1
|
Mikaelian I, Gadet R, Deygas M, Bertolino P, Hennino A, Gillet G, Rimokh R, Berremila SA, Péoc’h M, Gonzalo P. EGFR-dependent aerotaxis is a common trait of breast tumour cells. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:324. [PMID: 36380366 PMCID: PMC9667613 DOI: 10.1186/s13046-022-02514-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND Aerotaxis, the chemotactism to oxygen, is well documented in prokaryotes. We previously reported for the first time that non-tumorigenic breast epithelial cells also display unequivocal directional migration towards oxygen. This process is independent of the hypoxia-inducible factor (HIF)/prolyl hydroxylase domain (PHD) pathway but controlled by the redox regulation of epidermal growth factor receptor (EGFR), with a reactive oxygen species (ROS) gradient overlapping the oxygen gradient at low oxygen concentration. Since hypoxia is an acknowledged hallmark of cancers, we addressed the putative contribution of aerotaxis to cancer metastasis by studying the directed migration of cancer cells from an hypoxic environment towards nearby oxygen sources, modelling the in vivo migration of cancer cells towards blood capillaries. METHODS We subjected to the aerotactic test described in our previous papers cells isolated from fresh breast tumours analysed by the Pathology Department of the Saint-Etienne University Hospital (France) over a year. The main selection criterion, aside from patient consent, was the size of the tumour, which had to be large enough to perform the aerotactic tests without compromising routine diagnostic tests. Finally, we compared the aerotactic properties of these primary cells with those of commonly available breast cancer cell lines. RESULTS We show that cells freshly isolated from sixteen human breast tumour biopsies, representative of various histological characteristics and grades, are endowed with strong aerotactic properties similar to normal mammary epithelial cell lines. Strikingly, aerotaxis of these primary cancerous cells is also strongly dependent on both EGFR activation and ROS. In addition, we demonstrate that aerotaxis can trigger directional invasion of tumour cells within the extracellular matrix contrary to normal mammary epithelial cells. This contrasts with results obtained with breast cancer cell lines, in which aerotactic properties were either retained or impaired, and in some cases, even lost during the establishment of these cell lines. CONCLUSIONS Altogether, our results support that aerotaxis may play an important role in breast tumour metastasis. In view of these findings, we discuss the prospects for combating metastatic spread. TRIAL REGISTRATION IRBN1462021/CHUSTE.
Collapse
Affiliation(s)
- Ivan Mikaelian
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France
| | - Rudy Gadet
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France
| | - Mathieu Deygas
- grid.4444.00000 0001 2112 9282Institut Curie, Paris Sciences et Lettres (PSL) Research University, Centre National de la Recherche Scientifique (CNRS), Unité Mixte de Recherche (UMR) 144, Paris, France ,grid.440907.e0000 0004 1784 3645Institut Pierre-Gilles de Gennes, PSL Research University, Paris, France
| | - Philippe Bertolino
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France
| | - Anca Hennino
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France
| | - Germain Gillet
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France
| | - Ruth Rimokh
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France
| | - Sid-Ali Berremila
- grid.412954.f0000 0004 1765 1491Pathology department, UFR Medecine Saint-Etienne, CHU of Saint-Etienne, Saint-Etienne, France
| | - Michel Péoc’h
- grid.412954.f0000 0004 1765 1491Pathology department, UFR Medecine Saint-Etienne, CHU of Saint-Etienne, Saint-Etienne, France
| | - Philippe Gonzalo
- grid.418116.b0000 0001 0200 3174Centre de Recherche en Cancérologie de Lyon - Université Claude Bernard Lyon 1, UMR CNRS 5286, INSERM 1052, Centre Léon Bérard, 69373 Lyon, France ,grid.412954.f0000 0004 1765 1491Biochemistry and Pharmacology department, UFR Medecine Saint-Etienne, CHU of Saint-Etienne, Saint-Etienne, France
| |
Collapse
|
2
|
Hoffman JA, Trotter KW, Day CR, Ward JM, Inoue K, Rodriguez J, Archer TK. Multimodal regulatory elements within a hormone-specific super enhancer control a heterogeneous transcriptional response. Mol Cell 2022; 82:803-815.e5. [PMID: 35077705 PMCID: PMC8897972 DOI: 10.1016/j.molcel.2021.12.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 11/02/2021] [Accepted: 12/22/2021] [Indexed: 12/16/2022]
Abstract
The hormone-stimulated glucocorticoid receptor (GR) modulates transcription by interacting with thousands of enhancers and GR binding sites (GBSs) throughout the genome. Here, we examined the effects of GR binding on enhancer dynamics and investigated the contributions of individual GBSs to the hormone response. Hormone treatment resulted in genome-wide reorganization of the enhancer landscape in breast cancer cells. Upstream of the DDIT4 oncogene, GR bound to four sites constituting a hormone-dependent super enhancer. Three GBSs were required as hormone-dependent enhancers that differentially promoted histone acetylation, transcription frequency, and burst size. Conversely, the fourth site suppressed transcription and hormone treatment alleviated this suppression. GR binding within the super enhancer promoted a loop-switching mechanism that allowed interaction of the DDIT4 TSS with the active GBSs. The unique functions of each GR binding site contribute to hormone-induced transcriptional heterogeneity and demonstrate the potential for targeted modulation of oncogene expression.
Collapse
Affiliation(s)
- Jackson A Hoffman
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Kevin W Trotter
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Christopher R Day
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - James M Ward
- Integrative Bioinformatics, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Kaoru Inoue
- Clinical Research Branch, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Joseph Rodriguez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC, USA 27709
| | - Trevor K Archer
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, Research Triangle Park, Durham, NC 27709, USA.
| |
Collapse
|
3
|
Kitakaze K, Tsuboi K, Tsuda M, Takenouchi Y, Ishimaru H, Okamoto Y. Development of a selective fluorescence-based enzyme assay for glycerophosphodiesterase family members GDE4 and GDE7. J Lipid Res 2021; 62:100141. [PMID: 34673020 PMCID: PMC8591415 DOI: 10.1016/j.jlr.2021.100141] [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: 06/29/2021] [Revised: 10/08/2021] [Accepted: 10/12/2021] [Indexed: 01/02/2023] Open
Abstract
Lysophosphatidic acid (LPA) is a lipid mediator that regulates various processes, including cell migration and cancer progression. Autotaxin (ATX) is a lysophospholipase D-type exoenzyme that produces extracellular LPA. In contrast, glycerophosphodiesterase (GDE) family members GDE4 and GDE7 are intracellular lysophospholipases D that form LPA, depending on Mg2+ and Ca2+, respectively. Since no fluorescent substrate for these GDEs has been reported, in the present study, we examined whether a fluorescent ATX substrate, FS-3, could be applied to study GDE activity. We found that the membrane fractions of human GDE4- and GDE7-overexpressing human embryonic kidney 293T cells hydrolyzed FS-3 in a manner almost exclusively dependent on Mg2+ and Ca2+, respectively. Using these assay systems, we found that several ATX inhibitors, including α-bromomethylene phosphonate analog of LPA and 3-carbacyclic phosphatidic acid, also potently inhibited GDE4 and GDE7 activities. In contrast, the ATX inhibitor S32826 hardly inhibited these activities. Furthermore, FS-3 was hydrolyzed in a Mg2+-dependent manner by the membrane fraction of human prostate cancer LNCaP cells that express GDE4 endogenously but not by those of GDE4-deficient LNCaP cells. Similar Ca2+-dependent GDE7 activity was observed in human breast cancer MCF-7 cells but not in GDE7-deficient MCF-7 cells. Finally, our assay system could selectively measure GDE4 and GDE7 activities in a mixture of the membrane fractions of GDE4- and GDE7-overexpressing human embryonic kidney 293T cells in the presence of S32826. These findings allow high-throughput assays of GDE4 and GDE7 activities, which could lead to the development of selective inhibitors and stimulators as well as a better understanding of the biological roles of these enzymes.
Collapse
Affiliation(s)
- Keisuke Kitakaze
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan.
| | - Kazuhito Tsuboi
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan.
| | - Maho Tsuda
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Yasuhiro Takenouchi
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Hironobu Ishimaru
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| | - Yasuo Okamoto
- Department of Pharmacology, Kawasaki Medical School, Kurashiki, Okayama, Japan
| |
Collapse
|
4
|
Khalil AIS, Chattopadhyay A, Sanyal A. Analysis of Aneuploidy Spectrum From Whole-Genome Sequencing Provides Rapid Assessment of Clonal Variation Within Established Cancer Cell Lines. Cancer Inform 2021; 20:11769351211049236. [PMID: 34671179 PMCID: PMC8521761 DOI: 10.1177/11769351211049236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Accepted: 09/02/2021] [Indexed: 11/16/2022] Open
Abstract
BACKGROUND The revolution in next-generation sequencing (NGS) technology has allowed easy access and sharing of high-throughput sequencing datasets of cancer cell lines and their integrative analyses. However, long-term passaging and culture conditions introduce high levels of genomic and phenotypic diversity in established cell lines resulting in strain differences. Thus, clonal variation in cultured cell lines with respect to the reference standard is a major barrier in systems biology data analyses. Therefore, there is a pressing need for a fast and entry-level assessment of clonal variations within cell lines using their high-throughput sequencing data. RESULTS We developed a Python-based software, AStra, for de novo estimation of the genome-wide segmental aneuploidy to measure and visually interpret strain-level similarities or differences of cancer cell lines from whole-genome sequencing (WGS). We demonstrated that aneuploidy spectrum can capture the genetic variations in 27 strains of MCF7 breast cancer cell line collected from different laboratories. Performance evaluation of AStra using several cancer sequencing datasets revealed that cancer cell lines exhibit distinct aneuploidy spectra which reflect their previously-reported karyotypic observations. Similarly, AStra successfully identified large-scale DNA copy number variations (CNVs) artificially introduced in simulated WGS datasets. CONCLUSIONS AStra provides an analytical and visualization platform for rapid and easy comparison between different strains or between cell lines based on their aneuploidy spectra solely using the raw BAM files representing mapped reads. We recommend AStra for rapid first-pass quality assessment of cancer cell lines before integrating scientific datasets that employ deep sequencing. AStra is an open-source software and is available at https://github.com/AISKhalil/AStra.
Collapse
Affiliation(s)
| | - Anupam Chattopadhyay
- School of Computer Science and Engineering, Nanyang Technological University, Singapore, Singapore
| | - Amartya Sanyal
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| |
Collapse
|
5
|
Tran V, Kim R, Maertens M, Hartung T, Maertens A. Similarities and Differences in Gene Expression Networks Between the Breast Cancer Cell Line Michigan Cancer Foundation-7 and Invasive Human Breast Cancer Tissues. Front Artif Intell 2021; 4:674370. [PMID: 34056582 PMCID: PMC8155268 DOI: 10.3389/frai.2021.674370] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/23/2021] [Indexed: 12/31/2022] Open
Abstract
Failure to adequately characterize cell lines, and understand the differences between in vitro and in vivo biology, can have serious consequences on the translatability of in vitro scientific studies to human clinical trials. This project focuses on the Michigan Cancer Foundation-7 (MCF-7) cells, a human breast adenocarcinoma cell line that is commonly used for in vitro cancer research, with over 42,000 publications in PubMed. In this study, we explore the key similarities and differences in gene expression networks of MCF-7 cell lines compared to human breast cancer tissues. We used two MCF-7 data sets, one data set collected by ARCHS4 including 1032 samples and one data set from Gene Expression Omnibus GSE50705 with 88 estradiol-treated MCF-7 samples. The human breast invasive ductal carcinoma (BRCA) data set came from The Cancer Genome Atlas, including 1212 breast tissue samples. Weighted Gene Correlation Network Analysis (WGCNA) and functional annotations of the data showed that MCF-7 cells and human breast tissues have only minimal similarity in biological processes, although some fundamental functions, such as cell cycle, are conserved. Scaled connectivity—a network topology metric—also showed drastic differences in the behavior of genes between MCF-7 and BRCA data sets. Finally, we used canSAR to compute ligand-based druggability scores of genes in the data sets, and our results suggested that using MCF-7 to study breast cancer may lead to missing important gene targets. Our comparison of the networks of MCF-7 and human breast cancer highlights the nuances of using MCF-7 to study human breast cancer and can contribute to better experimental design and result interpretation of study involving this cell line.
Collapse
Affiliation(s)
- Vy Tran
- Department of Environmental Health and Engineering, Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Robert Kim
- Department of Environmental Health and Engineering, Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Mikhail Maertens
- Department of Environmental Health and Engineering, Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Thomas Hartung
- Department of Environmental Health and Engineering, Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States.,Department of Biology, Center for Alternatives to Animal Testing-Europe, University of Konstanz, Konstanz, Germany.,Department of Environmental Health and Engineering, Doerenkamp-Zbinden Professor and Chair for Evidence-Based Toxicology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| | - Alexandra Maertens
- Department of Environmental Health and Engineering, Center for Alternatives to Animal Testing, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States
| |
Collapse
|
6
|
Li S, Garay JP, Tubbs CA, Franco HL. CRISPR-based knock-in mutagenesis of the pioneer transcription factor FOXA1: optimization of strategies for multi-allelic proteins in cancer cells. FEBS Open Bio 2021; 11:1537-1551. [PMID: 33666335 PMCID: PMC8167868 DOI: 10.1002/2211-5463.13139] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 02/23/2021] [Accepted: 03/03/2021] [Indexed: 12/24/2022] Open
Abstract
Precise genome engineering of living cells has been revolutionized by the introduction of the highly specific and easily programmable properties of the clustered regularly interspaced short palindromic repeats (CRISPR) technology. This has greatly accelerated research into human health and has facilitated the discovery of novel therapeutics. CRISPR‐Cas9 is most widely employed for its ability to inactivate or knockout specific genes, but can be also used to introduce subtle site‐specific substitutions of DNA sequences that can lead to changes in the amino acid composition of proteins. Despite the proven success of CRISPR‐based knock‐in strategies of genes in typical diploid cells (i.e., cells containing two sets of chromosomes), precise editing of cancer cells, that typically have unstable genomes and multiple copies of chromosomes, is more challenging and not adequately addressed in the literature. Herein, we detail our methodology for replacing endogenous proteins with intended knock‐in mutants in polyploid cancer cells and discuss our experimental design, screening strategy, and facile allele frequency estimation methodology. As proof of principle, we performed genome editing of specific amino acids within the pioneer transcription factor FOXA1, a critical component of estrogen and androgen receptor signaling, in MCF‐7 breast cancer cells. We confirm mutant FOXA1 protein expression and intended amino acid substitutions via western blotting and mass spectrometry. In addition, we show that mutant allele frequency estimation is easily achieved by topoisomerase‐based cloning combined with allele‐specific PCR, which we later confirmed by next‐generation RNA‐sequencing. Typically, there are 4 ‐ 5 copies (alleles) of FOXA1 in breast cancer cells, making the editing of this protein inherently challenging. As a result, most studies that focus on FOXA1 mutants rely on ectopic overexpression of FOXA1 from a plasmid. Therefore, we provide an optimized methodology for replacing endogenous wild‐type FOXA1 with precise knock‐in mutants to enable the systematic analysis of its molecular mechanisms within the appropriate physiological context.
Collapse
Affiliation(s)
- Shen Li
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Joseph P Garay
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Colby A Tubbs
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| | - Hector L Franco
- The Lineberger Comprehensive Cancer Center, Department of Genetics, University of North Carolina at Chapel Hill, NC, USA
| |
Collapse
|
7
|
Franzini S, Di Stefano M, Micheletti C. essHi-C: Essential component analysis of Hi-C matrices. Bioinformatics 2021; 37:2088-2094. [PMID: 33523102 DOI: 10.1093/bioinformatics/btab062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/18/2021] [Accepted: 01/28/2021] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Hi-C matrices are cornerstones for qualitative and quantitative studies of genome folding, from its territorial organization to compartments and topological domains. The high dynamic range of genomic distances probed in Hi-C assays reflects in an inherent stochastic background of the interactions matrices, which inevitably convolve the features of interest with largely non-specific ones. RESULTS Here we introduce and discuss essHi-C, a method to isolate the specific, or essential component of Hi-C matrices from the non-specific portion of the spectrum that is compatible with random matrices. Systematic comparisons show that essHi-C improves the clarity of the interaction patterns, enhances the robustness against sequencing depth of topologically associating domains identification, allows the unsupervised clustering of experiments in different cell lines and recovers the cell-cycle phasing of single-cells based on Hi-C data. Thus, essHi-C provides means for isolating significant biological and physical features from Hi-C matrices. AVAILABILITY The essHi-C software package is available at: https://github.com/stefanofranzini/essHIC . SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Stefano Franzini
- SISSA - Scuola internazionale Superiore di Studi Avanzati, Via Bonomea 265, I-34077 Trieste, Italy
| | - Marco Di Stefano
- Structural genomics Group, CNAG-CRG Centre Nacional d'Análisi Genómica - Centre de Regulació Genómica, Barcelona, 08028, Spain
| | - Cristian Micheletti
- SISSA - Scuola internazionale Superiore di Studi Avanzati, Via Bonomea 265, I-34077 Trieste, Italy
| |
Collapse
|
8
|
Vargas-Rondón N, Pérez-Mora E, Villegas VE, Rondón-Lagos M. Role of chromosomal instability and clonal heterogeneity in the therapy response of breast cancer cell lines. Cancer Biol Med 2020; 17:970-985. [PMID: 33299647 PMCID: PMC7721098 DOI: 10.20892/j.issn.2095-3941.2020.0028] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Accepted: 05/20/2020] [Indexed: 01/08/2023] Open
Abstract
Objective Chromosomal instability (CIN) is a hallmark of cancer characterized by cell-to-cell variability in the number or structure of chromosomes, frequently observed in cancer cell populations and is associated with poor prognosis, metastasis, and therapeutic resistance. Breast cancer (BC) is characterized by unstable karyotypes and recent reports have indicated that CIN may influence the response of BC to chemotherapy regimens. However, paradoxical associations between extreme CIN and improved outcome have been observed. Methods This study aimed to 1) evaluate CIN levels and clonal heterogeneity (CH) in MCF7, ZR-751, MDA-MB468, BT474, and KPL4 BC cells treated with low doses of tamoxifen (TAM), docetaxel (DOC), doxorubicin (DOX), Herceptin (HT), and combined treatments (TAM/DOC, TAM/DOX, TAM/HT, HT/DOC, and HT/DOX) by using fluorescence in situ hybridization (FISH), and 2) examine the association with response to treatments by comparing FISH results with cell proliferation. Results Intermediate CIN was linked to drug sensitivity according to three characteristics: estrogen receptor α (ERα) and HER2 status, pre-existing CIN level in cancer cells, and the CIN induced by the treatments. ERα+/HER2- cells with intermediate CIN were sensitive to treatment with taxanes (DOC) and anthracyclines (DOX), while ERα-/HER2-, ERα+/HER2+, and ERα-/HER2+ cells with intermediate CIN were resistant to these treatments. Conclusions A greater understanding of CIN and CH in BC could assist in the optimization of existing therapeutic regimens and/or in supporting new strategies to improve cancer outcomes.
Collapse
Affiliation(s)
- Natalia Vargas-Rondón
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Erika Pérez-Mora
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Victoria E. Villegas
- Biology Program, Faculty of Natural Sciences, Universidad del Rosario, Bogotá 111221, Colombia
| | - Milena Rondón-Lagos
- School of Biological Sciences, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| |
Collapse
|
9
|
Liu X, Gygi SP, Paulo JA. Isobaric Tag-Based Protein Profiling across Eight Human Cell Lines Using High-Field Asymmetric Ion Mobility Spectrometry and Real-Time Database Searching. Proteomics 2020; 21:e2000218. [PMID: 33015980 DOI: 10.1002/pmic.202000218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/26/2020] [Indexed: 12/11/2022]
Abstract
A vast number of human cell lines are available for cell culture model-based studies, and as such the potential exists for discrepancies in findings due to cell line selection. To investigate this concept, the authors determine the relative protein abundance profiles of a panel of eight diverse, but commonly studied human cell lines. This panel includes HAP1, HEK293T, HeLa, HepG2, Jurkat, Panc1, SH-SY5Y, and SVGp12. A mass spectrometry-based proteomics workflow designed to enhance quantitative accuracy while maintaining analytical depth is used. To this end, this strategy leverages TMTpro16-based sample multiplexing, high-field asymmetric ion mobility spectrometry, and real-time database searching. The data show that the differences in the relative protein abundance profiles reflect cell line diversity. The authors also determine several hundred proteins to be highly enriched for a given cell line, and perform gene ontology and pathway analysis on these cell line-enriched proteins. An R Shiny application is designed to query protein abundance profiles and retrieve proteins with similar patterns. The workflows used herein can be applied to additional cell lines to aid cell line selection for addressing a given scientific inquiry or for improving an experimental design.
Collapse
Affiliation(s)
- Xinyue Liu
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Steven P Gygi
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| | - Joao A Paulo
- Department of Cell Biology, Harvard Medical School, Boston, MA, 02115, USA
| |
Collapse
|
10
|
DiScala M, Najor MS, Yung T, Morgan D, Abukhdeir AM, Cobleigh MA. Loss of STAT6 leads to anchorage-independent growth and trastuzumab resistance in HER2+ breast cancer cells. PLoS One 2020; 15:e0234146. [PMID: 32525891 PMCID: PMC7289443 DOI: 10.1371/journal.pone.0234146] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 05/19/2020] [Indexed: 11/22/2022] Open
Abstract
Approximately 20% of breast cancers are HER2-positive. Trastuzumab has improved patient outcomes significantly for these cancers. However, acquired resistance remains a major hurdle in the clinical management of these patients. Therefore, identifying molecular changes that cause trastuzumab resistance is worthwhile. STAT6 is a transcription factor that regulates a variety of genes involved in cell cycle regulation, growth inhibition, and apoptosis. STAT6 expression is lost in approximately 3% of breast cancers, but little work has been done in the context of trastuzumab resistance in breast cancer. In isogenic cell line pairs, we observed that trastuzumab-resistant cells expressed significantly lower levels of STAT6 compared to trastuzumab-sensitive cells. Therefore, in order to study the consequences of STAT6 loss in HER2+ breast cancer, we knocked out both alleles of the STAT6 gene using somatic cell gene targeting. Interestingly, loss of STAT6 resulted in anchorage-independent growth and changes in several genes involved in epithelial to mesenchymal transition. This study suggests that STAT6 may play a role in the pathophysiology of HER2+ human breast cancer.
Collapse
Affiliation(s)
- Molly DiScala
- Division of Hematology, Oncology, and Cell Therapy, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Matthew S. Najor
- Division of Hematology, Oncology, and Cell Therapy, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Timothy Yung
- Division of Hematology, Oncology, and Cell Therapy, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Deri Morgan
- Department of Radiation Oncology, University of Kansas Medical Center, Kansas City, Missouri, United States of America
| | - Abde M. Abukhdeir
- Division of Hematology, Oncology, and Cell Therapy, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
| | - Melody A. Cobleigh
- Division of Hematology, Oncology, and Cell Therapy, Department of Medicine, Rush University Medical Center, Chicago, Illinois, United States of America
| |
Collapse
|
11
|
Pancholi S, Ribas R, Simigdala N, Schuster E, Nikitorowicz-Buniak J, Ressa A, Gao Q, Leal MF, Bhamra A, Thornhill A, Morisset L, Montaudon E, Sourd L, Fitzpatrick M, Altelaar M, Johnston SR, Marangoni E, Dowsett M, Martin LA. Tumour kinome re-wiring governs resistance to palbociclib in oestrogen receptor positive breast cancers, highlighting new therapeutic modalities. Oncogene 2020; 39:4781-4797. [PMID: 32307447 PMCID: PMC7299844 DOI: 10.1038/s41388-020-1284-6] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Revised: 03/18/2020] [Accepted: 03/24/2020] [Indexed: 01/13/2023]
Abstract
Combination of CDK4/6 inhibitors and endocrine therapy improves clinical outcome in advanced oestrogen receptor (ER)-positive breast cancer, however relapse is inevitable. Here, we show in model systems that other than loss of RB1 few gene-copy number (CN) alterations are associated with irreversible-resistance to endocrine therapy and subsequent secondary resistance to palbociclib. Resistance to palbociclib occurred as a result of tumour cell re-wiring leading to increased expression of EGFR, MAPK, CDK4, CDK2, CDK7, CCNE1 and CCNE2. Resistance altered the ER genome wide-binding pattern, leading to decreased expression of ‘classical’ oestrogen-regulated genes and was accompanied by reduced sensitivity to fulvestrant and tamoxifen. Persistent CDK4 blockade decreased phosphorylation of tuberous sclerosis complex 2 (TSC2) enhancing EGFR signalling, leading to the re-wiring of ER. Kinome-knockdown confirmed dependency on ERBB-signalling and G2/M–checkpoint proteins such as WEE1, together with the cell cycle master regulator, CDK7. Noteworthy, sensitivity to CDK7 inhibition was associated with loss of ER and RB1 CN. Overall, we show that resistance to CDK4/6 inhibitors is dependent on kinase re-wiring and the redeployment of signalling cascades previously associated with endocrine resistance and highlights new therapeutic networks that can be exploited upon relapse after CDK4/6 inhibition.
Collapse
Affiliation(s)
- Sunil Pancholi
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK
| | - Ricardo Ribas
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK
| | - Nikiana Simigdala
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK
| | - Eugene Schuster
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Anna Ressa
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Qiong Gao
- CRUK, Bioinformatic Cofacility, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | - Mariana Ferreira Leal
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK
| | - Amandeep Bhamra
- Proteomic Unit, Institute of Cancer Research, London, SW7 3RP, UK
| | - Allan Thornhill
- Centre for Cancer Imaging, Institute of Cancer Research, Sutton, SM2 5NG, UK
| | | | - Elodie Montaudon
- Department of Translational Research, Institut Curie, Paris, France
| | - Laura Sourd
- Department of Translational Research, Institut Curie, Paris, France
| | - Martin Fitzpatrick
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Maarten Altelaar
- Biomolecular Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | | | | | - Mitch Dowsett
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK.,Ralph Lauren Centre for Breast Cancer Research, Royal Marsden Hospital, London, SW3 6JJ, UK
| | - Lesley-Ann Martin
- Breast Cancer Now Toby Robins Research Centre, Institute of Cancer Research, London, SW7 3RP, UK.
| |
Collapse
|
12
|
Lafta IJ, Kudhair BK, Alabid NN. Characterization of the major human STAG3 variants using some proteomics and bioinformatics assays. EGYPTIAN JOURNAL OF MEDICAL HUMAN GENETICS 2020. [DOI: 10.1186/s43042-020-0051-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Abstract
Background
STAG3 is the meiotic component of cohesin and a member of the Cancer Testis Antigen (CTA) family. This gene has been found to be overexpressed in many types of cancer, and recently, its variants have been implicated in other disorders and many human diseases. Therefore, this study aimed to analyze the major variants of STAG3. Western blot (WB) and immunoprecipitation (IP) assays were performed using two different anti-STAG3 antibodies that targeted the relevant protein in MCF-7, T-47D, MDA-MB-468, and MDA-MB-231 breast cancer cells with Jurkat and MCF-10A cells as positive and negative controls, respectively. In silico analyses were searched to study the major isoforms.
Results
WB and IP assays revealed two abundant polypeptides < 191 kDa and ~ 75 kDa in size. Specific bioinformatics tools successfully determined the three-dimensional (3-D) structure, the subcellular localization, and the secondary structures of the isoforms. Furthermore, some of the physicochemical properties of the STAG3 proteins were also determined.
Conclusions
The results of this study revealed the power of applying the biological techniques (WB and IP) with the bioinformatics assays and the possibility of their exploitation in understanding diseased genes. Exploring the major variants of STAG3 at the protein level could help decipher some disorders associated with their occurrence, along with designing drugs effective at least for some relevant diseases.
Collapse
|
13
|
Rycenga HB, Wolfe KB, Yeh ES, Long DT. Uncoupling of p97 ATPase activity has a dominant negative effect on protein extraction. Sci Rep 2019; 9:10329. [PMID: 31316150 PMCID: PMC6637110 DOI: 10.1038/s41598-019-46949-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 07/04/2019] [Indexed: 12/13/2022] Open
Abstract
p97 is a highly abundant, homohexameric AAA+ ATPase that performs a variety of essential cellular functions. Characterized as a ubiquitin-selective chaperone, p97 recognizes proteins conjugated to K48-linked polyubiquitin chains and promotes their removal from chromatin and other molecular complexes. Changes in p97 expression or activity are associated with the development of cancer and several related neurodegenerative disorders. Although pathogenic p97 mutations cluster in and around p97’s ATPase domains, mutant proteins display normal or elevated ATPase activity. Here, we show that one of the most common p97 mutations (R155C) retains ATPase activity, but is functionally defective. p97-R155C can be recruited to ubiquitinated substrates on chromatin, but is unable to promote substrate removal. As a result, p97-R155C acts as a dominant negative, blocking protein extraction by a similar mechanism to that observed when p97’s ATPase activity is inhibited or inactivated. However, unlike ATPase-deficient proteins, p97-R155C consumes excess ATP, which can hinder high-energy processes. Together, our results shed new insight into how pathogenic mutations in p97 alter its cellular function, with implications for understanding the etiology and treatment of p97-associated diseases.
Collapse
Affiliation(s)
- Halley B Rycenga
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Kelly B Wolfe
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA
| | - Elizabeth S Yeh
- Department of Pharmacology and Toxicology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - David T Long
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, Charleston, SC, 29425, USA.
| |
Collapse
|
14
|
Yılmaz MB, Tunç E, Ilgaz NS, Öksüz H, Öztecik E, Özpak L, Öcal I, Pazarbaşı A, Demirhan O. Kanserli hücre hatları, pasaj sayısı arttıkça genomik organizasyonunu ve karyotipini değiştirir: sitogenetik bir çalışma. CUKUROVA MEDICAL JOURNAL 2018. [DOI: 10.17826/cumj.375325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
|
15
|
Dixon JR, Xu J, Dileep V, Zhan Y, Song F, Le VT, Yardımcı GG, Chakraborty A, Bann DV, Wang Y, Clark R, Zhang L, Yang H, Liu T, Iyyanki S, An L, Pool C, Sasaki T, Rivera-Mulia JC, Ozadam H, Lajoie BR, Kaul R, Buckley M, Lee K, Diegel M, Pezic D, Ernst C, Hadjur S, Odom DT, Stamatoyannopoulos JA, Broach JR, Hardison RC, Ay F, Noble WS, Dekker J, Gilbert DM, Yue F. Integrative detection and analysis of structural variation in cancer genomes. Nat Genet 2018; 50:1388-1398. [PMID: 30202056 PMCID: PMC6301019 DOI: 10.1038/s41588-018-0195-8] [Citation(s) in RCA: 217] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/16/2018] [Indexed: 01/19/2023]
Abstract
Structural variants (SVs) can contribute to oncogenesis through a variety of mechanisms. Despite their importance, the identification of SVs in cancer genomes remains challenging. Here, we present a framework that integrates optical mapping, high-throughput chromosome conformation capture (Hi-C), and whole-genome sequencing to systematically detect SVs in a variety of normal or cancer samples and cell lines. We identify the unique strengths of each method and demonstrate that only integrative approaches can comprehensively identify SVs in the genome. By combining Hi-C and optical mapping, we resolve complex SVs and phase multiple SV events to a single haplotype. Furthermore, we observe widespread structural variation events affecting the functions of noncoding sequences, including the deletion of distal regulatory sequences, alteration of DNA replication timing, and the creation of novel three-dimensional chromatin structural domains. Our results indicate that noncoding SVs may be underappreciated mutational drivers in cancer genomes.
Collapse
Affiliation(s)
- Jesse R Dixon
- Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Jie Xu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Vishnu Dileep
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | - Ye Zhan
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Fan Song
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Victoria T Le
- Salk Institute for Biological Studies, La Jolla, CA, USA
| | | | | | - Darrin V Bann
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Yanli Wang
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Royden Clark
- Penn State College of Medicine, Informatics and Technology, Hershey, PA, USA
| | - Lijun Zhang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Hongbo Yang
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Tingting Liu
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Sriranga Iyyanki
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Lin An
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA
| | - Christopher Pool
- Division of Otolaryngology, Head & Neck Surgery, Milton S. Hershey Medical Center, Hershey, PA, USA
| | - Takayo Sasaki
- Department of Biological Science, Florida State University, Tallahassee, FL, USA
| | | | - Hakan Ozadam
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Bryan R Lajoie
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA
| | - Rajinder Kaul
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | | | - Kristen Lee
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Morgan Diegel
- Altius institute for Biomedical Sciences, Seattle, WA, USA
| | - Dubravka Pezic
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Christina Ernst
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Suzana Hadjur
- Research Department of Cancer Biology, Cancer Institute, University College London, London, UK
| | - Duncan T Odom
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
- German Cancer Research Center (DKFZ), Division Signaling and Functional Genomics, Heidelberg, Germany
| | | | - James R Broach
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA
| | - Ross C Hardison
- Center for Comparative Genomics and Bioinformatics, Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, State College, PA, USA
| | - Ferhat Ay
- La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.
- School of Medicine, University of California San Diego, La Jolla, CA, USA.
| | | | - Job Dekker
- Program in Systems Biology, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA, USA.
- Howard Hughes Medical Institute, Chevy Chase, MD, USA.
| | - David M Gilbert
- Department of Biological Science, Florida State University, Tallahassee, FL, USA.
| | - Feng Yue
- Department of Biochemistry and Molecular Biology, College of Medicine, The Pennsylvania State University, Hershey, PA, USA.
- Bioinformatics and Genomics Program, The Pennsylvania State University, University Park, State College, PA, USA.
| |
Collapse
|
16
|
Ghader A, Ardakani AA, Ghaznavi H, Shakeri-Zadeh A, Minaei SE, Mohajer S, Ara MHM. Evaluation of nonlinear optical differences between breast cancer cell lines SK-BR-3 and MCF-7; an in vitro study. Photodiagnosis Photodyn Ther 2018; 23:171-175. [DOI: 10.1016/j.pdpdt.2018.06.015] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 06/17/2018] [Accepted: 06/18/2018] [Indexed: 01/30/2023]
|
17
|
Elbaz M, Ahirwar D, Ravi J, Nasser MW, Ganju RK. Novel role of cannabinoid receptor 2 in inhibiting EGF/EGFR and IGF-I/IGF-IR pathways in breast cancer. Oncotarget 2018; 8:29668-29678. [PMID: 27213582 PMCID: PMC5444694 DOI: 10.18632/oncotarget.9408] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Accepted: 04/10/2016] [Indexed: 12/18/2022] Open
Abstract
Breast cancer is the second leading cause of cancer deaths among women. Cannabinoid receptor 2 (CNR2 or CB2) is an integral part of the endocannabinoid system. Although CNR2 is highly expressed in the breast cancer tissues as well as breast cancer cell lines, its functional role in breast tumorigenesis is not well understood. We observed that estrogen receptor-α negative (ERα-) breast cancer cells highly express epidermal growth factor receptor (EGFR) as well as insulin-like growth factor-I receptor (IGF-IR). We also observed IGF-IR upregulation in ERα+ breast cancer cells. In addition, we found that higher CNR2 expression correlates with better recurrence free survival in ERα- and ERα+ breast cancer patients. Therefore, we analyzed the role of CNR2 specific agonist (JWH-015) on EGF and/or IGF-I-induced tumorigenic events in ERα- and ERα+ breast cancers. Our studies showed that CNR2 activation inhibited EGF and IGF-I-induced migration and invasion of ERα+ and ERα- breast cancer cells. At the molecular level, JWH-015 inhibited EGFR and IGF-IR activation and their downstream targets STAT3, AKT, ERK, NF-kB and matrix metalloproteinases (MMPs). In vivo studies showed that JWH-015 significantly reduced breast cancer growth in ERα+ and ERα- breast cancer mouse models. Furthermore, we found that the tumors derived from JWH-015-treated mice showed reduced activation of EGFR and IGF-IR and their downstream targets. In conclusion, we show that CNR2 activation suppresses breast cancer through novel mechanisms by inhibiting EGF/EGFR and IGF-I/IGF-IR signaling axes.
Collapse
Affiliation(s)
- Mohamad Elbaz
- Department of Pathology and The Comprehensive Cancer Center, The Ohio State University, Wexner Medical Center, Columbus, OH, USA.,Department of Pharmacology, Pharmacy School, Helwan University, Helwan, Egypt
| | - Dinesh Ahirwar
- Department of Pathology and The Comprehensive Cancer Center, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Janani Ravi
- Department of Pathology and The Comprehensive Cancer Center, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Mohd W Nasser
- Department of Pathology and The Comprehensive Cancer Center, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| | - Ramesh K Ganju
- Department of Pathology and The Comprehensive Cancer Center, The Ohio State University, Wexner Medical Center, Columbus, OH, USA
| |
Collapse
|
18
|
Schukken KM, Foijer F. CIN and Aneuploidy: Different Concepts, Different Consequences. Bioessays 2017; 40. [PMID: 29160563 DOI: 10.1002/bies.201700147] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 10/10/2017] [Indexed: 12/19/2022]
Abstract
Chromosomal instability (CIN) and aneuploidy are similar concepts but not synonymous. CIN is the process that leads to chromosome copy number alterations, and aneuploidy is the result. While CIN and resulting aneuploidy often cause growth defects, they are also selected for in cancer cells. Although such contradicting fates may seem paradoxical at first, they can be better understood when CIN and aneuploidy are assessed separately, taking into account the in vitro or in vivo context, the rate of CIN, and severity of the aneuploid karyotype. As CIN can only be measured in living cells, which proves to be technically challenging in vivo, aneuploidy is more frequently quantified. However, CIN rates might be more predictive for tumor outcome than assessing aneuploidy rates alone. In reviewing the literature, we therefore conclude that there is an urgent need for new models in which we can monitor chromosome mis-segregation and its consequences in vivo. Also see the video abstract here: https://youtu.be/fL3LxZduchg.
Collapse
Affiliation(s)
- Klaske M Schukken
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
| | - Floris Foijer
- European Research Institute for the Biology of Ageing (ERIBA), University of Groningen, University Medical Center Groningen, 9713 AV, Groningen, The Netherlands
| |
Collapse
|
19
|
Chakraborty A, Ay F. Identification of copy number variations and translocations in cancer cells from Hi-C data. Bioinformatics 2017; 34:338-345. [PMID: 29048467 DOI: 10.1093/bioinformatics/btx664] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Revised: 09/21/2017] [Accepted: 10/17/2017] [Indexed: 11/14/2022] Open
Abstract
MOTIVATION Eukaryotic chromosomes adapt a complex and highly dynamic three-dimensional (3D) structure, which profoundly affects different cellular functions and outcomes including changes in epigenetic landscape and in gene expression. Making the scenario even more complex, cancer cells harbor chromosomal abnormalities [e.g. copy number variations (CNVs) and translocations] altering their genomes both at the sequence level and at the level of 3D organization. High-throughput chromosome conformation capture techniques (e.g. Hi-C), which are originally developed for decoding the 3D structure of the chromatin, provide a great opportunity to simultaneously identify the locations of genomic rearrangements and to investigate the 3D genome organization in cancer cells. Even though Hi-C data has been used for validating known rearrangements, computational methods that can distinguish rearrangement signals from the inherent biases of Hi-C data and from the actual 3D conformation of chromatin, and can precisely detect rearrangement locations de novo have been missing. RESULTS In this work, we characterize how intra and inter-chromosomal Hi-C contacts are distributed for normal and rearranged chromosomes to devise a new set of algorithms (i) to identify genomic segments that correspond to CNV regions such as amplifications and deletions (HiCnv), (ii) to call inter-chromosomal translocations and their boundaries (HiCtrans) from Hi-C experiments and (iii) to simulate Hi-C data from genomes with desired rearrangements and abnormalities (AveSim) in order to select optimal parameters for and to benchmark the accuracy of our methods. Our results on 10 different cancer cell lines with Hi-C data show that we identify a total number of 105 amplifications and 45 deletions together with 90 translocations, whereas we identify virtually no such events for two karyotypically normal cell lines. Our CNV predictions correlate very well with whole genome sequencing data among chromosomes with CNV events for a breast cancer cell line (r = 0.89) and capture most of the CNVs we simulate using Avesim. For HiCtrans predictions, we report evidence from the literature for 30 out of 90 translocations for eight of our cancer cell lines. Furthermore, we show that our tools identify and correctly classify relatively understudied rearrangements such as double minutes and homogeneously staining regions. Considering the inherent limitations of existing techniques for karyotyping (i.e. missing balanced rearrangements and those near repetitive regions), the accurate identification of CNVs and translocations in a cost-effective and high-throughput setting is still a challenge. Our results show that the set of tools we develop effectively utilize moderately sequenced Hi-C libraries (100-300 million reads) to identify known and de novo chromosomal rearrangements/abnormalities in well-established cancer cell lines. With the decrease in required number of cells and the increase in attainable resolution, we believe that our framework will pave the way towards comprehensive mapping of genomic rearrangements in primary cells from cancer patients using Hi-C. AVAILABILITY AND IMPLEMENTATION CNV calling: https://github.com/ay-lab/HiCnv, Translocation calling: https://github.com/ay-lab/HiCtrans and Hi-C simulation: https://github.com/ay-lab/AveSim. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Collapse
Affiliation(s)
- Abhijit Chakraborty
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA
| | - Ferhat Ay
- Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA.,School of Medicine, University of California San Diego, 9500 Gilman Drive, La Jolla, CA, USA
| |
Collapse
|
20
|
Rondón-Lagos M, Rangel N, Di Cantogno LV, Annaratone L, Castellano I, Russo R, Manetta T, Marchiò C, Sapino A. Effect of low doses of estradiol and tamoxifen on breast cancer cell karyotypes. Endocr Relat Cancer 2016; 23:635-50. [PMID: 27357940 PMCID: PMC5064758 DOI: 10.1530/erc-16-0078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 06/29/2016] [Indexed: 12/21/2022]
Abstract
Evidence supports a role of 17&-estradiol (E2) in carcinogenesis and the large majority of breast carcinomas are dependent on estrogen. The anti-estrogen tamoxifen (TAM) is widely used for both treatment and prevention of breast cancer; however, it is also carcinogenic in human uterus and rat liver, highlighting the profound complexity of its actions. The nature of E2- or TAM-induced chromosomal damage has been explored using relatively high concentrations of these agents, and only some numerical aberrations and chromosomal breaks have been analyzed. This study aimed to determine the effects of low doses of E2 and TAM (10(&8 )mol L(&1) and 10(&6 )mol L(&1) respectively) on karyotypes of MCF7, T47D, BT474, and SKBR3 breast cancer cells by comparing the results of conventional karyotyping and multi-FISH painting with cell proliferation. Estrogen receptor (ER)-positive (+) cells showed an increase in cell proliferation after E2 treatment (MCF7, T47D, and BT474) and a decrease after TAM treatment (MCF7 and T47D), whereas in ER& cells (SKBR3), no alterations in cell proliferation were observed, except for a small increase at 96 h. Karyotypes of both ER+ and ER& breast cancer cells increased in complexity after treatments with E2 and TAM leading to specific chromosomal abnormalities, some of which were consistent throughout the treatment duration. This genotoxic effect was higher in HER2+ cells. The ER&/HER2+ SKBR3 cells were found to be sensitive to TAM, exhibiting an increase in chromosomal aberrations. These in vitro results provide insights into the potential role of low doses of E2 and TAM in inducing chromosomal rearrangements in breast cancer cells.
Collapse
Affiliation(s)
| | - Nelson Rangel
- Department of Medical SciencesUniversity of Turin, Turin, Italy Natural and Mathematical Sciences FacultyUniversidad del Rosario, Bogotá, Colombia
| | | | | | | | - Rosalia Russo
- Department of Medical SciencesUniversity of Turin, Turin, Italy
| | - Tilde Manetta
- Department of Public Health and PediatricsUniversity of Turin, Turin, Italy
| | | | - Anna Sapino
- Department of Medical SciencesUniversity of Turin, Turin, Italy Candiolo Cancer InstituteFPO-IRCCS, Candiolo, Italy
| |
Collapse
|
21
|
Kleensang A, Vantangoli MM, Odwin-DaCosta S, Andersen ME, Boekelheide K, Bouhifd M, Fornace AJ, Li HH, Livi CB, Madnick S, Maertens A, Rosenberg M, Yager JD, Zhao L, Hartung T. Genetic variability in a frozen batch of MCF-7 cells invisible in routine authentication affecting cell function. Sci Rep 2016; 6:28994. [PMID: 27456714 PMCID: PMC4960662 DOI: 10.1038/srep28994] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/13/2016] [Indexed: 12/30/2022] Open
Abstract
Common recommendations for cell line authentication, annotation and quality control fall short addressing genetic heterogeneity. Within the Human Toxome Project, we demonstrate that there can be marked cellular and phenotypic heterogeneity in a single batch of the human breast adenocarcinoma cell line MCF-7 obtained directly from a cell bank that are invisible with the usual cell authentication by short tandem repeat (STR) markers. STR profiling just fulfills the purpose of authentication testing, which is to detect significant cross-contamination and cell line misidentification. Heterogeneity needs to be examined using additional methods. This heterogeneity can have serious consequences for reproducibility of experiments as shown by morphology, estrogenic growth dose-response, whole genome gene expression and untargeted mass-spectroscopy metabolomics for MCF-7 cells. Using Comparative Genomic Hybridization (CGH), differences were traced back to genetic heterogeneity already in the cells from the original frozen vials from the same ATCC lot, however, STR markers did not differ from ATCC reference for any sample. These findings underscore the need for additional quality assurance in Good Cell Culture Practice and cell characterization, especially using other methods such as CGH to reveal possible genomic heterogeneity and genetic drifts within cell lines.
Collapse
Affiliation(s)
- Andre Kleensang
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
| | | | - Shelly Odwin-DaCosta
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
| | - Melvin E Andersen
- The Hamner Institutes for Health Sciences, Research Triangle Park, NC, USA
| | - Kim Boekelheide
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Mounir Bouhifd
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
| | - Albert J Fornace
- Department of Biochemistry and Molecular &Cellular Biology, and Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | - Heng-Hong Li
- Department of Biochemistry and Molecular &Cellular Biology, and Lombardi Comprehensive Cancer Center, Georgetown University, Washington, DC, USA
| | | | - Samantha Madnick
- Department of Pathology and Laboratory Medicine, Brown University, Providence, RI, USA
| | - Alexandra Maertens
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
| | | | - James D Yager
- Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Liang Zhao
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
| | - Thomas Hartung
- Center for Alternatives to Animal Testing (CAAT), Department of Environmental Health Sciences, Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA.,University of Konstanz, CAAT-Europe, Germany
| |
Collapse
|
22
|
Whole genome sequence analysis of BT-474 using complete Genomics' standard and long fragment read technologies. Gigascience 2016; 5:8. [PMID: 26865974 PMCID: PMC4748558 DOI: 10.1186/s13742-016-0113-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 01/19/2016] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND The cell line BT-474 is a popular cell line for studying the biology of cancer and developing novel drugs. However, there is no complete, published genome sequence for this highly utilized scientific resource. In this study we sought to provide a comprehensive and useful data set for the scientific community by generating a whole genome sequence for BT-474. FINDINGS Five μg of genomic DNA, isolated from an early passage of the BT-474 cell line, was used to generate a whole genome sequence (114X coverage) using Complete Genomics' standard sequencing process. To provide additional variant phasing and structural variation data we also processed and analyzed two separate libraries of 5 and 6 individual cells to depths of 99X and 87X, respectively, using Complete Genomics' Long Fragment Read (LFR) technology. CONCLUSIONS BT-474 is a highly aneuploid cell line with an extremely complex genome sequence. This ~300X total coverage genome sequence provides a more complete understanding of this highly utilized cell line at the genomic level.
Collapse
|
23
|
de Oliveira-Júnior RJ, Ueira-Vieira C, Sena AAS, Reis CF, Mineo JR, Goulart LR, Morelli S. Chromosomal disruption and rearrangements during murine sarcoma development converge to stable karyotypic formation kept by telomerase overexpression. J Biomed Sci 2016; 23:22. [PMID: 26841871 PMCID: PMC4739385 DOI: 10.1186/s12929-016-0230-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/12/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tumor initiation presents a complex and unstable genomic landscape; one of the earliest hallmark events of cancer, and its progression is probably based on selection mechanisms under specific environments that lead to functional tumor cell speciation. We hypothesized that viable tumor phenotypes possess common and highly stable karyotypes and their proliferation is facilitated by an attuned high telomerase activity. Very few investigations have focused on the evolution of common chromosomal rearrangements associated to molecular events that result in functional phenotypes during tumor development. RESULTS We have used cytogenetic, flow cytometry and cell culture tools to investigate chromosomal rearrangements and clonality during cancer development using the murine sarcoma TG180 model, and also molecular biology techniques to establish a correlation between chromosome instability and telomerase activity, since telomeres are highly affected during cancer evolution. Cytogenetic analysis showed a near-tetraploid karyotype originated by endoreduplication. Chromosomal rearrangements were random events in response to in vitro conditions, but a stable karyotypic equilibrium was achieved during tumor progression in different in vivo conditions, suggesting that a specific microenvironment may stabilize the chromosomal number and architecture. Specific chromosome aberrations (marker chromosomes) and activated regions (rDNAs) were ubiquitous in the karyotype, suggesting that the conservation of these patterns may be advantageous for tumor progression. High telomerase expression was also correlated with the chromosomal rearrangements stabilization. CONCLUSIONS Our data reinforce the notion that the sarcoma cell evolution converges from a highly unstable karyotype to relatively stable and functional chromosome rearrangements, which are further enabled by telomerase overexpression.
Collapse
Affiliation(s)
| | - Carlos Ueira-Vieira
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | | | - Carolina Fernandes Reis
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - José Roberto Mineo
- Institute of Biomedical Sciences, Federal University of Uberlândia, Uberlândia, MG, Brazil
| | - Luiz Ricardo Goulart
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil. .,Department of Medical Microbiology and Immunology, University of California Davis, Davis, CA, USA.
| | - Sandra Morelli
- Institute of Genetics and Biochemistry, Federal University of Uberlândia, Uberlândia, MG, Brazil.
| |
Collapse
|
24
|
Eletxigerra U, Martinez-Perdiguero J, Merino S, Barderas R, Ruiz-Valdepeñas Montiel V, Villalonga R, Pingarrón JM, Campuzano S. Electrochemical Magnetoimmunosensor for Progesterone Receptor Determination. Application to the Simultaneous Detection of Estrogen and Progesterone Breast-cancer Related Receptors in Raw Cell Lysates. ELECTROANAL 2015. [DOI: 10.1002/elan.201501090] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
| | | | - S. Merino
- Micro-NanoFabrication Unit; IK4-Tekniker; Eibar Spain
| | - R. Barderas
- Departamento de Bioquímica y Biología Molecular, Facultad de CC. Químicas; Universidad Complutense de Madrid; Madrid Spain
| | - V. Ruiz-Valdepeñas Montiel
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; Madrid Spain
| | - R. Villalonga
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; Madrid Spain
| | - J. M. Pingarrón
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; Madrid Spain
| | - S. Campuzano
- Departamento de Química Analítica, Facultad de CC. Químicas; Universidad Complutense de Madrid; Madrid Spain
| |
Collapse
|
25
|
Li Y, Arao Y, Hall JM, Burkett S, Liu L, Gerrish K, Cavailles V, Korach KS. Research Resource: STR DNA profile and gene expression comparisons of human BG-1 cells and a BG-1/MCF-7 clonal variant. Mol Endocrinol 2015; 28:2072-81. [PMID: 25321415 DOI: 10.1210/me.2014-1229] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Human ovarian cancer BG-1 cells are a valuable in vitro model that has enabled several laboratories to study the estrogenic responses of ovarian cancers. We recently discovered that there are two different BG-1 cell lines being used for experiments, denoted here as BG-1 FR and BG-1 NIEHS, which exhibit striking morphological differences. The objective of this study was to methodically analyze these two BG-1 variants and compare their characteristics. Short tandem repeat analysis revealed that the DNA profile of BG-1 FR cells was unique, yet the Short tandem repeat pattern of BG-1 NIEHS was identical with that of MCF-7 cells. From a cytogenetic analysis, it became apparent that the BG-1 FR line had the same profile as previously reported, whereas the BG-1 NIEHS and MCF-7 cells share a similar genetic display. A significant number of unique chromosomal translocations were observed between the BG-1 NIEHS and MCF-7 cells, suggesting that acquired genotypic differences resulted in the formation of two lines from a common origin. Although all cell types demonstrated a similar estrogen responsiveness in reporter gene assays, a microarray analysis revealed distinct estrogen-responsive gene expression patterns with surprisingly moderate to low overlap. We conclude that BG-1 FR is the original ovarian cancer cell line, whereas the BG-1 NIEHS is a variant from the MCF-7 cells. These findings provide much needed clarification of the identities and characteristics of key cell line models that are widely used to study estrogen action in female reproductive cancers.
Collapse
Affiliation(s)
- Yin Li
- Laboratory of Reproductive and Developmental Toxicology (Y.L., Y.A., K.S.K.) and Molecular Genomics Core Facility (L.L., K.G.), National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709; College of Pharmacy and Health Sciences (J.M.H.), Campbell University, Buies Creek, North Carolina 27506; Center for Cancer Research (S.B.), National Cancer Institute, National Institutes of Health, Frederick, Maryland 21702; and Institut de Recherche en Cancérologie de Montpellier (V.C.), Institut de Recherche en Cancerologie de Montpellier and INSERM Unité 896, Universite Montpellier1, F-34298 Montpellier, France
| | | | | | | | | | | | | | | |
Collapse
|
26
|
Abstract
The most widely used approach for defining gene function is to reduce or completely disrupt its normal expression. For over a decade, RNAi has ruled the lab, offering a magic bullet to disrupt gene expression in many organisms. However, new biotechnological tools--specifically CRISPR-based technologies--have become available and are squeezing out RNAi dominance in mammalian cell studies. These seemingly competing technologies leave research investigators with the question: "Which technology should I use in my experiment?" This review offers a practical resource to compare and contrast these technologies, guiding the investigator when and where to use this fantastic array of powerful tools.
Collapse
Affiliation(s)
- Michael Boettcher
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Michael T McManus
- Department of Microbiology and Immunology, UCSF Diabetes Center, Keck Center for Noncoding RNA, University of California, San Francisco, San Francisco, CA 94143, USA.
| |
Collapse
|
27
|
Sakamoto R, Rahman MM, Shimomura M, Itoh M, Nakatsura T. Time-lapse imaging assay using the BioStation CT: a sensitive drug-screening method for three-dimensional cell culture. Cancer Sci 2015; 106:757-765. [PMID: 25865675 PMCID: PMC4471796 DOI: 10.1111/cas.12667] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 12/24/2022] Open
Abstract
Three-dimensional (3D) cell culture is beneficial for physiological studies of tumor cells, due to its potential to deliver a high quantity of cell culture information that is representative of the cancer microenvironment and predictive of drug responses in vivo. Currently, gel-associated or matrix-associated 3D cell culture is comprised of intricate procedures that often result in experimental complexity. Therefore, we developed an innovative anti-cancer drug sensitivity screening technique for 3D cell culture on NanoCulture Plates (NCP) by employing the imaging device BioStation CT. Here, we showed that the human breast cancer cell lines BT474 and T47D form multicellular spheroids on NCP plates and compared their sensitivity to the anti-cancer drugs trastuzumab and paclitaxel using the BioStation CT. The anticancer drugs reduced spheroid migration velocity and suppressed spheroid fusion. In addition, primary cells derived from the human breast cancer tissues B58 and B61 grown on NCP plates also exhibited similar drug sensitivity. These results were in good agreement with the conventional assay method using ATP quantification. We confirmed the antitumor effects of the drugs on cells seeded in 96-well plates using the BioStation CT imaging technique. We expect this method to be useful in research for new antitumor agents and for drug sensitivity tests in individually-tailored cancer treatments.
Collapse
Affiliation(s)
| | | | - Manami Shimomura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| | - Manabu Itoh
- SCIVAX Life Sciences, Kawasaki, Kanagawa, Japan
| | - Tetsuya Nakatsura
- Division of Cancer Immunotherapy, Exploratory Oncology Research and Clinical Trial Center, National Cancer Center, Kashiwa, Chiba, Japan
| |
Collapse
|
28
|
Wang YK, Chen Z, Yun T, Li CY, Jiang B, Lv XX, Chu GH, Wang SN, Yan H, Shi LF. Human epidermal growth factor receptor 2 expression in mixed gastric carcinoma. World J Gastroenterol 2015; 21:4680-4687. [PMID: 25914479 PMCID: PMC4402317 DOI: 10.3748/wjg.v21.i15.4680] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Revised: 12/29/2014] [Accepted: 02/11/2015] [Indexed: 02/07/2023] Open
Abstract
AIM: To investigate human epidermal growth factor receptor 2 (HER2) amplification and protein expression in mixed gastric carcinoma.
METHODS: Fluorescence in situ hybridization and immunohistochemistry were used to detect HER2 amplification and protein expression in 277 cases of mixed gastric carcinoma. Protein staining intensity was rate as 1+, 2+, or 3+.
RESULTS: Of the 277 cases, 114 (41.2%) expressed HER2 protein. HER2 3+ staining was observed in 28/277 (10.1%) cases, 2+ in 37/277 (13.4%) cases, and 1+ in 49/277 (17.7%) cases. A HER2 amplification rate of 17% was detected, of which 25/28 (89.3%) were observed in the HER2 3+ staining group, 17/37 (45.9%) in 2+, and 5/49 (10.2%) in 1+. Of the 47 patients with HER2 amplification who received chemotherapy plus trastuzumab, 22 demonstrated median progression-free and overall survivals of 9.1 mo and 16.7 mo, respectively, which were significantly better than those achieved with chemotherapy alone (5.6 mo and 12.1 mo, respectively) in 19 previously treated patients (Ps < 0.05).
CONCLUSION: HER2 detection in mixed gastric carcinoma displays high heterogeneity. Relatively quantitative parameters are needed for assessing the level of HER2 amplification and protein expression.
Collapse
MESH Headings
- Adult
- Aged
- Antineoplastic Agents/therapeutic use
- Biomarkers, Tumor/analysis
- Biomarkers, Tumor/genetics
- Carcinoma/chemistry
- Carcinoma/drug therapy
- Carcinoma/genetics
- Carcinoma/mortality
- Carcinoma/pathology
- Disease Progression
- Disease-Free Survival
- Female
- Gene Amplification
- Humans
- Immunohistochemistry
- In Situ Hybridization, Fluorescence
- Male
- Middle Aged
- Neoplasms, Complex and Mixed/chemistry
- Neoplasms, Complex and Mixed/drug therapy
- Neoplasms, Complex and Mixed/genetics
- Neoplasms, Complex and Mixed/mortality
- Neoplasms, Complex and Mixed/pathology
- Patient Selection
- Predictive Value of Tests
- RNA, Messenger/analysis
- Receptor, ErbB-2/analysis
- Receptor, ErbB-2/antagonists & inhibitors
- Receptor, ErbB-2/genetics
- Stomach Neoplasms/chemistry
- Stomach Neoplasms/drug therapy
- Stomach Neoplasms/genetics
- Stomach Neoplasms/mortality
- Stomach Neoplasms/pathology
- Time Factors
- Trastuzumab/therapeutic use
- Treatment Outcome
Collapse
|
29
|
Schug ZT, Peck B, Jones DT, Zhang Q, Grosskurth S, Alam IS, Goodwin LM, Smethurst E, Mason S, Blyth K, McGarry L, James D, Shanks E, Kalna G, Saunders RE, Jiang M, Howell M, Lassailly F, Thin MZ, Spencer-Dene B, Stamp G, van den Broek NJF, Mackay G, Bulusu V, Kamphorst JJ, Tardito S, Strachan D, Harris AL, Aboagye EO, Critchlow SE, Wakelam MJO, Schulze A, Gottlieb E. Acetyl-CoA synthetase 2 promotes acetate utilization and maintains cancer cell growth under metabolic stress. Cancer Cell 2015; 27:57-71. [PMID: 25584894 PMCID: PMC4297291 DOI: 10.1016/j.ccell.2014.12.002] [Citation(s) in RCA: 553] [Impact Index Per Article: 61.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/05/2014] [Accepted: 12/09/2014] [Indexed: 12/17/2022]
Abstract
A functional genomics study revealed that the activity of acetyl-CoA synthetase 2 (ACSS2) contributes to cancer cell growth under low-oxygen and lipid-depleted conditions. Comparative metabolomics and lipidomics demonstrated that acetate is used as a nutritional source by cancer cells in an ACSS2-dependent manner, and supplied a significant fraction of the carbon within the fatty acid and phospholipid pools. ACSS2 expression is upregulated under metabolically stressed conditions and ACSS2 silencing reduced the growth of tumor xenografts. ACSS2 exhibits copy-number gain in human breast tumors, and ACSS2 expression correlates with disease progression. These results signify a critical role for acetate consumption in the production of lipid biomass within the harsh tumor microenvironment.
Collapse
Affiliation(s)
- Zachary T Schug
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Barrie Peck
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Dylan T Jones
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Qifeng Zhang
- Babraham Institute, Babraham Research Campus, Cambridge CB22 3AT, UK
| | | | - Israt S Alam
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | | | | | - Susan Mason
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Karen Blyth
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Lynn McGarry
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Daniel James
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Emma Shanks
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gabriela Kalna
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Rebecca E Saunders
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Ming Jiang
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Michael Howell
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Francois Lassailly
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - May Zaw Thin
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Bradley Spencer-Dene
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Gordon Stamp
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Niels J F van den Broek
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Gillian Mackay
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Vinay Bulusu
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Jurre J Kamphorst
- Institute of Cancer Sciences, University of Glasgow, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Saverio Tardito
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - David Strachan
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK
| | - Adrian L Harris
- Molecular Oncology Laboratories, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Eric O Aboagye
- Department of Surgery and Cancer, Imperial College London, Hammersmith Hospital, Du Cane Road, London W12 0NN, UK
| | | | | | - Almut Schulze
- Cancer Research UK, London Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Eyal Gottlieb
- Cancer Research UK, Beatson Institute, Garscube Estate, Switchback Road, Glasgow G61 1BD, UK.
| |
Collapse
|
30
|
Rondón-Lagos M, Verdun Di Cantogno L, Rangel N, Mele T, Ramírez-Clavijo SR, Scagliotti G, Marchiò C, Sapino A. Unraveling the chromosome 17 patterns of FISH in interphase nuclei: an in-depth analysis of the HER2 amplicon and chromosome 17 centromere by karyotyping, FISH and M-FISH in breast cancer cells. BMC Cancer 2014; 14:922. [PMID: 25481507 PMCID: PMC4295336 DOI: 10.1186/1471-2407-14-922] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Accepted: 11/27/2014] [Indexed: 11/10/2022] Open
Abstract
Background In diagnostic pathology, HER2 status is determined in interphase nuclei by fluorescence in situ hybridization (FISH) with probes for the HER2 gene and for the chromosome 17 centromere (CEP17). The latter probe is used as a surrogate for chromosome 17 copies, however chromosome 17 (Chr17) is frequently rearranged. The frequency and type of specific structural Chr17 alterations in breast cancer have been studied by using comparative genomic hybridization and spectral karyotyping, but not fully detailed. Actually, balanced chromosome rearrangements (e.g. translocations or inversions) and low frequency mosaicisms are assessable on metaphases using G-banding karyotype and multicolor FISH (M-FISH) only. Methods We sought to elucidate the CEP17 and HER2 FISH patterns of interphase nuclei by evaluating Chr17 rearrangements in metaphases of 9 breast cancer cell lines and a primary culture from a triple negative breast carcinoma by using G-banding, FISH and M-FISH. Results Thirty-nine rearranged chromosomes containing a portion of Chr17 were observed. Chromosomes 8 and 11 were the most frequent partners of Chr17 translocations. The lowest frequency of Chr17 abnormalities was observed in the HER2-negative cell lines, while the highest was observed in the HER2-positive SKBR3 cells. The MDA-MB231 triple negative cell line was the sole to show only non-altered copies of Chr17, while the SKBR3, MDA-MB361 and JIMT-1 HER2-positive cells carried no normal Chr17 copies. True polysomy was observed in MDA-MB231 as the only Chr17 alteration. In BT474 cells polysomy was associated to Chr17 structural alterations. By comparing M-FISH and FISH data, in 8 out of 39 rearranged chromosomes only CEP17 signals were detectable, whereas in 14 rearranged chromosomes HER2 and STARD3 genes were present without CEP17 signals. HER2 and STARD3 always co-localized on the same chromosomes and were always co-amplified, whereas TOP2A also mapped to different derivatives and was co-amplified with HER2 and STARD3 on SKBR3 cells only. Conclusion The high frequency of complex Chr17 abnormalities suggests that the interpretation of FISH results on interphase nuclei using a dual probe assay to assess gene amplification should be performed “with caution”, given that CEP17 signals are not always indicative of normal unaltered or rearranged copies of Chr17.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Caterina Marchiò
- Department of Medical Sciences, University of Turin, Via Santena 7, 10126 Turin, Italy.
| | | |
Collapse
|