackson RA, Chen ES. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs. Pharmacol Ther 2016; 162:69-85. [DOI: 10.1016/j.pharmthera.2016.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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23
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Jiang C, Starr S, Chen F, Wu J. Low-fidelity alternative DNA repair carcinogenesis theory may interpret many cancer features and anticancer strategies. Future Oncol 2016; 12:1897-910. [PMID: 27166654 DOI: 10.2217/fon-2016-0066] [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: 11/21/2022] Open
Abstract
We have proposed that the low-fidelity compensatory backup alternative DNA repair pathways drive multistep carcinogenesis. Here, we apply it to interpret the clinical features of cancer, such as mutator phenotype, tissue specificity, age specificity, diverse types of cancers originated from the same type of tissue, cancer susceptibility of patients with DNA repair-defective syndromes, development of cancer only for a selected number of individuals among those that share the same genetic defect, invasion and metastasis. Clinically, the theory predicts that to improve the efficacy of molecular targeted or synthetic lethal therapy, it may be crucial to inhibit the low-fidelity compensatory alternative DNA repair either directly or by blocking the signal transducers of the sustained microenvironmental stress.
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Affiliation(s)
- Chuo Jiang
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China.,Central Laboratories, Xuhui Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences, 966 Middle Huaihai Road, Shanghai 200031, China
| | - Shane Starr
- Department of Pathology & Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, USA and currently Flint Medical Laboratory, 3490 Calkins Road, Flint, MI 48532, USA
| | - Fuxue Chen
- School of Life Sciences, Shanghai University, 99 Shangda Road, Shanghai 200444, China
| | - Jiaxi Wu
- Central Laboratories, Xuhui Central Hospital, Shanghai Clinical Center, Chinese Academy of Sciences, 966 Middle Huaihai Road, Shanghai 200031, China.,Department of Pathology & Laboratory Medicine, Brody School of Medicine, East Carolina University, 600 Moye Boulevard, Greenville, North Carolina 27834, USA and currently Flint Medical Laboratory, 3490 Calkins Road, Flint, MI 48532, USA
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24
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Calzone L, Barillot E, Zinovyev A. Predicting genetic interactions from Boolean models of biological networks. Integr Biol (Camb) 2015; 7:921-9. [PMID: 25958956 DOI: 10.1039/c5ib00029g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Genetic interaction can be defined as a deviation of the phenotypic quantitative effect of a double gene mutation from the effect predicted from single mutations using a simple (e.g., multiplicative or linear additive) statistical model. Experimentally characterized genetic interaction networks in model organisms provide important insights into relationships between different biological functions. We describe a computational methodology allowing us to systematically and quantitatively characterize a Boolean mathematical model of a biological network in terms of genetic interactions between all loss of function and gain of function mutations with respect to all model phenotypes or outputs. We use the probabilistic framework defined in MaBoSS software, based on continuous time Markov chains and stochastic simulations. In addition, we suggest several computational tools for studying the distribution of double mutants in the space of model phenotype probabilities. We demonstrate this methodology on three published models for each of which we derive the genetic interaction networks and analyze their properties. We classify the obtained interactions according to their class of epistasis, dependence on the chosen initial conditions and the phenotype. The use of this methodology for validating mathematical models from experimental data and designing new experiments is discussed.
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25
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Doherty R, Madhusudan S. DNA Repair Endonucleases: Physiological Roles and Potential as Drug Targets. ACTA ACUST UNITED AC 2015; 20:829-41. [PMID: 25877151 DOI: 10.1177/1087057115581581] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2014] [Accepted: 03/22/2015] [Indexed: 12/15/2022]
Abstract
Genomic DNA is constantly exposed to endogenous and exogenous damaging agents. To overcome these damaging effects and maintain genomic stability, cells have robust coping mechanisms in place, including repair of the damaged DNA. There are a number of DNA repair pathways available to cells dependent on the type of damage induced. The removal of damaged DNA is essential to allow successful repair. Removal of DNA strands is achieved by nucleases. Exonucleases are those that progressively cut from DNA ends, and endonucleases make single incisions within strands of DNA. This review focuses on the group of endonucleases involved in DNA repair pathways, their mechanistic functions, roles in cancer development, and how targeting these enzymes is proving to be an exciting new strategy for personalized therapy in cancer.
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Affiliation(s)
- Rachel Doherty
- Laboratory of Molecular Oncology, Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, UK
| | - Srinivasan Madhusudan
- Laboratory of Molecular Oncology, Academic Unit of Oncology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham University Hospitals, Nottingham, UK
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26
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Pearl LH, Schierz AC, Ward SE, Al-Lazikani B, Pearl FMG. Therapeutic opportunities within the DNA damage response. Nat Rev Cancer 2015; 15:166-80. [PMID: 25709118 DOI: 10.1038/nrc3891] [Citation(s) in RCA: 384] [Impact Index Per Article: 42.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The DNA damage response (DDR) is essential for maintaining the genomic integrity of the cell, and its disruption is one of the hallmarks of cancer. Classically, defects in the DDR have been exploited therapeutically in the treatment of cancer with radiation therapies or genotoxic chemotherapies. More recently, protein components of the DDR systems have been identified as promising avenues for targeted cancer therapeutics. Here, we present an in-depth analysis of the function, role in cancer and therapeutic potential of 450 expert-curated human DDR genes. We discuss the DDR drugs that have been approved by the US Food and Drug Administration (FDA) or that are under clinical investigation. We examine large-scale genomic and expression data for 15 cancers to identify deregulated components of the DDR, and we apply systematic computational analysis to identify DDR proteins that are amenable to modulation by small molecules, highlighting potential novel therapeutic targets.
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Affiliation(s)
- Laurence H Pearl
- Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9RQ, UK
| | - Amanda C Schierz
- 1] Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK. [2] Bluefool Innovations, 4 May Close, Sandhurst, Berkshire GU47 0UG, UK
| | - Simon E Ward
- Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
| | - Bissan Al-Lazikani
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK
| | - Frances M G Pearl
- 1] Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London SM2 5NG, UK. [2] Translational Drug Discovery Group, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, UK
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