Use of antisense oligonucleotide libraries for identifying gene function
AssigneeIsis Pharmaceuticals, Inc.
InventorsC. Frank Bennett, Alexander H. Borchers, James G. Karras
Life of this patent
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Abstract
A method for identifying one or more genes involved in a phenotype of cells, tissues or organisms, comprising the steps of contacting cells, tissues or organisms which exhibit the phenotype with a library of antisense oligonucleotides and performing a primary phenotypic assay to determine which antisense oligonucleotides in the library attenuate the phenotype. These antisense oligonucleotides correspond to genes involved in the phenotype. The method may be used to identify genes involved in various disease states.
Claims29
A method for identifying one or more genes involved in a response by a cell, tissue or organism to a stimulus, comprising the steps of:
- a.) contacting cells, tissues or organisms which are capable of exhibiting a particular response to said stimulus with a library of antisense oligonucleotides prior to treatment with said stimulus;
- and
- b.) determining which antisense oligonucleotides within said library modulate said response, wherein antisense oligonucleotides which modulate said response correspond to gene products involved in said response.
A method for identifying one or more genes involved in a phenotype of a cell, tissue or organism, comprising the steps of:
- a.) contacting one or more substantially identical subpopulations of said cell, tissue or organism which exhibits said phenotype with a library of antisense oligonucleotides, wherein each subpopulation is contacted with one member of said library of antisense oligonucleotides;
- and
- b.) performing a primary phenotypic assay to determine which antisense oligonucleotides within said library modulate said phenotype, wherein antisense oligonucleotides which modulate said phenotype correspond to genes involved in said phenotype.
A method for identifying genes expressed in dendritic cells that regulate co-stimulation of T-cells, comprising the steps of:
- a.) culturing dendritic cells in the presence of one or more cytokines to activate said dendritic cells;
- b.) contacting one or more substantially identical subpopulations of said activated dendritic cells with a library of antisense oligonucleotides, wherein each subpopulation is contacted with one member of said library;
- c.) adding T-cells to said antisense oligonucleotide-treated activated dendritic cells;
- and
- d.) measuring IL-2 production, wherein antisense oligonucleotides which modulate IL-2 production correspond to genes which play a role in co-stimulation of T cells.
A method for identifying genes that play a role in T cell-mediated inflammation, comprising the steps of:
- a.) culturing dendritic cells in the presence of one or more cytokines to activate said dendritic cells;
- b.) contacting one or more substantially identical subpopulations of said activated dendritic cells with a library of antisense oligonucleotides, wherein each subpopulation is contacted with one member of said library;
- c.) adding T-cells to said antisense oligonucleotide-treated activated dendritic cells;
- and
- d.) measuring IL-2 production, wherein antisense oligonucleotides which inhibit IL-2 production correspond to genes which increase inflammation.
A library comprising between about 10 and 10,000 prevalidated antisense oligonucleotides.
Dependencies are inferred from the claim text.