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Organ, Edward L.; Sheng, Jinsong; Ruley, H E; Rubin, Donald H.

doi:10.1186/1471-2121-5-41

Cited by 16 publications

(9 citation statements)

References 72 publications

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“…The present study suggests that MNU and HU can be used to enhance the recovery of clones homozygous for recessive mutations during phenotype-based genetic screens in mammalian cells (31,32,42). The vector may also allow mutagenesis screens to be carried out in a greater variety of cell backgrounds.…”

Section: Resultsmentioning

confidence: 99%

Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability

Donahue

Lin

Cao

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Widespread losses of heterozygosity (LOH) in human cancer have been thought to result from chromosomal instability caused by mutations affecting DNA repair͞genome maintenance. However, the origin of LOH in most tumors is unknown. The present study examined the ability of carcinogenic agents to induce LOH at 53 sites throughout the genome of normal diploid mouse ES cells. Brief exposures to nontoxic levels of methylnitrosourea, diepoxybutane, mitomycin C, hydroxyurea, doxorubicin, and UV light stimulated LOH at all loci at frequencies ranging from 1-8 ؋ 10 ؊3 per cell (10 -123 times higher than in untreated cells). This greatly exceeds the frequencies at which these agents have been reported to induce point mutations and is comparable to the rates of LOH observed in ES cells lacking the gene responsible for Bloom syndrome, an inherited DNA repair defect that results in greatly increased risk of cancer. These results suggest that LOH contributes significantly to the carcinogenicity of a variety of mutagens and raises the possibility that genome-wide LOH observed in some human cancers may reflect prior exposure to genotoxic agents rather than a state of chromosomal instability during the carcinogenic process. Finally, as a practical matter, chemically induced LOH is expected to enhance the recovery of homozygous recessive mutants from phenotype-based genetic screens in mammalian cells.cancer etiology ͉ cancer genetics ͉ carcinogenesis ͉ genome stability

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Section: Resultsmentioning

confidence: 99%

Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability

Donahue

Lin

Cao

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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“…Methods describing the preparation of clonal gene-trap library cell lines resisting lytic infection using RIE-1 cells (reovirus), Sup-T1 (HIV-1), TZM-bl cells (human rhinovirus 2 and 16), and Vero E6 cells (cowpox, Ebola, Herpes simplex virus 1 and 2, Marburg, and poliovirus) were described previously [ 18 , 75 – 79 ]. Briefly, gene-trap libraries, each harboring approximately 10 4 gene entrapment events, were expanded to 80–90% confluency until ~10 3 daughter cells represented each clone.…”

Section: Methodsmentioning

confidence: 99%

“…After incubating each cell type with indicated toxin or bacterium, resistant clones were expanded in separate wells of multi-well plates. The detailed protocols were described previously [ 18 , 75 – 79 ].…”

Section: Methodsmentioning

confidence: 99%

“…Genomic DNA from clonal, virus-resistant cell lines was extracted using the QIAamp DNA Blood Mini Kit (Qiagen, Inc., Valencia, CA). Shuttle vectors and genomic DNA fragments flanking the U3neoSV1 integration site were recovered by digesting genomic DNA with either BamH1 or EcoRI, self-ligating the resulting genomic DNA fragments, transforming Escherichia coli , and selecting for bacteria harboring carbenicillin-resistant plasmids, as described [ 75 ]. DNA sequences flanking the U3neoSV1 integration sites were sequenced using primers annealing to the U3neoSV1 shuttle vector.…”

Section: Methodsmentioning

confidence: 99%

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Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

Cheng

Murray²,

Zhao

et al. 2016

PLoS Comput Biol

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Viruses require host cellular factors for successful replication. A comprehensive systems-level investigation of the virus-host interactome is critical for understanding the roles of host factors with the end goal of discovering new druggable antiviral targets. Gene-trap insertional mutagenesis is a high-throughput forward genetics approach to randomly disrupt (trap) host genes and discover host genes that are essential for viral replication, but not for host cell survival. In this study, we used libraries of randomly mutagenized cells to discover cellular genes that are essential for the replication of 10 distinct cytotoxic mammalian viruses, 1 gram-negative bacterium, and 5 toxins. We herein reported 712 candidate cellular genes, characterizing distinct topological network and evolutionary signatures, and occupying central hubs in the human interactome. Cell cycle phase-specific network analysis showed that host cell cycle programs played critical roles during viral replication (e.g. MYC and TAF4 regulating G0/1 phase). Moreover, the viral perturbation of host cellular networks reflected disease etiology in that host genes (e.g. CTCF, RHOA, and CDKN1B) identified were frequently essential and significantly associated with Mendelian and orphan diseases, or somatic mutations in cancer. Computational drug repositioning framework via incorporating drug-gene signatures from the Connectivity Map into the virus-host interactome identified 110 putative druggable antiviral targets and prioritized several existing drugs (e.g. ajmaline) that may be potential for antiviral indication (e.g. anti-Ebola). In summary, this work provides a powerful methodology with a tight integration of gene-trap insertional mutagenesis testing and systems biology to identify new antiviral targets and drugs for the development of broadly acting and targeted clinical antiviral therapeutics.

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“…Using this system, Murray et al, identified Rab9 as a factor required for infection of several enveloped viruses such as Marburg virus, measles virus, HIV and Ebola virus [59]. Furthermore, a number of cytoskeletal associated proteins, insulin growth factor II (IGF-II) pathway and a putative cell surface protein OL-16 were identified as factors required for reovirus infection [61,63]. …”

Section: Cell-based Screens and Virusesmentioning

confidence: 99%

Cell-based genomic screening: elucidating virus–host interactions

Panda

Cherry

2012

Current Opinion in Virology

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Brief summary Viruses rely on host cell machinery for successful infection, while at the same time evading the host immune response. Characterization of these processes has revealed insights both into fundamental cellular processes as well as the nuances of viral replication. The recent advent of cell-based screening coupled with RNAi technology, has greatly facilitated studies focused on characterizing the virus-host interface and has expanded our understanding of cellular factors that impact viral infection. These findings have led to the discovery of potential therapeutic targets, but there is certainly more to be discovered. In this article we will review the recent progress in this arena and discuss the challenges and future of this emerging field.

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Cited by 16 publications

References 72 publications

Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability

Carcinogens induce genome-wide loss of heterozygosity in normal stem cells without persistent chromosomal instability

Systems Biology-Based Investigation of Cellular Antiviral Drug Targets Identified by Gene-Trap Insertional Mutagenesis

Cell-based genomic screening: elucidating virus–host interactions

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