In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens

Ryan D Chow; Guangchuan Wang; Lupeng Ye; Adan Codina; Hyunu Ray Kim; Li Shen; Matthew B Dong; Youssef Errami; Sidi Chen

doi:10.1038/s41592-019-0371-5

In vivo profiling of metastatic double knockouts through CRISPR-Cpf1 screens

Nat Methods. 2019 May;16(5):405-408. doi: 10.1038/s41592-019-0371-5. Epub 2019 Apr 8.

Authors

Ryan D Chow^#^{1

2

3

4}, Guangchuan Wang^#^{1

2

3}, Lupeng Ye^#^{1

2

3}, Adan Codina^{1

2

3

5}, Hyunu Ray Kim^{1

2

3}, Li Shen^{1

2

3}, Matthew B Dong^{1

2

3

4

6}, Youssef Errami^{1

2

3}, Sidi Chen^{7

8

9

10

11

12

13

14}

Affiliations

¹ Department of Genetics, Yale University School of Medicine, New Haven, CT, USA.
² System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA.
³ Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA.
⁴ Yale MD-PhD Program, Yale University, New Haven, CT, USA.
⁵ Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA.
⁶ Yale Immunobiology Program, The Anlyan Center for Medical Research & Education, New Haven, CT, USA.
⁷ Department of Genetics, Yale University School of Medicine, New Haven, CT, USA. sidi.chen@yale.edu.
⁸ System Biology Institute, Integrated Science & Technology Center, Yale University, West Haven, CT, USA. sidi.chen@yale.edu.
⁹ Center for Cancer Systems Biology, Integrated Science & Technology Center, West Haven, CT, USA. sidi.chen@yale.edu.
¹⁰ Yale MD-PhD Program, Yale University, New Haven, CT, USA. sidi.chen@yale.edu.
¹¹ Yale Combined Program in the Biological and Biomedical Sciences, Yale University, New Haven, CT, USA. sidi.chen@yale.edu.
¹² Yale Immunobiology Program, The Anlyan Center for Medical Research & Education, New Haven, CT, USA. sidi.chen@yale.edu.
¹³ Yale Comprehensive Cancer Center, New Haven, CT, USA. sidi.chen@yale.edu.
¹⁴ Yale Stem Cell Center, New Haven, CT, USA. sidi.chen@yale.edu.

^# Contributed equally.

Abstract

Systematic investigation of the genetic interactions that influence metastatic potential has been challenging. Here we developed massively parallel CRISPR-Cpf1/Cas12a crRNA array profiling (MCAP), an approach for combinatorial interrogation of double knockouts in vivo. We designed an MCAP library of 11,934 arrays targeting 325 pairwise combinations of genes implicated in metastasis. By assessing the metastatic potential of the double knockouts in mice, we unveiled a quantitative landscape of genetic interactions that drive metastasis.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Animals
Bacterial Proteins / genetics*
CRISPR-Associated Protein 9 / genetics
CRISPR-Cas Systems / genetics*
Cell Line, Tumor
Clustered Regularly Interspaced Short Palindromic Repeats / genetics*
Endonucleases / genetics*
Gene Editing / methods*
Gene Knockout Techniques / methods*
Mice
Neoplasm Metastasis / genetics*
Sequence Analysis, RNA

Substances

Bacterial Proteins
CRISPR-Associated Protein 9
Cas12a protein
Endonucleases

Abstract

Publication types

MeSH terms

Substances

Grants and funding