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Compositions and methods for mammalian genetics and uses thereof

a technology of mammalian genetics and composition methods, applied in the field of mammalian genetic composition and methods, can solve the problems of limiting the contribution of mutagenesis-based genetics to the understanding of human diseases, generating and recovering,

Inactive Publication Date: 2012-07-26
WHITEHEAD INST FOR BIOMEDICAL RES
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  • Summary
  • Abstract
  • Description
  • Claims
  • Application Information

AI Technical Summary

Benefits of technology

[0007]In another aspect, the invention provides a method of identifying a gene that encodes a gene product that plays a role in drug activity of an agent in mammalian cells, the method comprising steps of: (a) introducing a gene trap vector into near-haploid mammalian cells, wherein the gene trap vector comprises a nucleic acid construct comprising a nucleic acid encoding a reporter that allows the identification of a cell expressing said nucleic acid, wherein said nucleic acid construct integrates into the genome of at least some of said near-haploid mammalian cells; (b) contacting the mammalian cells with an agent drug at a concentration sufficient to cause a detectable effect on said non-mutant near-haploid cells; (c) identifying a cell that contains said nucleic acid construct integrated into its genome and does not exhibit said effect; and (d) identifying a gene into which the nucleic acid construct integrated, thereby identifying a gene that encodes a gene product that plays a role in drug activity of the agent in mammalian cells. In some embodiments the agent is a drug.

Problems solved by technology

However, the inability to generate and recover bi-allelic mutants in human diploid cells limits the contribution of mutagenesis-based genetics to the understanding of human disease.

Method used

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  • Compositions and methods for mammalian genetics and uses thereof
  • Compositions and methods for mammalian genetics and uses thereof
  • Compositions and methods for mammalian genetics and uses thereof

Examples

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example 1

Characterization and Retroviral Infection of KBM7 Subclones

[0149]We first characterized a haploid genome setting in human cells that we believed would be permissive for efficient forward genetic approaches. A subclone of the CML cell line KBM7 has been described to carry a near haploid chromosome set [14]. First we examined if this cell line (generously provided by Dr. B. H. Cochran, Tufts University School of Medicine, Boston, Mass.) could be easily propagated, was tolerant to viral infection and could be efficiently subcloned. The term “KBM7 cell line” is used herein to refer to this near-haploid cell line or to a subclone thereof. Cells of the KBM7 cell line of a subclone thereof may be referred to as “KBM7 cells”. KBM7 cells had a high subcloning efficiency (of around ˜80%), and several of the subclones were examined further. The KBM7 subclones proliferated readily with a generation time of approximately 24 hrs and could be maintained at sparse and very high cell densities (e.g....

example 2

Selection of Gene Trap Vectors for Insertional Mutagenesis in KBM7 Cells

[0151]We next determined whether the observed haploid nature of the great majority of the genome sequence in the KBM7 subclone allowed the generation of knockout cells by mutagenesis. Since we knew that the cells could be readily infected by retroviruses, we explored the use in these cells of several viral gene-trap vectors designed to trap expressed genes. The large majority of promotorless gene trap vectors described in the literature are based on neomycin (G418, geneticin) selection. Surprisingly, initial experiments showed that KBM7 cells were inherently resistant to very high concentrations of neomycin, precluding use of preexisting vectors. A potentia exception was the UPA-Trap vector (described in Shigeoka et al. 2005 Nucleic Acids Res. 2005 33(2):e20.) that in addition to neomycin contains GFP. To test this vector, virus was produced by transfection of this vector with retroviral packaging vectors in 293...

example 3

Construction of Gene Trap Vectors Containing Vectors Containing Puromycin and GFP Selectable Markers

[0152]Novel retroviral gene trap vectors that contain an inactivated LTR, a strong splice-acceptor site derived from the long fiber gene of Adenovirus serotype 40 (Carette et al. 2005 The Journal of Gene Medicine 7(8) 1053-1062), and either GFP or the puromycin resistance gene (PURO) followed by a SV40 polyadenylation signal were constructed as follows. The coding sequence of the PURO or GFP was obtained by PCR amplification with primers containing overhanging ClaI and NheI restriction sites as well as partial splice acceptor sites: (GFP:5′-GATCGCTAGCCGCATTTCTTTTTTCCAGATGGTGAGCAAGGGCGAGG-3′ (SEQ ID NO: 126) and 5′-GATCGGATCCTTACTTGTACAGCTCGTCCATGC-3′ (SEQ ID NO: 127) PURO: 5′-GATCGCTAGCCGCATTTCTTTTTTCCAGATGACCGAGTACAAGCCCAC-3′ (SEQ ID NO: 128) and 5′-GATCGGATCCTCAGGCACCGGGCTTGCGGGTC-3′ (SEQ ID NO:129)). These PCR products were inserted in pEGFPC1(Clontech) replacing EGFP. Subsequently...

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Abstract

The invention provides compositions and methods for performing mammalian cell genetics, e.g., genetic screens, using near-haploid cells. The invention further provides genes and gene products isolated using the inventive methods and methods of use thereof.

Description

RELATED APPLICATIONS[0001]This application claims the benefit of U.S. Provisional Application Ser. No. 61 / 224,338, filed Jul. 9, 2009, the entire teachings of which are incorporated herein by reference.BACKGROUND OF THE INVENTION[0002]Large-scale gene inactivation through mutagenesis in genetically tractable model organisms such as the budding yeast, the fruit-fly, and the worm is one of the most powerful tools for gaining insight into biological processes. Despite recent advances in RNA interference, successful whole-genome genetic screening in mammalian cells remains a daunting task.SUMMARY OF THE INVENTION[0003]Classical genetics using induced mutations has developed into one of the most powerful approaches to elucidate the genetic components that underlie biological processes, independently of prior knowledge or assumptions. The study of cultured human cells allows the recapitulation of aspects of human disease. However, the inability to generate and recover bi-allelic mutants i...

Claims

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Application Information

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Patent Type & Authority Applications(United States)
IPC IPC(8): C12Q1/70
CPCC12N15/1051C12N15/1079C12N15/86C12N2840/44C12N2800/107C12N2800/60C12N2740/13043
Inventor BRUMMELKAMP, THIJN R.CARETTE, JAN E.
Owner WHITEHEAD INST FOR BIOMEDICAL RES
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