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Murchan P, Baird AM, Ó Broin P, Sheils O, Finn SP. Surrogate Biomarker Prediction from Whole-Slide Images for Evaluating Overall Survival in Lung Adenocarcinoma. Diagnostics (Basel) 2024; 14:462. [PMID: 38472935 DOI: 10.3390/diagnostics14050462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 02/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Recent advances in computational pathology have shown potential in predicting biomarkers from haematoxylin and eosin (H&E) whole-slide images (WSI). However, predicting the outcome directly from WSIs remains a substantial challenge. In this study, we aimed to investigate how gene expression, predicted from WSIs, could be used to evaluate overall survival (OS) in patients with lung adenocarcinoma (LUAD). METHODS Differentially expressed genes (DEGs) were identified from The Cancer Genome Atlas (TCGA)-LUAD cohort. Cox regression analysis was performed on DEGs to identify the gene prognostics of OS. Attention-based multiple instance learning (AMIL) models were trained to predict the expression of identified prognostic genes from WSIs using the TCGA-LUAD dataset. Models were externally validated in the Clinical Proteomic Tumour Analysis Consortium (CPTAC)-LUAD dataset. The prognostic value of predicted gene expression values was then compared to the true gene expression measurements. RESULTS The expression of 239 prognostic genes could be predicted in TCGA-LUAD with cross-validated Pearson's R > 0.4. Predicted gene expression demonstrated prognostic performance, attaining a cross-validated concordance index of up to 0.615 in TCGA-LUAD through Cox regression. In total, 36 genes had predicted expression in the external validation cohort that was prognostic of OS. CONCLUSIONS Gene expression predicted from WSIs is an effective method of evaluating OS in patients with LUAD. These results may open up new avenues of cost- and time-efficient prognosis assessment in LUAD treatment.
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Affiliation(s)
- Pierre Murchan
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, H91 CF50 Galway, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
| | - Anne-Marie Baird
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
- School of Medicine, Trinity Translational Medicine Institute, Trinity College Dublin, D02 A440 Dublin, Ireland
| | - Pilib Ó Broin
- School of Mathematical & Statistical Sciences, University of Galway, H91 TK33 Galway, Ireland
| | - Orla Sheils
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
| | - Stephen P Finn
- Department of Histopathology and Morbid Anatomy, Trinity Translational Medicine Institute, Trinity College Dublin, D08 W9RT Dublin, Ireland
- Trinity St. James's Cancer Institute (TSJCI), St. James's Hospital, D08 RX0X Dublin, Ireland
- Department of Histopathology, St. James's Hospital, James's Street, D08 X4RX Dublin, Ireland
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2
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Campos Gudiño R, Rutherford KA, McManus KJ. Evaluating Chromosome Instability and Genotoxicity Through Single Cell Quantitative Imaging Microscopy. Methods Mol Biol 2024; 2825:309-331. [PMID: 38913318 DOI: 10.1007/978-1-0716-3946-7_18] [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: 06/25/2024]
Abstract
Across eukaryotes, genome stability is essential for normal cell function, physiology, and species survival. Aberrant expression of key genes or exposure to genotoxic agents can have detrimental effects on genome stability and contribute to the development of various diseases, including cancer. Chromosome instability (CIN), or ongoing changes in chromosome complements, is a frequent form of genome instability observed in cancer and is a driver of genetic and cell-to-cell heterogeneity that can be rapidly detected and quantitatively assessed using surrogate markers of CIN. For example, single cell quantitative imaging microscopy (QuantIM) can be used to simultaneously identify changes in nuclear areas and micronucleus formation. While changes in nuclear areas are often associated with large-scale changes in chromosome complements (i.e., ploidy), micronuclei are small extra-nuclear bodies found outside the primary nucleus that have previously been employed as a measure of genotoxicity of test compounds. Here, we present a facile QuantIM approach that allows for the rapid assessment and quantification of CIN associated phenotypes and genotoxicity. First, we provide protocols to optimize and execute CIN and genotoxicity assays. Secondly, we present the critical imaging settings, optimization steps, downstream statistical analyses, and data visualization strategies employed to obtain high quality and robust data. These approaches can be easily applied to assess the prevalence of CIN associated phenotypes and genotoxic stress for a myriad of experimental and clinical contexts ranging from direct tests to large-scale screens of various genetic contexts (i.e., aberrant gene expression) or chemical compounds. In summary, this QuantIM approach facilitates the identification of novel CIN genes and/or genotoxic agents that will provide greater insight into the aberrant genes and pathways underlying CIN and genotoxicity.
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Affiliation(s)
- Rubi Campos Gudiño
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kailee A Rutherford
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada
- Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kirk J McManus
- Paul Albrechtsen Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.
- Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada.
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3
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Goncharov NV, Kovalskaia VA, Romanishin AO, Shved NA, Belousov AS, Tiasto VS, Gulaia VS, Neergheen VS, Rummun N, Liskovykh M, Larionov V, Kouprina N, Kumeiko VV. Novel assay to measure chromosome instability identifies Punica granatum extract that elevates CIN and has a potential for tumor- suppressing therapies. Front Bioeng Biotechnol 2022; 10:989932. [PMID: 36601386 PMCID: PMC9806258 DOI: 10.3389/fbioe.2022.989932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Accepted: 11/22/2022] [Indexed: 12/23/2022] Open
Abstract
Human artificial chromosomes (HACs) have provided a useful tool to study kinetochore structure and function, gene delivery, and gene expression. The HAC propagates and segregates properly in the cells. Recently, we have developed an experimental high-throughput imaging (HTI) HAC-based assay that allows the identification of genes whose depletion leads to chromosome instability (CIN). The HAC carries a GFP transgene that facilitates quantitative measurement of CIN. The loss of HAC/GFP may be measured by flow cytometry or fluorescence scanning microscope. Therefore, CIN rate can be measured by counting the proportion of fluorescent cells. Here, the HAC/GFP-based assay has been adapted to screen anticancer compounds for possible induction or elevation of CIN. We analyzed 24 cytotoxic plant extracts. Punica granatum leaf extract (PLE) indeed sharply increases CIN rate in HT1080 fibrosarcoma cells. PLE treatment leads to cell cycle arrest, reduction of mitotic index, and the increased numbers of micronuclei (MNi) and nucleoplasmic bridges (NPBs). PLE-mediated increased CIN correlates with the induction of double-stranded breaks (DSBs). We infer that the PLE extract contains a component(s) that elevate CIN, making it a candidate for further study as a potential cancer treatment. The data also provide a proof of principle for the utility of the HAC/GFP-based system in screening for natural products and other compounds that elevate CIN in cancer cells.
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Affiliation(s)
- Nikolay V. Goncharov
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, Russia,Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia,*Correspondence: Nikolay V. Goncharov, ; Vadim V. Kumeiko,
| | | | | | - Nikita A. Shved
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, Russia,Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Andrei S. Belousov
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vladlena S. Tiasto
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Valeriia S. Gulaia
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia
| | - Vidushi S. Neergheen
- Biopharmaceutical Unit, Centre for Biomedical and Biomaterials Research (CBBR), University of Mauritius, Réduit, Mauritius
| | - Nawraj Rummun
- Biopharmaceutical Unit, Centre for Biomedical and Biomaterials Research (CBBR), University of Mauritius, Réduit, Mauritius
| | - Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, United States
| | - Vadim V. Kumeiko
- A.V. Zhirmunsky National Scientific Center of Marine Biology, Russian Academy of Sciences, Vladivostok, Russia,Institute of Life Sciences and Biomedicine, Far Eastern Federal University, Vladivostok, Russia,*Correspondence: Nikolay V. Goncharov, ; Vadim V. Kumeiko,
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Neudorf NM, Thompson LL, Lichtensztejn Z, Razi T, McManus KJ. Reduced SKP2 Expression Adversely Impacts Genome Stability and Promotes Cellular Transformation in Colonic Epithelial Cells. Cells 2022; 11:cells11233731. [PMID: 36496990 PMCID: PMC9738323 DOI: 10.3390/cells11233731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/17/2022] [Accepted: 11/19/2022] [Indexed: 11/24/2022] Open
Abstract
Despite the high morbidity and mortality rates associated with colorectal cancer (CRC), the underlying molecular mechanisms driving CRC development remain largely uncharacterized. Chromosome instability (CIN), or ongoing changes in chromosome complements, occurs in ~85% of CRCs and is a proposed driver of cancer development, as the genomic changes imparted by CIN enable the acquisition of karyotypes that are favorable for cellular transformation and the classic hallmarks of cancer. Despite these associations, the aberrant genes and proteins driving CIN remain elusive. SKP2 encodes an F-box protein, a variable subunit of the SKP1-CUL1-F-box (SCF) complex that selectively targets proteins for polyubiquitylation and degradation. Recent data have identified the core SCF complex components (SKP1, CUL1, and RBX1) as CIN genes; however, the impact reduced SKP2 expression has on CIN, cellular transformation, and oncogenesis remains unknown. Using both short- small interfering RNA (siRNA) and long-term (CRISPR/Cas9) approaches, we demonstrate that diminished SKP2 expression induces CIN in both malignant and non-malignant colonic epithelial cell contexts. Moreover, temporal assays reveal that reduced SKP2 expression promotes cellular transformation, as demonstrated by enhanced anchorage-independent growth. Collectively, these data identify SKP2 as a novel CIN gene in clinically relevant models and highlight its potential pathogenic role in CRC development.
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Affiliation(s)
- Nicole M. Neudorf
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Laura L. Thompson
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Zelda Lichtensztejn
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Tooba Razi
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Kirk J. McManus
- CancerCare Manitoba Research Institute, Winnipeg, MB R3E 0V9, Canada
- Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0V9, Canada
- Correspondence: ; Tel.: +1-204-787-2833
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Rasool R, Ullah I, Mubeen B, Alshehri S, Imam SS, Ghoneim MM, Alzarea SI, Al-Abbasi FA, Murtaza BN, Kazmi I, Nadeem MS. Theranostic Interpolation of Genomic Instability in Breast Cancer. Int J Mol Sci 2022; 23:ijms23031861. [PMID: 35163783 PMCID: PMC8836911 DOI: 10.3390/ijms23031861] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/26/2022] [Accepted: 01/27/2022] [Indexed: 12/14/2022] Open
Abstract
Breast cancer is a diverse disease caused by mutations in multiple genes accompanying epigenetic aberrations of hazardous genes and protein pathways, which distress tumor-suppressor genes and the expression of oncogenes. Alteration in any of the several physiological mechanisms such as cell cycle checkpoints, DNA repair machinery, mitotic checkpoints, and telomere maintenance results in genomic instability. Theranostic has the potential to foretell and estimate therapy response, contributing a valuable opportunity to modify the ongoing treatments and has developed new treatment strategies in a personalized manner. “Omics” technologies play a key role while studying genomic instability in breast cancer, and broadly include various aspects of proteomics, genomics, metabolomics, and tumor grading. Certain computational techniques have been designed to facilitate the early diagnosis of cancer and predict disease-specific therapies, which can produce many effective results. Several diverse tools are used to investigate genomic instability and underlying mechanisms. The current review aimed to explore the genomic landscape, tumor heterogeneity, and possible mechanisms of genomic instability involved in initiating breast cancer. We also discuss the implications of computational biology regarding mutational and pathway analyses, identification of prognostic markers, and the development of strategies for precision medicine. We also review different technologies required for the investigation of genomic instability in breast cancer cells, including recent therapeutic and preventive advances in breast cancer.
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Affiliation(s)
- Rabia Rasool
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (R.R.); (I.U.); (B.M.)
| | - Inam Ullah
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (R.R.); (I.U.); (B.M.)
| | - Bismillah Mubeen
- Institute of Molecular Biology and Biotechnology, The University of Lahore, Lahore 54000, Pakistan; (R.R.); (I.U.); (B.M.)
| | - Sultan Alshehri
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Syed Sarim Imam
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia; (S.A.); (S.S.I.)
| | - Mohammed M. Ghoneim
- Department of Pharmacy Practice, College of Pharmacy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia;
| | - Sami I. Alzarea
- Department of Pharmacology, College of Pharmacy, Jouf University, Sakaka 72341, Saudi Arabia;
| | - Fahad A. Al-Abbasi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
| | - Bibi Nazia Murtaza
- Department of Zoology, Abbottabad University of Science and Technology (AUST), Abbottabad 22310, Pakistan;
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (I.K.); (M.S.N.)
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia;
- Correspondence: (I.K.); (M.S.N.)
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6
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Campos Gudiño R, Farrell AC, Neudorf NM, McManus KJ. A Comprehensive Assessment of Genetic and Epigenetic Alterations Identifies Frequent Variations Impacting Six Prototypic SCF Complex Members. Int J Mol Sci 2021; 23:ijms23010084. [PMID: 35008511 PMCID: PMC8744973 DOI: 10.3390/ijms23010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/14/2021] [Accepted: 12/20/2021] [Indexed: 11/24/2022] Open
Abstract
The SKP1, CUL1, F-box protein (SCF) complex represents a family of 69 E3 ubiquitin ligases that poly-ubiquitinate protein substrates marking them for proteolytic degradation via the 26S proteasome. Established SCF complex targets include transcription factors, oncoproteins and tumor suppressors that modulate cell cycle activity and mitotic fidelity. Accordingly, genetic and epigenetic alterations involving SCF complex member genes are expected to adversely impact target regulation and contribute to disease etiology. To gain novel insight into cancer pathogenesis, we determined the prevalence of genetic and epigenetic alterations in six prototypic SCF complex member genes (SKP1, CUL1, RBX1, SKP2, FBXW7 and FBXO5) from patient datasets extracted from The Cancer Genome Atlas (TCGA). Collectively, ~45% of observed SCF complex member mutations are predicted to impact complex structure and/or function in 10 solid tumor types. In addition, the distribution of encoded alterations suggest SCF complex members may exhibit either tumor suppressor or oncogenic mutational profiles in a cancer type dependent manner. Further bioinformatic analyses reveal the potential functional implications of encoded alterations arising from missense mutations by examining predicted deleterious mutations with available crystal structures. The SCF complex also exhibits frequent copy number alterations in a variety of cancer types that generally correspond with mRNA expression levels. Finally, we note that SCF complex member genes are differentially methylated across cancer types, which may effectively phenocopy gene copy number alterations. Collectively, these data show that SCF complex member genes are frequently altered at the genetic and epigenetic levels in many cancer types, which will adversely impact the normal targeting and timely destruction of protein substrates, which may contribute to the development and progression of an extensive array of cancer types.
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Affiliation(s)
- Rubi Campos Gudiño
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (R.C.G.); (A.C.F.); (N.M.N.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Ally C. Farrell
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (R.C.G.); (A.C.F.); (N.M.N.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Nicole M. Neudorf
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada; (R.C.G.); (A.C.F.); (N.M.N.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
| | - Kirk J. McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-787-2833
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7
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Palmer MCL, Neudorf NM, Farrell AC, Razi T, Lichtensztejn Z, McManus KJ. The F-box protein, FBXO7 is required to maintain chromosome stability in humans. Hum Mol Genet 2021; 31:1471-1486. [PMID: 34791250 PMCID: PMC9071473 DOI: 10.1093/hmg/ddab330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/06/2021] [Accepted: 11/08/2021] [Indexed: 11/19/2022] Open
Abstract
Despite the high morbidity and mortality rates associated with colorectal cancer (CRC), the aberrant genes and mechanisms driving CRC pathogenesis remain poorly understood. Chromosome instability (CIN), or ongoing changes in chromosome numbers, is a predominant form of genome instability associated with ~85% of CRCs, suggesting it may be a key mechanism driving CRC oncogenesis. CIN enables the acquisition of copy number alterations conferring selective growth, proliferation and survival advantages that promote cellular transformation. Despite these associations, the aberrant genes underlying CIN remain largely unknown. Candidate CIN gene FBXO7 encodes an F-box protein, a subunit of the SKP1-CUL1-FBOX (SCF) complex that confers substrate specificity to the complex and targets proteins for subsequent degradation by the 26S proteasome. Recently, the genes encoding the three core SCF complex members were identified as CIN genes; however, it is unknown whether F-box proteins exhibit similar integral roles in maintaining chromosome stability. Using short- small interfering RNA (siRNA) and long- (CRISPR/Cas9) term approaches, we show that reduced FBXO7 expression induces CIN in various colonic epithelial cell contexts, whereas FBXO7 knockout clones also exhibit hallmarks associated with cellular transformation, namely increased clonogenic and anchorage-independent growth. Collectively, these data demonstrate that FBXO7 is required to maintain genome stability identifying FBXO7 a novel CIN gene whose reduced expression may contribute to CRC development and progression.
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Affiliation(s)
- Michaela C L Palmer
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Nicole M Neudorf
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Ally C Farrell
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Tooba Razi
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Zelda Lichtensztejn
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
| | - Kirk J McManus
- CancerCare Manitoba Research Institute, CancerCare Manitoba, Winnipeg, MB, Canada.,Department of Biochemistry & Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB, Canada
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8
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Xu Z, Verma A, Naveed U, Bakhoum SF, Khosravi P, Elemento O. Deep learning predicts chromosomal instability from histopathology images. iScience 2021; 24:102394. [PMID: 33997679 PMCID: PMC8099498 DOI: 10.1016/j.isci.2021.102394] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 03/03/2021] [Accepted: 04/01/2021] [Indexed: 12/13/2022] Open
Abstract
Chromosomal instability (CIN) is a hallmark of human cancer yet not readily testable for patients with cancer in routine clinical setting. In this study, we sought to explore whether CIN status can be predicted using ubiquitously available hematoxylin and eosin histology through a deep learning-based model. When applied to a cohort of 1,010 patients with breast cancer (Training set: n = 858, Test set: n = 152) from The Cancer Genome Atlas where 485 patients have high CIN status, our model accurately classified CIN status, achieving an area under the curve of 0.822 with 81.2% sensitivity and 68.7% specificity in the test set. Patch-level predictions of CIN status suggested intra-tumor heterogeneity within slides. Moreover, presence of patches with high predicted CIN score within an entire slide was more predictive of clinical outcome than the average CIN score of the slide, thus underscoring the clinical importance of intra-tumor heterogeneity.
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Affiliation(s)
- Zhuoran Xu
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York 10065, USA
- Pathology and Laboratory Medicine, Weill Cornell Medicine, New York 10065, USA
| | - Akanksha Verma
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York 10065, USA
| | - Uska Naveed
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York 10065, USA
| | - Samuel F. Bakhoum
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York 10021, USA
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York 10021, USA
| | - Pegah Khosravi
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York 10065, USA
- Computational Oncology, Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York 10021, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York 10065, USA
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9
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Lepage CC, Palmer MCL, Farrell AC, Neudorf NM, Lichtensztejn Z, Nachtigal MW, McManus KJ. Reduced SKP1 and CUL1 expression underlies increases in Cyclin E1 and chromosome instability in cellular precursors of high-grade serous ovarian cancer. Br J Cancer 2021; 124:1699-1710. [PMID: 33731859 PMCID: PMC8110794 DOI: 10.1038/s41416-021-01317-w] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 12/23/2020] [Accepted: 02/12/2021] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND High-grade serous ovarian cancer (HGSOC) is the most common and lethal ovarian cancer histotype. Chromosome instability (CIN, an increased rate of chromosome gains and losses) is believed to play a fundamental role in the development and evolution of HGSOC. Importantly, overexpression of Cyclin E1 protein induces CIN, and genomic amplification of CCNE1 contributes to HGSOC pathogenesis in ~20% of patients. Cyclin E1 levels are normally regulated in a cell cycle-dependent manner by the SCF (SKP1-CUL1-FBOX) complex, an E3 ubiquitin ligase that includes the proteins SKP1 and CUL1. Conceptually, diminished SKP1 or CUL1 expression is predicted to underlie increases in Cyclin E1 levels and induce CIN. METHODS This study employs fallopian tube secretory epithelial cell models to evaluate the impact diminished SKP1 or CUL1 expression has on Cyclin E1 and CIN in both short-term (siRNA) and long-term (CRISPR/Cas9) studies. RESULTS Single-cell quantitative imaging microscopy approaches revealed changes in CIN-associated phenotypes and chromosome numbers and increased Cyclin E1 in response to diminished SKP1 or CUL1 expression. CONCLUSIONS These data identify SKP1 and CUL1 as novel CIN genes in HGSOC precursor cells that may drive early aetiological events contributing to HGSOC development.
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Affiliation(s)
- Chloe Camille Lepage
- grid.21613.370000 0004 1936 9609Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba Canada ,grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada
| | - Michaela Cora Lynn Palmer
- grid.21613.370000 0004 1936 9609Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba Canada ,grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada
| | - Ally Catherina Farrell
- grid.21613.370000 0004 1936 9609Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba Canada ,grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada
| | - Nicole Marie Neudorf
- grid.21613.370000 0004 1936 9609Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba Canada ,grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada
| | - Zelda Lichtensztejn
- grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada
| | - Mark William Nachtigal
- grid.21613.370000 0004 1936 9609Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba Canada ,grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada ,grid.21613.370000 0004 1936 9609Department of Obstetrics, Gynecology & Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba Canada
| | - Kirk James McManus
- grid.21613.370000 0004 1936 9609Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba Canada ,grid.419404.c0000 0001 0701 0170Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba Canada
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Chromosome instability is prevalent and dynamic in high-grade serous ovarian cancer patient samples. Gynecol Oncol 2021; 161:769-778. [PMID: 33714608 DOI: 10.1016/j.ygyno.2021.02.038] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 02/27/2021] [Indexed: 12/18/2022]
Abstract
OBJECTIVE High-grade serous ovarian cancer (HGSOC) is the most lethal gynaecological malignancy in women with a high level of mortality, metastatic disease, disease recurrence and multi-drug resistance. Many previous studies have focused on characterising genome instability in recurrent resistant HGSOC and while this has advanced our understanding of HGSOC, our fundamental knowledge of the mechanisms driving genome instability remains limited. Chromosome instability (CIN; an increased rate of chromosome gains and losses) is a form of genome instability that is commonly associated with recurrence and multi-drug resistance in many cancer types but has just begun to be characterised in HGSOC. METHOD To examine the relationship between CIN and HGSOC, we employed single-cell quantitative imaging microscopy approaches capable of capturing the cell-to-cell heterogeneity associated with CIN, to assess the prevalence and dynamics of CIN within individual and patient-matched HGSOC ascites and solid tumour samples. RESULTS CIN occurs in 90.9% of ascites samples and 100% of solid tumours, while in-depth analyses identified statistically significant temporal dynamics within the serial ascites samples. In general, aneuploidy and CIN increase with disease progression and frequently decrease following chemotherapy treatments in responsive disease. Finally, our work identified higher levels of CIN in solid tumours relative to ascites samples isolated from the same individual, which identifies a novel difference existing between solid tumours and ascites samples. CONCLUSIONS Our findings provide novel insight into the relationship between CIN and HGSOC, and uncover a previously unknown relationship existing between CIN in solid tumours and metastatic disease (ascites).
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Jeusset LM, Guppy BJ, Lichtensztejn Z, McDonald D, McManus KJ. Reduced USP22 Expression Impairs Mitotic Removal of H2B Monoubiquitination, Alters Chromatin Compaction and Induces Chromosome Instability That May Promote Oncogenesis. Cancers (Basel) 2021; 13:cancers13051043. [PMID: 33801331 PMCID: PMC7958346 DOI: 10.3390/cancers13051043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2020] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 12/19/2022] Open
Abstract
Chromosome instability (CIN) is an enabling feature of oncogenesis associated with poor patient outcomes, whose genetic determinants remain largely unknown. As mitotic chromatin compaction defects can compromise the accuracy of chromosome segregation into daughter cells and drive CIN, characterizing the molecular mechanisms ensuring accurate chromatin compaction may identify novel CIN genes. In vitro, histone H2B monoubiquitination at lysine 120 (H2Bub1) impairs chromatin compaction, while in vivo H2Bub1 is rapidly depleted from chromatin upon entry into mitosis, suggesting that H2Bub1 removal may be a pre-requisite for mitotic fidelity. The deubiquitinating enzyme USP22 catalyzes H2Bub1 removal in interphase and may also be required for H2Bub1 removal in early mitosis to maintain chromosome stability. In this study, we demonstrate that siRNA-mediated USP22 depletion increases H2Bub1 levels in early mitosis and induces CIN phenotypes associated with mitotic chromatin compaction defects revealed by super-resolution microscopy. Moreover, USP22-knockout models exhibit continuously changing chromosome complements over time. These data identify mitotic removal of H2Bub1 as a critical determinant of chromatin compaction and faithful chromosome segregation. We further demonstrate that USP22 is a CIN gene, indicating that USP22 deletions, which are frequent in many tumor types, may drive genetic heterogeneity and contribute to cancer pathogenesis.
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Affiliation(s)
- Lucile M. Jeusset
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E0J9, Canada
| | - Brent J. Guppy
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E0J9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
| | - Darin McDonald
- Department of Oncology, University of Alberta, Edmonton, AB T6G2H7, Canada;
| | - Kirk J. McManus
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E0V9, Canada; (L.M.J.); (B.J.G.); (Z.L.)
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E0J9, Canada
- Correspondence: ; Tel.: +1-(204)-787-2833
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12
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RUNX3 Transcript Variants Have Distinct Roles in Ovarian Carcinoma and Differently Influence Platinum Sensitivity and Angiogenesis. Cancers (Basel) 2021; 13:cancers13030476. [PMID: 33530588 PMCID: PMC7866085 DOI: 10.3390/cancers13030476] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 01/15/2021] [Accepted: 01/21/2021] [Indexed: 12/14/2022] Open
Abstract
Simple Summary Epithelial ovarian cancer treatment is limited by missing predictive markers, frequent chemotherapy resistance and an incomplete understanding of the biology of tumors. Earlier work proved that hypermethylation of the gene RUNX3 coding for a transcription factor has prognostic value, and RUNX3 transcript variant overexpression, regulated by this epigenetic mechanism, influences cisplatin sensitivity and malignant properties of cells contrary. The present data validate RUNX3 transcript variant-specific effects for high-grade serous ovarian cancer and identify RUNX3-regulated genes and processes. Specifically, DNA damage repair and angiogenesis are influenced by RUNX3, and transcript variant 1 mediates stronger carcinogenic properties. Abstract The prognosis of late-stage epithelial ovarian cancer (EOC) patients is affected by chemotherapy response and the malignant potential of the tumor cells. In earlier work, we identified hypermethylation of the runt-related transcription factor 3 gene (RUNX3) as a prognostic biomarker and contrary functions of transcript variants (TV1 and TV2) in A2780 and SKOV3 cells. The aim of the study was to further validate these results and to increase the knowledge about RUNX3 function in EOC. New RUNX3 overexpression models of high-grade serous ovarian cancer (HGSOC) were established and analyzed for phenotypic (IC50 determination, migration, proliferation and angiogenesis assay, DNA damage analysis) and transcriptomic consequences (NGS) of RUNX3 TV1 and TV2 overexpression. Platinum sensitivity was affected by a specific transcript variant depending on BRCA background. RUNX3 TV2 induced an increased sensitivity in BRCA1wt cells (OVCAR3), whereas TV1 increased the sensitivity and induced a G2/M arrest under treatment in BRCA1mut cells (A13-2-12). These different phenotypes relate to differences in DNA repair: homologous recombination deficient A13-2-12 cells show less γH2AX foci despite higher levels of Pt-DNA adducts. RNA-Seq analyses prove transcript variant and cell-line-specific RUNX3 effects. Pathway analyses revealed another clinically important function of RUNX3—regulation of angiogenesis. This was confirmed by thrombospondin1 analyses, HUVEC spheroid sprouting assays and proteomic profiling. Importantly, conditioned media (CM) from RUNX3 TV1 overexpressing A13-2-12 cells induced an increased HUVEC sprouting. Altogether, the presented data support the hypothesis of different functions of RUNX3 transcript variants related to the clinically relevant processes—platinum resistance and angiogenesis.
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13
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Bungsy M, Palmer MCL, Jeusset LM, Neudorf NM, Lichtensztejn Z, Nachtigal MW, McManus KJ. Reduced RBX1 expression induces chromosome instability and promotes cellular transformation in high-grade serous ovarian cancer precursor cells. Cancer Lett 2020; 500:194-207. [PMID: 33290867 DOI: 10.1016/j.canlet.2020.11.051] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 11/26/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022]
Abstract
Despite high-grade serous ovarian cancer (HGSOC) being the most common and lethal gynecological cancer in women, the early etiological events driving disease development remain largely unknown. Emerging evidence now suggests that chromosome instability (CIN; ongoing changes in chromosome numbers) may play a central role in the development and progression of HGSOC. Importantly, genomic amplification of the Cyclin E1 gene (CCNE1) contributes to HGSOC pathogenesis in ~20% of patients, while Cyclin E1 overexpression induces CIN in model systems. Cyclin E1 levels are normally regulated by the SCF (SKP1-CUL1-FBOX) complex, an E3 ubiquitin ligase that includes RBX1 as a core component. Interestingly, RBX1 is heterozygously lost in ~80% of HGSOC cases and reduced expression corresponds with worse outcomes, suggesting it may be a pathogenic event. Using both short (siRNA) and long (CRISPR/Cas9) term approaches, we show that reduced RBX1 expression corresponds with significant increases in CIN phenotypes in fallopian tube secretory epithelial cells, a cellular precursor of HGSOC. Moreover, reduced RBX1 expression corresponds with increased Cyclin E1 levels and anchorage-independent growth. Collectively, these data identify RBX1 as a novel CIN gene with pathogenic implications for HGSOC.
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Affiliation(s)
- Manisha Bungsy
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Michaela C L Palmer
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Lucile M Jeusset
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Nicole M Neudorf
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Mark W Nachtigal
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Obstetrics, Gynecology & Reproductive Sciences, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J McManus
- Research Institute in Oncology & Hematology, Winnipeg, Manitoba, R3E 0V9, Canada; Department of Biochemistry and Medical Genetics, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada.
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14
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Vishwakarma R, McManus KJ. Chromosome Instability; Implications in Cancer Development, Progression, and Clinical Outcomes. Cancers (Basel) 2020; 12:cancers12040824. [PMID: 32235397 PMCID: PMC7226245 DOI: 10.3390/cancers12040824] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/15/2022] Open
Abstract
Chromosome instability (CIN) refers to an ongoing rate of chromosomal changes and is a driver of genetic, cell-to-cell heterogeneity. It is an aberrant phenotype that is intimately associated with cancer development and progression. The presence, extent, and level of CIN has tremendous implications for the clinical management and outcomes of those living with cancer. Despite its relevance in cancer, there is still extensive misuse of the term CIN, and this has adversely impacted our ability to identify and characterize the molecular determinants of CIN. Though several decades of genetic research have provided insight into CIN, the molecular determinants remain largely unknown, which severely limits its clinical potential. In this review, we provide a definition of CIN, describe the two main types, and discuss how it differs from aneuploidy. We subsequently detail its impact on cancer development and progression, and describe how it influences metastatic potential with reference to cancer prognosis and outcomes. Finally, we end with a discussion of how CIN induces genetic heterogeneity to influence the use and efficacy of several precision medicine strategies, including patient and risk stratification, as well as its impact on the acquisition of drug resistance and disease recurrence.
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Affiliation(s)
- Raghvendra Vishwakarma
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada;
| | - Kirk J. McManus
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada;
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-787-2833
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15
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Thompson LL, Baergen AK, Lichtensztejn Z, McManus KJ. Reduced SKP1 Expression Induces Chromosome Instability through Aberrant Cyclin E1 Protein Turnover. Cancers (Basel) 2020; 12:E531. [PMID: 32106628 PMCID: PMC7139525 DOI: 10.3390/cancers12030531] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Revised: 02/21/2020] [Accepted: 02/24/2020] [Indexed: 12/22/2022] Open
Abstract
Chromosome instability (CIN), or progressive changes in chromosome numbers, is an enabling feature of many cancers; however, the mechanisms giving rise to CIN remain poorly understood. To expand our mechanistic understanding of the molecular determinants of CIN in humans, we employed a cross-species approach to identify 164 human candidates to screen. Using quantitative imaging microscopy (QuantIM), we show that silencing 148 genes resulted in significant changes in CIN-associated phenotypes in two distinct cellular contexts. Ten genes were prioritized for validation based on cancer patient datasets revealing frequent gene copy number losses and associations with worse patient outcomes. QuantIM determined silencing of each gene-induced CIN, identifying novel roles for each as chromosome stability genes. SKP1 was selected for in-depth analyses as it forms part of SCF (SKP1, CUL1, FBox) complex, an E3 ubiquitin ligase that targets proteins for proteolytic degradation. Remarkably, SKP1 silencing induced increases in replication stress, DNA double strand breaks and chromothriptic events that were ascribed to aberrant increases in Cyclin E1 levels arising from reduced SKP1 expression. Collectively, these data reveal a high degree of evolutionary conservation between human and budding yeast CIN genes and further identify aberrant mechanisms associated with increases in chromothriptic events.
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Affiliation(s)
- Laura L. Thompson
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Allison K. Baergen
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
| | - Kirk J. McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, MB R3E 0J9, Canada; (L.L.T.); (A.K.B.); (Z.L.)
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, MB R3E 0V9, Canada
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16
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An Automated, Single Cell Quantitative Imaging Microscopy Approach to Assess Micronucleus Formation, Genotoxicity and Chromosome Instability. Cells 2020; 9:cells9020344. [PMID: 32024251 PMCID: PMC7072510 DOI: 10.3390/cells9020344] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/14/2020] [Accepted: 01/31/2020] [Indexed: 12/14/2022] Open
Abstract
Micronuclei are small, extranuclear bodies that are distinct from the primary cell nucleus. Micronucleus formation is an aberrant event that suggests a history of genotoxic stress or chromosome mis-segregation events. Accordingly, assays evaluating micronucleus formation serve as useful tools within the fields of toxicology and oncology. Here, we describe a novel micronucleus formation assay that utilizes a high-throughput imaging platform and automated image analysis software for accurate detection and rapid quantification of micronuclei at the single cell level. We show that our image analysis parameters are capable of identifying dose-dependent increases in micronucleus formation within three distinct cell lines following treatment with two established genotoxic agents, etoposide or bleomycin. We further show that this assay detects micronuclei induced through silencing of the established chromosome instability gene, SMC1A. Thus, the micronucleus formation assay described here is a versatile and efficient alternative to more laborious cytological approaches, and greatly increases throughput, which will be particularly beneficial for large-scale chemical or genetic screens.
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17
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Leylek TR, Jeusset LM, Lichtensztejn Z, McManus KJ. Reduced Expression of Genes Regulating Cohesion Induces Chromosome Instability that May Promote Cancer and Impact Patient Outcomes. Sci Rep 2020; 10:592. [PMID: 31953484 PMCID: PMC6969069 DOI: 10.1038/s41598-020-57530-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 01/03/2020] [Indexed: 12/15/2022] Open
Abstract
Chromosome instability (CIN), or continual changes in chromosome complements, is an enabling feature of cancer; however, the molecular determinants of CIN remain largely unknown. Emerging data now suggest that aberrant sister chromatid cohesion may induce CIN and contribute to cancer. To explore this possibility, we employed clinical and fundamental approaches to systematically assess the impact reduced cohesion gene expression has on CIN and cancer. Ten genes encoding critical functions in cohesion were evaluated and remarkably, each exhibits copy number losses in 12 common cancer types, and reduced expression is associated with worse patient survival. To gain mechanistic insight, we combined siRNA-based silencing with single cell quantitative imaging microscopy to comprehensively assess the impact reduced expression has on CIN in two karyotypically stable cell lines. We show that reduced expression induces CIN phenotypes, namely increases in micronucleus formation and nuclear areas. Subsequent direct tests involving a subset of prioritized genes also revealed significant changes in chromosome numbers with corresponding increases in moderate and severe cohesion defects within mitotic chromosome spreads. Collectively, our clinical and fundamental findings implicate reduced sister chromatid cohesion, resulting from gene copy number losses, as a key pathogenic event in the development and progression of many cancer types.
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Affiliation(s)
- Tarik R Leylek
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
| | - Lucile M Jeusset
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Zelda Lichtensztejn
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada
| | - Kirk J McManus
- Department of Biochemistry & Medical Genetics, University of Manitoba, Winnipeg, Manitoba, R3E 0J9, Canada.
- Research Institute in Oncology & Hematology, CancerCare Manitoba, Winnipeg, Manitoba, R3E 0V9, Canada.
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18
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Kouprina N, Liskovykh M, Petrov N, Larionov V. Human artificial chromosome (HAC) for measuring chromosome instability (CIN) and identification of genes required for proper chromosome transmission. Exp Cell Res 2019; 387:111805. [PMID: 31877307 DOI: 10.1016/j.yexcr.2019.111805] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 12/20/2019] [Accepted: 12/22/2019] [Indexed: 01/24/2023]
Abstract
Chromosomal instability (CIN) is one of the characteristics of cancer inherent for tumor initiation and progression, which is defined as a persistent, high rate of gain/loss of whole chromosomes. In the vast majority of human tumors the molecular basis of CIN remains unknown. The development of a conceptually simple colony color sectoring assay that measures yeast artificial chromosome (YAC) loss provided a powerful genetic tool to assess the rate of chromosome mis-segregation and also identified 937 yeast genes involved in this process. Similarly, a human artificial chromosome (HAC)-based assay has been recently developed and applied to quantify chromosome mis-segregation events in human cells. This assay allowed identification of novel human CIN genes in the library of protein kinases. Among them are PINK1, TRIO, IRAK1, PNCK, and TAOK1. The HAC-based assay may be applied to screen siRNA, shRNA and CRISPR-based libraries to identify the complete spectrum of CIN genes. This will reveal new insights into mechanisms of chromosome segregation and may expedite the development of novel therapeutic strategies to target the CIN phenotype in cancer cells.
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Affiliation(s)
- Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
| | - Mikhail Liskovykh
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Nikolai Petrov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
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19
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Diminished Condensin Gene Expression Drives Chromosome Instability That May Contribute to Colorectal Cancer Pathogenesis. Cancers (Basel) 2019; 11:cancers11081066. [PMID: 31357676 PMCID: PMC6721357 DOI: 10.3390/cancers11081066] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 07/17/2019] [Accepted: 07/25/2019] [Indexed: 12/28/2022] Open
Abstract
Chromosome instability (CIN), or constantly evolving chromosome complements, is a form of genome instability implicated in the development and progression of many cancer types, however, the molecular determinants of CIN remain poorly understood. Condensin is a protein complex involved in chromosome compaction, and recent studies in model organisms show that aberrant compaction adversely impacts mitotic fidelity. To systematically assess the clinical and fundamental impacts that reduced condensin gene expression have in cancer, we first assessed gene copy number alterations of all eight condensin genes. Using patient derived datasets, we show that shallow/deep deletions occur frequently in 12 common cancer types. Furthermore, we show that reduced expression of each gene is associated with worse overall survival in colorectal cancer patients. To determine the overall impact that reduced condensin gene expression has on CIN, a comprehensive siRNA-based screen was performed in two karyotypically stable cell lines. Following gene silencing, quantitative imaging microscopy identified increases in CIN-associated phenotypes, including changes in nuclear areas, micronucleus formation, and chromosome numbers. Although silencing corresponded with increases in CIN phenotypes, the most pronounced phenotypes were observed following SMC2 and SMC4 silencing. Collectively, our clinical and fundamental findings suggest reduced condensin expression and function may be a significant, yet, underappreciated driver of colorectal cancer.
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20
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Detecting Chromosome Instability in Cancer: Approaches to Resolve Cell-to-Cell Heterogeneity. Cancers (Basel) 2019; 11:cancers11020226. [PMID: 30781398 PMCID: PMC6406658 DOI: 10.3390/cancers11020226] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/11/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
Chromosome instability (CIN) is defined as an increased rate of chromosome gains and losses that manifests as cell-to-cell karyotypic heterogeneity and drives cancer initiation and evolution. Current research efforts are aimed at identifying the etiological origins of CIN, establishing its roles in cancer pathogenesis, understanding its implications for patient prognosis, and developing novel therapeutics that are capable of exploiting CIN. Thus, the ability to accurately identify and evaluate CIN is critical within both research and clinical settings. Here, we provide an overview of quantitative single cell approaches that evaluate and resolve cell-to-cell heterogeneity and CIN, and discuss considerations when selecting the most appropriate approach to suit both research and clinical contexts.
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21
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Guo X, Ni J, Liang Z, Xue J, Fenech MF, Wang X. The molecular origins and pathophysiological consequences of micronuclei: New insights into an age-old problem. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2018; 779:1-35. [PMID: 31097147 DOI: 10.1016/j.mrrev.2018.11.001] [Citation(s) in RCA: 77] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 02/07/2023]
Abstract
Micronuclei (MN), the small nucleus-like bodies separated from the primary nucleus, can exist in cells with numerical and/or structural chromosomal aberrations in apparently normal tissues and more so in tumors in humans. While MN have been observed for over 100 years, they were merely and constantly considered as passive indicators of chromosome instability (CIN) for a long time. Relatively little is known about the molecular origins and biological consequences of MN. Rapid technological advances are helping to close these gaps. Very recent studies provide exciting evidence that MN act as key platform for chromothripsis and a trigger of innate immune response, suggesting that MN could affect cellular functions by both genetic and nongenetic means. These previously unappreciated findings have reawakened widespread interests in MN. In this review, the diverse mechanisms leading to MN generation and the complex fate profiles of MN are discussed, together with the evidence for their contribution to CIN, inflammation, senescence and cell death. Moreover, we put this knowledge together into a speculative perspective on how MN may be responsible for cancer development and how their presence may influence the choice of treatment. We suggest that the heterogeneous responses to MN may function physiological to ensure the arrestment, elimination and immune clearance of damaged cells, but pathologically, may enable the survival and oncogenic transformation of cells bearing CIN. These insights not only underscore the complexity of MN biology, but also raise a host of new questions and provide fertile ground for future research.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Juan Ni
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Ziqing Liang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Michael F Fenech
- University of South Australia, Adelaide, SA, 5000, Australia; Genome Health Foundation, North Brighton, SA, 5048, Australia.
| | - Xu Wang
- School of Life Sciences, The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Yunnan Normal University, Kunming, Yunnan, 650500, China.
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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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Asbaghi Y, Thompson LL, Lichtensztejn Z, McManus KJ. KIF11 silencing and inhibition induces chromosome instability that may contribute to cancer. Genes Chromosomes Cancer 2017; 56:668-680. [PMID: 28510357 DOI: 10.1002/gcc.22471] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/04/2017] [Accepted: 05/04/2017] [Indexed: 12/25/2022] Open
Abstract
Understanding the aberrant pathways that contribute to oncogenesis and identifying the altered genes involved in these pathways is a critical first step to develop effective strategies to better combat cancer. Chromosome instability (CIN) is an aberrant phenotype that occurs in ∼80% of all cancer types and is associated with aggressive tumors, the acquisition of multidrug resistance and poor patient prognosis. Despite these associations however, the aberrant genes and molecular defects underlying CIN remain poorly understood. KIF11 is an evolutionarily conserved microtubule motor protein that functions in centrosome and chromosome dynamics in mitosis. Interestingly, the yeast ortholog of KIF11, namely CIN8 is a CIN gene and thus aberrant KIF11 expression and function is suspected to underlie CIN. In support of this possibility, KIF11 is somatically altered in a large number of cancer types. Using a complementary biochemical and genetic approach we examined whether KIF11 silencing with siRNAs or inhibition with monastrol was able to convert two distinct and karyotypically stable cell lines into karyotypically unstable cell lines. Indeed, quantitative imaging microscopy and flow cytometry revealed that KIF11 silencing induced increases in nuclear areas, micronucleus formation, DNA content and chromosome numbers relative to controls that was also observed following KIF11 inhibition. Collectively, this study identifies and validates KIF11 as an evolutionarily conserved CIN gene, and further suggests that aberrant expression and function may contribute to the pathogenesis of a subset of cancers.
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Affiliation(s)
- Yasamin Asbaghi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Laura L Thompson
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Zelda Lichtensztejn
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J McManus
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada.,Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
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Penner-Goeke S, Lichtensztejn Z, Neufeld M, Ali JL, Altman AD, Nachtigal MW, McManus KJ. The temporal dynamics of chromosome instability in ovarian cancer cell lines and primary patient samples. PLoS Genet 2017; 13:e1006707. [PMID: 28376088 PMCID: PMC5395197 DOI: 10.1371/journal.pgen.1006707] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 04/18/2017] [Accepted: 03/20/2017] [Indexed: 01/12/2023] Open
Abstract
Epithelial ovarian cancer (EOC) is the most prevalent form of ovarian cancer and has the highest mortality rate. Novel insight into EOC is required to minimize the morbidity and mortality rates caused by recurrent, drug resistant disease. Although numerous studies have evaluated genome instability in EOC, none have addressed the putative role chromosome instability (CIN) has in disease progression and drug resistance. CIN is defined as an increase in the rate at which whole chromosomes or large parts thereof are gained or lost, and can only be evaluated using approaches capable of characterizing genetic or chromosomal heterogeneity within populations of cells. Although CIN is associated with numerous cancer types, its prevalence and dynamics in EOC is unknown. In this study, we assessed CIN within serial samples collected from the ascites of five EOC patients, and in two well-established ovarian cancer cell models of drug resistance (PEO1/4 and A2780s/cp). We quantified and compared CIN (as measured by nuclear areas and CIN Score (CS) values) within and between serial samples to glean insight into the association and dynamics of CIN within EOC, with a particular focus on resistant and recurrent disease. Using quantitative, single cell analyses we determined that CIN is associated with every sample evaluated and further show that many EOC samples exhibit a large degree of nuclear size and CS value heterogeneity. We also show that CIN is dynamic and generally increases within resistant disease. Finally, we show that both drug resistance models (PEO1/4 and A2780s/cp) exhibit heterogeneity, albeit to a much lesser extent. Surprisingly, the two cell line models exhibit remarkably similar levels of CIN, as the nuclear areas and CS values are largely overlapping between the corresponding paired lines. Accordingly, these data suggest CIN may represent a novel biomarker capable of monitoring changes in EOC progression associated with drug resistance.
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Affiliation(s)
- Signe Penner-Goeke
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Zelda Lichtensztejn
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Megan Neufeld
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
| | - Jennifer L. Ali
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Alon D. Altman
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Mark W. Nachtigal
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
- Department of Obstetrics, Gynecology and Reproductive Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Kirk J. McManus
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Manitoba, Canada
- Research Institute in Oncology and Hematology, CancerCare Manitoba, Winnipeg, Manitoba, Canada
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Kim JH, Lee HS, Lee NCO, Goncharov NV, Kumeiko V, Masumoto H, Earnshaw WC, Kouprina N, Larionov V. Development of a novel HAC-based "gain of signal" quantitative assay for measuring chromosome instability (CIN) in cancer cells. Oncotarget 2016; 7:14841-56. [PMID: 26943579 PMCID: PMC4924756 DOI: 10.18632/oncotarget.7854] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Accepted: 01/29/2016] [Indexed: 12/14/2022] Open
Abstract
Accumulating data indicates that chromosome instability (CIN) common to cancer cells can be used as a target for cancer therapy. At present the rate of chromosome mis-segregation is quantified by laborious techniques such as coupling clonal cell analysis with karyotyping or fluorescence in situ hybridization (FISH). Recently, a novel assay was developed based on the loss of a non-essential human artificial chromosome (HAC) carrying a constitutively expressed EGFP transgene ("loss of signal" assay). Using this system, anticancer drugs can be easily ranked on by their effect on HAC loss. However, it is problematic to covert this "loss of signal" assay into a high-throughput screen to identify drugs and mutations that increase CIN levels. To address this point, we re-designed the HAC-based assay. In this new system, the HAC carries a constitutively expressed shRNA against the EGFP transgene integrated into human genome. Thus, cells that inherit the HAC display no green fluorescence, while cells lacking the HAC do. We verified the accuracy of this "gain of signal" assay by measuring the level of CIN induced by known antimitotic drugs and added to the list of previously ranked CIN inducing compounds, two newly characterized inhibitors of the centromere-associated protein CENP-E, PF-2771 and GSK923295 that exhibit the highest effect on chromosome instability measured to date. The "gain of signal" assay was also sensitive enough to detect increase of CIN after siRNA depletion of known genes controlling mitotic progression through distinct mechanisms. Hence this assay can be utilized in future experiments to uncover novel human CIN genes, which will provide novel insight into the pathogenesis of cancer. Also described is the possible conversion of this new assay into a high-throughput screen using a fluorescence microplate reader to characterize chemical libraries and identify new conditions that modulate CIN level.
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Affiliation(s)
- Jung-Hyun Kim
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Hee-Sheung Lee
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Nicholas C. O. Lee
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Nikolay V. Goncharov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
- School of Biomedicine, Far Eastern Federal University, A. V. Zhirmunsky Institute of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Vadim Kumeiko
- School of Biomedicine, Far Eastern Federal University, A. V. Zhirmunsky Institute of Marine Biology, FEB RAS, Vladivostok, Russia
| | - Hiroshi Masumoto
- Laboratory of Cell Engineering, Department of Human Genome Research, Kazusa DNA Research Institute, Kisarazu, Japan
| | - William C. Earnshaw
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Edinburgh, Scotland
| | - Natalay Kouprina
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
| | - Vladimir Larionov
- Developmental Therapeutics Branch, National Cancer Institute, NIH, Bethesda, MD, USA
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