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Choudhuri S, Patton GW, Chanderbhan RF, Mattia A, Klaassen CD. From Classical Toxicology to Tox21: Some Critical Conceptual and Technological Advances in the Molecular Understanding of the Toxic Response Beginning From the Last Quarter of the 20th Century. Toxicol Sci 2018; 161:5-22. [PMID: 28973688 PMCID: PMC5837539 DOI: 10.1093/toxsci/kfx186] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Toxicology has made steady advances over the last 60+ years in understanding the mechanisms of toxicity at an increasingly finer level of cellular organization. Traditionally, toxicological studies have used animal models. However, the general adoption of the principles of 3R (Replace, Reduce, Refine) provided the impetus for the development of in vitro models in toxicity testing. The present commentary is an attempt to briefly discuss the transformation in toxicology that began around 1980. Many genes important in cellular protection and metabolism of toxicants were cloned and characterized in the 80s, and gene expression studies became feasible, too. The development of transgenic and knockout mice provided valuable animal models to investigate the role of specific genes in producing toxic effects of chemicals or protecting the organism from the toxic effects of chemicals. Further developments in toxicology came from the incorporation of the tools of "omics" (genomics, proteomics, metabolomics, interactomics), epigenetics, systems biology, computational biology, and in vitro biology. Collectively, the advances in toxicology made during the last 30-40 years are expected to provide more innovative and efficient approaches to risk assessment. A goal of experimental toxicology going forward is to reduce animal use and yet be able to conduct appropriate risk assessments and make sound regulatory decisions using alternative methods of toxicity testing. In that respect, Tox21 has provided a big picture framework for the future. Currently, regulatory decisions involving drugs, biologics, food additives, and similar compounds still utilize data from animal testing and human clinical trials. In contrast, the prioritization of environmental chemicals for further study can be made using in vitro screening and computational tools.
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Affiliation(s)
- Supratim Choudhuri
- Office of Food Additive Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Geoffrey W Patton
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington
| | - Ronald F Chanderbhan
- Office of Food Additive Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Antonia Mattia
- Office of Food Additive Safety, Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration, College Park, Maryland
| | - Curtis D Klaassen
- Department of Environmental and Occupational Health Sciences, School of Public Health, University of Washington, Seattle, Washington
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302
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Sun Q, Choudhary S, Mannion C, Kissin Y, Zilberberg J, Lee WY. Ex vivo replication of phenotypic functions of osteocytes through biomimetic 3D bone tissue construction. Bone 2018; 106:148-155. [PMID: 29066313 PMCID: PMC5694355 DOI: 10.1016/j.bone.2017.10.019] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/16/2017] [Accepted: 10/20/2017] [Indexed: 12/11/2022]
Abstract
Osteocytes, residing as 3-dimensionally (3D) networked cells in bone, are well known to regulate bone and mineral homeostasis and have been recently implicated to interact with cancer cells to influence the progression of bone metastases. In this study, a bone tissue consisting of 3D-networked primary human osteocytes and MLO-A5 cells was constructed using: (1) the biomimetic close-packed assembly of 20-25μm microbeads with primary cells isolated from human bone samples and MLO-A5 cells and (2) subsequent perfusion culture in a microfluidic device. With this 3D tissue construction approach, we replicated ex vivo, for the first time, the mechanotransduction function of human primary osteocytes and MLO-A5 cells by correlating the effects of cyclic compression on down-regulated SOST and DKK1 expressions. Also, as an example of using our ex vivo model to evaluate therapeutic agents, we confirmed previously reported findings that parathyroid hormone (PTH) decreases SOST and increases the ratio of RANKL and OPG. In comparison to other in vitro models, our ex vivo model: (1) replicates the cell density, phenotype, and functions of primary human osteocytes and MLO-A5 cells and (2) thus provides a clinically relevant means of studying bone diseases and metastases.
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Affiliation(s)
- Qiaoling Sun
- Department of Materials Science and Chemical Engineering, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Saba Choudhary
- Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Ciaran Mannion
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Yair Kissin
- Department of Orthopeidc Surgery, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Jenny Zilberberg
- Department of Biomedical Research, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Woo Y Lee
- Department of Materials Science and Chemical Engineering, Stevens Institute of Technology, Hoboken, NJ, USA.
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303
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Lee Y, Choi YR, Kim KY, Shin DH. The impact of intermittent versus continuous exposure to EGFR tyrosine kinase inhibitor on selection of EGFR T790M-mutant drug-resistant clones in a lung cancer cell line carrying activating EGFR mutation. Oncotarget 2017; 7:43315-43323. [PMID: 27270313 PMCID: PMC5190025 DOI: 10.18632/oncotarget.9703] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 05/09/2016] [Indexed: 01/01/2023] Open
Abstract
Drug-resistant cell lines are essential tools for investigating the mechanisms of resistance to molecular-targeted anti-cancer drugs. However, little is known about how to establish clinically relevant drug-resistant cell lines. Our study examined the impact of a drug-free period on the establishment of a cell line with clinically relevant resistance to molecular-targeted drugs. We used PC9 cells, a lung cancer cell line carrying EGFR mutation, because this is a validated target for EGFR tyrosine kinase inhibitors (TKI). PC9 cells were intermittently or continuously exposed to increasing concentrations of gefitinib (0.01 μM to 1.0 μM) and the emergence of the most common acquired resistance mutation in EGFR, T790M, was determined. T790M was detected at a 25-fold lower drug concentration in cells continuously exposed to gefitinib (PC9/GRc) than in cells intermittently exposed to gefitinib (PC9/GRi) (0.04 μM vs 1.0 μM, respectively). The mutation frequencies at those drug concentrations were 19.8% and 8.0% in PC9/GRc and PC9/GRi cells, respectively. After drug-free culture for 8 weeks, resistance to gefitinib decreased in the PC9/GRi cells but not in the PC9/GRc cells. In the PC9/GRc cells, the frequency of the T790M mutation was consistently about 20% from 0.04 μM to 1.0 μM of gefitinib. In the PC9/GRc cells, the T790M mutation was detected in all single-cell clones, at frequencies ranging from 7.0% to 37.0%, with a median of 19.5% (95% confidence interval, 17.3%–20.9%). In conclusion, compared with intermittent drug exposure, continuous exposure might select better minor drug-resistant clones when creating cell lines resistant to molecular-targeted drugs.
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Affiliation(s)
- Youngjoo Lee
- Center for Lung Cancer, National Cancer Center, Goyang, Republic of Korea.,Lung Cancer Branch, Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Yu-Ra Choi
- Lung Cancer Branch, Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Kyoung-Yeon Kim
- Lung Cancer Branch, Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
| | - Dong Hoon Shin
- Lung Cancer Branch, Research Institute and Hospital, National Cancer Center, Goyang, Republic of Korea
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304
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Yoshida T, Kates M, Sopko NA, Liu X, Singh AK, Bishai WR, Joice G, McConkey DJ, Bivalacqua TJ. Ex vivo culture of tumor cells from N-methyl-N-nitrosourea-induced bladder cancer in rats: Development of organoids and an immortalized cell line. Urol Oncol 2017; 36:160.e23-160.e32. [PMID: 29288005 DOI: 10.1016/j.urolonc.2017.11.024] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Revised: 11/24/2017] [Accepted: 11/30/2017] [Indexed: 01/09/2023]
Abstract
OBJECTIVE We ex vivo cultured primary tumor cells from N-methyl-N-nitrosourea (MNU)-induced bladder tumors in rats and established an immortalized cell line from them. MATERIALS AND METHODS Bladder tumors in rats were induced by instillation of MNU into the murine bladder. Primary tumor cells were prepared by the cancer-tissue originated spheroid method. An immortalized cell line was established by co-culture with fibroblasts. The cultured tumor cells were molecularly and functionally characterized by quantitative real-time polymerase chain reaction, Western blot, growth assay, and transwell migration assay. RESULTS Primary tumor cells were successfully prepared as multicellular spheroids from MNU-induced bladder tumors. The differentiation marker expression patterns observed in the original tumors were largely retained in the spheroids. We succeeded in establishing a cell line from the spheroids and named it T-MNU-1. Although basal markers (CK14 and CK5) were enriched in T-MNU-1 compared to the spheroids, T-MNU-1 expressed both luminal and basal markers. T-MNU-1 was able to migrate through a transwell. CONCLUSIONS Tumor cells in MNU-induced bladder tumors were successfully cultured ex vivo as organoids, and an immortalized cell line was also established from them. The ex vivo models offer a platform that enables analysis of intrinsic characteristics of tumor cells excluding influence of microenvironment in MNU-induced bladder tumors.
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Affiliation(s)
- Takahiro Yoshida
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD.
| | - Max Kates
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Nikolai A Sopko
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Xiaopu Liu
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - Alok K Singh
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, MD
| | - William R Bishai
- Center for Tuberculosis Research, Johns Hopkins School of Medicine, Baltimore, MD
| | - Gregory Joice
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD
| | - David J McConkey
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD; The Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD
| | - Trinity J Bivalacqua
- The James Buchanan Brady Urological Institute and Department of Urology, Johns Hopkins School of Medicine, Baltimore, MD; The Johns Hopkins Greenberg Bladder Cancer Institute, Baltimore, MD
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305
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Moreira L, Bakir B, Chatterji P, Dantes Z, Reichert M, Rustgi AK. Pancreas 3D Organoids: Current and Future Aspects as a Research Platform for Personalized Medicine in Pancreatic Cancer. Cell Mol Gastroenterol Hepatol 2017; 5. [PMID: 29541683 PMCID: PMC5849862 DOI: 10.1016/j.jcmgh.2017.12.004] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Pancreatic ductal adenocarcinoma is one of the most aggressive forms of cancer, and the third leading cause of cancer-related mortality in the United States. Although important advances have been made in the last decade, the mortality rate of pancreatic ductal adenocarcinoma has not changed appreciably. This review summarizes a rapidly emerging model of pancreatic cancer research, focusing on 3-dimensional organoids as a powerful tool for several applications, but above all, representing a step toward personalized medicine.
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Affiliation(s)
- Leticia Moreira
- Division of Gastroenterology, Departments of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania,Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas, IDIBAPS, University of Barcelona, Catalonia, Spain
| | - Basil Bakir
- Division of Gastroenterology, Departments of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Priya Chatterji
- Division of Gastroenterology, Departments of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania
| | - Zahra Dantes
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Maximilian Reichert
- II. Medizinische Klinik und Poliklinik, Klinikum Rechts der Isar, Technische Universität München, Munich, Germany
| | - Anil K. Rustgi
- Division of Gastroenterology, Departments of Medicine and Genetics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania,Correspondence Address correspondence to: Anil K. Rustgi, MD, 951 Biomedical Research Building II/III, University of Pennsylvania, 415 Curie Boulevard, Philadelphia, Pennsylvania 19104. fax: (215) 573–5412.951 Biomedical Research Building II/IIIUniversity of Pennsylvania415 Curie BoulevardPhiladelphiaPennsylvania 19104
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306
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Ding KF, Petricoin EF, Finlay D, Yin H, Hendricks WPD, Sereduk C, Kiefer J, Sekulic A, LoRusso PM, Vuori K, Trent JM, Schork NJ. Nonlinear mixed effects dose response modeling in high throughput drug screens: application to melanoma cell line analysis. Oncotarget 2017; 9:5044-5057. [PMID: 29435161 PMCID: PMC5797032 DOI: 10.18632/oncotarget.23495] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/30/2017] [Indexed: 11/25/2022] Open
Abstract
Cancer cell lines are often used in high throughput drug screens (HTS) to explore the relationship between cell line characteristics and responsiveness to different therapies. Many current analysis methods infer relationships by focusing on one aspect of cell line drug-specific dose-response curves (DRCs), the concentration causing 50% inhibition of a phenotypic endpoint (IC50). Such methods may overlook DRC features and do not simultaneously leverage information about drug response patterns across cell lines, potentially increasing false positive and negative rates in drug response associations. We consider the application of two methods, each rooted in nonlinear mixed effects (NLME) models, that test the relationship relationships between estimated cell line DRCs and factors that might mitigate response. Both methods leverage estimation and testing techniques that consider the simultaneous analysis of different cell lines to draw inferences about any one cell line. One of the methods is designed to provide an omnibus test of the differences between cell line DRCs that is not focused on any one aspect of the DRC (such as the IC50 value). We simulated different settings and compared the different methods on the simulated data. We also compared the proposed methods against traditional IC50-based methods using 40 melanoma cell lines whose transcriptomes, proteomes, and, importantly, BRAF and related mutation profiles were available. Ultimately, we find that the NLME-based methods are more robust, powerful and, for the omnibus test, more flexible, than traditional methods. Their application to the melanoma cell lines reveals insights into factors that may be clinically useful.
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Affiliation(s)
- Kuan-Fu Ding
- J. Craig Venter Institute, La Jolla, CA, USA.,University of California, San Diego, CA, USA
| | | | - Darren Finlay
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Hongwei Yin
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Chris Sereduk
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Jeffrey Kiefer
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | | | - Kristiina Vuori
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA.,Yale University, New Haven, CT, USA
| | - Jeffrey M Trent
- The Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Nicholas J Schork
- J. Craig Venter Institute, La Jolla, CA, USA.,University of California, San Diego, CA, USA.,The Translational Genomics Research Institute, Phoenix, AZ, USA
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307
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Winters IP, Chiou SH, Paulk NK, McFarland CD, Lalgudi PV, Ma RK, Lisowski L, Connolly AJ, Petrov DA, Kay MA, Winslow MM. Multiplexed in vivo homology-directed repair and tumor barcoding enables parallel quantification of Kras variant oncogenicity. Nat Commun 2017; 8:2053. [PMID: 29233960 PMCID: PMC5727199 DOI: 10.1038/s41467-017-01519-y] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022] Open
Abstract
Large-scale genomic analyses of human cancers have cataloged somatic point mutations thought to initiate tumor development and sustain cancer growth. However, determining the functional significance of specific alterations remains a major bottleneck in our understanding of the genetic determinants of cancer. Here, we present a platform that integrates multiplexed AAV/Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple genomic alterations in de novo cancers in mice. Using this approach, we introduce a barcoded library of non-synonymous mutations into hotspot codons 12 and 13 of Kras in adult somatic cells to initiate tumors in the lung, pancreas, and muscle. High-throughput sequencing of barcoded Kras HDR alleles from bulk lung and pancreas reveals surprising diversity in Kras variant oncogenicity. Rapid, cost-effective, and quantitative approaches to simultaneously investigate the function of precise genomic alterations in vivo will help uncover novel biological and clinically actionable insights into carcinogenesis.
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Affiliation(s)
- Ian P Winters
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Shin-Heng Chiou
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nicole K Paulk
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | | | - Pranav V Lalgudi
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Rosanna K Ma
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Leszek Lisowski
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Translational Vectorology Group, Children's Medical Research Institute, Westmead, NSW, 2145, Australia
- Military Institute of Hygiene and Epidemiology, Puławy, 24-100, Poland
| | - Andrew J Connolly
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Dmitri A Petrov
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Mark A Kay
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA, 94305, USA.
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308
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Azuaje F. Computational models for predicting drug responses in cancer research. Brief Bioinform 2017; 18:820-829. [PMID: 27444372 PMCID: PMC5862310 DOI: 10.1093/bib/bbw065] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Indexed: 02/06/2023] Open
Abstract
The computational prediction of drug responses based on the analysis of multiple types of genome-wide molecular data is vital for accomplishing the promise of precision medicine in oncology. This will benefit cancer patients by matching their tumor characteristics to the most effective therapy available. As larger and more diverse layers of patient-related data become available, further demands for new bioinformatics approaches and expertise will arise. This article reviews key strategies, resources and techniques for the prediction of drug sensitivity in cell lines and patient-derived samples. It discusses major advances and challenges associated with the different model development steps. This review highlights major trends in this area, and will assist researchers in the assessment of recent progress and in the selection of approaches to emerging applications in oncology.
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Affiliation(s)
- Francisco Azuaje
- NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg, Luxembourg
- Corresponding author: Francisco Azuaje, NorLux Neuro-Oncology Laboratory, Department of Oncology, Luxembourg Institute of Health (LIH), Luxembourg L-1526, Luxembourg. Tel.: +352-26970875; Fax: +352-26970396; E-mail:
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309
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Sun Q, Choudhary S, Mannion C, Kissin Y, Zilberberg J, Lee WY. Ex vivo construction of human primary 3D-networked osteocytes. Bone 2017; 105:245-252. [PMID: 28942121 PMCID: PMC5690542 DOI: 10.1016/j.bone.2017.09.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 09/06/2017] [Accepted: 09/20/2017] [Indexed: 02/07/2023]
Abstract
A human bone tissue model was developed by constructing ex vivo the 3D network of osteocytes via the biomimetic assembly of primary human osteoblastic cells with 20-25μm microbeads and subsequent microfluidic perfusion culture. The biomimetic assembly: (1) enabled 3D-constructed cells to form cellular network via processes with an average cell-to-cell distance of 20-25μm, and (2) inhibited cell proliferation within the interstitial confine between the microbeads while the confined cells produced extracellular matrix (ECM) to form a mechanically integrated structure. The mature osteocytic expressions of SOST and FGF23 genes became significantly higher, especially for SOST by 250 folds during 3D culture. The results validate that the bone tissue model: (1) consists of 3D cellular network of primary human osteocytes, (2) mitigates the osteoblastic differentiation and proliferation of primary osteoblast-like cells encountered in 2D culture, and (3) therefore reproduces ex vivo the phenotype of human 3D-networked osteocytes. The 3D tissue construction approach is expected to provide a clinically relevant and high-throughput means for evaluating drugs and treatments that target bone diseases with in vitro convenience.
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Affiliation(s)
- Qiaoling Sun
- Department of Materials Science and Chemical Engineering, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Saba Choudhary
- Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology, Hoboken, NJ, USA
| | - Ciaran Mannion
- Department of Pathology, Hackensack University Medical Center, Hackensack, NJ, USA
| | - Yair Kissin
- Hackensack University Medical Center, Hackensack, NJ, USA
| | - Jenny Zilberberg
- Research Department, Hackensack University Medical Center, Hackensack, NJ, USA.
| | - Woo Y Lee
- Department of Materials Science and Chemical Engineering, Stevens Institute of Technology, Hoboken, NJ, USA.
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310
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Prina-Mello A, Jain N, Liu B, Kilpatrick JI, Tutty MA, Bell AP, Jarvis SP, Volkov Y, Movia D. Culturing substrates influence the morphological, mechanical and biochemical features of lung adenocarcinoma cells cultured in 2D or 3D. Tissue Cell 2017; 50:15-30. [PMID: 29429514 DOI: 10.1016/j.tice.2017.11.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 10/31/2017] [Accepted: 11/26/2017] [Indexed: 01/04/2023]
Abstract
Alternative models such as three-dimensional (3D) cell cultures represent a distinct milestone towards capturing the realities of cancer biology in vitro and reduce animal experimentation in the preclinical stage of drug discovery. Significant work remains to be done to understand how substrates used in in vitro alternatives influence cancer cells phenotype and drug efficacy responses, so that to accurately link such models to specific in vivo disease scenarios. Our study describes how the morphological, mechanical and biochemical properties of adenocarcinoma (A549) cells change in response to a 3D environment and varying substrates. Confocal Laser Scanning (LSCM), He-Ion (HIM) and Atomic Force (AFM) microscopies, supported by ELISA and Western blotting, were used. These techniques enabled us to evaluate the shape, cytoskeletal organization, roughness, stiffness and biochemical signatures of cells grown within soft 3D matrices (PuraMatrix™ and Matrigel™), and to compare them to those of cells cultured on two-dimensional glass substrates. Cell cultures are also characterized for their biological response to docetaxel, a taxane-type drug used in Non-Small-Cell Lung Cancer (NSCLC) treatment. Our results offer an advanced biophysical insight into the properties and potential application of 3D cultures of A549 cells as in vitro alternatives in lung cancer research.
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Affiliation(s)
- Adriele Prina-Mello
- CRANN Institute and AMBER Centre, Trinity College Dublin, Ireland; Laboratory for Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland
| | - Namrata Jain
- CRANN Institute and AMBER Centre, Trinity College Dublin, Ireland
| | - Baiyun Liu
- School of Physics, University College Dublin, Ireland
| | - Jason I Kilpatrick
- Conway Institute of Biomedical and Biomolecular Research, University College Dublin, Ireland
| | - Melissa A Tutty
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland
| | - Alan P Bell
- CRANN Institute and AMBER Centre, Trinity College Dublin, Ireland; Advanced Microscopy Laboratory (AML), Trinity College Dublin, Ireland
| | - Suzanne P Jarvis
- Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland; School of Physics, University College Dublin, Ireland
| | - Yuri Volkov
- CRANN Institute and AMBER Centre, Trinity College Dublin, Ireland; Laboratory for Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland
| | - Dania Movia
- Laboratory for Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute (TTMI), Trinity College Dublin, Ireland; Department of Clinical Medicine, School of Medicine, Trinity College Dublin, Ireland.
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311
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Miserocchi G, Mercatali L, Liverani C, De Vita A, Spadazzi C, Pieri F, Bongiovanni A, Recine F, Amadori D, Ibrahim T. Management and potentialities of primary cancer cultures in preclinical and translational studies. J Transl Med 2017; 15:229. [PMID: 29116016 PMCID: PMC5688825 DOI: 10.1186/s12967-017-1328-z] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2017] [Accepted: 10/27/2017] [Indexed: 02/07/2023] Open
Abstract
The use of patient-derived primary cell cultures in cancer preclinical assays has increased in recent years. The management of resected tumor tissue remains complex and a number of parameters must be respected to obtain complete sample digestion and optimal vitality yield. We provide an overview of the benefits of correct primary cell culture management using different preclinical methodologies, and describe the pros and cons of this model with respect to other kinds of samples. One important advantage is that the heterogeneity of the cell populations composing a primary culture partially reproduces the tumor microenvironment and crosstalk between malignant and healthy cells, neither of which is possible with cell lines. Moreover, the use of patient-derived specimens in innovative preclinical technologies, such as 3D systems or bioreactors, represents an important opportunity to improve the translational value of the results obtained. In vivo models could further our understanding of the crosstalk between tumor and other tissues as they enable us to observe the systemic and biological interactions of a complete organism. Although engineered mice are the most common model used in this setting, the zebrafish (Danio rerio) species has recently been recognized as an innovative experimental system. In fact, the transparent body and incomplete immune system of zebrafish embryos are especially useful for evaluating patient-derived tumor tissue interactions in healthy hosts. In conclusion, ex vivo systems represent an important tool for cancer research, but samples require correct manipulation to maximize their translational value.
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Affiliation(s)
- Giacomo Miserocchi
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Laura Mercatali
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy.
| | - Chiara Liverani
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Alessandro De Vita
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Chiara Spadazzi
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Federica Pieri
- Pathology Unit, Morgagni-Pierantoni Hospital, Via Carlo Forlanini 34, 47121, Forlì, Italy
| | - Alberto Bongiovanni
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Federica Recine
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Dino Amadori
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
| | - Toni Ibrahim
- Osteoncology and Rare Tumors Center, Istituto Scientifico Romagnolo per lo Studio e la Cura dei Tumori (IRST) IRCCS, Via Piero Maroncelli 40, 47014, Meldola, FC, Italy
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312
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Ao L, Guo Y, Song X, Guan Q, Zheng W, Zhang J, Huang H, Zou Y, Guo Z, Wang X. Evaluating hepatocellular carcinoma cell lines for tumour samples using within-sample relative expression orderings of genes. Liver Int 2017; 37:1688-1696. [PMID: 28481424 DOI: 10.1111/liv.13467] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 04/28/2017] [Indexed: 12/11/2022]
Abstract
BACKGROUND & AIMS Concerns are raised about the representativeness of cell lines for tumours due to the culture environment and misidentification. Liver is a major metastatic destination of many cancers, which might further confuse the origin of hepatocellular carcinoma cell lines. Therefore, it is of crucial importance to understand how well they can represent hepatocellular carcinoma. METHODS The HCC-specific gene pairs with highly stable relative expression orderings in more than 99% of hepatocellular carcinoma but with reversed relative expression orderings in at least 99% of one of the six types of cancer, colorectal carcinoma, breast carcinoma, non-small-cell lung cancer, gastric carcinoma, pancreatic carcinoma and ovarian carcinoma, were identified. RESULTS With the simple majority rule, the HCC-specific relative expression orderings from comparisons with colorectal carcinoma and breast carcinoma could exactly discriminate primary hepatocellular carcinoma samples from both primary colorectal carcinoma and breast carcinoma samples. Especially, they correctly classified more than 90% of liver metastatic samples from colorectal carcinoma and breast carcinoma to their original tumours. Finally, using these HCC-specific relative expression orderings from comparisons with six cancer types, we identified eight of 24 hepatocellular carcinoma cell lines in the Cancer Cell Line Encyclopedia (Huh-7, Huh-1, HepG2, Hep3B, JHH-5, JHH-7, C3A and Alexander cells) that are highly representative of hepatocellular carcinoma. Evaluated with a REOs-based prognostic signature for hepatocellular carcinoma, all these eight cell lines showed the same metastatic properties of the high-risk metastatic hepatocellular carcinoma tissues. CONCLUSIONS Caution should be taken for using hepatocellular carcinoma cell lines. Our results should be helpful to select proper hepatocellular carcinoma cell lines for biological experiments.
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Affiliation(s)
- Lu Ao
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - You Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Department of Preventive Medicine, School of Basic Medicine Sciences, Gannan Medical University, Ganzhou, China
| | - Xuekun Song
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, China
| | - Qingzhou Guan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Weicheng Zheng
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Jiahui Zhang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Haiyan Huang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
| | - Yi Zou
- Department of Automation and Key Laboratory of China MOE for System Control and Information Processing, Shanghai Jiao Tong University, Shanghai, China
| | - Zheng Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China.,Fujian Key Laboratory of Tumour Microbiology, Fujian Medical University, Fuzhou, China
| | - Xianlong Wang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, School of Basic Medical Sciences, Fujian Medical University, Fuzhou, China
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313
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Alvi MA, Wilson RH, Salto-Tellez M. Rare cancers: the greatest inequality in cancer research and oncology treatment. Br J Cancer 2017; 117:1255-1257. [PMID: 28934760 PMCID: PMC5672935 DOI: 10.1038/bjc.2017.321] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Muhammad A Alvi
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, UK
| | - Richard H Wilson
- Colorectal Cancer Focus Group, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, UK
| | - Manuel Salto-Tellez
- Northern Ireland Molecular Pathology Laboratory, Centre for Cancer Research and Cell Biology, Queen’s University Belfast, Northern Ireland BT9 7AE, UK
- Tissue Pathology Department, Belfast Health and Social Care Trust, Northern Ireland BT12 6BA, UK
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314
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Patient-derived xenografts undergo mouse-specific tumor evolution. Nat Genet 2017; 49:1567-1575. [PMID: 28991255 PMCID: PMC5659952 DOI: 10.1038/ng.3967] [Citation(s) in RCA: 499] [Impact Index Per Article: 71.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 09/13/2017] [Indexed: 12/14/2022]
Abstract
Patient-derived xenografts (PDXs) have become a prominent cancer model system, as they are presumed to faithfully represent the genomic features of primary tumors. Here we monitored the dynamics of copy number alterations (CNAs) in 1,110 PDX samples across 24 cancer types. We observed rapid accumulation of CNAs during PDX passaging, often due to selection of pre-existing minor clones. CNA acquisition in PDXs was correlated with the tissue-specific levels of aneuploidy and genetic heterogeneity observed in primary tumors. However, the particular CNAs acquired during PDX passaging differed from those acquired during tumor evolution in patients. Several CNAs recurrently observed in primary tumors gradually disappeared in PDXs, indicating that events undergoing positive selection in humans can become dispensable during propagation in mice. Importantly, the genomic stability of PDXs was associated with their response to chemotherapy and targeted drugs. These findings have important implications for PDX-based modeling of human cancer.
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315
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Liu Z, Delavan B, Roberts R, Tong W. Lessons Learned from Two Decades of Anticancer Drugs. Trends Pharmacol Sci 2017; 38:852-872. [DOI: 10.1016/j.tips.2017.06.005] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/09/2017] [Accepted: 06/19/2017] [Indexed: 02/08/2023]
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316
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Application of standard cell cultures and 3D in vitro tissue models as an effective tool in drug design and development. Pharmacol Rep 2017. [DOI: 10.1016/j.pharep.2017.03.014] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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317
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Rapid identification and validation of novel targeted approaches for Glioblastoma: A combined ex vivo-in vivo pharmaco-omic model. Exp Neurol 2017; 299:281-288. [PMID: 28923369 DOI: 10.1016/j.expneurol.2017.09.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 07/25/2017] [Accepted: 09/10/2017] [Indexed: 01/08/2023]
Abstract
Tumor heterogeneity is a major factor in glioblastoma's poor response to therapy and seemingly inevitable recurrence. Only two glioblastoma drugs have received Food and Drug Administration approval since 1998, highlighting the urgent need for new therapies. Profiling "omics" analyses have helped characterize glioblastoma molecularly and have thus identified multiple molecular targets for precision medicine. These molecular targets have influenced clinical trial design; many "actionable" mutation-focused trials are underway, but because they have not yet led to therapeutic breakthroughs, new strategies for treating glioblastoma, especially those with a pharmacological functional component, remain in high demand. In that regard, high-throughput screening that allows for expedited preclinical drug testing and the use of GBM models that represent tumor heterogeneity more accurately than traditional cancer cell lines is necessary to maximize the successful translation of agents into the clinic. High-throughput screening has been successfully used in the testing, discovery, and validation of potential therapeutics in various cancer models, but it has not been extensively utilized in glioblastoma models. In this report, we describe the basic aspects of high-throughput screening and propose a modified high-throughput screening model in which ex vivo and in vivo drug testing is complemented by post-screening pharmacological, pan-omic analysis to expedite anti-glioma drugs' preclinical testing and develop predictive biomarker datasets that can aid in personalizing glioblastoma therapy and inform clinical trial design.
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318
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Martin-Trujillo A, Vidal E, Monteagudo-Sánchez A, Sanchez-Delgado M, Moran S, Hernandez Mora JR, Heyn H, Guitart M, Esteller M, Monk D. Copy number rather than epigenetic alterations are the major dictator of imprinted methylation in tumors. Nat Commun 2017; 8:467. [PMID: 28883545 PMCID: PMC5589900 DOI: 10.1038/s41467-017-00639-9] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Accepted: 07/17/2017] [Indexed: 02/07/2023] Open
Abstract
It has been postulated that imprinting aberrations are common in tumors. To understand the role of imprinting in cancer, we have characterized copy-number and methylation in over 280 cancer cell lines and confirm our observations in primary tumors. Imprinted differentially methylated regions (DMRs) regulate parent-of-origin monoallelic expression of neighboring transcripts in cis. Unlike single-copy CpG islands that may be prone to hypermethylation, imprinted DMRs can either loose or gain methylation during tumorigenesis. Here, we show that methylation profiles at imprinted DMRs often not represent genuine epigenetic changes but simply the accumulation of underlying copy-number aberrations (CNAs), which is independent of the genome methylation state inferred from cancer susceptible loci. Our results reveal that CNAs also influence allelic expression as loci with copy-number neutral loss-of-heterozygosity or amplifications may be expressed from the appropriate parental chromosomes, which is indicative of maintained imprinting, although not observed as a single expression foci by RNA FISH.Altered genomic imprinting is frequently reported in cancer. Here, the authors analyze copy number and methylation in cancer cell lines and primary tumors to show that imprinted methylation profiles represent the accumulation of copy number alteration, rather than epigenetic alterations.
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Affiliation(s)
- Alex Martin-Trujillo
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Enrique Vidal
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain
| | - Ana Monteagudo-Sánchez
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Marta Sanchez-Delgado
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Sebastian Moran
- Cancer Epigenetics group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Jose Ramon Hernandez Mora
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain
| | - Holger Heyn
- Universitat Pompeu Fabra (UPF), Barcelona, Spain Universitat Pompeu Fabra (UPF), 08003, Barcelona, Spain.,CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028, Barcelona, Spain
| | - Miriam Guitart
- Genetics Laboratory, UDIAT- Diagnostic Centre, Corporació Sanitària Parc Taulí, 08208, Sabadell, Spain
| | - Manel Esteller
- Cancer Epigenetics group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain.,Department of Physiological Sciences II, School of Medicine, University of Barcelona, Barcelona, 08907, Catalonia, Spain.,Institucio Catalana de Recerca i Estudis Avançats (ICREA), 08010, Barcelona, Spain
| | - David Monk
- Imprinting and Cancer group, Cancer Epigenetic and Biology Program (PEBC), Institut d'Investigació Biomedica de Bellvitge (IDIBELL), Avinguda Granvia, L'Hospitalet de Llobregat, 08907, Barcelona, Spain.
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319
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Persson CU, von Stedingk K, Bexell D, Merselius M, Braekeveldt N, Gisselsson D, Arsenian-Henriksson M, Påhlman S, Wigerup C. Neuroblastoma patient-derived xenograft cells cultured in stem-cell promoting medium retain tumorigenic and metastatic capacities but differentiate in serum. Sci Rep 2017; 7:10274. [PMID: 28860499 PMCID: PMC5579187 DOI: 10.1038/s41598-017-09662-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/19/2017] [Indexed: 12/26/2022] Open
Abstract
Cultured cancer cells serve as important models for preclinical testing of anti-cancer compounds. However, the optimal conditions for retaining original tumor features during in vitro culturing of cancer cells have not been investigated in detail. Here we show that serum-free conditions are critical for maintaining an immature phenotype of neuroblastoma cells isolated from orthotopic patient-derived xenografts (PDXs). PDX cells could be grown either as spheres or adherent on laminin in serum-free conditions with retained patient-specific genomic aberrations as well as tumorigenic and metastatic capabilities. However, addition of serum led to morphological changes, neuronal differentiation and reduced cell proliferation. The epidermal growth factor (EGF) and basic fibroblast growth factor (bFGF) were central for PDX cell proliferation and MYCN expression, and also hindered the serum-induced differentiation. Although serum induced a robust expression of neurotrophin receptors, stimulation with their cognate ligands did not induce further sympathetic differentiation, which likely reflects a block in PDX cell differentiation capacity coupled to their tumor genotype. Finally, PDX cells cultured as spheres or adherent on laminin responded similarly to various cytotoxic drugs, suggesting that both conditions are suitable in vitro screening models for neuroblastoma-targeting compounds.
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Affiliation(s)
- Camilla U Persson
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | | | - Daniel Bexell
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - My Merselius
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Noémie Braekeveldt
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - David Gisselsson
- Department of Clinical Genetics, Lund University, Department of Pathology, University and Regional Laboratories, Lund, Sweden
| | - Marie Arsenian-Henriksson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, SE-171 77, Stockholm, Sweden
| | - Sven Påhlman
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden
| | - Caroline Wigerup
- Translational Cancer Research, Lund University Cancer Center at Medicon Village, Lund University, Lund, Sweden.
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320
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Choudhary S, Sun Q, Mannion C, Kissin Y, Zilberberg J, Lee WY. Hypoxic Three-Dimensional Cellular Network Construction Replicates Ex Vivo the Phenotype of Primary Human Osteocytes. Tissue Eng Part A 2017; 24:458-468. [PMID: 28594289 DOI: 10.1089/ten.tea.2017.0103] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Osteocytes are deeply embedded in the mineralized matrix of bone and are nonproliferative, making them a challenge to isolate and maintain using traditional in vitro culture methods without sacrificing their inimitable phenotype. We studied the synergistic effects of two microenvironmental factors that are vital in retaining, ex vivo, the phenotype of primary human osteocytes: hypoxia and three-dimensional (3D) cellular network. To recapitulate the lacunocanalicular structure of bone tissue, we assembled and cultured primary human osteocytic cells with biphasic calcium phosphate microbeads in a microfluidic perfusion culture device. The 3D cellular network was constructed by the following: (1) the inhibited proliferation of cells entrapped by microbeads, biomimetically resembling lacunae, and (2) the connection of neighboring cells by dendrites through the mineralized, canaliculi-like interstitial spaces between the microbeads. We found that hypoxia synergistically and remarkably upregulated the mature osteocytic gene expressions of the 3D-networked cells, SOST (encoding sclerostin) and FGF23 (encoding fibroblast growth factor 23), by several orders of magnitude in comparison to those observed from two-dimensional and normoxic culture controls. Intriguingly, hypoxia facilitated the self-assembly of a nonproliferating, osteoblastic monolayer on the surface of the 3D-networked cells, replicating the osteoblastic endosteal cell layer found at the interface between native bone and bone marrow tissues. Our ability to replicate, with hypoxia, the strong expressions of these mature osteocytic markers, SOST and FGF23, is important since these (1) could not be significantly produced in vitro and (2) are new important targets for treating bone diseases. Our findings are therefore expected to facilitate ex vivo studies of human bone diseases using primary human bone cells and enable high-throughput evaluation of potential bone-targeting therapies with clinical relevance.
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Affiliation(s)
- Saba Choudhary
- 1 Department of Biomedical Engineering, Chemistry and Biological Sciences, Stevens Institute of Technology , Hoboken, New Jersey
| | - Qiaoling Sun
- 2 Department of Chemical Engineering and Materials Science, Stevens Institute of Technology , Hoboken, New Jersey
| | - Ciaran Mannion
- 3 Department of Pathology, Hackensack University Medical Center , Hackensack, New Jersey
| | - Yair Kissin
- 4 Insall Scott Kelly Institute for Orthopaedics and Sports Medicine , New York, New York.,5 Hackensack University Medical Center , Hackensack, New Jersey.,6 Lenox Hill Hospital , New York, New York
| | - Jenny Zilberberg
- 7 John Theurer Cancer Center, Hackensack University Medical Center , Hackensack, New Jersey
| | - Woo Y Lee
- 2 Department of Chemical Engineering and Materials Science, Stevens Institute of Technology , Hoboken, New Jersey
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321
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A computational integrative approach based on alternative splicing analysis to compare immortalized and primary cancer cells. Int J Biochem Cell Biol 2017; 91:116-123. [PMID: 28757458 DOI: 10.1016/j.biocel.2017.07.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Revised: 07/03/2017] [Accepted: 07/15/2017] [Indexed: 11/20/2022]
Abstract
Immortalized cell lines are widely used to study the effectiveness and toxicity of anti cancer drugs as well as to assess the phenotypic characteristics of cancer cells, such as proliferation and migration ability. Unfortunately, cell lines often show extremely different properties than tumor tissues. Also the primary cells, that are deprived of the in vivo environment, might adapt to artificial conditions, and differ from the tissue they should represent. Despite these considerations, cell lines are still one of the most used cancer models due to their availability and capability to expand without limitation, but the clinical relevance of their use is still a big issue in cancer research. Many studies tried to overcome this task, comparing cell lines and tumor samples through the definition of the genomic and transcriptomic differences. To this aim, most of them used nucleotide variation or gene expression data. Here we introduce a different strategy based on alternative splicing detection and integration of DNA and RNA sequencing data, to explore the differences between immortalized and tissue-derived cells at isoforms level. Furthermore, in order to better investigate the heterogeneity of both cell populations, we took advantage of a public available dataset obtained with a new simultaneous omics single cell sequencing methodology. The proposed pipeline allowed us to identify, through a computational and prediction approach, putative mutated and alternative spliced transcripts responsible for the dissimilarity between immortalized and primary hepato carcinoma cells.
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322
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Ahonen I, Åkerfelt M, Toriseva M, Oswald E, Schüler J, Nees M. A high-content image analysis approach for quantitative measurements of chemosensitivity in patient-derived tumor microtissues. Sci Rep 2017; 7:6600. [PMID: 28747710 PMCID: PMC5529420 DOI: 10.1038/s41598-017-06544-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Accepted: 06/14/2017] [Indexed: 11/17/2022] Open
Abstract
Organotypic, three-dimensional (3D) cancer models have enabled investigations of complex microtissues in increasingly realistic conditions. However, a drawback of these advanced models remains the poor biological relevance of cancer cell lines, while higher clinical significance would be obtainable with patient-derived cell cultures. Here, we describe the generation and data analysis of 3D microtissue models from patient-derived xenografts (PDX) of non-small cell lung carcinoma (NSCLC). Standard of care anti-cancer drugs were applied and the altered multicellular morphologies were captured by confocal microscopy, followed by automated image analyses to quantitatively measure phenotypic features for high-content chemosensitivity tests. The obtained image data were thresholded using a local entropy filter after which the image foreground was split into local regions, for a supervised classification into tumor or fibroblast cell types. Robust statistical methods were applied to evaluate treatment effects on growth and morphology. Both novel and existing computational approaches were compared at each step, while prioritizing high experimental throughput. Docetaxel was found to be the most effective drug that blocked both tumor growth and invasion. These effects were also validated in PDX tumors in vivo. Our research opens new avenues for high-content drug screening based on patient-derived cell cultures, and for personalized chemosensitivity testing.
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Affiliation(s)
- Ilmari Ahonen
- Department of Mathematics and Statistics, University of Turku, Turku, Finland. .,Institute of Biomedicine, University of Turku, Turku, Finland.
| | - Malin Åkerfelt
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Mervi Toriseva
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eva Oswald
- Discovery Services, Charles River, Freiburg, Germany
| | - Julia Schüler
- Discovery Services, Charles River, Freiburg, Germany
| | - Matthias Nees
- Institute of Biomedicine, University of Turku, Turku, Finland
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323
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BKM120 induces apoptosis and inhibits tumor growth in medulloblastoma. PLoS One 2017; 12:e0179948. [PMID: 28662162 PMCID: PMC5491106 DOI: 10.1371/journal.pone.0179948] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/07/2017] [Indexed: 11/19/2022] Open
Abstract
Medulloblastoma (MB) is the most common malignant brain tumor in children, accounting for nearly 20 percent of all childhood brain tumors. New treatment strategies are needed to improve patient survival outcomes and to reduce adverse effects of current therapy. The phosphatidylinositol-3-kinase (PI3K)/AKT/mammalian target of rapamycin (mTOR) intracellular signaling pathway plays a key role in cellular metabolism, proliferation, survival and angiogenesis, and is often constitutively activated in human cancers, providing unique opportunities for anticancer therapeutic intervention. The aim of this study was to evaluate the pre-clinical activity of BKM120, a selective pan-class I PI3K inhibitor, on MB cell lines and primary samples. IC50 values of BKM120 in the twelve MB cell lines tested ranged from 0.279 to 4.38 μM as determined by cell viability assay. IncuCyte ZOOM Live-Cell Imaging system was used for kinetic monitoring of cytotoxicity of BKM120 and apoptosis in MB cells. BKM120 exhibited cytotoxicity in MB cells in a dose and time-dependent manner by inhibiting activation of downstream signaling molecules AKT and mTOR, and activating caspase-mediated apoptotic pathways. Furthermore, BKM120 decreased cellular glycolytic metabolic activity in MB cell lines in a dose-dependent manner demonstrated by ATP level per cell. In MB xenograft mouse study, DAOY cells were implanted in the flank of nude mice and treated with vehicle, BKM120 at 30 mg/kg and 60 mg/kg via oral gavage daily. BKM120 significantly suppressed tumor growth and prolonged mouse survival. These findings help to establish a basis for clinical trials of BKM120, which could be a novel therapy for the treatment of medulloblastoma patients.
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324
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Lovitt CJ, Shelper TB, Avery VM. Cancer drug discovery: recent innovative approaches to tumor modeling. Expert Opin Drug Discov 2017; 11:885-94. [PMID: 27454169 DOI: 10.1080/17460441.2016.1214562] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
INTRODUCTION Cell culture models have been at the heart of anti-cancer drug discovery programs for over half a century. Advancements in cell culture techniques have seen the rapid evolution of more complex in vitro cell culture models investigated for use in drug discovery. Three-dimensional (3D) cell culture research has become a strong focal point, as this technique permits the recapitulation of the tumor microenvironment. Biologically relevant 3D cellular models have demonstrated significant promise in advancing cancer drug discovery, and will continue to play an increasing role in the future. AREAS COVERED In this review, recent advances in 3D cell culture techniques and their application in tumor modeling and anti-cancer drug discovery programs are discussed. The topics include selection of cancer cells, 3D cell culture assays (associated endpoint measurements and analysis), 3D microfluidic systems and 3D bio-printing. EXPERT OPINION Although advanced cancer cell culture models and techniques are becoming commonplace in many research groups, the use of these approaches has yet to be fully embraced in anti-cancer drug applications. Furthermore, limitations associated with analyzing information-rich biological data remain unaddressed.
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Affiliation(s)
- Carrie J Lovitt
- a Discovery Biology, Eskitis Institute for Drug Discovery , Griffith University , Nathan , Australia
| | - Todd B Shelper
- a Discovery Biology, Eskitis Institute for Drug Discovery , Griffith University , Nathan , Australia
| | - Vicky M Avery
- a Discovery Biology, Eskitis Institute for Drug Discovery , Griffith University , Nathan , Australia
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325
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Abstract
Hematological malignancies manifest as lymphoma, leukemia, and myeloma, and remain a burden on society. From initial therapy to endless relapse-related treatment, societal burden is felt not only in the context of healthcare cost, but also in the compromised quality of life of patients. Long-term therapeutic strategies have become the standard in keeping hematological malignancies at bay as these cancers develop resistance to each round of therapy with time. As a result, there is a continual need for the development of new drugs to combat resistant disease in order to prolong patient life, if not to produce a cure. This review aims to summarize advances in targeting lymphoma, leukemia, and myeloma through both cutting-edge and well established platforms. Current standard of treatment will be reviewed for these malignancies and emphasis will be made on new therapy development in the areas of antibody engineering, epigenetic small molecule inhibiting drugs, vaccine development, and chimeric antigen receptor cell engineering. In addition, platforms for the delivery of these and other drugs will be reviewed including antibody-drug conjugates, micro- and nanoparticles, and multimodal hydrogels. Lastly, we propose that tissue engineered constructs for hematological malignancies are the missing link in targeted drug discovery alongside mouse and patient-derived xenograft models.
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326
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Roubaud G, Liaw BC, Oh WK, Mulholland DJ. Strategies to avoid treatment-induced lineage crisis in advanced prostate cancer. Nat Rev Clin Oncol 2017; 14:269-283. [PMID: 27874061 PMCID: PMC5567685 DOI: 10.1038/nrclinonc.2016.181] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The increasing potency of therapies that target the androgen receptor (AR) signalling axis has correlated with a rise in the proportion of patients with prostate cancer harbouring an adaptive phenotype, termed treatment-induced lineage crisis. This phenotype is characterized by features that include soft-tissue metastasis and/or resistance to standard anticancer therapies. Potent anticancer treatments might force cancer cells to evolve and develop alternative cell lineages that are resistant to primary therapies, a mechanism similar to the generation of multidrug- resistant microorganisms after continued antibiotic use. Herein, we assess the hypothesis that treatment-adapted phenotypes harbour reduced AR expression and/or activity, and acquire compensatory strategies for cell survival. We highlight the striking similarities between castration-resistant prostate cancer and triple-negative breast cancer, another poorly differentiated endocrine malignancy. Alternative treatment paradigms are needed to avoid therapy-induced resistance. Herein, we present a new clinical trial strategy designed to evaluate the potential of rapid drug cycling as an approach to delay the onset of resistance and treatment-induced lineage crisis in patients with metastatic castration-resistant prostate cancer.
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Affiliation(s)
- Guilhem Roubaud
- Department of Medical Oncology, Institut Bergonié, 229 Cours de l'Argonne, Bordeaux 33076, France
| | - Bobby C Liaw
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, New York 10029, USA
| | - William K Oh
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, New York 10029, USA
| | - David J Mulholland
- Icahn School of Medicine at Mount Sinai, Tisch Cancer Institute, 1470 Madison Avenue, New York, New York 10029, USA
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327
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Vaughan L, Glänzel W, Korch C, Capes-Davis A. Widespread Use of Misidentified Cell Line KB (HeLa): Incorrect Attribution and Its Impact Revealed through Mining the Scientific Literature. Cancer Res 2017; 77:2784-2788. [PMID: 28455420 DOI: 10.1158/0008-5472.can-16-2258] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Revised: 09/26/2016] [Accepted: 03/24/2017] [Indexed: 02/07/2023]
Abstract
Continuous cell lines are widely used, but can result in invalid, irreproducible research data. Cell line misidentification is a common problem that can be detected by authentication testing; however, misidentified cell lines continue to be used in publications. Here we explore the impact of one misidentified cell line, KB (HeLa), on the scientific literature. We identified 574 articles between 2000 and 2014 that provided an incorrect attribution for KB, in accordance with its false identity as oral epidermoid carcinoma, but only 57 articles that provided a correct attribution for KB, as HeLa or cervical adenocarcinoma. Statistical analysis of 57 correct and 171 incorrect articles showed that the number of citations to these articles increased over time. Content analysis of 200 citing articles showed there was a tendency to describe the cell line in accordance with the description in the cited paper. Analysis of journal impact factor showed no significant difference between correct and incorrect groups. Articles using KB or citing that usage were most frequently published in the subject areas of pharmacology, pharmacy, oncology, and medicinal chemistry. These findings are important for science policy and support the need for journals to require authentication testing as a condition of publication. Cancer Res; 77(11); 2784-8. ©2017 AACR.
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Affiliation(s)
- Liwen Vaughan
- Faculty of Information and Media Studies, University of Western Ontario, London, Ontario, Canada
| | - Wolfgang Glänzel
- Centre for R&D Monitoring (ECOOM) and Department of MSI, KU Leuven, Leuven, Belgium.,Department of Science Policy & Scientometrics, LHAS, Budapest, Hungary
| | - Christopher Korch
- Division of Medical Oncology, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, New South Wales, Australia.
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328
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Murahari M, Kharkar PS, Lonikar N, Mayur YC. Design, synthesis, biological evaluation, molecular docking and QSAR studies of 2,4-dimethylacridones as anticancer agents. Eur J Med Chem 2017; 130:154-170. [PMID: 28246041 DOI: 10.1016/j.ejmech.2017.02.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 02/07/2017] [Accepted: 02/08/2017] [Indexed: 02/05/2023]
Affiliation(s)
- Manikanta Murahari
- Department of Pharmaceutical Chemistry, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai 400 056, India; Department of Pharmaceutical Chemistry, Faculty of Pharmacy, M.S. Ramaiah University of Applied Sciences, Bangalore 560 054, India
| | - Prashant S Kharkar
- Department of Pharmaceutical Chemistry, SPP School of Pharmacy & Technology Management, SVKM's NMIMS, Mumbai 400 056, India
| | - Nitin Lonikar
- Department of Pharmaceutical Chemistry, AME's V.L. College of Pharmacy, Raichur 584103, India
| | - Y C Mayur
- Department of Pharmaceutical Chemistry, SPP School of Pharmacy & Technology Management, SVKM's NMIMS, Mumbai 400 056, India.
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329
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Yu S, Kim T, Yoo KH, Kang K. The T47D cell line is an ideal experimental model to elucidate the progesterone-specific effects of a luminal A subtype of breast cancer. Biochem Biophys Res Commun 2017; 486:752-758. [PMID: 28342866 DOI: 10.1016/j.bbrc.2017.03.114] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2017] [Accepted: 03/21/2017] [Indexed: 12/31/2022]
Abstract
Cell lines are often used as in vitro tools to mimic certain types of in vivo system; several cell lines, including MCF-7 and T47D, have been widely used in breast cancer studies without investigating the cell lines' characteristics. In this study, we compared the genome-wide binding profiles of ERα, PR, and P300, and the gene expression changes between MCF-7 and T47D cell lines that represent the luminal A subtype of breast cancer. Surprisingly, several thousand genes were differentially expressed under estrogenic condition. In addition, ERα, PR, and P300 binding to regulatory elements showed distinct genomic landscapes between MCF-7 and T47D cell lines in the same hormonal states. In particular, the T47D cell line was markedly susceptible to progesterone, whereas the MCF-7 cell line did not respond to progesterone in the presence of estrogen. Consistently, changes in the expression level of the PR-target gene, STAT5A, were only observed in the T47D cell line, not the MCF-7 cell line, when treated with progesterone. Overall, the results highlight the importance of selecting appropriate cell lines for breast cancer studies and suggest that T47D cell lines can be an ideal experimental model to elucidate the progesterone-specific effects of a luminal A subtype of breast cancer.
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Affiliation(s)
- Sungryul Yu
- Department of Clinical Laboratory Science, Semyung University, Jecheon 27136, Republic of Korea
| | - Taemook Kim
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea
| | - Kyung Hyun Yoo
- Department of Biological Sciences, Sookmyung Women's University, Seoul, 04310, Republic of Korea
| | - Keunsoo Kang
- Department of Microbiology, College of Natural Sciences, Dankook University, Cheonan 31116, Republic of Korea.
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330
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Ronchetti L, Melucci E, De Nicola F, Goeman F, Casini B, Sperati F, Pallocca M, Terrenato I, Pizzuti L, Vici P, Sergi D, Di Lauro L, Amoreo CA, Gallo E, Diodoro MG, Pescarmona E, Vitale I, Barba M, Buglioni S, Mottolese M, Fanciulli M, De Maria R, Maugeri-Saccà M. DNA damage repair and survival outcomes in advanced gastric cancer patients treated with first-line chemotherapy. Int J Cancer 2017; 140:2587-2595. [PMID: 28233295 DOI: 10.1002/ijc.30668] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 02/08/2017] [Accepted: 02/17/2017] [Indexed: 12/22/2022]
Abstract
The DNA damage response (DDR) network is exploited by cancer cells to withstand chemotherapy. Gastric cancer (GC) carries deregulation of the DDR and harbors genetic defects that fuel its activation. The ATM-Chk2 and ATR-Chk1-Wee1 axes are deputed to initiate DNA repair. Overactivation of these pathways in cancer cells may represent an adaptive response for compensating genetic defects deregulating G1 -S transition (e.g., TP53) and ATM/ATR-initiated DNA repair (e.g., ARID1A). We hypothesized that DDR-linked biomarkers may predict clinical outcomes in GC patients treated with chemotherapy. Immunohistochemical assessment of DDR kinases (pATM, pChk2, pChk1 and pWee1) and DNA damage markers (γ-H2AX and pRPA32) was performed in biological samples from 110 advanced GC patients treated with first-line chemotherapy, either in phase II trials or in routine clinical practice. In 90 patients, this characterization was integrated with targeted ultra-deep sequencing for evaluating the mutational status of TP53 and ARID1A. We recorded a positive association between the investigated biomarkers. The combination of two biomarkers (γ-H2AXhigh /pATMhigh ) was an adverse factor for both progression-free survival (multivariate Cox: HR 2.23, 95%CI: 1.47-3.40) and overall survival (multivariate Cox: HR: 2.07, 95%CI: 1.20-3.58). The relationship between the γ-H2AXhigh /pATMhigh model and progression-free survival was consistent across the different TP53 backgrounds and was maintained in the ARID1A wild-type setting. Conversely, this association was no longer observed in an ARID1A-mutated subgroup. The γ-H2AXhigh /pATMhigh model negatively impacted survival outcomes in GC patients treated with chemotherapy. The mutational status of ARID1A, but apparently not TP53 mutations, affects its predictive significance.
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Affiliation(s)
- Livia Ronchetti
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Elisa Melucci
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Francesca De Nicola
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Frauke Goeman
- Oncogenomic and Epigenetic Unit, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Beatrice Casini
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Francesca Sperati
- Biostatistics-Scientific Direction, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Matteo Pallocca
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Irene Terrenato
- Biostatistics-Scientific Direction, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Laura Pizzuti
- Division of Medical Oncology 2, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Patrizia Vici
- Division of Medical Oncology 2, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Domenico Sergi
- Division of Medical Oncology 2, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Luigi Di Lauro
- Division of Medical Oncology 2, "Regina Elena" National Cancer Institute, Rome, Italy
| | | | - Enzo Gallo
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | | | - Edoardo Pescarmona
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Ilio Vitale
- Department of Biology, University of Rome "Tor Vergata", Rome, Italy.,Scientific Direction, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Maddalena Barba
- Division of Medical Oncology 2, "Regina Elena" National Cancer Institute, Rome, Italy.,Scientific Direction, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Simonetta Buglioni
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Marcella Mottolese
- Department of Pathology, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Maurizio Fanciulli
- SAFU Laboratory, Department of Research, Advanced Diagnostic, and Technological Innovation, "Regina Elena" National Cancer Institute, Rome, Italy
| | - Ruggero De Maria
- Institute of General Pathology, Catholic University of the Sacred Heart, Rome, Italy
| | - Marcello Maugeri-Saccà
- Division of Medical Oncology 2, "Regina Elena" National Cancer Institute, Rome, Italy.,Scientific Direction, "Regina Elena" National Cancer Institute, Rome, Italy
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331
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Affiliation(s)
- Diana Behrens
- EPO - Experimental Pharmacology and Oncology GmbH - GmbH, Robert-Roessle-Str. 10, 13125 Berlin, Germany.
| | - Wolfgang Walther
- Experimental and Clinical Research Center (ECRC), Charité, University Medicine, Berlin; Max-Delbrueck-Center for Molecular Medicine, Robert-Roessle-Str. 10, 13125 Berlin, Germany
| | - Iduna Fichtner
- EPO - Experimental Pharmacology and Oncology GmbH - GmbH, Robert-Roessle-Str. 10, 13125 Berlin, Germany
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332
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Liu X, Krawczyk E, Suprynowicz FA, Palechor-Ceron N, Yuan H, Dakic A, Simic V, Zheng YL, Sripadhan P, Chen C, Lu J, Hou TW, Choudhury S, Kallakury B, Tang DG, Darling T, Thangapazham R, Timofeeva O, Dritschilo A, Randell SH, Albanese C, Agarwal S, Schlegel R. Conditional reprogramming and long-term expansion of normal and tumor cells from human biospecimens. Nat Protoc 2017; 12:439-451. [PMID: 28125105 PMCID: PMC6195120 DOI: 10.1038/nprot.2016.174] [Citation(s) in RCA: 213] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Historically, it has been difficult to propagate cells in vitro that are derived directly from human tumors or healthy tissue. However, in vitro preclinical models are essential tools for both the study of basic cancer biology and the promotion of translational research, including drug discovery and drug target identification. This protocol describes conditional reprogramming (CR), which involves coculture of irradiated mouse fibroblast feeder cells with normal and tumor human epithelial cells in the presence of a Rho kinase inhibitor (Y-27632). CR cells can be used for various applications, including regenerative medicine, drug sensitivity testing, gene expression profiling and xenograft studies. The method requires a pathologist to differentiate healthy tissue from tumor tissue, and basic tissue culture skills. The protocol can be used with cells derived from both fresh and cryopreserved tissue samples. As approximately 1 million cells can be generated in 7 d, the technique is directly applicable to diagnostic and predictive medicine. Moreover, the epithelial cells can be propagated indefinitely in vitro, yet retain the capacity to become fully differentiated when placed into conditions that mimic their natural environment.
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Affiliation(s)
- Xuefeng Liu
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
- Correspondence should be addressed to X.L. () or R.S. ()
| | - Ewa Krawczyk
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
- Correspondence should be addressed to X.L. () or R.S. ()
| | - Frank A Suprynowicz
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Nancy Palechor-Ceron
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Hang Yuan
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Aleksandra Dakic
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Vera Simic
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Yun-Ling Zheng
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Praathibha Sripadhan
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Chen Chen
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Jie Lu
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Tung-Wei Hou
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Sujata Choudhury
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Bhaskar Kallakury
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Dean G Tang
- Department of Epigenetics and Molecular Carcinogenesis, University of Texas MD Anderson Cancer Center, Smithville, Texas, USA
| | - Thomas Darling
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Rajesh Thangapazham
- Department of Dermatology, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Olga Timofeeva
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
- Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Anatoly Dritschilo
- Department of Radiation Medicine, Georgetown University Medical Center, Washington, DC, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA
| | - Christopher Albanese
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
- Department of Oncology, Georgetown University Medical Center, Washington, DC, USA
| | - Seema Agarwal
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
| | - Richard Schlegel
- Department of Pathology, Georgetown University Medical Center, Washington, DC, USA
- Center for Cell Reprogramming, Georgetown University Medical Center, Washington, DC, USA
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333
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Chicaybam L, Barcelos C, Peixoto B, Carneiro M, Limia CG, Redondo P, Lira C, Paraguassú-Braga F, Vasconcelos ZFMD, Barros L, Bonamino MH. An Efficient Electroporation Protocol for the Genetic Modification of Mammalian Cells. Front Bioeng Biotechnol 2017; 4:99. [PMID: 28168187 PMCID: PMC5253374 DOI: 10.3389/fbioe.2016.00099] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2016] [Accepted: 12/20/2016] [Indexed: 01/14/2023] Open
Abstract
Genetic modification of cell lines and primary cells is an expensive and cumbersome approach, often involving the use of viral vectors. Electroporation using square-wave generating devices, like Lonza's Nucleofector, is a widely used option, but the costs associated with the acquisition of electroporation kits and the transient transgene expression might hamper the utility of this methodology. In the present work, we show that our in-house developed buffers, termed Chicabuffers, can be efficiently used to electroporate cell lines and primary cells from murine and human origin. Using the Nucleofector II device, we electroporated 14 different cell lines and also primary cells, like mesenchymal stem cells and cord blood CD34+, providing optimized protocols for each of them. Moreover, when combined with sleeping beauty-based transposon system, long-term transgene expression could be achieved in all types of cells tested. Transgene expression was stable and did not interfere with CD34+ differentiation to committed progenitors. We also show that these buffers can be used in CRISPR-mediated editing of PDCD1 gene locus in 293T and human peripheral blood mononuclear cells. The optimized protocols reported in this study provide a suitable and cost-effective platform for the genetic modification of cells, facilitating the widespread adoption of this technology.
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Affiliation(s)
- Leonardo Chicaybam
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil; Fundação Instituto Oswaldo Cruz, Vice-presidência de Pesquisa e Laboratórios de Referência, Rio de Janeiro, Brazil
| | - Camila Barcelos
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA) , Rio de Janeiro , Brazil
| | - Barbara Peixoto
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA) , Rio de Janeiro , Brazil
| | - Mayra Carneiro
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA) , Rio de Janeiro , Brazil
| | - Cintia Gomez Limia
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA) , Rio de Janeiro , Brazil
| | - Patrícia Redondo
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil; Centro de Transplante de Medula Óssea, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - Carla Lira
- Banco de Cordão Umbilical e Placentário, Instituto Nacional de Cancer (INCA), Rio de Janeiro, Brazil; Instituto Fernandes Figueira, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Flávio Paraguassú-Braga
- Banco de Cordão Umbilical e Placentário, Instituto Nacional de Cancer (INCA) , Rio de Janeiro , Brazil
| | | | - Luciana Barros
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA) , Rio de Janeiro , Brazil
| | - Martin Hernán Bonamino
- Programa de Carcinogênese Molecular, Coordenação de Pesquisa, Instituto Nacional de Câncer (INCA), Rio de Janeiro, Brazil; Fundação Instituto Oswaldo Cruz, Vice-presidência de Pesquisa e Laboratórios de Referência, Rio de Janeiro, Brazil
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334
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Zhao H, Lu Z, Bauzon F, Fu H, Cui J, Locker J, Zhu L. p27T187A knockin identifies Skp2/Cks1 pocket inhibitors for advanced prostate cancer. Oncogene 2017; 36:60-70. [PMID: 27181203 PMCID: PMC5112153 DOI: 10.1038/onc.2016.175] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 03/04/2016] [Accepted: 04/11/2016] [Indexed: 12/27/2022]
Abstract
SCFSkp2/Cks1 ubiquitinates Thr187-phosphorylated p27 for degradation. Overexpression of Skp2 coupled with underexpression of p27 are frequent characteristics of cancer cells. When the role of SCFSkp2/Cks1-mediated p27 ubiquitination in cancer was specifically tested by p27 Thr187-to-Ala knockin (p27T187A KI), it was found dispensable for KrasG12D-induced lung tumorigenesis but essential for Rb1-deficient pituitary tumorigenesis. Here we identify pRb and p53 doubly deficient (DKO) prostate tumorigenesis as a context in which p27 ubiquitination by SCFSkp2/Cks1 is required for p27 downregulation. p27 protein accumulated in prostate when p27T187A KI mice underwent DKO prostate tumorigenesis. p27T187A KI or Skp2 knockdown (KD) induced similar degrees of p27 protein accumulation in DKO prostate cells, and Skp2 KD did not further increase p27 protein in DKO prostate cells that contained p27T187A KI (AADKO prostate cells). p27T187A KI activated an E2F1-p73-apoptosis axis in DKO prostate tumorigenesis, slowed disease progression and significantly extended survival. Querying co-occurrence relationships among RB1, TP53, PTEN, NKX3-1 and MYC in TCGA of prostate cancer identified co-inactivation of RB1 and TP53 as the only statistically significant co-occurrences in metastatic castration-resistant prostate cancer (mCRPC). Together, our study identifies Skp2/Cks1 pocket inhibitors as potential therapeutics for mCRPC. Procedures for establishing mCRPC organoid cultures from contemporary patients were recently established. An Skp2/Cks1 pocket inhibitor preferentially collapsed DKO prostate tumor organoids over AADKO organoids, which spontaneously disintegrated over time when DKO prostate tumor organoids grew larger, setting the stage to translate mouse model findings to precision medicine in the clinic on the organoid platform.
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Affiliation(s)
- Hongling Zhao
- Department of Developmental and Molecular Biology, and Ophthalmology & Visual Sciences, and Medicine, The Albert Einstein Comprehensive Cancer Center and Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Zhonglei Lu
- Department of Developmental and Molecular Biology, and Ophthalmology & Visual Sciences, and Medicine, The Albert Einstein Comprehensive Cancer Center and Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Frederick Bauzon
- Department of Developmental and Molecular Biology, and Ophthalmology & Visual Sciences, and Medicine, The Albert Einstein Comprehensive Cancer Center and Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Hao Fu
- Department of Developmental and Molecular Biology, and Ophthalmology & Visual Sciences, and Medicine, The Albert Einstein Comprehensive Cancer Center and Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Jinhua Cui
- Department of Developmental and Molecular Biology, and Ophthalmology & Visual Sciences, and Medicine, The Albert Einstein Comprehensive Cancer Center and Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Joseph Locker
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Liang Zhu
- Department of Developmental and Molecular Biology, and Ophthalmology & Visual Sciences, and Medicine, The Albert Einstein Comprehensive Cancer Center and Liver Research Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
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335
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TODAKA A, UMEHARA R, SASAKI K, SERIZAWA M, URAKAMI K, KUSUHARA M, YAMAGUCHI K, YASUI H. Metabolic profiling of gemcitabine- and paclitaxel-treated immortalized human pancreatic cell lines with K-RASG12D . Biomed Res 2017; 38:29-40. [DOI: 10.2220/biomedres.38.29] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Akiko TODAKA
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center
- Shizuoka Cancer Center
- Department of Surgery, Keio University Graduate School of Medicine
| | - Rina UMEHARA
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
| | | | - Masakuni SERIZAWA
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
| | - Kenichi URAKAMI
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute
| | - Masatoshi KUSUHARA
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute
- Regional Resources Division, Shizuoka Cancer Center Research Institute
| | | | - Hirofumi YASUI
- Division of Gastrointestinal Oncology, Shizuoka Cancer Center
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336
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Efficient and simple approach to in vitro culture of primary epithelial cancer cells. Biosci Rep 2016; 36:BSR20160208. [PMID: 27803125 PMCID: PMC5146827 DOI: 10.1042/bsr20160208] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 08/31/2016] [Accepted: 10/29/2016] [Indexed: 12/11/2022] Open
Abstract
Primary breast and prostate epithelial cancer cells may be efficiently cultured in vitro using simple and easily validatable approach–plates coated with a mixture of extracellular matrix components and tissue-specific primary cell medium. Primary cancer cells constitute a favourable testing platform for in vitro research in oncology field as they reflect tumour state more accurately than the most commonly employed stable cell lines. Unfortunately, due to limited availability of material and difficulties with protocols validation, primary models are rarely implemented into laboratory practice. We have compared protocols for primary cultures, differing in media components and plate coatings. In terms of culture establishment, application of Geltrex® coating demonstrated equal efficiency to feeder layer (83% compared with 72% successfully established breast and 80% compared with 80% prostate tumour specimens), yet it was substantially less complicated and easier to validate. Both Geltrex® coating and tissue-specific primary cell medium were permanently required to successfully maintain primary epithelial prostate cancer cells (PEPCs) in culture. In case of primary epithelial breast cancer cells (PEBCs), collagen I coating enabled to obtain comparable number of passages to Geltrex® coating (P=0.438). Commercial primary cell media demonstrated lower efficiency than tissue-specific ones (PEPCs–5 compared with 8 and PEBCs–6 compared with 9 passages). Interestingly, both analysed tumour types were unsusceptible to induction of culture lifespan extension when transduced with SV40LT, BMI-1 or hEST2 genes, commonly applied as potential immortalizing agents. In conclusion, the approach based on extracellular matrix reconstitution and tissue-specific primary cell media is easy to validate and provides in vitro expansion sufficient for analytical purposes (approximately 8 passages). Therefore, it may facilitate implementation of hardly available experimental models for a variety of analyses.
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337
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Müller R. PPARβ/δ in human cancer. Biochimie 2016; 136:90-99. [PMID: 27916645 DOI: 10.1016/j.biochi.2016.10.019] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Revised: 10/06/2016] [Accepted: 10/19/2016] [Indexed: 12/31/2022]
Abstract
The nuclear receptor factor peroxisome proliferator-activated receptor (PPARβ/δ) can regulate its target genes by transcriptional activation or repression through both ligand-dependent and independent mechanism as well as by interactions with other transcription factors. PPARβ/δ exerts essential regulatory functions in intermediary metabolism that have been elucidated in detail, but clearly also plays a role in inflammation, differentiation, apoptosis and other cancer-associated processes, which is, however, mechanistically only partly understood. Consistent with these functions clinical associations link the expression of PPARβ/δ and its target genes to an unfavorable outcome of several human cancers. However, the available data do not yield a clear picture of PPARβ/δ's role in cancer-associated processes and are in fact partly controversial. This article provides an overview of this research area and discusses the role of PPARβ/δ in cancer in light of the complex mechanisms of its transcriptional regulation and its potential as a druggable anti-cancer target.
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Affiliation(s)
- Rolf Müller
- Institute of Molecular Biology and Tumor Research, Center for Tumor Biology and Immunology, Philipps University, Hans-Meerwein-Str. 3, 35043 Marburg, Germany.
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338
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Wang D, Pham NA, Tong J, Sakashita S, Allo G, Kim L, Yanagawa N, Raghavan V, Wei Y, To C, Trinh QM, Starmans MHW, Chan-Seng-Yue MA, Chadwick D, Li L, Zhu CQ, Liu N, Li M, Lee S, Ignatchenko V, Strumpf D, Taylor P, Moghal N, Liu G, Boutros PC, Kislinger T, Pintilie M, Jurisica I, Shepherd FA, McPherson JD, Muthuswamy L, Moran MF, Tsao MS. Molecular heterogeneity of non-small cell lung carcinoma patient-derived xenografts closely reflect their primary tumors. Int J Cancer 2016; 140:662-673. [PMID: 27750381 DOI: 10.1002/ijc.30472] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Accepted: 09/29/2016] [Indexed: 01/10/2023]
Abstract
Availability of lung cancer models that closely mimic human tumors remains a significant gap in cancer research, as tumor cell lines and mouse models may not recapitulate the spectrum of lung cancer heterogeneity seen in patients. We aimed to establish a patient-derived tumor xenograft (PDX) resource from surgically resected non-small cell lung cancer (NSCLC). Fresh tumor tissue from surgical resection was implanted and grown in the subcutaneous pocket of non-obese severe combined immune deficient (NOD SCID) gamma mice. Subsequent passages were in NOD SCID mice. A subset of matched patient and PDX tumors and non-neoplastic lung tissues were profiled by whole exome sequencing, single nucleotide polymorphism (SNP) and methylation arrays, and phosphotyrosine (pY)-proteome by mass spectrometry. The data were compared to published NSCLC datasets of NSCLC primary and cell lines. 127 stable PDXs were established from 441 lung carcinomas representing all major histological subtypes: 52 adenocarcinomas, 62 squamous cell carcinomas, one adeno-squamous carcinoma, five sarcomatoid carcinomas, five large cell neuroendocrine carcinomas, and two small cell lung cancers. Somatic mutations, gene copy number and expression profiles, and pY-proteome landscape of 36 PDXs showed greater similarity with patient tumors than with established cell lines. Novel somatic mutations on cancer associated genes were identified but only in PDXs, likely due to selective clonal growth in the PDXs that allows detection of these low allelic frequency mutations. The results provide the strongest evidence yet that PDXs established from lung cancers closely mimic the characteristics of patient primary tumors.
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Affiliation(s)
- Dennis Wang
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Sheffield Institute of Translational Neuroscience, University of Sheffield, Sheffield, UK, S1O 2HQ
| | - Nhu-An Pham
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Jiefei Tong
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Shingo Sakashita
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Ghassan Allo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Lucia Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Naoki Yanagawa
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Vibha Raghavan
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Yuhong Wei
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Christine To
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Quang M Trinh
- Ontario Institute of Cancer Research, Toronto, ON, Canada
| | | | | | - Dianne Chadwick
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Lei Li
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Chang-Qi Zhu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ni Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Ming Li
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Sharon Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Dan Strumpf
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Paul Taylor
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada
| | - Nadeem Moghal
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Geoffrey Liu
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - Paul C Boutros
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Pharmacology and Toxicology, University of Toronto, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Melania Pintilie
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Igor Jurisica
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.,Department of Computer Science, University of Toronto, Toronto, ON, Canada
| | - Frances A Shepherd
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Medicine, University of Toronto, Toronto, ON, Canada
| | - John D McPherson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Lakshmi Muthuswamy
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael F Moran
- Program in Molecular Structure and Function, Hospital for Sick Children, Toronto, ON, Canada.,Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Ming-Sound Tsao
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.,Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
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339
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Identifying clinically relevant drug resistance genes in drug-induced resistant cancer cell lines and post-chemotherapy tissues. Oncotarget 2016; 6:41216-27. [PMID: 26515599 PMCID: PMC4747401 DOI: 10.18632/oncotarget.5649] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 09/12/2015] [Indexed: 12/13/2022] Open
Abstract
Until recently, few molecular signatures of drug resistance identified in drug-induced resistant cancer cell models can be translated into clinical practice. Here, we defined differentially expressed genes (DEGs) between pre-chemotherapy colorectal cancer (CRC) tissue samples of non-responders and responders for 5-fluorouracil and oxaliplatin-based therapy as clinically relevant drug resistance genes (CRG5-FU/L-OHP). Taking CRG5-FU/L-OHP as reference, we evaluated the clinical relevance of several types of genes derived from HCT116 CRC cells with resistance to 5-fluorouracil and oxaliplatin, respectively. The results revealed that DEGs between parental and resistant cells, when both were treated with the corresponding drug for a certain time, were significantly consistent with the CRG5-FU/L-OHP as well as the DEGs between the post-chemotherapy CRC specimens of responders and non-responders. This study suggests a novel strategy to extract clinically relevant drug resistance genes from both drug-induced resistant cell models and post-chemotherapy cancer tissue specimens.
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340
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Schneeberger VE, Allaj V, Gardner EE, Poirier JT, Rudin CM. Quantitation of Murine Stroma and Selective Purification of the Human Tumor Component of Patient-Derived Xenografts for Genomic Analysis. PLoS One 2016; 11:e0160587. [PMID: 27611664 PMCID: PMC5017757 DOI: 10.1371/journal.pone.0160587] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Accepted: 07/21/2016] [Indexed: 01/16/2023] Open
Abstract
Patient-derived xenograft (PDX) mouse models are increasingly used for preclinical therapeutic testing of human cancer. A limitation in molecular and genetic characterization of PDX tumors is the presence of integral murine stroma. This is particularly problematic for genomic sequencing of PDX models. Rapid and dependable approaches for quantitating stromal content and purifying the malignant human component of these tumors are needed. We used a recently developed technique exploiting species-specific polymerase chain reaction (PCR) amplicon length (ssPAL) differences to define the fractional composition of murine and human DNA, which was proportional to the fractional composition of cells in a series of lung cancer PDX lines. We compared four methods of human cancer cell isolation: fluorescence-activated cell sorting (FACS), an immunomagnetic mouse cell depletion (MCD) approach, and two distinct EpCAM-based immunomagnetic positive selection methods. We further analyzed DNA extracted from the resulting enriched human cancer cells by targeted sequencing using a clinically validated multi-gene panel. Stromal content varied widely among tumors of similar histology, but appeared stable over multiple serial tumor passages of an individual model. FACS and MCD were superior to either positive selection approach, especially in cases of high stromal content, and consistently allowed high quality human-specific genomic profiling. ssPAL is a dependable approach to quantitation of murine stromal content, and MCD is a simple, efficient, and high yield approach to human cancer cell isolation for genomic analysis of PDX tumors.
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Affiliation(s)
- Valentina E. Schneeberger
- Molecular Pharmacology & Chemistry Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Viola Allaj
- Molecular Pharmacology & Chemistry Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Eric E. Gardner
- Pharmacology Graduate Training Program, Johns Hopkins University, Baltimore, MD, United States of America
| | - J. T. Poirier
- Molecular Pharmacology & Chemistry Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- * E-mail: (JP); (CR)
| | - Charles M. Rudin
- Molecular Pharmacology & Chemistry Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Department of Medicine, Weill Cornell Medical College, New York, NY, United States of America
- * E-mail: (JP); (CR)
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341
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Wang S, Nie S, Zhu F. Chemical constituents and health effects of sweet potato. Food Res Int 2016; 89:90-116. [PMID: 28460992 DOI: 10.1016/j.foodres.2016.08.032] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/20/2016] [Accepted: 08/23/2016] [Indexed: 11/18/2022]
Abstract
Sweet potatoes are becoming a research focus in recent years due to their unique nutritional and functional properties. Bioactive carbohydrates, proteins, lipids, carotenoids, anthocyanins, conjugated phenolic acids, and minerals represent versatile nutrients in different parts (tubers, leaves, stems, and stalks) of sweet potato. The unique composition of sweet potato contributes to their various health benefits, such as antioxidative, hepatoprotective, antiinflammatory, antitumor, antidiabetic, antimicrobial, antiobesity, antiaging effects. Factors affecting the nutritional composition and bio-functions of sweet potato include the varieties, plant parts, extraction time and solvents, postharvest storage, and processing. The assays for bio-function evaluation also contribute to the variations among different studies. This review summarizes the current knowledge of the chemical composition of sweet potato, and their bio-functions studied in vitro and in vivo. Leaves, stems, and stalks of sweet potato remain much underutilized on commercial levels. Sweet potato can be further developed as a sustainable crop for diverse nutritionally enhanced and value-added food products to promote human health.
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Affiliation(s)
- Sunan Wang
- Canadian Food and Wine Institute, Niagara College, 135 Taylor Road, Niagara-on-the-Lake, Ontario, Canada L0S 1J0; School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
| | - Shaoping Nie
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang 330047, China
| | - Fan Zhu
- School of Chemical Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand.
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342
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Salawu A, Fernando M, Hughes D, Reed MWR, Woll P, Greaves C, Day C, Alhajimohammed M, Sisley K. Establishment and molecular characterisation of seven novel soft-tissue sarcoma cell lines. Br J Cancer 2016; 115:1058-1068. [PMID: 27560552 PMCID: PMC5117779 DOI: 10.1038/bjc.2016.259] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Revised: 07/20/2016] [Accepted: 07/26/2016] [Indexed: 12/17/2022] Open
Abstract
Background: Soft-tissue sarcomas (STS) are a diverse group of malignancies that remain a diagnostic and therapeutic challenge. Relatively few reliable cell lines currently exist. Rapidly developing technology for genomic profiling with emerging insights into candidate functional (driver) aberrations raises the need for more models for in vitro functional validation of molecular targets. Methods: Primary cell culture was performed on STS tumours utilising a differential attachment approach. Cell lines were characterised by morphology, immunocytochemistry, proliferation assays, short tandem repeat (STR) and microarray-based genomic copy number profiling. Results: Of 47 STS cases of various subtypes, half formed adherent monolayers. Seven formed self-immortalised cell lines, including three undifferentiated pleomorphic sarcomas, two dedifferentiated liposarcomas (one of which had received radiotherapy), a leiomyosarcoma and a myxofibrosarcoma. Two morphologically distinct yet genetically identical variants were established in separate cultures for the latter two tumours. All cell lines demonstrated genomic and phenotypic features that not only confirm their malignant characteristics but also confirm retention of DNA copy number aberrations present in their parent tumours that likely include drivers. Conclusions: These primary cell lines are much-needed additions to the number of reliable cell lines of STS with complex genomics available for initial functional validation of candidate molecular targets.
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Affiliation(s)
- Abdulazeez Salawu
- Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Malee Fernando
- Department of Histopathology, Sheffield Teaching Hospitals, Royal Hallamshire Hospital, Glossop Road Sheffield S10 2JF, UK
| | - David Hughes
- Department of Histopathology, Sheffield Teaching Hospitals, Royal Hallamshire Hospital, Glossop Road Sheffield S10 2JF, UK
| | - Malcolm W R Reed
- Brighton and Sussex Medical School, University of Sussex, Falmer, Brighton BN1 9PX, UK
| | - Penella Woll
- Academic Unit of Clinical Oncology, Weston Park Hospital, University of Sheffield, Whitham Road, Sheffield S10 2SJ, UK
| | - Claire Greaves
- Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Chris Day
- Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
| | - Meshal Alhajimohammed
- Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK.,Prince Sultan Military Medical City, Post Box 7897 Riyadh 11159, Kingdom of Saudi Arabia
| | - Karen Sisley
- Department of Oncology and Metabolism, The University of Sheffield, Medical School, Beech Hill Road, Sheffield S10 2RX, UK
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343
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Jimbo M, Blanco FF, Huang YH, Telonis AG, Screnci BA, Cosma GL, Alexeev V, Gonye GE, Yeo CJ, Sawicki JA, Winter JM, Brody JR. Targeting the mRNA-binding protein HuR impairs malignant characteristics of pancreatic ductal adenocarcinoma cells. Oncotarget 2016; 6:27312-31. [PMID: 26314962 PMCID: PMC4694992 DOI: 10.18632/oncotarget.4743] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Accepted: 07/13/2015] [Indexed: 12/21/2022] Open
Abstract
Post-transcriptional regulation is a powerful mediator of gene expression, and can rapidly alter the expression of numerous transcripts involved in tumorigenesis. We have previously shown that the mRNA-binding protein HuR (ELAVL1) is elevated in human pancreatic ductal adenocarcinoma (PDA) specimens compared to normal pancreatic tissues, and its cytoplasmic localization is associated with increased tumor stage. To gain a better insight into HuR’s role in PDA biology and to assess it as a candidate therapeutic target, we altered HuR expression in PDA cell lines and characterized the resulting phenotype in preclinical models. HuR silencing by short hairpin and small interfering RNAs significantly decreased cell proliferation and anchorage-independent growth, as well as impaired migration and invasion. In comparison, HuR overexpression increased migration and invasion, but had no significant effects on cell proliferation and anchorage-independent growth. Importantly, two distinct targeted approaches to HuR silencing showed marked impairment in tumor growth in mouse xenografts. NanoString nCounter® analyses demonstrated that HuR regulates core biological processes, highlighting that HuR inhibition likely thwarts PDA viability through post-transcriptional regulation of diverse signaling pathways (e.g. cell cycle, apoptosis, DNA repair). Taken together, our study suggests that targeted inhibition of HuR may be a novel, promising approach to the treatment of PDA.
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Affiliation(s)
- Masaya Jimbo
- Department of Surgery and The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Fernando F Blanco
- Department of Surgery and The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.,Department of Pharmacology & Experimental Therapeutics, Division of Clinical Pharmacology, Thomas Jefferson University, Philadelphia, PA, USA
| | - Yu-Hung Huang
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College, Thomas Jefferson University, Philadelphia, PA, USA
| | - Brad A Screnci
- Department of Surgery and The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Gabriela L Cosma
- Department of Microbiology and Immunology, Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Vitali Alexeev
- Department of Dermatology, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Charles J Yeo
- Department of Surgery and The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | | | - Jordan M Winter
- Department of Surgery and The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Jonathan R Brody
- Department of Surgery and The Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
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344
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Ordikhani F, Erdem Arslan M, Marcelo R, Sahin I, Grigsby P, Schwarz JK, Azab AK. Drug Delivery Approaches for the Treatment of Cervical Cancer. Pharmaceutics 2016; 8:E23. [PMID: 27447664 PMCID: PMC5039442 DOI: 10.3390/pharmaceutics8030023] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Revised: 07/12/2016] [Accepted: 07/13/2016] [Indexed: 12/22/2022] Open
Abstract
Cervical cancer is a highly prevalent cancer that affects women around the world. With the availability of new technologies, researchers have increased their efforts to develop new drug delivery systems in cervical cancer chemotherapy. In this review, we summarized some of the recent research in systematic and localized drug delivery systems and compared the advantages and disadvantages of these methods.
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Affiliation(s)
- Farideh Ordikhani
- Department of Radiation Oncology, Cancer Biology Division, Washington University School of Medicine, Saint Louis, MO 63108, USA.
| | - Mustafa Erdem Arslan
- Department of Radiation Oncology, Cancer Biology Division, Washington University School of Medicine, Saint Louis, MO 63108, USA.
| | - Raymundo Marcelo
- Department of Radiation Oncology, Cancer Biology Division, Washington University School of Medicine, Saint Louis, MO 63108, USA.
| | - Ilyas Sahin
- Department of Medicine, Mount Auburn Hospital, Harvard Medical School, Cambridge, MA 02138, USA.
| | - Perry Grigsby
- Department of Radiation Oncology, Radiology and Obstetrics and Gynecology, Washington University School of Medicine, Saint Louis, MO 63108, USA.
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO 63108, USA.
| | - Julie K Schwarz
- Department of Radiation Oncology, Cancer Biology Division, Washington University School of Medicine, Saint Louis, MO 63108, USA.
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO 63108, USA.
- Department of Radiation Oncology, Cell Biology and Physiology, Washington University School of Medicine, Saint Louis, MO 63108, USA.
| | - Abdel Kareem Azab
- Department of Radiation Oncology, Cancer Biology Division, Washington University School of Medicine, Saint Louis, MO 63108, USA.
- Alvin J. Siteman Cancer Center, Washington University School of Medicine, Saint Louis, MO 63108, USA.
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345
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Tong M, Zheng W, Li H, Li X, Ao L, Shen Y, Liang Q, Li J, Hong G, Yan H, Cai H, Li M, Guan Q, Guo Z. Multi-omics landscapes of colorectal cancer subtypes discriminated by an individualized prognostic signature for 5-fluorouracil-based chemotherapy. Oncogenesis 2016; 5:e242. [PMID: 27429074 PMCID: PMC5399173 DOI: 10.1038/oncsis.2016.51] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/27/2016] [Accepted: 06/17/2016] [Indexed: 12/11/2022] Open
Abstract
Until recently, few prognostic signatures for colorectal cancer (CRC) patients receiving 5-fluorouracil (5-FU)-based chemotherapy could be used in clinical practice. Here, using transcriptional profiles for a panel of cancer cell lines and three cohorts of CRC patients, we developed a prognostic signature based on within-sample relative expression orderings (REOs) of six gene pairs for stage II-III CRC patients receiving 5-FU-based chemotherapy. This REO-based signature had the unique advantage of being insensitive to experimental batch effects and free of the impractical data normalization requirement. After stratifying 184 CRC samples with multi-omics data from The Cancer Genome Atlas into two prognostic groups using the REO-based signature, we further revealed that patients with high recurrence risk were characterized by frequent gene copy number aberrations reducing 5-FU efficacy and DNA methylation aberrations inducing distinct transcriptional alternations to confer 5-FU resistance. In contrast, patients with low recurrence risk exhibited deficient mismatch repair and carried frequent gene mutations suppressing cell adhesion. These results reveal the multi-omics landscapes determining prognoses of stage II-III CRC patients receiving 5-FU-based chemotherapy.
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Affiliation(s)
- M Tong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - W Zheng
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - H Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - X Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - L Ao
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Y Shen
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Q Liang
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - J Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - G Hong
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - H Yan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - H Cai
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - M Li
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Q Guan
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
| | - Z Guo
- Department of Bioinformatics, Key Laboratory of Ministry of Education for Gastrointestinal Cancer, Fujian Medical University, Fuzhou, China
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346
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Thu KL, Papari-Zareei M, Stastny V, Song K, Peyton M, Martinez VD, Zhang YA, Castro IB, Varella-Garcia M, Liang H, Xing C, Kittler R, Milchgrub S, Castrillon DH, Davidson HL, Reynolds CP, Lam WL, Lea J, Gazdar AF. A comprehensively characterized cell line panel highly representative of clinical ovarian high-grade serous carcinomas. Oncotarget 2016; 8:50489-50499. [PMID: 28881577 PMCID: PMC5584155 DOI: 10.18632/oncotarget.9929] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Accepted: 05/22/2016] [Indexed: 12/26/2022] Open
Abstract
Recent literature suggests that most widely used ovarian cancer (OVCA) cell models do not recapitulate the molecular features of clinical tumors. To address this limitation, we generated 18 cell lines and 3 corresponding patient-derived xenografts predominantly from high-grade serous carcinoma (HGSOC) peritoneal effusions. Comprehensive genomic characterization and comparison of each model to its parental tumor demonstrated a high degree of molecular similarity. Our characterization included whole exome-sequencing and copy number profiling for cell lines, xenografts, and matched non-malignant tissues, and DNA methylation, gene expression, and spectral karyotyping for a subset of specimens. Compared to the Cancer Genome Atlas (TCGA), our models more closely resembled HGSOC than any other tumor type, justifying their validity as OVCA models. Our meticulously characterized models provide a crucial resource for the OVCA research community that will advance translational findings and ultimately lead to clinical applications.
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Affiliation(s)
- Kelsie L Thu
- British Columbia Cancer Agency Research Centre and University of British Columbia, Vancouver, BC, Canada
| | - Mahboubeh Papari-Zareei
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Victor Stastny
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Kai Song
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA.,School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
| | - Michael Peyton
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Victor D Martinez
- British Columbia Cancer Agency Research Centre and University of British Columbia, Vancouver, BC, Canada
| | - Yu-An Zhang
- Hamon Center for Therapeutic Oncology Research, UT Southwestern Medical Center, Dallas, TX, USA
| | - Isabel B Castro
- Division of Medical Oncology, University of Colorado Denver School of Medicine, Aurora, CO, USA
| | | | - Hanquan Liang
- Eugene McDermott Center for Human Growth & Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Chao Xing
- Eugene McDermott Center for Human Growth & Development, UT Southwestern Medical Center, Dallas, TX, USA
| | - Ralf Kittler
- Eugene McDermott Center for Human Growth & Development, UT Southwestern Medical Center, Dallas, TX, USA.,Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Sara Milchgrub
- Department of Pathology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Diego H Castrillon
- Department of Pathology and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
| | - Heather L Davidson
- Cell Biology & Biochemistry, Internal Medicine, and Pediatrics, School of Medicine Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - C Patrick Reynolds
- Cell Biology & Biochemistry, Internal Medicine, and Pediatrics, School of Medicine Texas Tech University Health Sciences Center, Lubbock, TX, USA
| | - Wan L Lam
- British Columbia Cancer Agency Research Centre and University of British Columbia, Vancouver, BC, Canada
| | - Jayanthi Lea
- Obstetrics & Gynecology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Adi F Gazdar
- Hamon Center for Therapeutic Oncology Research, Department of Pathology and Simmons Comprehensive Cancer Center, UT Southwestern Medical Center, Dallas, TX, USA
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347
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Pal D, Blair HJ, Elder A, Dormon K, Rennie KJ, Coleman DJL, Weiland J, Rankin KS, Filby A, Heidenreich O, Vormoor J. Long-term in vitro maintenance of clonal abundance and leukaemia-initiating potential in acute lymphoblastic leukaemia. Leukemia 2016; 30:1691-700. [PMID: 27109511 PMCID: PMC4980562 DOI: 10.1038/leu.2016.79] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Revised: 03/18/2016] [Accepted: 03/30/2016] [Indexed: 12/31/2022]
Abstract
Lack of suitable in vitro culture conditions for primary acute lymphoblastic leukaemia (ALL) cells severely impairs their experimental accessibility and the testing of new drugs on cell material reflecting clonal heterogeneity in patients. We show that Nestin-positive human mesenchymal stem cells (MSCs) support expansion of a range of biologically and clinically distinct patient-derived ALL samples. Adherent ALL cells showed an increased accumulation in the S phase of the cell cycle and diminished apoptosis when compared with cells in the suspension fraction. Moreover, surface expression of adhesion molecules CD34, CDH2 and CD10 increased several fold. Approximately 20% of the ALL cells were in G0 phase of the cell cycle, suggesting that MSCs may support quiescent ALL cells. Cellular barcoding demonstrated long-term preservation of clonal abundance. Expansion of ALL cells for >3 months compromised neither feeder dependence nor cancer initiating ability as judged by their engraftment potential in immunocompromised mice. Finally, we demonstrate the suitability of this co-culture approach for the investigation of drug combinations with luciferase-expressing primograft ALL cells. Taken together, we have developed a preclinical platform with patient-derived material that will facilitate the development of clinically effective combination therapies for ALL.
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Affiliation(s)
- D Pal
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - H J Blair
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - A Elder
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - K Dormon
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - K J Rennie
- Musculoskeletal Research Group, Institute of Cellular Medicine, Newcastle University, Newcastle Upon Tyne, UK
| | - D J L Coleman
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - J Weiland
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK.,Department of Hematology, Oncology, Hemostaseology, and Stem Cell Transplantation, Faculty of Medicine, RWTH Aachen University, Aachen, Germany
| | - K S Rankin
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - A Filby
- Flow Cytometry Core Facility, Faculty of Medical Sciences, Newcastle University, Newcastle Upon Tyne, UK
| | - O Heidenreich
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK
| | - J Vormoor
- Newcastle Cancer Centre at the Northern Institute for Cancer Research, Newcastle University, Newcastle Upon Tyne, UK.,Great North Children's Hospital, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle Upon Tyne, UK
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348
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van der Sligte NE, Kampen KR, ter Elst A, Scherpen FJG, Meeuwsen-de Boer TGJ, Guryev V, van Leeuwen FN, Kornblau SM, de Bont ESJM. Essential role for cyclic-AMP responsive element binding protein 1 (CREB) in the survival of acute lymphoblastic leukemia. Oncotarget 2016; 6:14970-81. [PMID: 26008971 PMCID: PMC4558129 DOI: 10.18632/oncotarget.3911] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 04/24/2015] [Indexed: 01/27/2023] Open
Abstract
Acute lymphoblastic leukemia (ALL) relapse remains a leading cause of cancer related death in children, therefore, new therapeutic options are needed. Recently, we showed that a peptide derived from Cyclic-AMP Responsive Element Binding Protein (CREB) was highly phosphorylated in pediatric leukemias. In this study, we determined CREB phosphorylation and mRNA levels showing that CREB expression was significantly higher in ALL compared to normal bone marrow (phosphorylation: P < 0.0001, mRNA: P = 0.004). High CREB and phospho-CREB expression was correlated with a lower median overall survival in a cohort of 140 adult ALL patients. ShRNA mediated knockdown of CREB in ALL cell lines blocked leukemic cell growth by inducing cell cycle arrest and apoptosis. Gene expression array analysis showed downregulation of CREB target genes regulating cell proliferation and glucose metabolism and upregulation of apoptosis inducing genes. Similar to CREB knockdown, the CREB inhibitor KG-501 decreased leukemic cell viability and induced apoptosis in ALL cell lines, as well as primary T-ALL samples, with cases showing high phospho-CREB levels being more sensitive than those with lower phospho-CREB levels. Together, these in vitro findings support an important role for CREB in the survival of ALL cells and identify this transcription factor as a potential target for treatment.
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Affiliation(s)
- Naomi E van der Sligte
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Kim R Kampen
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Arja ter Elst
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Frank J G Scherpen
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Tiny G J Meeuwsen-de Boer
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Victor Guryev
- European Research Institute for The Biology of Ageing, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
| | - Frank N van Leeuwen
- Laboratory of Pediatric Oncology, Department of Pediatrics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Steven M Kornblau
- Department of Leukemia, The University of Texas, MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Eveline S J M de Bont
- Division of Pediatric Oncology/Hematology, Department of Pediatrics, Beatrix Children's Hospital, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands
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349
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Grossenbacher SK, Canter RJ, Murphy WJ. Natural killer cell immunotherapy to target stem-like tumor cells. J Immunother Cancer 2016; 4:19. [PMID: 27096096 PMCID: PMC4835831 DOI: 10.1186/s40425-016-0124-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 03/11/2016] [Indexed: 11/10/2022] Open
Abstract
Advances in cancer immunotherapy are leading to its increasing and successful application for the treatment of solid-tissue cancers. Despite the recent advances there are still significant barriers, in particular, evidence for significant tumor heterogeneity, both genetic and epigenetic that limit long-term efficacy. Subpopulations of "stem-like" tumor cells have been identified in nearly all human malignancies based on both morphologic and functional criteria. Also called cancer stem cells or CSCs, these quiescent cells display enhanced tumorigenic potential and are capable of repopulating tumors in the wake of traditional cytoreductive therapies. These CSCs may be best targeted via immunotherapy. Our lab has identified activated natural killer (NK) cell-based therapy as an effective method to target CSCs particularly after radiation therapy for solid tumors. Using a variety of in vitro and in vivo methods, including the utilization of primary tumor tissue and patient-derived xenografts, we observed that autologous and allogeneic NK cells possess the ability to preferentially kill stem-like cells or CSCs from freshly isolated patient samples representing a broad spectrum of tumor types, including pancreatic cancers, breast cancers, and sarcomas. The results indicated that CSCs express stress ligand molecules capable of being targeted by NKG2D on NK cells and that prior radiation therapy can both deplete the cycling non-CSCs bulk tumor population and upregulate these stress ligands on the CSC making this an effective combination approach.
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Affiliation(s)
- Steven K Grossenbacher
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA 95817 USA
| | - Robert J Canter
- Division of Surgical Oncology, Department of Surgery, University of California Davis School of Medicine, Sacramento, CA 95817 USA
| | - William J Murphy
- Department of Dermatology, University of California Davis School of Medicine, Sacramento, CA 95817 USA ; Division of Hematology and Oncology, Department of Internal Medicine, University of California Davis Medical Center, Sacramento, CA 95817 USA
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350
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Lai ZW, Bolm L, Fuellgraf H, Biniossek ML, Makowiec F, Hopt UT, Werner M, Keck T, Bausch D, Sorio C, Scarpa A, Schilling O, Bronsert P, Wellner UF. Characterization of various cell lines from different ampullary cancer subtypes and cancer associated fibroblast-mediated responses. BMC Cancer 2016; 16:195. [PMID: 26951071 PMCID: PMC4782372 DOI: 10.1186/s12885-016-2193-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Accepted: 02/17/2016] [Indexed: 12/20/2022] Open
Abstract
Background Ampullary cancer is a relatively rare form of cancer and usually treated by pancreatoduodenectomy, followed by adjuvant therapy. The intestinal subtype is associated with markedly improved prognosis after resection. At present, only few cell lines are available for in vitro studies of ampullary cancer and they have not been collectively characterized. Methods We characterize five ampullary cancer cell lines by subtype maker expression, epithelial-mesenchymal transition (EMT) features, growth and invasion, drug sensitivity and response to cancer-associated fibroblast conditioned medium (CAF-CM). Results On the basis of EMT features, subtype marker expression, growth, invasion and drug sensitivity three types of cell lines could be distinguished: mesenchymal-like, pancreatobiliary-like and intestinal-like. Heterogeneous effects from the cell lines in response to CAF-CM, such as different growth rates, induction of EMT markers as well as suppression of intestinal differentiation markers were observed. In addition, proteomic analysis showed a clear difference in intestinal-like cell line from other cell lines. Conclusion Most of the available AMPAC cell lines seem to reflect a poorly differentiated pancreatobiliary or mesenchymal-like phenotype, which is consistent to their origin. We suggest that the most appropriate cell line model for intestinal-like AMPAC is the SNU869, while others seem to reflect aggressive AMPAC subtypes. Electronic supplementary material The online version of this article (doi:10.1186/s12885-016-2193-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zon Weng Lai
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Louisa Bolm
- Clinic for Surgery, UKSH Campus Lübeck, Lübeck, Germany
| | - Hannah Fuellgraf
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany
| | - Martin L Biniossek
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany
| | - Frank Makowiec
- Clinic for General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany
| | - Ulrich Theodor Hopt
- Clinic for General and Visceral Surgery, University Medical Center Freiburg, Freiburg, Germany.,Klinik für Chirurgie, Ratzeburger Allee 160, 23562, Lübeck, Germany
| | - Martin Werner
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany.,Comprehensive Cancer Center Freiburg, Freiburg, Germany
| | - Tobias Keck
- Clinic for Surgery, UKSH Campus Lübeck, Lübeck, Germany
| | - Dirk Bausch
- Clinic for Surgery, UKSH Campus Lübeck, Lübeck, Germany
| | - Claudio Sorio
- Dipartimento di Patologia, Universita di Verona, Verona, Italy
| | - Aldo Scarpa
- Dipartimento di Patologia, Universita di Verona, Verona, Italy
| | - Oliver Schilling
- Institute of Molecular Medicine and Cell Research, University of Freiburg, Freiburg, Germany. .,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Freiburg, Germany. .,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany.
| | - Peter Bronsert
- Department of Pathology, University Medical Center Freiburg, Freiburg, Germany.,German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), D-69120, Heidelberg, Germany.,Comprehensive Cancer Center Freiburg, Freiburg, Germany
| | - Ulrich Friedrich Wellner
- Clinic for Surgery, UKSH Campus Lübeck, Lübeck, Germany.,Comprehensive Cancer Center Freiburg, Freiburg, Germany.,Klinik für Chirurgie, Ratzeburger Allee 160, 23562, Lübeck, Germany
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