Browse
Submit Data
Databases
API
Help

Dataset Information

9 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Susceptibility to SARS-CoV-2 of Cell Lines and Substrates Commonly Used to Diagnose and Isolate Influenza and Other Viruses.

ABSTRACT: Co-infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other viruses has been reported. We evaluated cell lines commonly used to isolate viruses and diagnose related diseases for their susceptibility to SARS-CoV-2. Although multiple kidney cell lines from monkeys were susceptible to SARS-CoV-2, we found many cell types derived from humans, dogs, minks, cats, mice, and chicken were not. We analyzed MDCK cells, which are most commonly used for surveillance and study of influenza viruses, and found that they were not susceptible to SARS-CoV-2. The low expression level of the angiotensin converting enzyme 2 receptor and lower receptor affinity to SARS-CoV-2 spike, which could be overcome by overexpression of canine angiotensin converting enzyme 2 in trans, strengthened the cellular barrier to productive infection. Moreover, a D614G mutation in the spike protein did not appear to affect SARS-CoV-2 cell tropism. Our findings should help avert inadvertent propagation of SARS-CoV-2 from diagnostic cell lines.

SUBMITTER: Wang L

PROVIDER: S-EPMC8084484 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Adventitious viruses persistently infect three commonly used mosquito cell lines.

Project description:Mosquito cell lines have been used extensively in research to isolate and propagate arthropod-borne viruses and understand virus-vector interactions. Despite their utility as an in vitro tool, these cell lines are poorly defined and may harbor insect-specific viruses. Accordingly, we screened four commonly-used mosquito cell lines, C6/36 and U4.4 cells from Aedes albopictus, Aag2 cells from Aedes aegypti, and Hsu cells from Culex quinquefasciatus, for the presence of adventitious (i.e. exogenous) viruses. All four cell lines stained positive for double-stranded RNA, indicative of RNA virus replication. We subsequently identified viruses infecting Aag2, U4.4 and Hsu cell lines using untargeted next-generation sequencing, but not C6/36 cells. PCR confirmation revealed that these sequences stem from active viral replication and/or integration into the cellular genome. Our results show that these commonly-used mosquito cell lines are persistently-infected with several viruses. This finding may be critical to interpreting data generated in these systems.

| S-EPMC6764424 | biostudies-literature

Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.

Project description:Neuroblastoma cell lines are an important and cost-effective model used to study oncogenic drivers of the disease. While many of these cell lines have been previously characterized with SNP, methylation, and/or mRNA expression microarrays, there has not been an effort to comprehensively sequence these cell lines. Here, we present raw whole transcriptome data generated by RNA sequencing of 39 commonly-used neuroblastoma cell lines. These data can be used to perform differential expression analysis based on a genetic aberration or phenotype in neuroblastoma (e.g., MYCN amplification status, ALK mutation status, chromosome arm 1p, 11q and/or 17q status, sensitivity to pharmacologic perturbation). Additionally, we designed this experiment to enable structural variant and/or long-noncoding RNA analysis across these cell lines. Finally, as more DNase/ATAC and histone/transcription factor ChIP sequencing is performed in these cell lines, our RNA-Seq data will be an important complement to inform transcriptional targets as well as regulatory (enhancer or repressor) elements in neuroblastoma.

| S-EPMC5369315 | biostudies-literature

Corrigendum: Transcriptomic profiling of 39 commonly-used neuroblastoma cell lines.

Project description:This corrects the article DOI: 10.1038/sdata.2017.33.

| S-EPMC5716011 | biostudies-literature

RNA-seq of 675 commonly used human cancer cell lines

Project description:"Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels24, the transcriptome which represents the active program of a cell remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines. The raw sequence files were submitted to the European Genome-Phenome Archive (EGA) under accession EGAS00001000610 ( https://www.ebi.ac.uk/ega/datasets/EGAD00001000725 ). Processed, human non-identifiable data, together with a README file describing the data (140625_Klijn_README.txt) are available here in E-MTAB-2706.additional.*.zip files: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2706/files ."

| S-ECPF-MTAB-2706 | biostudies-other

Genetic Ancestry Analysis Reveals Misclassification of Commonly Used Cancer Cell Lines.

Project description:BACKGROUND:Given the scarcity of cell lines from underrepresented populations, it is imperative that genetic ancestry for these cell lines is characterized. Consequences of cell line mischaracterization include squandered resources and publication retractions. METHODS:We calculated genetic ancestry proportions for 15 cell lines to assess the accuracy of previous race/ethnicity classification and determine previously unknown estimates. DNA was extracted from cell lines and genotyped for ancestry informative markers representing West African (WA), Native American (NA), and European (EUR) ancestry. RESULTS:Of the cell lines tested, all previously classified as White/Caucasian were accurately described with mean EUR ancestry proportions of 97%. Cell lines previously classified as Black/African American were not always accurately described. For instance, the 22Rv1 prostate cancer cell line was recently found to carry mixed genetic ancestry using a much smaller panel of markers. However, our more comprehensive analysis determined the 22Rv1 cell line carries 99% EUR ancestry. Most notably, the E006AA-hT prostate cancer cell line, classified as African American, was found to carry 92% EUR ancestry. We also determined the MDA-MB-468 breast cancer cell line carries 23% NA ancestry, suggesting possible Afro-Hispanic/Latina ancestry. CONCLUSIONS:Our results suggest predominantly EUR ancestry for the White/Caucasian-designated cell lines, yet high variance in ancestry for the Black/African American-designated cell lines. In addition, we revealed an extreme misclassification of the E006AA-hT cell line. IMPACT:Genetic ancestry estimates offer more sophisticated characterization leading to better contextualization of findings. Ancestry estimates should be provided for all cell lines to avoid erroneous conclusions in disparities literature.

| S-EPMC6548687 | biostudies-literature

H9N2 influenza viruses from birds used in falconry.

Project description:H9N2 avian influenza viruses continue to spread in poultry and wild birds throughout Eurasia.To characterize H9N2 influenza viruses from pheasants, quail, and white-bellied bustards (WBBs) used to train falcons in the United Arab Emirates (UAE).Four H9N2 viruses were isolated from pheasants, quail, and WBB used for falconry in the UAE, and antigenic, molecular, phylogenetic analysis, and invivo characterization of H9N2 viruses were performed.The pheasant and WBB isolates were antigenically and molecularly clearly related and along with the quail isolates contained multiple "avian-human" substitutions. The release of smuggled H9N2-infected birds for falconry may contribute to the spread of these viruses to wild birds, domestic poultry, and humans.

| S-EPMC3823638 | biostudies-other

Genomic characterization of five commonly used endometrial cancer cell lines

Project description:An in-depth examination of five endometrial cancer cell lines in which mutation profiles, copy number variation, micro-satellite instability and homolgous recombination repair ability were determined and assessed in the context of TCGA endometrial cancer groups.

2020-05-27 | GSE151207 | GEO

Identification of replication competent murine gammaretroviruses in commonly used prostate cancer cell lines.

Project description:A newly discovered gammaretrovirus, termed XMRV, was recently reported to be present in the prostate cancer cell line CWR22Rv1. Using a combination of both immunohistochemistry with broadly-reactive murine leukemia virus (MLV) anti-sera and PCR, we determined if additional prostate cancer or other cell lines contain XMRV or MLV-related viruses. Our study included a total of 72 cell lines, which included 58 of the 60 human cancer cell lines used in anticancer drug screens and maintained at the NCI-Frederick (NCI-60). We have identified gammaretroviruses in two additional prostate cancer cell lines: LAPC4 and VCaP, and show that these viruses are replication competent. Viral genome sequencing identified the virus in LAPC4 and VCaP as nearly identical to another known xenotropic MLV, Bxv-1. We also identified a gammaretrovirus in the non-small-cell lung carcinoma cell line EKVX. Prostate cancer cell lines appear to have a propensity for infection with murine gammaretroviruses, and we propose that this may be in part due to cell line establishment by xenograft passage in immunocompromised mice. It is unclear if infection with these viruses is necessary for cell line establishment, or what confounding role they may play in experiments performed with these commonly used lines. Importantly, our results suggest a need for regular screening of cancer cell lines for retroviral "contamination", much like routine mycoplasma testing.

| S-EPMC3117837 | biostudies-literature

Tropism of SARS-CoV-2 in commonly used laboratory cell-lines and their proteomic landscape during infection

Project description:The present pandemic by Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is driving increased research activities in order to understand the basic biology of the virus and determining effective therapeutic strategies. The commonly used laboratory cell-lines of human origin are the first line of experimental models to study the pathogenicity and performing antiviral assays. Thus, to find a suitable cell model to study SARS-CoV-2, we assessed the tropism and cytopathogenicity of the first Swedish isolate of SARS-CoV-2 in six different cell-lines of human origin and compared their growth characteristics to other globally isolated strains. Overall, majority of the strains showed high to moderate level of susceptibility in Caco2, Huh7, Calu 3 and 293FT cell-lines and in Caco2 cells the virus can achieve high titers in absence of any prominent cytopathic effect. The protein expression profile during SARS-CoV-2 infection revealed cell-type specific regulation of cellular pathways. Type-I interferon signaling was identified as the common dysregulated cellular response in Caco2, Calu-3 and Huh7 cells. Overall, cell-type specific variability was noted with respect to cytopathogenicity, susceptibility and cellular response to SARS-CoV-2. This study provides important clues regarding SARS-CoV-2 pathogenesis and can represent as a guide for future studies.

2021-04-14 | PXD023760 | Pride

RNA-seq of 675 commonly used human cancer cell lines

Project description:Tumor-derived cell lines have served as vital models to advance our understanding of oncogene function and therapeutic response1. Although substantial effort has been directed to defining the genomic constitution of cancer cell line panels24, the transcriptome which represents the active program of a cell remains understudied. Here, we describe RNA sequencing and SNP array analysis of 675 commonly used human cancer cell lines. We explore numerous transcriptome features including coding and non-coding gene expression, transcribed mutations, gene fusion and expression of non-human sequences. Aside from many known aberrations we find new surprising characteristics, including more than 2200 unique fusion gene pairs representing a vast, testable repertoire of oncogenic fusions, many of which have analogs found in primary human tumors. We show that a combination of multiple genome and transcriptome features in a novel pathway-based approach enhances prediction of response to various targeted therapeutics. Our results provide valuable new insights into these critical pre-clinical models and provide added context for interpreting the numerous studies that employ these widely used cell lines. The raw sequence files were submitted to the European Genome-Phenome Archive (EGA) under accession EGAS00001000610 ( https://www.ebi.ac.uk/ega/datasets/EGAD00001000725 ). Processed, human non-identifiable data, together with a README file describing the data (140625_Klijn_README.txt) are available here in E-MTAB-2706.additional.*.zip files: https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-2706/files .

2014-11-25 | E-MTAB-2706 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data