Methods for genome-wide screening and construction of genetic interaction maps

Patent metadata

Field	Value
Publication number	US-10144927-B2
Application number	US-201414458114-A
Country	US
Kind code	B2
Filing date	Aug 12, 2014
Priority date	Feb 13, 2012
Publication date	Dec 4, 2018
Grant date	Dec 4, 2018

Abstract

The present invention provides methods for conducting screens using nucleic acid elements (e.g., interfering RNAs) to confidently identify hit genetic elements. The present invention further comprises constructing vectors that contain two or more nucleic acid elements to knock down all pairwise combinations of the hit genetic elements identified from the screen. Following quantitation of the single and double-knockdown phenotypes, genetic interactions between all gene pairs can be calculated. Genes can then be clustered according to the similarity of the pattern of their interactions with all of the other genes to obtain a genetic interaction map, which can advantageously be used to predict functional associations between genes and identify drug targets for therapy such as combination cancer therapy.

First claim

What is claimed is:

1. A method for identifying a first and a second modulating nucleic acid element that target a first and a second genetic element, said method comprising:
(a) cloning a first modulating nucleic acid element with a second modulating nucleic acid element to form a double-modulating viral vector comprising said first modulating nucleic acid element linked to said second modulating nucleic acid element, wherein said first modulating nucleic acid element targets a first genetic element and said second modulating nucleic acid element targets a second genetic element and wherein said first modulating nucleic acid element and said second modulating nucleic acid element are an interfering RNA, and further wherein said first genetic element is phenotypically responsive to said first modulating nucleic acid element and said second genetic element is phenotypically responsive to said second modulating nucleic acid element;
(b) repeating step (a) using a plurality of different first modulating nucleic acid elements and a plurality of different second modulating nucleic acid elements, thereby forming a plurality of different double-modulating viral vectors;
(c) infecting a plurality of mammalian cells with said plurality of different double-modulating viral vectors, thereby forming a plurality of double-modulating viral vector-infected mammalian cells;
(d) separating a selected pool of said plurality of double-modulating viral vector-infected mammalian cells expressing a detectable phenotype from a non-selected pool of said plurality of double-modulating viral vector-infected mammalian cells not expressing said detectable phenotype;
(e) quantitating the frequencies of said first modulating nucleic acid element linked to said second modulating nucleic acid element in said selected pool relative to the frequencies of said first modulating nucleic acid element linked to said second modulating nucleic acid element in said non-selected pool, thereby identifying a first and a second modulating nucleic acid element that target a first and a second genetic element;
(f) cloning a first non-modulating nucleic acid element with a second non-modulating nucleic acid element to form a double non-modulating viral vector comprising said first non-modulating nucleic acid element linked to said second non-modulating nucleic acid element, wherein said first non-modulating nucleic acid element and said second modulating nucleic acid element do not target a genetic element and wherein said first non-modulating nucleic acid element and said second non-modulating nucleic acid element are an interfering RNA;
(g) repeating step (f) using a plurality of different first non-modulating nucleic acid elements and a plurality of different second non-modulating nucleic acid elements, thereby forming a plurality of different double non-modulating viral vectors;
(h) infecting a plurality of mammalian cells with said plurality of different double non-modulating viral vectors, thereby forming a plurality of double non-modulating viral vector-infected mammalian cells;
(i) separating a selected pool of said plurality of double non-modulating viral vector-infected mammalian cells expressing a detectable phenotype from a non-selected pool of said plurality of double non-modulating viral vector-infected mammalian cells not expressing said detectable phenotype; and
(j) quantitating the frequencies of said first non-modulating nucleic acid element linked to said second non-modulating nucleic acid element in said selected pool relative to the frequencies of said first non-modulating nucleic acid element linked to said second non-modulating nucleic acid element in said non-selected pool.

2. The method of claim 1 , further comprising:
detecting differences between said frequencies of said first modulating nucleic acid element linked to said second modulating nucleic acid element in said selected pool relative to a calculated control frequency and based at least in part on said differences detecting a genetic interaction between said first and second genetic elements.

3. The method of claim 2 , wherein said genetic interaction corresponds to a buffering genetic interaction or a synergistic genetic interaction.

4. The method of claim 3 , wherein the presence of a synergistic genetic interaction indicates that said first and second genetic elements act in parallel pathways.

5. The method of claim 3 , wherein the presence of a buffering genetic interaction indicates that said first and second genetic elements act in a linear pathway.

6. The method of claim 5 , further comprising screening said double-modulating viral vector for different phenotypes and/or in different cell lines.

7. The method of claim 6 , wherein said double-modulating viral vector comprises a unique barcode for each of said first and second modulating nucleic acid elements.

8. The method of claim 7 , wherein step (j) comprises quantitating the frequencies of said first and second modulating nucleic acid elements by deep sequencing.

9. A method for identifying a first and a second modulating nucleic acid element that target a first and a second genetic element, said method comprising:
(a) cloning a first modulating nucleic acid element with a second modulating nucleic acid element to form a double-modulating viral vector comprising said first modulating nucleic acid element linked to said second modulating nucleic acid element, wherein said first modulating nucleic acid element targets a first genetic element and said second modulating nucleic acid element targets a second genetic element and wherein said first modulating nucleic acid element and said second modulating nucleic acid element are an interfering RNA, and further wherein said first genetic element is phenotypically responsive to said first modulating nucleic acid element and said second genetic element is phenotypically responsive to said second modulating nucleic acid element;
(b) repeating step (a) using a plurality of different first modulating nucleic acid elements and a plurality of different second modulating nucleic acid elements, thereby forming a plurality of different double-modulating viral vectors;
(c) infecting a plurality of mammalian cells with said plurality of different double-modulating viral vectors, thereby forming a plurality of double-modulating viral vector-infected mammalian cells;
(d) separating a selected pool of said plurality of double-modulating viral vector-infected mammalian cells expressing a detectable phenotype from a non-selected pool of said plurality of double-modulating viral vector-infected mammalian cells not expressing said detectable phenotype;
(e) quantitating the frequencies of said first modulating nucleic acid element linked to said second modulating nucleic acid element in said selected pool relative to the frequencies of said first modulating nucleic acid element linked to said second modulating nucleic acid element in said non-selected pool, thereby identifying a first and a second modulating nucleic acid element that target a first and a second genetic element;
(f) cloning said first or second modulating nucleic acid element with a first non-modulating nucleic acid element to form a mixed-modulating/non-modulating viral vector comprising said first or second modulating nucleic acid element linked to said first non-modulating nucleic acid element, wherein said first non-modulating nucleic acid element does not target a genetic element and wherein said first non-modulating nucleic acid element is an interfering RNA;
(g) repeating step (f) using a plurality of different first or second modulating nucleic acid elements and a plurality of different first non-modulating nucleic acid elements, thereby form

Assignees

• Univ California

Inventors

• Kampmann Martin
• Bassik Michael
• Weissman Jonathan

Classifications

• C12Q2525/301

  Hairpin oligonucleotides · CPC title

• C12N15/1075 Primary

  by coupling phenotype to genotype, not provided for in other groups of this subclass · CPC title

• C12Q2600/142

  Toxicological screening, e.g. expression profiles which identify toxicity · CPC title

• C12Q1/68

  involving nucleic acids · CPC title

• C12N2310/531

  Stem-loop; Hairpin · CPC title