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Archambaud C, Nunez N, da Silva RAG, Kline KA, Serror P. Enterococcus faecalis: an overlooked cell invader. Microbiol Mol Biol Rev 2024:e0006924. [PMID: 39239986 DOI: 10.1128/mmbr.00069-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/07/2024] Open
Abstract
SUMMARYEnterococcus faecalis and Enterococcus faecium are human pathobionts that exhibit a dual lifestyle as commensal and pathogenic bacteria. The pathogenic lifestyle is associated with specific conditions involving host susceptibility and intestinal overgrowth or the use of a medical device. Although the virulence of E. faecium appears to benefit from its antimicrobial resistance, E. faecalis is recognized for its higher pathogenic potential. E. faecalis has long been considered a predominantly extracellular pathogen; it adheres to and is taken up by a wide range of mammalian cells, albeit with less efficiency than classical intracellular enteropathogens. Carbohydrate structures, rather than proteinaceous moieties, are likely to be primarily involved in the adhesion of E. faecalis to epithelial cells. Consistently, few adhesins have been implicated in the adhesion of E. faecalis to epithelial cells. On the host side, very little is known about cognate receptors, except for the role of glycosaminoglycans during macrophage infection. Several lines of evidence indicate that E. faecalis internalization may involve a zipper-like mechanism as well as a macropinocytosis pathway. Conversely, E. faecalis can use several strategies to prevent engulfment in phagocytes. However, the bacterial and host mechanisms underlying cell infection by E. faecalis are still in their infancy. The most recent striking finding is the existence of an intracellular lifestyle where E. faecalis can replicate within a variety of host cells. In this review, we summarize and discuss the current knowledge of E. faecalis-host cell interactions and argue on the need for further mechanistic studies to prevent or reduce infections.
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Affiliation(s)
- Cristel Archambaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Natalia Nunez
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
| | - Ronni A G da Silva
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Drug Resistance Interdisciplinary Research Group, Singapore, Singapore
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Kimberly A Kline
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Pascale Serror
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Jouy-en-Josas, France
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2
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Makowska A, Weiskirchen R. Nasopharyngeal Carcinoma Cell Lines: Reliable Alternatives to Primary Nasopharyngeal Cells? Cells 2024; 13:559. [PMID: 38606998 PMCID: PMC11011377 DOI: 10.3390/cells13070559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/17/2024] [Accepted: 03/20/2024] [Indexed: 04/13/2024] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a type of cancer that originates from the mucosal lining of the nasopharynx and can invade and spread. Although contemporary chemoradiotherapy effectively manages the disease locally, there are still challenges with locoregional recurrence and distant failure. Therefore, it is crucial to have a deeper understanding of the molecular basis of NPC cell movement in order to develop a more effective treatment and to improve patient survival rates. Cancer cell line models are invaluable in studying health and disease and it is not surprising that they play a critical role in NPC research. Consequently, scientists have established around 80 immortalized human NPC lines that are commonly used as in vitro models. However, over the years, it has been observed that many cell lines are misidentified or contaminated by other cells. This cross-contamination leads to the creation of false cell lines that no longer match the original donor. In this commentary, we discuss the impact of misidentified NPC cell lines on the scientific literature. We found 1159 articles from 2000 to 2023 that used NPC cell lines contaminated with HeLa cells. Alarmingly, the number of publications and citations using these contaminated cell lines continued to increase, even after information about the contamination was officially published. These articles were most commonly published in the fields of oncology, pharmacology, and experimental medicine research. These findings highlight the importance of science policy and support the need for journals to require authentication testing before publication.
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Affiliation(s)
- Anna Makowska
- Division of Pediatric Hematology, Oncology and Stem Cell Transplantation, RWTH University Hospital Aachen, D-52074 Aachen, Germany
| | - Ralf Weiskirchen
- Institute of Molecular Pathobiochemistry, Experimental Gene Therapy and Clinical Chemistry (IFMPEGKC), RWTH University Hospital Aachen, D-52074 Aachen, Germany
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3
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Lang OW, Srivastava D, Pugh BF, Lai WKM. GenoPipe: identifying the genotype of origin within (epi)genomic datasets. Nucleic Acids Res 2023; 51:12054-12068. [PMID: 37933851 PMCID: PMC10711449 DOI: 10.1093/nar/gkad950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 09/19/2023] [Accepted: 10/11/2023] [Indexed: 11/08/2023] Open
Abstract
Confidence in experimental results is critical for discovery. As the scale of data generation in genomics has grown exponentially, experimental error has likely kept pace despite the best efforts of many laboratories. Technical mistakes can and do occur at nearly every stage of a genomics assay (i.e. cell line contamination, reagent swapping, tube mislabelling, etc.) and are often difficult to identify post-execution. However, the DNA sequenced in genomic experiments contains certain markers (e.g. indels) encoded within and can often be ascertained forensically from experimental datasets. We developed the Genotype validation Pipeline (GenoPipe), a suite of heuristic tools that operate together directly on raw and aligned sequencing data from individual high-throughput sequencing experiments to characterize the underlying genome of the source material. We demonstrate how GenoPipe validates and rescues erroneously annotated experiments by identifying unique markers inherent to an organism's genome (i.e. epitope insertions, gene deletions and SNPs).
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Affiliation(s)
- Olivia W Lang
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Divyanshi Srivastava
- Department of Biochemistry & Molecular Biology, Pennsylvania State University, University Park, PA, 16801, USA
| | - B Franklin Pugh
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - William K M Lai
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
- Department of Computational Biology, Cornell University, Ithaca, NY 14850, USA
- Cornell Institute of Biotechnology, Cornell University, Ithaca, NY 14850, USA
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4
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Lang O, Srivastava D, Pugh BF, Lai WK. GenoPipe: identifying the genotype of origin within (epi)genomic datasets. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532660. [PMID: 36993164 PMCID: PMC10055126 DOI: 10.1101/2023.03.14.532660] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
Confidence in experimental results is critical for discovery. As the scale of data generation in genomics has grown exponentially, experimental error has likely kept pace despite the best efforts of many laboratories. Technical mistakes can and do occur at nearly every stage of a genomics assay (i.e., cell line contamination, reagent swapping, tube mislabelling, etc.) and are often difficult to identify post-execution. However, the DNA sequenced in genomic experiments contains certain markers (e.g., indels) encoded within and can often be ascertained forensically from experimental datasets. We developed the Genotype validation Pipeline (GenoPipe), a suite of heuristic tools that operate together directly on raw and aligned sequencing data from individual high-throughput sequencing experiments to characterize the underlying genome of the source material. We demonstrate how GenoPipe validates and rescues erroneously annotated experiments by identifying unique markers inherent to an organism’s genome (i.e., epitope insertions, gene deletions, and SNPs).
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5
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Tutty MA, Holmes S, Prina-Mello A. Cancer Cell Culture: The Basics and Two-Dimensional Cultures. Methods Mol Biol 2023; 2645:3-40. [PMID: 37202610 DOI: 10.1007/978-1-0716-3056-3_1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Despite significant advances in investigative and therapeutic methodologies for cancer, 2D cell culture remains an essential and evolving competency in this fast-paced industry. From basic monolayer cultures and functional assays to more recent and ever-advancing cell-based cancer interventions, 2D cell culture plays a crucial role in cancer diagnosis, prognosis, and treatment. Research and development in this field call for a great deal of optimization, while the heterogenous nature of cancer itself demands personalized precision for its intervention. In this way, 2D cell culture is ideal, providing a highly adaptive and responsive platform, where skills can be honed and techniques modified. Furthermore, it is arguably the most efficient, economical, and sustainable methodology available to researchers and clinicians alike.In this chapter, we discuss the history of cell culture and the varying types of cell and cell lines used today, the techniques used to characterize and authenticate them, the applications of 2D cell culture in cancer diagnosis and prognosis, and more recent developments in the area of cell-based cancer interventions and vaccines.
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Affiliation(s)
- Melissa Anne Tutty
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
| | - Sarah Holmes
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland.
| | - Adriele Prina-Mello
- Laboratory of Biological Characterization of Advanced Materials (LBCAM), Trinity Translational Medicine Institute, Trinity College, Dublin, Ireland
- Nanomedicine and Molecular Imaging Group, Trinity Translational Medicine Institute (TTMI), School of Medicine, Trinity College Dublin, Dublin, Ireland
- Trinity St. James's Cancer Institute, St. James's Hospital, Trinity College Dublin, Dublin, Ireland
- Advanced Materials and Bioengineering Research (AMBER) Centre, CRANN Institute, Trinity College Dublin, Dublin, Ireland
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6
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Miao X, Hu J, Chai C, Tang H, Zhao Z, Luo W, Zhou W, Xu H. Establishment and characterization of a new intrahepatic cholangiocarcinoma cell line derived from a Chinese patient. Cancer Cell Int 2022; 22:418. [PMID: 36578029 PMCID: PMC9795767 DOI: 10.1186/s12935-022-02840-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 12/23/2022] [Indexed: 12/29/2022] Open
Abstract
Patients with intrahepatic cholangiocarcinoma (ICC) require chemotherapy due to late detection, rapid disease progression, and low surgical resection rate. Tumor cell lines are extremely important in cancer research for drug discovery and development. Here, we established and characterized a new intrahepatic cholangiocarcinoma cell line, ICC-X1. STR testing confirmed the absence of cross-contamination and high similarity to the original tissue. ICC-X1 exhibited typical epithelial morphology and formed tumor spheres in the suspension culture. The population doubling time was approximately 48 h. The cell line had a complex hypotriploid karyotype. The cell line exhibited a strong migration ability in vitro and cell inoculation into BALB/c nude mice led to the formation of xenografts. Additionally, ICC-X1 cells were sensitive to gemcitabine and paclitaxel but resistant to 5-fluorouracil and oxaliplatin. RNA sequencing revealed that the upregulated cancer-related genes were mainly enriched in several signaling pathways, including the TNF signaling pathway, NOD-like receptor signaling pathway, and NF-κB signaling pathway. The downregulated cancer-related genes were mainly enriched in the Rap1 signaling pathway and Hippo signaling pathway among other pathways. In conclusion, we have created a new ICC cell line derived from Chinese patients. This cell line can be used as a preclinical model to study ICC, specifically tumor metastasis and drug resistance mechanisms.
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Affiliation(s)
- Xin Miao
- grid.410727.70000 0001 0526 1937State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Animal Virology of the Ministry of Agriculture, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730000 China
| | - Jinjing Hu
- grid.412643.60000 0004 1757 2902The Forth Department of General Surgery, The First Hospital of Lanzhou University, No. 1, Donggang West Road, Lanzhou, 730000 Gansu China
| | - Changpeng Chai
- grid.412643.60000 0004 1757 2902The Forth Department of General Surgery, The First Hospital of Lanzhou University, No. 1, Donggang West Road, Lanzhou, 730000 Gansu China
| | - Huan Tang
- grid.412643.60000 0004 1757 2902The Forth Department of General Surgery, The First Hospital of Lanzhou University, No. 1, Donggang West Road, Lanzhou, 730000 Gansu China
| | - Zhenjie Zhao
- grid.412643.60000 0004 1757 2902The Forth Department of General Surgery, The First Hospital of Lanzhou University, No. 1, Donggang West Road, Lanzhou, 730000 Gansu China
| | - Wei Luo
- grid.412643.60000 0004 1757 2902The Forth Department of General Surgery, The First Hospital of Lanzhou University, No. 1, Donggang West Road, Lanzhou, 730000 Gansu China
| | - Wence Zhou
- grid.411294.b0000 0004 1798 9345Department of General Surgery, The Second Hospital of Lanzhou University, Lanzhou, 730000 China ,grid.32566.340000 0000 8571 0482The Second Clinical Medical College, Lanzhou University, Lanzhou, 730000 China
| | - Hao Xu
- grid.412643.60000 0004 1757 2902The Forth Department of General Surgery, The First Hospital of Lanzhou University, No. 1, Donggang West Road, Lanzhou, 730000 Gansu China
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7
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Hayder H, Shan Y, Chen Y, O’Brien JA, Peng C. Role of microRNAs in trophoblast invasion and spiral artery remodeling: Implications for preeclampsia. Front Cell Dev Biol 2022; 10:995462. [PMID: 36263015 PMCID: PMC9575991 DOI: 10.3389/fcell.2022.995462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
It is now well-established that microRNAs (miRNAs) are important regulators of gene expression. The role of miRNAs in placental development and trophoblast function is constantly expanding. Trophoblast invasion and their ability to remodel uterine spiral arteries are essential for proper placental development and successful pregnancy outcome. Many miRNAs are reported to be dysregulated in pregnancy complications, especially preeclampsia and they exert various regulatory effects on trophoblasts. In this review, we provide a brief overview of miRNA biogenesis and their mechanism of action, as well as of trophoblasts differentiation, invasion and spiral artery remodeling. We then discuss the role of miRNAs in trophoblasts invasion and spiral artery remodeling, focusing on miRNAs that have been thoroughly investigated, especially using multiple model systems. We also discuss the potential role of miRNAs in the pathogenesis of preeclampsia.
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Affiliation(s)
- Heyam Hayder
- Department of Biology, York University, Toronto, ON, Canada
| | - Yanan Shan
- Department of Biology, York University, Toronto, ON, Canada
| | - Yan Chen
- Department of Biology, York University, Toronto, ON, Canada
| | | | - Chun Peng
- Department of Biology, York University, Toronto, ON, Canada
- Centre for Research on Biomolecular Interactions, York University, Toronto, ON, Canada
- *Correspondence: Chun Peng,
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8
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Isidan A, Yenigun A, Soma D, Aksu E, Lopez K, Park Y, Cross-Najafi A, Li P, Kundu D, House MG, Chakraborty S, Glaser S, Kennedy L, Francis H, Zhang W, Alpini G, Ekser B. Development and Characterization of Human Primary Cholangiocarcinoma Cell Lines. THE AMERICAN JOURNAL OF PATHOLOGY 2022; 192:1200-1217. [PMID: 35640676 PMCID: PMC9472155 DOI: 10.1016/j.ajpath.2022.05.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/12/2022] [Accepted: 05/18/2022] [Indexed: 06/15/2023]
Abstract
Cholangiocarcinoma (CCA) is the second most common primary liver tumor and is associated with late diagnosis, limited treatment options, and a 5-year survival rate of around 30%. CCA cell lines were first established in 1971, and since then, only 70 to 80 CCA cell lines have been established. These cell lines have been essential in basic and translational research to understand and identify novel mechanistic pathways, biomarkers, and disease-specific genes. Each CCA cell line has unique characteristics, reflecting a specific genotype, sex-related properties, and patient-related signatures, making them scientifically and commercially valuable. CCA cell lines are crucial in the use of novel technologies, such as three-dimensional organoid models, which help to model the tumor microenvironment and cell-to-cell crosstalk between tumor-neighboring cells. This review highlights crucial information on CCA cell lines, including: i) type of CCA (eg, intra- or extrahepatic), ii) isolation source (eg, primary tumor or xenograft), iii) chemical digestion method (eg, trypsin or collagenase), iv) cell-sorting method (colony isolation or removal of fibroblasts), v) maintenance-medium choice (eg, RPMI or Dulbecco's modified Eagle's medium), vi) cell morphology (eg, spindle or polygonal shape), and vii) doubling time of cells.
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Affiliation(s)
- Abdulkadir Isidan
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ali Yenigun
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana; Department of General Surgery, Yeditepe University Faculty of Medicine, Istanbul, Turkey
| | - Daiki Soma
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana; Division of Transplantation & Hepatobiliary Surgery, Department of Surgery, University of Florida College of Medicine, Gainesville, Florida
| | - Eric Aksu
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Kevin Lopez
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Yujin Park
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Arthur Cross-Najafi
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Ping Li
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Debjyoti Kundu
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Division of Research, Richard L. Roudebush VA Medical Center, Indianapolis, Indiana
| | - Michael G House
- Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Sanjukta Chakraborty
- Department of Medical Physiology, Texas A&M University College of Medicine, Bryan, Texas
| | - Shannon Glaser
- Department of Medical Physiology, Texas A&M University College of Medicine, Bryan, Texas
| | - Lindsey Kennedy
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Division of Research, Richard L. Roudebush VA Medical Center, Indianapolis, Indiana
| | - Heather Francis
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Division of Research, Richard L. Roudebush VA Medical Center, Indianapolis, Indiana
| | - Wenjun Zhang
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Gianfranco Alpini
- Division of Gastroenterology and Hepatology, Department of Medicine, Indiana University School of Medicine, Indianapolis, Indiana; Division of Research, Richard L. Roudebush VA Medical Center, Indianapolis, Indiana
| | - Burcin Ekser
- Transplant Division, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana.
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Melo G, Silva CAB, Hague A, Parkinson EK, Rivero ERC. Anticancer effects of putative and validated BH3-mimetic drugs in head and neck squamous cell carcinomas: An overview of current knowledge. Oral Oncol 2022; 132:105979. [PMID: 35816876 DOI: 10.1016/j.oraloncology.2022.105979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 05/20/2022] [Accepted: 06/17/2022] [Indexed: 11/16/2022]
Abstract
The purpose of this review was to summarise available literature concerning the anticancer effects of both putative and validated BH3-mimetics in head and neck squamous cell carcinomas. A literature search was performed and studies assessing malignant cell lines, xenograft models, and/or humans were considered eligible. A total of 501 studies were identified, of which 40 were included. One phase-II clinical trial assessing gossypol (combined with docetaxel) was found. The remaining 39 preclinical studies investigated cell lines and/or xenograft models involving the use of six validated BH3-mimetics (A-1210477, A-1331852, ABT-737, navitoclax, S63845, venetoclax) and six putative BH3-mimetics (ApoG2, gossypol, obatoclax, sabutoclax, TW-37, and YC137). In preclinical settings, most validated BH3-mimetics were capable of inducing apoptosis (in-vitro) and tumour growth inhibition (in-vivo). The majority of putative BH3-mimetics were also capable of inducing cell death, although important off-target effects, such as autophagy induction, were also described. Combinations with conventional anticancer drugs, ionising radiation, or multiple BH3-mimetics generally resulted in enhanced anticancer effects, such as increased sensitivity to apoptotic stimuli, especially considering some cell lines that showed resistance to either treatment alone. In conclusion, although clinical data are still insufficient to evaluate the anticancer effects of BH3-mimetics in head and neck squamous cell carcinomas, promising results in preclinical settings were observed concerning induction of cell death and inhibition of tumour growth. Therefore, further clinical trials are highly encouraged.
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Affiliation(s)
- Gilberto Melo
- Postgraduate Program in Dentistry, Federal University of Santa Catarina, Florianópolis, Brazil.
| | - Carolina Amália Barcellos Silva
- Department of Morphological Sciences, Biological Sciences Center, Federal University of Santa Catarina, Florianópolis, Brazil.
| | - Angela Hague
- Senior Lecturer, Bristol Dental School, Bristol, United Kingdom.
| | - Eric Kenneth Parkinson
- Centre for Oral Immunobiology and Regenerative Medicine, Institute of Dentistry, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, United Kingdom.
| | - Elena Riet Correa Rivero
- Department of Pathology, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, Brazil.
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Blaszczak W, Swietach P. What do cellular responses to acidity tell us about cancer? Cancer Metastasis Rev 2021; 40:1159-1176. [PMID: 34850320 PMCID: PMC8825410 DOI: 10.1007/s10555-021-10005-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 11/22/2021] [Indexed: 12/20/2022]
Abstract
The notion that invasive cancer is a product of somatic evolution is a well-established theory that can be modelled mathematically and demonstrated empirically from therapeutic responses. Somatic evolution is by no means deterministic, and ample opportunities exist to steer its trajectory towards cancer cell extinction. One such strategy is to alter the chemical microenvironment shared between host and cancer cells in a way that no longer favours the latter. Ever since the first description of the Warburg effect, acidosis has been recognised as a key chemical signature of the tumour microenvironment. Recent findings have suggested that responses to acidosis, arising through a process of selection and adaptation, give cancer cells a competitive advantage over the host. A surge of research efforts has attempted to understand the basis of this advantage and seek ways of exploiting it therapeutically. Here, we review key findings and place these in the context of a mathematical framework. Looking ahead, we highlight areas relating to cellular adaptation, selection, and heterogeneity that merit more research efforts in order to close in on the goal of exploiting tumour acidity in future therapies.
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Affiliation(s)
- Wiktoria Blaszczak
- Department of Physiology, Anatomy & Genetics, Parks Road, Oxford, OX1 3PT, England
| | - Pawel Swietach
- Department of Physiology, Anatomy & Genetics, Parks Road, Oxford, OX1 3PT, England.
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11
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Avalos-Soriano A, García-Gasca A, Yáñez-Rivera B. The Development and Evaluation of Brain and Heart Cell Lines from a Marine Fish for Use in Xenobiotic-Induced Cytotoxicity Testing. Altern Lab Anim 2021; 49:147-156. [PMID: 34814757 DOI: 10.1177/02611929211052565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Two cell lines derived from the brain and heart of a Pacific white snook specimen (Centropomus viridis) were developed and evaluated in terms of their responsiveness to glyphosate-induced cytotoxicity. The cells were grown in Leibovitz-15 (L-15) medium supplemented with 10% fetal bovine serum (FBS) and were passaged 36 times. Growth was tested at different concentrations of FBS (5, 10 and 20%) at 27°C. The cell lines were cryopreserved at different passages and were successfully thawed, with a survival rate greater than 80% without detectable contamination. At passage 36, the cells were used to assess the deleterious effects of glyphosate, and cell proliferation was measured by direct counting and with the MTT assay. Similar LC50 values were obtained with both methods. Although the principles behind these two assessment methods differ, our results show that both are suitable for evaluating glyphosate toxicity. In addition, heart- and brain-derived cells showed similar sensitivity, suggesting that the same mode of action might be responsible for the toxicity of glyphosate at the cellular level. The newly developed Pacific white snook brain and heart cell lines could be useful to investigate cellular and molecular mechanisms of toxicity, satisfying the need to reduce the use of animals in experiments. Glyphosate-related toxicological data obtained in the present study will allow us to continue investigating the effects of this herbicide directly on brain and heart fish cells since similar studies have only been carried out on either live organisms or on human cell lines such as neuroblastoma, which are immortalised by oncogenes or similar.
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Affiliation(s)
- Anaguiven Avalos-Soriano
- Cátedras CONACyT-Molecular Biology and Tissue Culture Laboratory, 42575Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán, Mazatlán Sinaloa, México
| | - Alejandra García-Gasca
- Molecular Biology and Tissue Culture Laboratory, 42575Centro de Investigación en Alimentación y Desarrollo, Unidad Mazatlán, Mazatlán Sinaloa, México
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Shimizu K, Gi M, Suzuki S, North BJ, Watahiki A, Fukumoto S, Asara JM, Tokunaga F, Wei W, Inuzuka H. Interplay between protein acetylation and ubiquitination controls MCL1 protein stability. Cell Rep 2021; 37:109988. [PMID: 34758305 PMCID: PMC8621139 DOI: 10.1016/j.celrep.2021.109988] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 06/02/2021] [Accepted: 10/21/2021] [Indexed: 01/29/2023] Open
Abstract
The anti-apoptotic myeloid cell leukemia 1 (MCL1) protein belongs to the pro-survival BCL2 family and is frequently amplified or elevated in human cancers. MCL1 is highly unstable, with its stability being regulated by phosphorylation and ubiquitination. Here, we identify acetylation as another critical post-translational modification regulating MCL1 protein stability. We demonstrate that the lysine acetyltransferase p300 targets MCL1 at K40 for acetylation, which is counteracted by the deacetylase sirtuin 3 (SIRT3). Mechanistically, acetylation enhances MCL1 interaction with USP9X, resulting in deubiquitination and subsequent MCL1 stabilization. Therefore, ectopic expression of acetylation-mimetic MCL1 promotes apoptosis evasion of cancer cells, enhances colony formation potential, and facilitates xenografted tumor progression. We further demonstrate that elevated MCL1 acetylation sensitizes multiple cancer cells to pharmacological inhibition of USP9X. These findings reveal that acetylation of MCL1 is a critical post-translational modification enhancing its oncogenic function and provide a rationale for developing innovative therapeutic strategies for MCL1-dependent tumors. MCL1, an anti-apoptotic BCL2 family protein, is frequently overexpressed in a variety of cancers, and its oncogenic function is finely regulated by post-translational modifications such as phosphorylation and ubiquitination. Shimizu et al. dissect the molecular mechanism of acetylation-mediated MCL1 stability control, providing insights into potential therapeutic intervention targeting the MCL1 protein.
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Affiliation(s)
- Kouhei Shimizu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA; Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan.
| | - Min Gi
- Department of Molecular Pathology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; Department of Environmental Risk Assessment, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Shugo Suzuki
- Department of Molecular Pathology, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Brian J North
- Department of Biomedical Sciences, Creighton University, Omaha, NE 68178, USA
| | - Asami Watahiki
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan
| | - Satoshi Fukumoto
- Center for Advanced Stem Cell and Regenerative Research, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai 980-8575, Japan; Section of Pediatric Dentistry, Division of Oral Health, Growth and Development, Kyushu University Faculty of Dental Science, Fukuoka 812-8582, Japan
| | - John M Asara
- Division of Signal Transduction, Beth Israel Deaconess Medical Center and Department of Medicine, Harvard Medical School, Boston, MA 02215, USA
| | - Fuminori Tokunaga
- Department of Pathobiochemistry, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA.
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13
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Korch CT, Capes-Davis A. The Extensive and Expensive Impacts of HEp-2 [HeLa], Intestine 407 [HeLa], and Other False Cell Lines in Journal Publications. SLAS DISCOVERY 2021; 26:1268-1279. [PMID: 34697958 DOI: 10.1177/24725552211051963] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Cell lines are essential models for biomedical research. However, they have a common and important problem that needs to be addressed. Cell lines can be misidentified, meaning that they no longer correspond to the donor from whom the cells were first obtained. This problem may arise due to cross-contamination: the accidental introduction of cells from another culture. The contaminant, which is often a rapidly dividing cell line, will overgrow and replace the original culture. The end result is a false cell line, also known as a misidentified or imposter cell line. False cell lines may come from an entirely different species, tissue, or cell type than the original donor. If undetected, false cell lines produce unreliable and irreproducible results that pollute the biomedical literature and threaten the development of reliable drug discovery and meaningful patient treatments.The goal of this study was to ascertain how widespread this problem is and how it affects the literature, as well as to estimate how much funding has been used to produce pools of scientific literature of questionable value. We focus on HEp-2 [HeLa] and Intestine 407 [HeLa], two false cell lines that are widely used in the scientific literature but were shown to be cross-contaminated in 1967. These two cell lines have been used in 8497 and 1397 published articles and extensively described as laryngeal cancer and normal intestine, respectively, rather than their true identity: the cervical cancer cell line HeLa. Discussed are tools, approaches, and resources that can address this issue-both retrospectively and prospectively.
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Affiliation(s)
- Christopher T Korch
- Divisions of Medical Oncology and Endocrinology, Metabolism, and Diabetes, University of Colorado School of Medicine, Anschutz Medical Campus, Aurora, CO, USA
| | - Amanda Capes-Davis
- CellBank Australia, Children's Medical Research Institute, The University of Sydney, Westmead, NSW, Australia
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14
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Han S, Basting PJ, Dias GB, Luhur A, Zelhof AC, Bergman CM. Transposable element profiles reveal cell line identity and loss of heterozygosity in Drosophila cell culture. Genetics 2021; 219:6321957. [PMID: 34849875 PMCID: PMC8633141 DOI: 10.1093/genetics/iyab113] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2021] [Accepted: 07/01/2021] [Indexed: 11/28/2022] Open
Abstract
Cell culture systems allow key insights into biological mechanisms yet suffer from irreproducible outcomes in part because of cross-contamination or mislabeling of cell lines. Cell line misidentification can be mitigated by the use of genotyping protocols, which have been developed for human cell lines but are lacking for many important model species. Here, we leverage the classical observation that transposable elements (TEs) proliferate in cultured Drosophila cells to demonstrate that genome-wide TE insertion profiles can reveal the identity and provenance of Drosophila cell lines. We identify multiple cases where TE profiles clarify the origin of Drosophila cell lines (Sg4, mbn2, and OSS_E) relative to published reports, and also provide evidence that insertions from only a subset of long-terminal repeat retrotransposon families are necessary to mark Drosophila cell line identity. We also develop a new bioinformatics approach to detect TE insertions and estimate intra-sample allele frequencies in legacy whole-genome sequencing data (called ngs_te_mapper2), which revealed loss of heterozygosity as a mechanism shaping the unique TE profiles that identify Drosophila cell lines. Our work contributes to the general understanding of the forces impacting metazoan genomes as they evolve in cell culture and paves the way for high-throughput protocols that use TE insertions to authenticate cell lines in Drosophila and other organisms.
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Affiliation(s)
- Shunhua Han
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Preston J Basting
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA
| | - Guilherme B Dias
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
| | - Arthur Luhur
- Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Andrew C Zelhof
- Drosophila Genomics Resource Center, Indiana University, Bloomington, IN 47405, USA.,Department of Biology, Indiana University, Bloomington, IN 47405, USA
| | - Casey M Bergman
- Department of Genetics and Institute of Bioinformatics, University of Georgia, Athens, GA 30602, USA.,Department of Genetics, University of Georgia, Athens, GA 30602, USA
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15
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Khaseb S, Orooji M, Pour MG, Safavi SM, Eghbal MJ, Rezai Rad M. Dental stem cell banking: Techniques and protocols. Cell Biol Int 2021; 45:1851-1865. [PMID: 33979004 DOI: 10.1002/cbin.11626] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Revised: 04/21/2021] [Accepted: 05/01/2021] [Indexed: 12/13/2022]
Abstract
Dental tissue-derived stem cells (DSCs) provide an easy, accessible, relatively noninvasive promising source of adult stem cells (ASCs), which brought encouraging prospective for their clinical applications. DSCs provide a perfect opportunity to apply for a patient's own ASC, which poses a low risk of immune rejection. However, problems associated with the long-term culture of stem cells, including loss of proliferation and differentiation capacities, senescence, genetic instability, and the possibility of microbial contamination, make cell banking necessary. With the rapid development of advanced cryopreservation technology, various international DSC banks have been established for both research and clinical applications around the world. However, few studies have been published that provide step-by-step guidance on DSCs isolation and banking methods. The purpose of this review is to present protocols and technical details for all steps of cryopreserved DSCs, from donor selection, isolation, cryopreservation, to characterization and quality control. Here, the emphasis is on presenting practical principles in accordance with the available valid guidelines.
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Affiliation(s)
- Sanaz Khaseb
- Department of Hematology, Faculty of Medical Sciences, Tarbiat Modares University (TMU), Tehran, Iran
| | - Mahdi Orooji
- Department of Electrical and Computer Engineering, Tarbiat Modares University (TMU), Tehran, Iran
| | - Majid Ghasemian Pour
- Research Institute for Dental Sciences, Dental Research Center, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Seyed Mohammadreza Safavi
- Research Institute for Dental Sciences, Dental Research Center, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Jafar Eghbal
- Research Institute for Dental Sciences, Dental Research Center, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Maryam Rezai Rad
- Research Institute for Dental Sciences, Dental Research Center, School of Dentistry, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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16
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Chatzimichail S, Supramaniam P, Salehi-Reyhani A. Absolute Quantification of Protein Copy Number in Single Cells With Immunofluorescence Microscopy Calibrated Using Single-Molecule Microarrays. Anal Chem 2021; 93:6656-6664. [PMID: 33876929 DOI: 10.1021/acs.analchem.0c05177] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Great strides toward routine single-cell analyses have been made over the last decade, particularly in the field of transcriptomics. For proteomics, amplification is not currently possible and has necessitated the development of ultrasensitive platforms capable of performing such analyses on single cells. These platforms are improving in terms of throughput and multiplexability but still fall short in relation to more established methods such as fluorescence microscopy. However, microscopy methods rely on fluorescence intensity as a proxy for protein abundance and are not currently capable of reporting this in terms of an absolute copy number. Here, a microfluidic implementation of single-molecule microarrays for single-cell analysis is assessed in its ability to calibrate fluorescence microscopy data. We show that the equivalence of measurements of the steady-state distribution of protein abundance to single-molecule microarray data can be exploited to pave the way for absolute quantitation by fluorescence and immunofluorescence microscopy. The methods presented have been developed using GFP but are extendable to other proteins and other biomolecules of interest.
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Affiliation(s)
| | | | - Ali Salehi-Reyhani
- Department of Surgery & Cancer, Imperial College London, London W12 0HS, U.K
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17
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Colombo E, Cattaneo MG. Multicellular 3D Models to Study Tumour-Stroma Interactions. Int J Mol Sci 2021; 22:ijms22041633. [PMID: 33562840 PMCID: PMC7915117 DOI: 10.3390/ijms22041633] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/02/2021] [Accepted: 02/03/2021] [Indexed: 12/11/2022] Open
Abstract
Two-dimensional (2D) cell cultures have been the standard for many different applications, ranging from basic research to stem cell and cancer research to regenerative medicine, for most of the past century. Hence, almost all of our knowledge about fundamental biological processes has been provided by primary and established cell lines cultured in 2D monolayer. However, cells in tissues and organs do not exist as single entities, and life in multicellular organisms relies on the coordination of several cellular activities, which depend on cell–cell communication across different cell types and tissues. In addition, cells are embedded within a complex non-cellular structure known as the extracellular matrix (ECM), which anchors them in a three-dimensional (3D) formation. Likewise, tumour cells interact with their surrounding matrix and tissue, and the physical and biochemical properties of this microenvironment regulate cancer differentiation, proliferation, invasion, and metastasis. 2D models are unable to mimic the complex and dynamic interactions of the tumour microenvironment (TME) and ignore spatial cell–ECM and cell–cell interactions. Thus, multicellular 3D models are excellent tools to recapitulate in vitro the spatial dimension, cellular heterogeneity, and molecular networks of the TME. This review summarizes the biological significance of the cell–ECM and cell–cell interactions in the onset and progression of tumours and focuses on the requirement for these interactions to build up representative in vitro models for the study of the pathophysiology of cancer and for the design of more clinically relevant treatments.
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18
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Peavey J, Malek G. Cell Line Authentication in Vision Research and Beyond: A Tale Retold. Invest Ophthalmol Vis Sci 2021; 61:19. [PMID: 32516405 PMCID: PMC7415283 DOI: 10.1167/iovs.61.6.19] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
We live in an age where new technologies, and organizations involved in the distribution of biological materials, such as cell culture lines, have eased accessibility to a variety of in vitro models, developed, and/or harvested from different sources. In translational and basic ophthalmology research, in vitro assays are an essential component to discovery and preclinical studies. It is, therefore, of utmost importance for vision researchers to be cognizant of the risks surrounding the use of newly developed cell culture models and how scientific integrity could be impacted when standard operating procedures are not followed for cell line validation and identification. Herein, we discuss authentication challenges we faced when we obtained a newly marketed human choroidal endothelial cell line for vision research, and outline our process of validating and characterizing primary human choroidal endothelial cell lines in the laboratory.
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19
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Loiseau V, Cordaux R, Giraud I, Beby-Defaux A, Lévêque N, Gilbert C. Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B). Sci Rep 2020; 10:16046. [PMID: 32994520 PMCID: PMC7524804 DOI: 10.1038/s41598-020-73169-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 08/31/2020] [Indexed: 11/09/2022] Open
Abstract
The use of misidentified cell lines contaminated by other cell lines and/or microorganisms has generated much confusion in the scientific literature. Detailed characterization of such contaminations is therefore crucial to avoid misinterpretation and ensure robustness and reproducibility of research. Here we use DNA-seq data produced in our lab to first confirm that the Hep2 (clone 2B) cell line (Sigma-Aldrich catalog number: 85011412-1VL) is indistinguishable from the HeLa cell line by mapping integrations of the human papillomavirus 18 (HPV18) at their expected loci on chromosome 8. We then show that the cell line is also contaminated by a xenotropic murine leukemia virus (XMLV) that is nearly identical to the mouse Bxv1 provirus and we characterize one Bxv1 provirus, located in the second intron of the pseudouridylate synthase 1 (PUS1) gene. Using an RNA-seq dataset, we confirm the high expression of the E6 and E7 HPV18 oncogenes, show that the entire Bxv1 genome is moderately expressed, and retrieve a Bxv1 splicing event favouring expression of the env gene. Hep2 (clone 2B) is the fourth human cell line so far known to be contaminated by the Bxv1 XMLV. This contamination has to be taken into account when using the cell line in future experiments.
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Affiliation(s)
- Vincent Loiseau
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France
| | - Richard Cordaux
- Université de Poitiers, CNRS UMR 7267 Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Isabelle Giraud
- Université de Poitiers, CNRS UMR 7267 Laboratoire Ecologie et Biologie des Interactions, Equipe Ecologie Evolution Symbiose, 5 Rue Albert Turpain, TSA 51106, 86073, Poitiers Cedex 9, France
| | - Agnès Beby-Defaux
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France.,Unité de Microbiologie Moléculaire et Séquençage, CHU de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et de Mycobactériologie, CHU de Poitiers, Poitiers, France.,EA4331-LITEC, Université de Poitiers, Poitiers, France
| | - Clément Gilbert
- Université Paris-Saclay, CNRS, IRD, UMR Évolution, Génomes, Comportement et Écologie, 91198, Gif-sur-Yvette, France.
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20
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Gao Y, Nihira NT, Bu X, Chu C, Zhang J, Kolodziejczyk A, Fan Y, Chan NT, Ma L, Liu J, Wang D, Dai X, Liu H, Ono M, Nakanishi A, Inuzuka H, North BJ, Huang YH, Sharma S, Geng Y, Xu W, Liu XS, Li L, Miki Y, Sicinski P, Freeman GJ, Wei W. Acetylation-dependent regulation of PD-L1 nuclear translocation dictates the efficacy of anti-PD-1 immunotherapy. Nat Cell Biol 2020; 22:1064-1075. [PMID: 32839551 PMCID: PMC7484128 DOI: 10.1038/s41556-020-0562-4] [Citation(s) in RCA: 202] [Impact Index Per Article: 50.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 07/21/2020] [Indexed: 12/16/2022]
Abstract
Immunotherapies that target programmed cell death protein 1 (PD-1) and its ligand PD-L1 as well as cytotoxic T-lymphocyte-associated protein 4 (CTLA4) have shown impressive clinical outcomes for multiple tumours. However, only a subset of patients achieves durable responses, suggesting that the mechanisms of the immune checkpoint pathways are not completely understood. Here, we report that PD-L1 translocates from the plasma membrane into the nucleus through interactions with components of the endocytosis and nucleocytoplasmic transport pathways, regulated by p300-mediated acetylation and HDAC2-dependent deacetylation of PD-L1. Moreover, PD-L1 deficiency leads to compromised expression of multiple immune-response-related genes. Genetically or pharmacologically modulating PD-L1 acetylation blocks its nuclear translocation, reprograms the expression of immune-response-related genes and, as a consequence, enhances the anti-tumour response to PD-1 blockade. Thus, our results reveal an acetylation-dependent regulation of PD-L1 nuclear localization that governs immune-response gene expression, and thereby advocate targeting PD-L1 translocation to enhance the efficacy of PD-1/PD-L1 blockade.
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Affiliation(s)
- Yang Gao
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Naoe Taira Nihira
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Division of Pediatric Dentistry, Department of Oral Health and Development Sciences, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Xia Bu
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Chen Chu
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Jinfang Zhang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Aleksandra Kolodziejczyk
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yizeng Fan
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Ngai Ting Chan
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - Leina Ma
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Jing Liu
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Dong Wang
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Xiaoming Dai
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Huadong Liu
- Center for Mitochondrial Biology and Medicine, The Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology and Frontier Institute of Science and Technology, Xi'an Jiaotong University, Xi' an, China
| | - Masaya Ono
- Department of Clinical Proteomics, National Cancer Center Research Institute, Tokyo, Japan
| | - Akira Nakanishi
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - Hiroyuki Inuzuka
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Brian J North
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Yu-Han Huang
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA, USA
| | - Samanta Sharma
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Yan Geng
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin-Madison, Madison, WI, USA
| | - X Shirley Liu
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Lei Li
- Department of Urology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Yoshio Miki
- Department of Molecular Genetics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan.
| | - Piotr Sicinski
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, USA.
| | - Gordon J Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
| | - Wenyi Wei
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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21
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Gloria-Soria A, Soghigian J, Kellner D, Powell JR. Genetic diversity of laboratory strains and implications for research: The case of Aedes aegypti. PLoS Negl Trop Dis 2019; 13:e0007930. [PMID: 31815934 PMCID: PMC6922456 DOI: 10.1371/journal.pntd.0007930] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 12/19/2019] [Accepted: 11/17/2019] [Indexed: 12/29/2022] Open
Abstract
The yellow fever mosquito (Aedes aegypti), is the primary vector of dengue, Zika, and chikungunya fever, among other arboviral diseases. It is also a popular laboratory model in vector biology due to its ease of rearing and manipulation in the lab. Established laboratory strains have been used worldwide in thousands of studies for decades. Laboratory evolution of reference strains and contamination among strains are potential severe problems that could dramatically change experimental outcomes and thus is a concern in vector biology. We analyzed laboratory and field colonies of Ae. aegypti and an Ae. aegypti-derived cell line (Aag2) using 12 microsatellites and ~20,000 SNPs to determine the extent of divergence among laboratory strains and relationships to their wild relatives. We found that 1) laboratory populations are less genetically variable than their field counterparts; 2) colonies bearing the same name obtained from different laboratories may be highly divergent; 3) present genetic composition of the LVP strain used as the genome reference is incompatible with its presumed origin; 4) we document changes in two wild caught colonies over ~16 generations of colonization; and 5) the Aag2 Ae. aegypti cell line has experienced minimal genetic changes within and across laboratories. These results illustrate the degree of variability within and among strains of Ae. aegypti, with implications for cross-study comparisons, and highlight the need of a common mosquito repository and the implementation of strain validation tools.
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Affiliation(s)
- Andrea Gloria-Soria
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - John Soghigian
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - David Kellner
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
| | - Jeffrey R. Powell
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, United States of America
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22
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Development of conventional and real time PCR assays for rapid species authentication of mammalian cell lines commonly used in veterinary diagnostic laboratories. Res Vet Sci 2019; 126:170-177. [PMID: 31505453 DOI: 10.1016/j.rvsc.2019.08.029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Revised: 08/21/2019] [Accepted: 08/27/2019] [Indexed: 12/19/2022]
Abstract
Mammalian cell lines are valuable tools in biomedical fields, with applications ranging from disease diagnosis to the production of biological reagents and vaccines. Here we report the development of new conventional (cPCR) and real time PCR (qPCR) assays for species identification of several mammalian kidney cell lines originated from swine, green monkey, hamster and bovine tissues that are extensively used in veterinary diagnostic laboratories. The PCR primers and probes were selected from highly conserved mitochondrial genes and analyzed in silico by nucleotide BLAST in the National Center for Biotechnology Information (NCBI) website to ensure target specificity. The assays were highly species-specific and had no cross-reactivity against other tested cell lines originated from different mammalian species. Assay sensitivity (limit of detection; LOD) was determined using serial dilutions of cell line DNA as template. The estimated LODs were between 2.95 and 48 pg (picogram) DNA/assay for cPCR, and between 1.5 × 10-3 and 4.8 × 10-2 pg DNA/assay for qPCR. Multiplex qPCR assays were developed for simultaneous detection of up to three species in a single assay. The multiplex qPCR assays exhibited the same sensitivity as the corresponding singleplex assays with the exception of the green monkey species that demonstrated a 10-100 fold decline in the sensitivity. Contamination of swine cells was detected in one of the rabbit cell lines. The contamination was further confirmed by Sanger and Next-Generation sequencing.
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23
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Cancer Cell Lines Are Useful Model Systems for Medical Research. Cancers (Basel) 2019; 11:cancers11081098. [PMID: 31374935 PMCID: PMC6721418 DOI: 10.3390/cancers11081098] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/17/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Cell lines are in vitro model systems that are widely used in different fields of medical research, especially basic cancer research and drug discovery. Their usefulness is primarily linked to their ability to provide an indefinite source of biological material for experimental purposes. Under the right conditions and with appropriate controls, authenticated cancer cell lines retain most of the genetic properties of the cancer of origin. During the last few years, comparing genomic data of most cancer cell lines has corroborated this statement and those that were observed studying the tumoral tissue equivalents included in the The Cancer Genome Atlas (TCGA) database. We are at the disposal of comprehensive open access cell line datasets describing their molecular and cellular alterations at an unprecedented level of accuracy. This aspect, in association with the possibility of setting up accurate culture conditions that mimic the in vivo microenvironment (e.g., three-dimensional (3D) coculture), has strengthened the importance of cancer cell lines for continuing to sustain medical research fields. However, it is important to consider that the appropriate use of cell lines needs to follow established guidelines for guaranteed data reproducibility and quality, and to prevent the occurrence of detrimental events (i.e., those that are linked to cross-contamination and mycoplasma contamination).
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24
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Almeida JL, Dakic A, Kindig K, Kone M, Letham DLD, Langdon S, Peat R, Holding-Pillai J, Hall EM, Ladd M, Shaffer MD, Berg H, Li J, Wigger G, Lund S, Steffen CR, Fransway BB, Geraghty B, Natoli M, Bauer B, Gollin SM, Lewis DW, Reid Y. Interlaboratory study to validate a STR profiling method for intraspecies identification of mouse cell lines. PLoS One 2019; 14:e0218412. [PMID: 31220119 PMCID: PMC6586308 DOI: 10.1371/journal.pone.0218412] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Accepted: 05/31/2019] [Indexed: 12/21/2022] Open
Abstract
The Consortium for Mouse Cell Line Authentication was formed to validate Short Tandem Repeat (STR) markers for intraspecies identification of mouse cell lines. The STR profiling method is a multiplex polymerase chain reaction (PCR) assay comprised of primers targeting 19 mouse STR markers and two human STR markers (for interspecies contamination screening). The goals of the Consortium were to perform an interlaboratory study to–(1) validate the mouse STR markers to uniquely identify mouse cell lines (intraspecies identification), (2) to provide a public database of mouse cell lines with the National Institute of Standards and Technology (NIST)-validated mouse STR profiles, and (3) to publish the results of the interlaboratory study. The interlaboratory study was an international effort that consisted of 12 participating laboratories representing institutions from academia, industry, biological resource centers, and government. The study was based on 50 of the most commonly used mouse cell lines obtained from the American Type Culture Collection (ATCC). Of the 50 mouse cell lines, 18 had unique STR profiles that were 100% concordant (match) among all Consortium laboratory members, and the remaining 32 cell lines had discordance that was resolved readily and led to improvement of the assay. The discordance was due to low signal and interpretation issues involving artifacts and genotyping errors. Although the total number of discordant STR profiles was relatively high in this study, the percent of labs agreeing on allele calls among the discordant samples was above 92%. The STR profiles, including electropherogram images, for NIST-validated mouse cell lines will be published on the NCBI BioSample Database (https://www.ncbi.nlm.nih.gov/biosample/). Overall, the interlaboratory study showed that the multiplex PCR method using 18 of the 19 mouse STR markers is capable of discriminating at the intraspecies level between mouse cell lines. Further studies are ongoing to refine the assay including (1) development of an allelic ladder for improving the accuracy of allele calling and (2) integration of stutter filters to identify true stutter.
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Affiliation(s)
- Jamie L. Almeida
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Gaithersburg, Maryland, United States of America
- * E-mail:
| | - Aleksandra Dakic
- ATCC, Standards Resource Center, Manassas, Virginia, United States of America
| | - Karin Kindig
- ATCC, Standards Resource Center, Manassas, Virginia, United States of America
| | - Maikan Kone
- ATCC, Standards Resource Center, Manassas, Virginia, United States of America
| | | | - Scott Langdon
- Duke University, Durham, North Carolina, United States of America
| | - Ruth Peat
- The Francis Crick Institute, Cell Services, London, United Kingdom
| | | | - Erin M. Hall
- Genetica Cell Line Testing –a LabCorp brand, Burlington, North Carolina, United States of America
| | - Mark Ladd
- Genetica Cell Line Testing –a LabCorp brand, Burlington, North Carolina, United States of America
| | - Megan D. Shaffer
- Genetica Cell Line Testing –a LabCorp brand, Burlington, North Carolina, United States of America
| | - Heath Berg
- IDEXX BioAnalytics, Columbia, Missouri, United States of America
| | - Jinliang Li
- Laragen Inc., Culver City, California, United States of America
| | | | - Steve Lund
- National Institute of Standards and Technology, Statistical Engineering Division, Gaithersburg, Maryland, United States of America
| | - Carolyn R. Steffen
- National Institute of Standards and Technology, Biomolecular Measurement Division, Gaithersburg, Maryland, United States of America
| | - Barbara B. Fransway
- University of Arizona, Genetics Core Lab, University of Arizona Genetics Core, Tucson, Arizona, United States of America
| | - Bob Geraghty
- University of Cambridge, Cancer Research UK, Cambridge Institute, Cambridge, United Kingdom
| | - Manuela Natoli
- University of Cambridge, Cancer Research UK, Cambridge Institute, Cambridge, United Kingdom
| | - Beth Bauer
- University of Maryland, College Park, Maryland
| | - Susanne M. Gollin
- University of Pittsburgh, Department of Human Genetics, Pittsburgh, Pennsylvania, United States of America
| | - Dale W. Lewis
- University of Pittsburgh, Department of Human Genetics, Pittsburgh, Pennsylvania, United States of America
| | - Yvonne Reid
- National Institute of Standards and Technology, Biosystems and Biomaterials Division, Gaithersburg, Maryland, United States of America
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Abstract
Indirect immunofluorescence assay (IFA) has been used for detection of autoantibodies against cellular antigens for more than 50 years. Originally using rodent tissue as substrate, the method was optimized by using the human immortal HEp-2 cell line derived from a larynx epidermal carcinoma. The HEp-2/IFA platform allows for optimal visualization of several cellular domains recognized by autoantibodies in the samples being tested. Serial dilution allows for the estimation of the concentration (titer) of the autoantibodies in the sample. Judicious analysis of the topographic distribution of the immunofluorescence (pattern) provides useful hints on the most plausible autoantigens being recognized, vis-à-vis the cognate autoantibodies. The importance of the HEp-2/IFA pattern has been recently emphasized by the International Consensus on ANA Patterns (ICAP), an initiative that established a comprehensive classification of the most relevant and prevalent HEp-2/IFA patterns (designated anti-cell (AC) patterns) and harmonized its nomenclature. The former designation "antinuclear antibody test" has been progressively replaced by the term "anti-cell antibody test," due to the recognition that the HEp-2/IFA method in fact allows the detection of autoantibodies to several cellular domains, such as the cytoplasm and mitotic apparatus.The performance of the HEp-2/IFA test is strongly influenced by several technical details, including cell culture conditions, cell fixation and permeabilization methods, choice and titration of fluorochrome-conjugated secondary antibody, use and choice of blocking solutions, washing buffers, and antifading mounting medium. The several steps of the procedure must be carefully performed in order to avoid the formation of false positive fluorescent artifacts. The quality control of the assay involves the use of serum standards for negative, low positive and strongly positive reaction in each run of the assay. In addition, every new lot or new brand of HEp-2 slides should be evaluated by using a panel of standard sera yielding the most relevant AC patterns. Special attention should be dedicated to the training of personnel for the analysis of the slides at the microscope. These should be able to identify possible artifacts, recognize all relevant AC patterns, and formulate possible reflex tests according to the observed AC patterns.
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Biology is the root of variability: cautionary tales in Caenorhabditis elegans biology. Biochem Soc Trans 2019; 47:887-896. [PMID: 31127069 DOI: 10.1042/bst20190001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Revised: 04/29/2019] [Accepted: 04/30/2019] [Indexed: 12/31/2022]
Abstract
Abstract
Reproducibility is critical for the standardization, interpretation, and progression of research. However, many factors increase variability and reduce reproducibility. In Caenorhabditis elegans research, there are many possible causes of variability that may explain why experimental outcomes sometimes differ between laboratories and between experiments. Factors contributing to experimental variability include the genetic background of both C. elegans and its bacterial diet, differences in media composition, intergenerational and transgenerational effects that may be carried over for generations, and the use of chemicals or reagents that may have unexpected consequences. This review summarizes sources of variability in C. elegans research and serves to identify laboratory practices that could influence reproducibility.
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Luhur A, Klueg KM, Zelhof AC. Generating and working with Drosophila cell cultures: Current challenges and opportunities. WILEY INTERDISCIPLINARY REVIEWS-DEVELOPMENTAL BIOLOGY 2018; 8:e339. [PMID: 30561900 DOI: 10.1002/wdev.339] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/30/2018] [Accepted: 11/21/2018] [Indexed: 12/26/2022]
Abstract
The use of Drosophila cell cultures has positively impacted both fundamental and biomedical research. The most widely used cell lines: Schneider, Kc, the CNS and imaginal disc lines continue to be the choice for many applications. Drosophila cell lines provide a homogenous source of cells suitable for biochemical experimentations, transcriptomics, functional genomics, and biomedical applications. They are amenable to RNA interference and serve as a platform for high-throughput screens to identify relevant candidate genes or drugs for any biological process. Currently, CRISPR-based functional genomics are also being developed for Drosophila cell lines. Even though many uniquely derived cell lines exist, cell genetic techniques such the transgenic UAS-GAL4-based RasV12 oncogene expression, CRISPR-Cas9 editing and recombination mediated cassette exchange are likely to drive the establishment of many more lines from specific tissues, cells, or genotypes. However, the pace of creating new lines is hindered by several factors inherent to working with Drosophila cell cultures: single cell cloning, optimal media formulations and culture conditions capable of supporting lines from novel tissue sources or genotypes. Moreover, even though many Drosophila cell lines are morphologically and transcriptionally distinct it may be necessary to implement a standard for Drosophila cell line authentication, ensuring the identity and purity of each cell line. Altogether, recent advances and a standardized authentication effort should improve the utility of Drosophila cell cultures as a relevant model for fundamental and biomedical research. This article is categorized under: Technologies > Analysis of Cell, Tissue, and Animal Phenotypes.
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Affiliation(s)
- Arthur Luhur
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Kristin M Klueg
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
| | - Andrew C Zelhof
- Department of Biology, Drosophila Genomics Resource Center, Indiana University Bloomington, Bloomington, Indiana
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Korch C, Varella-Garcia M. Tackling the Human Cell Line and Tissue Misidentification Problem Is Needed for Reproducible Biomedical Research. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.yamp.2018.07.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abdelmegeed SM, Mohammed S. Canine mammary tumors as a model for human disease. Oncol Lett 2018; 15:8195-8205. [PMID: 29928319 PMCID: PMC6004712 DOI: 10.3892/ol.2018.8411] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 02/12/2018] [Indexed: 12/13/2022] Open
Abstract
Animal models for examining human breast cancer (HBC) carcinogenesis have been extensively studied and proposed. With the recent advent of immunotherapy, significant attention has been focused on the dog as a model for human cancer. Dogs develop mammary tumors and other cancer types spontaneously with an intact immune system, which exhibit a number of clinical and molecular similarities to HBC. In addition to the spontaneous tumor presentation, the clinical similarities between human and canine mammary tumors (CMT) include the age at onset, hormonal etiology and course of the diseases. Furthermore, factors that affect the disease outcome, including tumor size, stage and lymph node invasion, are similar in HBC and CMT. Similarly, the molecular characteristics of steroid receptor, epidermal growth factor, proliferation marker, metalloproteinase and cyclooxygenase expression, and the mutation of the p53 tumor suppressor gene in CMT, mimic HBC. Furthermore, ductal carcinomas in situ in human and canine mammary glands are particularly similar in their pathological, molecular and visual characteristics. These CMT characteristics and their similarities to HBC indicate that the dog could be an excellent model for the study of human disease. These similarities are discussed in detail in the present review, and are compared with the in vitro and other in vivo animal models available.
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Affiliation(s)
- Somaia M Abdelmegeed
- Department of Comparative Pathobiology, Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
| | - Sulma Mohammed
- Department of Comparative Pathobiology, Purdue University Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA
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Fernando EH, Dicay M, Stahl M, Gordon MH, Vegso A, Baggio C, Alston L, Lopes F, Baker K, Hirota S, McKay DM, Vallance B, MacNaughton WK. A simple, cost-effective method for generating murine colonic 3D enteroids and 2D monolayers for studies of primary epithelial cell function. Am J Physiol Gastrointest Liver Physiol 2017; 313:G467-G475. [PMID: 28751424 DOI: 10.1152/ajpgi.00152.2017] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Revised: 07/20/2017] [Accepted: 07/20/2017] [Indexed: 01/31/2023]
Abstract
Cancer cell lines have been the mainstay of intestinal epithelial experimentation for decades, due primarily to their immortality and ease of culture. However, because of the inherent biological abnormalities of cancer cell lines, many cellular biologists are currently transitioning away from these models and toward more representative primary cells. This has been particularly challenging, but recent advances in the generation of intestinal organoids have brought the routine use of primary cells within reach of most epithelial biologists. Nevertheless, even with the proliferation of publications that use primary intestinal epithelial cells, there is still a considerable amount of trial and error required for laboratories to establish a consistent and reliable method to culture three-dimensional (3D) intestinal organoids and primary epithelial monolayers. We aim to minimize the time other laboratories spend troubleshooting the technique and present a standard method for culturing primary epithelial cells. Therefore, we have described our optimized, high-yield, cost-effective protocol to grow 3D murine colonoids for more than 20 passages and our detailed methods to culture these cells as confluent monolayers for at least 14 days, enabling a wide variety of potential future experiments. By supporting and expanding on the current literature of primary epithelial culture optimization and detailed use in experiments, we hope to help enable the widespread adoption of these innovative methods and allow consistency of results obtained across laboratories and institutions.NEW & NOTEWORTHY Primary intestinal epithelial monolayers are notoriously difficult to maintain culture, even with the recent advances in the field. We describe, in detail, the protocols required to maintain three-dimensional cultures of murine colonoids and passage these primary epithelial cells to confluent monolayers in a standardized, high-yield and cost-effective manner.
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Affiliation(s)
- Elizabeth H Fernando
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Michael Dicay
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Martin Stahl
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Marilyn H Gordon
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Andrew Vegso
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Cristiane Baggio
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Laurie Alston
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Fernando Lopes
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Kristi Baker
- Department of Oncology, University of Alberta, Edmonton, Alberta, Canada
| | - Simon Hirota
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Derek M McKay
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada
| | - Bruce Vallance
- Department of Pediatrics, British Columbia Children's Hospital, University of British Columbia, Vancouver, British Columbia, Canada; and
| | - Wallace K MacNaughton
- Department of Physiology and Pharmacology and Gastrointestinal Research Group, University of Calgary, Calgary, Alberta, Canada;
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31
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Horbach SPJM, Halffman W. The ghosts of HeLa: How cell line misidentification contaminates the scientific literature. PLoS One 2017; 12:e0186281. [PMID: 29023500 PMCID: PMC5638414 DOI: 10.1371/journal.pone.0186281] [Citation(s) in RCA: 91] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 09/28/2017] [Indexed: 01/11/2023] Open
Abstract
While problems with cell line misidentification have been known for decades, an unknown number of published papers remains in circulation reporting on the wrong cells without warning or correction. Here we attempt to make a conservative estimate of this ‘contaminated’ literature. We found 32,755 articles reporting on research with misidentified cells, in turn cited by an estimated half a million other papers. The contamination of the literature is not decreasing over time and is anything but restricted to countries in the periphery of global science. The decades-old and often contentious attempts to stop misidentification of cell lines have proven to be insufficient. The contamination of the literature calls for a fair and reasonable notification system, warning users and readers to interpret these papers with appropriate care.
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Affiliation(s)
| | - Willem Halffman
- Radboud University, Institute for Science in Society, Nijmegen, The Netherlands
- * E-mail:
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32
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Drexler HG, Dirks WG, MacLeod RAF, Uphoff CC. False and mycoplasma-contaminated leukemia-lymphoma cell lines: time for a reappraisal. Int J Cancer 2017; 140:1209-1214. [PMID: 27870004 DOI: 10.1002/ijc.30530] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Revised: 11/04/2016] [Accepted: 11/08/2016] [Indexed: 01/23/2023]
Abstract
Leukemia-lymphoma cell lines are important research tools in a variety of fields. To represent adequate model systems it is of utmost importance that cell lines faithfully model the primary tumor material and are not cross-contaminated with unrelated cell material (or contaminated with mycoplasma). As it has been previously reported that cross-contaminated cell lines represent a significant problem, it is of interest to know whether any improvement in the prevalence of such "false cell lines" had occurred since we called the alert in 1999. A retrospective review of our data archives covered 848 cell lines received from 1990 to 2014 from 290 laboratories in 23 countries spanning the spectrum of leukemia-lymphoma entities. Two variables were considered: authenticity and freedom from mycoplasma infection. Regarding provenance, we separately considered primary sources (original investigators having established the cell lines or reference repositories) and secondary sources. The percentages of mycoplasma-contaminated cell lines decreased significantly over the 25-year timespan. Among primary sourced material: mycoplasma-contamination fell from 23% to 0%; among secondary sourced: from 48% to 21%. The corresponding figures for cross-contamination declined from 15% to 6%, while among material obtained from secondary sources prevalence remained remarkably high, throughout the time periods at 14-18%. Taken together, our data indicate that using non-authenticated cell lines from secondary sources carries a risk of about 1:6 for obtaining a false cell line. The use of authentic leukemia-lymphoma cell lines holds important translational value for their model character and the reproducibility of the laboratory data in the clinical arena.
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Affiliation(s)
- Hans G Drexler
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wilhelm G Dirks
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Roderick A F MacLeod
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Cord C Uphoff
- Department of Human and Animal Cell Lines, Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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33
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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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Abstract
In light of an enhanced awareness of ethical questions and ever increasing costs when working with animals in biomedical research, there is a dedicated and sometimes fierce debate concerning the (lack of) reproducibility of animal models and their relevance for human inflammatory diseases. Despite evident advancements in searching for alternatives, that is, replacing, reducing, and refining animal experiments-the three R's of Russel and Burch (1959)-understanding the complex interactions of the cells of the immune system, the nervous system and the affected tissue/organ during inflammation critically relies on in vivo models. Consequently, scientific advancement and ultimately novel therapeutic interventions depend on improving the reproducibility of animal inflammation models. As a prelude to the remaining hands-on protocols described in this volume, here, we summarize potential pitfalls of preclinical animal research and provide resources and background reading on how to avoid them.
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35
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Gardner JK, Herbst-Kralovetz MM. Three-Dimensional Rotating Wall Vessel-Derived Cell Culture Models for Studying Virus-Host Interactions. Viruses 2016; 8:v8110304. [PMID: 27834891 PMCID: PMC5127018 DOI: 10.3390/v8110304] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Revised: 10/18/2016] [Accepted: 10/31/2016] [Indexed: 12/31/2022] Open
Abstract
The key to better understanding complex virus-host interactions is the utilization of robust three-dimensional (3D) human cell cultures that effectively recapitulate native tissue architecture and model the microenvironment. A lack of physiologically-relevant animal models for many viruses has limited the elucidation of factors that influence viral pathogenesis and of complex host immune mechanisms. Conventional monolayer cell cultures may support viral infection, but are unable to form the tissue structures and complex microenvironments that mimic host physiology and, therefore, limiting their translational utility. The rotating wall vessel (RWV) bioreactor was designed by the National Aeronautics and Space Administration (NASA) to model microgravity and was later found to more accurately reproduce features of human tissue in vivo. Cells grown in RWV bioreactors develop in a low fluid-shear environment, which enables cells to form complex 3D tissue-like aggregates. A wide variety of human tissues (from neuronal to vaginal tissue) have been grown in RWV bioreactors and have been shown to support productive viral infection and physiological meaningful host responses. The in vivo-like characteristics and cellular features of the human 3D RWV-derived aggregates make them ideal model systems to effectively recapitulate pathophysiology and host responses necessary to conduct rigorous basic science, preclinical and translational studies.
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Affiliation(s)
- Jameson K Gardner
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
| | - Melissa M Herbst-Kralovetz
- Department of Basic Medical Sciences, College of Medicine-Phoenix, University of Arizona, Phoenix, AZ 85004, USA.
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36
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Abstract
Different genomic technologies have been applied to cell line authentication, but only one method (short tandem repeat [STR] profiling) has been the subject of a comprehensive and definitive standard (ASN-0002). Here we discuss the power of this document and why standards such as this are so critical for establishing the consensus technical criteria and practices that can enable progress in the fields of research that use cell lines. We also examine other methods that could be used for authentication and discuss how a combination of methods could be used in a holistic fashion to assess various critical aspects of the quality of cell lines.
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Affiliation(s)
- Jamie L. Almeida
- Biosystems and Biomaterials Division, The National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Kenneth D. Cole
- Biosystems and Biomaterials Division, The National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
| | - Anne L. Plant
- Biosystems and Biomaterials Division, The National Institute of Standards and Technology, Gaithersburg, Maryland, United States of America
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37
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Lynn DE, Harrison RL. Routine Maintenance and Storage of Lepidopteran Insect Cell Lines and Baculoviruses. Methods Mol Biol 2016; 1350:197-221. [PMID: 26820859 DOI: 10.1007/978-1-4939-3043-2_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
The various methods for maintaining (i.e., subculturing, splitting, or passaging) established lepidopteran cell lines are described. Three procedures are presented that are appropriate for different cell lines dependent upon the growth characteristics (in particular, cell attachment properties) of the cells of interest. In addition to the routine maintenance of cells in active culture, methods are also described for both short-term (low temperature) and long-term (frozen in liquid nitrogen) storage of cell lines, as well as quality control procedures for the cultures. Methods for storing baculoviruses for use in cell cultures and issues of concern when using cell cultures for their production and study are also described.
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Affiliation(s)
| | - Robert L Harrison
- Invasive Insect Biocontrol & Behavior Laboratory, USDA, ARS, BARC, Building 007, Room 301, BARC-W, 10300 Baltimore Ave., Beltsville, MD, 20705, USA.
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Asprer JST, Lakshmipathy U. Current methods and challenges in the comprehensive characterization of human pluripotent stem cells. Stem Cell Rev Rep 2016; 11:357-72. [PMID: 25504379 DOI: 10.1007/s12015-014-9580-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Pluripotent stem cells (PSCs) are powerful tools for basic scientific research and promising agents for drug discovery and regenerative medicine. Technological advances have made it increasingly easy to generate PSCs but the various lines generated may differ in their characteristics based on their origin, derivation, number of passages, and culture conditions. In order to confirm the pluripotency, quality, identity, and safety of pluripotent cell lines as they are derived and maintained, it is critical to perform a panel of characterization assays. Functional pluripotency is determined using tests that rely on the expression of specific markers in the undifferentiated and differentiated states; tests for quality, identity and safety are less specialized. This article provides a comprehensive review of current practices in PSC characterization and explores challenges in the field, from the selection of markers to the development of simple and scalable methods. It also delves into emerging trends like the adoption of alternative assays that could be used to supplement or replace traditional methods, specifically the use of in silico assays for determining pluripotency.
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Affiliation(s)
- Joanna S T Asprer
- Cell Biology, Life Sciences Solutions, Thermo Fisher Scientific, 5781 Van Allen Way, Carlsbad, CA, 92008, USA
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Ye F, Chen C, Qin J, Liu J, Zheng C. Genetic profiling reveals an alarming rate of cross-contamination among human cell lines used in China. FASEB J 2015; 29:4268-72. [PMID: 26116706 DOI: 10.1096/fj.14-266718] [Citation(s) in RCA: 205] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 06/22/2015] [Indexed: 01/26/2023]
Abstract
Cell lines are widely used as in vitro model systems in biologic and medical research. However, much of the research has been invalidated by the unwitting use of false cell lines. A significant proportion of the research involving human cell lines was initiated in China. Paradoxically, the cell lines used in China have never been authenticated. Here, we present a comprehensive survey of cross-contamination in 380 samples from 113 independent sources in China using short tandem repeat profiling methods. High levels of cross-contamination were uncovered (95 of 380, 25%). Notable false cell lines (e.g., KB and WISH) are still actively used under their false identity and tissue attributions. Most strikingly, 85.51% of lines established in China were misidentified (59 of 69) and accounted for over half of the misidentifications (59 of 95, 62.11%). Further, 93.22% of the contaminants in cell lines established in laboratories of China were HeLa cells or a possible hybrid of HeLa with an unknown cell line. Results from these misidentified lines have been published in thousands of potentially erroneous articles and may have distorted the findings visible to the scientific community. False lines have been used in drug screening, potentially leading to unusable or even harmful therapeutic strategies. We also noted the causes of contamination and provided suggestions for remediation.
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Affiliation(s)
- Fang Ye
- *China Center for Type Culture Collection and State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; and Beijing Microread Genetics Company, Limited, Beijing, China
| | - Chuguang Chen
- *China Center for Type Culture Collection and State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; and Beijing Microread Genetics Company, Limited, Beijing, China
| | - Jian Qin
- *China Center for Type Culture Collection and State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; and Beijing Microread Genetics Company, Limited, Beijing, China
| | - Jie Liu
- *China Center for Type Culture Collection and State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; and Beijing Microread Genetics Company, Limited, Beijing, China
| | - Congyi Zheng
- *China Center for Type Culture Collection and State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, China; and Beijing Microread Genetics Company, Limited, Beijing, China
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HeLa nucleic acid contamination in the cancer genome atlas leads to the misidentification of human papillomavirus 18. J Virol 2015; 89:4051-7. [PMID: 25631090 DOI: 10.1128/jvi.03365-14] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
UNLABELLED We searched The Cancer Genome Atlas (TCGA) database for viruses by comparing non-human reads present in transcriptome sequencing (RNA-Seq) and whole-exome sequencing (WXS) data to viral sequence databases. Human papillomavirus 18 (HPV18) is an etiologic agent of cervical cancer, and as expected, we found robust expression of HPV18 genes in cervical cancer samples. In agreement with previous studies, we also found HPV18 transcripts in non-cervical cancer samples, including those from the colon, rectum, and normal kidney. However, in each of these cases, HPV18 gene expression was low, and single-nucleotide variants and positions of genomic alignments matched the integrated portion of HPV18 present in HeLa cells. Chimeric reads that match a known virus-cell junction of HPV18 integrated in HeLa cells were also present in some samples. We hypothesize that HPV18 sequences in these non-cervical samples are due to nucleic acid contamination from HeLa cells. This finding highlights the problems that contamination presents in computational virus detection pipelines. IMPORTANCE Viruses associated with cancer can be detected by searching tumor sequence databases. Several studies involving searches of the TCGA database have reported the presence of HPV18, a known cause of cervical cancer, in a small number of additional cancers, including those of the rectum, kidney, and colon. We have determined that the sequences related to HPV18 in non-cervical samples are due to nucleic acid contamination from HeLa cells. To our knowledge, this is the first report of the misidentification of viruses in next-generation sequencing data of tumors due to contamination with a cancer cell line. These results raise awareness of the difficulty of accurately identifying viruses in human sequence databases.
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Abstract
Next-generation sequencing results obtained to detect somatic mutations in human cancers can also be searched for viruses that contribute to cancer. Recently, human papillomavirus 18 RNA was detected in tumor types not typically associated with HPV infection. Analyses reported in this issue of Journal of Virology demonstrate that the apparent presence of HPV18 RNA in these atypical tumors is due in at least some cases to contamination of samples with HeLa cells, which harbor HPV18.
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Zorn-Kruppa M, Houdek P, Wladykowski E, Engelke M, Bartok M, Mewes KR, Moll I, Brandner JM. Determining the Depth of Injury in Bioengineered Tissue Models of Cornea and Conjunctiva for the Prediction of All Three Ocular GHS Categories. PLoS One 2014; 9:e114181. [PMID: 25494045 PMCID: PMC4262406 DOI: 10.1371/journal.pone.0114181] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Accepted: 11/05/2014] [Indexed: 11/19/2022] Open
Abstract
The depth of injury (DOI) is a mechanistic correlate to the ocular irritation response. Attempts to quantitatively determine the DOI in alternative tests have been limited to exvivo animal eyes by fluorescent staining for biomarkers of cell death and viability in histological cross sections. It was the purpose of this study to assess whether DOI could also be measured by means of cell viability detected by the MTT assay using 3-dimensional (3D) reconstructed models of cornea and conjunctiva. The formazan-free area of metabolically inactive cells in the tissue after topical substance application is used as the visible correlate of the DOI. Areas of metabolically active or inactive cells are quantitatively analyzed on cryosection images with ImageJ software analysis tools. By incorporating the total tissue thickness, the relative MTT-DOI (rMTT-DOI) was calculated. Using the rMTT-DOI and human reconstructed cornea equivalents, we developed a prediction model based on suitable viability cut-off values. We tested 25 chemicals that cover the whole range of eye irritation potential based on the globally harmonized system of classification and labelling of chemicals (GHS). Principally, the MTT-DOI test method allows distinguishing between the cytotoxic effects of the different chemicals in accordance with all 3 GHS categories for eye irritation. Although the prediction model is slightly over-predictive with respect to non-irritants, it promises to be highly valuable to discriminate between severe irritants (Cat. 1), and mild to moderate irritants (Cat. 2). We also tested 3D conjunctiva models with the aim to specifically address conjunctiva-damaging substances. Using the MTT-DOI method in this model delivers comparable results as the cornea model, but does not add additional information. However, the MTT-DOI method using reconstructed cornea models already provided good predictability that was superior to the already existing established invitro/exvivo methods.
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Affiliation(s)
- Michaela Zorn-Kruppa
- University Medical Center Hamburg-Eppendorf, Department of Dermatology and Venerology, 20246 Hamburg, Germany
- * E-mail:
| | - Pia Houdek
- University Medical Center Hamburg-Eppendorf, Department of Dermatology and Venerology, 20246 Hamburg, Germany
| | - Ewa Wladykowski
- University Medical Center Hamburg-Eppendorf, Department of Dermatology and Venerology, 20246 Hamburg, Germany
| | - Maria Engelke
- Jacobs University Bremen gGmbH, School of Engineering and Sciences, 28759 Bremen, Germany
| | - Melinda Bartok
- Jacobs University Bremen gGmbH, School of Engineering and Sciences, 28759 Bremen, Germany
| | | | - Ingrid Moll
- University Medical Center Hamburg-Eppendorf, Department of Dermatology and Venerology, 20246 Hamburg, Germany
| | - Johanna M. Brandner
- University Medical Center Hamburg-Eppendorf, Department of Dermatology and Venerology, 20246 Hamburg, Germany
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Abstract
Cell lines are often used in place of primary cells to study biological processes. However, care must be taken when interpreting the results as cell lines do not always accurately replicate the primary cells. In this article, we will briefly talk about advantages and disadvantages of cell lines and then discuss results using the mouse Sertoli cell line, MSC-1, compared with primary mouse Sertoli cells. MSC-1 cells resemble Sertoli cells morphologically and possess several biochemical markers associated with Sertoli cells. Studies have demonstrated that the function and regulation of retinoic acid receptor α (RARα) is similar between MSC-1 and rat Sertoli cells. However, MSC-1 cells lack some of the immune privilege properties associated with primary Sertoli cells, including survival in animals with a fully functional immune system. Therefore, it has to be kept in mind that cell lines do not behave identically with primary cells and should not be used to replace primary cells. In order to strengthen the findings, key control experiments using primary cells should always be performed.
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Affiliation(s)
- Gurvinder Kaur
- Department of Cell Biology and Biochemistry; Texas Tech University Health Sciences Center; Lubbock, TX USA
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June CH. Toward synthetic biology with engineered T cells: a long journey just begun. Hum Gene Ther 2014; 25:779-84. [PMID: 25244569 PMCID: PMC4174426 DOI: 10.1089/hum.2014.2533] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/03/2014] [Indexed: 01/16/2023] Open
Affiliation(s)
- Carl H June
- Abramson Cancer Center; Abramson Family Cancer Research Institute; and Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania , Philadelphia, PA 19104-5156
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Establishment of primary xenograft model from newly characterized patient extrauterine carcinosarcoma. Int J Gynecol Cancer 2014; 23:1552-60. [PMID: 24172092 DOI: 10.1097/01.igc.0000434105.98035.c7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND AND OBJECTIVE The aim of this study was to characterize primary cells from extrauterine carcinosarcoma (CS) and to establish a primary CS xenograft mouse model. METHODS Primary cells were isolated from a patient with CS and cultured in vitro. Primary CS cells were verified for their ability to consecutively generate tumorigenesis in NOD/SCID mice. The properties of xenograft tumor and explants cells were investigated by immunohistochemistry, cytogenetic, and FACS analysis. Anticancer drug susceptibility of primary CS was analyzed using CCK-8. RESULTS Primary CS cells greater than 27 passages in vitro showed an ability of a series of xenograft tumorigenesis in vivo having the same marker expression and cytogenetic character as that of original tumor. In addition, explants of xenograft tumors retained their original characteristics in the in vitro culture system. Finally, the analysis of the susceptibility to anticancer drug revealed that primary CS cells were susceptible to both doxorubicin and nilotinib, which are tyrosine kinase inhibitors. CONCLUSIONS The primary CS cells and the primary CS xenograft tumorigenesis introduce a new therapeutic model for targeting cancer and also explore a deeper understanding of generation of the tumor itself.
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Casadevall A, Steen RG, Fang FC. Sources of error in the retracted scientific literature. FASEB J 2014; 28:3847-55. [PMID: 24928194 DOI: 10.1096/fj.14-256735] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Accepted: 05/27/2014] [Indexed: 12/22/2022]
Abstract
Retraction of flawed articles is an important mechanism for correction of the scientific literature. We recently reported that the majority of retractions are associated with scientific misconduct. In the current study, we focused on the subset of retractions for which no misconduct was identified, in order to identify the major causes of error. Analysis of the retraction notices for 423 articles indexed in PubMed revealed that the most common causes of error-related retraction are laboratory errors, analytical errors, and irreproducible results. The most common laboratory errors are contamination and problems relating to molecular biology procedures (e.g., sequencing, cloning). Retractions due to contamination were more common in the past, whereas analytical errors are now increasing in frequency. A number of publications that have not been retracted despite being shown to contain significant errors suggest that barriers to retraction may impede correction of the literature. In particular, few cases of retraction due to cell line contamination were found despite recognition that this problem has affected numerous publications. An understanding of the errors leading to retraction can guide practices to improve laboratory research and the integrity of the scientific literature. Perhaps most important, our analysis has identified major problems in the mechanisms used to rectify the scientific literature and suggests a need for action by the scientific community to adopt protocols that ensure the integrity of the publication process.
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Affiliation(s)
- Arturo Casadevall
- Department of Microbiology and Immunology and Division of Infectious Diseases, Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, New York, USA;
| | - R Grant Steen
- MediCC! Medical Communications Consultants, Chapel Hill, North Carolina, USA; and
| | - Ferric C Fang
- Department of Laboratory Medicine and Department of Microbiology, University of Washington School of Medicine, Seattle, Washington, USA
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Leroy B, Girard L, Hollestelle A, Minna JD, Gazdar AF, Soussi T. Analysis of TP53 mutation status in human cancer cell lines: a reassessment. Hum Mutat 2014; 35:756-65. [PMID: 24700732 DOI: 10.1002/humu.22556] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2014] [Accepted: 03/20/2014] [Indexed: 12/14/2022]
Abstract
Tumor-derived cell lines play an important role in the investigation of tumor biology and genetics. Across a wide array of studies, they have been tools of choice for the discovery of important genes involved in cancer and for the analysis of the cellular pathways that are impaired by diverse oncogenic events. They are also invaluable for screening novel anticancer drugs. The TP53 protein is a major component of multiple pathways that regulate cellular response to various types of stress. Therefore, TP53 status affects the phenotype of tumor cell lines profoundly and must be carefully ascertained for any experimental project. In the present review, we use the 2014 release of the UMD TP53 database to show that TP53 status is still controversial for numerous cell lines, including some widely used lines from the NCI-60 panel. Our analysis clearly confirms that, despite numerous warnings, the misidentification of cell lines is still present as a silent and neglected issue, and that extreme care must be taken when determining the status of p53, because errors may lead to disastrous experimental interpretations. A novel compendium gathering the TP53 status of 2,500 cell lines has been made available (http://p53.fr). A stand-alone application can be used to browse the database and extract pertinent information on cell lines and associated TP53 mutations. It will be updated regularly to minimize any scientific issues associated with the use of misidentified cell lines (http://p53.fr).
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Affiliation(s)
- Bernard Leroy
- Université Pierre et Marie Curie-Paris 6, Paris, 75005, France
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Kofanova OA, Mathieson W, Thomas GA, Betsou F. DNA fingerprinting: a quality control case study for human biospecimen authentication. Biopreserv Biobank 2014; 12:151-3. [PMID: 24749883 DOI: 10.1089/bio.2013.0063] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
This case study illustrates the usefulness of the DNA fingerprinting method in biobank quality control (QC) procedures and emphasizes the need for detailed and accurate record keeping during processing of biological samples. It also underlines the value of independent third-party assessment to identify points at which errors are most likely to have occurred when unexpected results are obtained from biospecimens.
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Affiliation(s)
- Olga A Kofanova
- 1 Integrated Biobank of Luxembourg (IBBL) , 6 rue Nicolas Ernest Barblé, 1210 Luxembourg, Luxembourg
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50
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Kniss DA, Summerfield TL. Discovery of HeLa Cell Contamination in HES Cells: Call for Cell Line Authentication in Reproductive Biology Research. Reprod Sci 2014; 21:1015-1019. [PMID: 24520087 DOI: 10.1177/1933719114522518] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Continuous cell lines are used frequently in reproductive biology research to study problems in early pregnancy events and parturition. It has been recognized for 50 years that many mammalian cell lines contain inter- or intraspecies contaminations with other cells. However, most investigators do not routinely test their culture systems for cross-contamination. The most frequent contributor to cross-contamination of cell lines is the HeLa cell isolated from an aggressive cervical adenocarcinoma. We report on the discovery of HeLa cell contamination of the human endometrial epithelial cell line HES isolated in our laboratory. Short tandem repeat analysis of 9 unique genetic loci demonstrated molecular identity between HES and HeLa cells. In addition, we verified that WISH cells, isolated originally from human amnion epithelium, were also contaminated with HeLa cells. Inasmuch as our laboratory did not culture HeLa cells at the time of HES cell derivations, the source of contamination was the WISH cell line. These data highlight the need for continued diligence in authenticating cell lines used in reproductive biology research.
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Affiliation(s)
- Douglas A Kniss
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Laboratory of Perinatal Research, The Wexner Medical Center at Ohio State University, Columbus, OH, USA
| | - Taryn L Summerfield
- Department of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine, Laboratory of Perinatal Research, The Wexner Medical Center at Ohio State University, Columbus, OH, USA
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