A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens

Nicole M Mattson; Anthony K N Chan; Kazuya Miyashita; Elizaveta Mukhaleva; Wen-Han Chang; Lu Yang; Ning Ma; Yingyu Wang; Sheela Pangeni Pokharel; Mingli Li; Qiao Liu; Xiaobao Xu; Renee Chen; Priyanka Singh; Leisi Zhang; Zeinab Elsayed; Bryan Chen; Denise Keen; Patrick Pirrotte; Steven T Rosen; Jianjun Chen; Mark A LaBarge; John E Shively; Nagarajan Vaidehi; Russell C Rockne; Mingye Feng; Chun-Wei Chen

doi:10.1038/s41594-024-01211-y

A novel class of inhibitors that disrupts the stability of integrin heterodimers identified by CRISPR-tiling-instructed genetic screens

Nat Struct Mol Biol. 2024 Mar;31(3):465-475. doi: 10.1038/s41594-024-01211-y. Epub 2024 Feb 5.

Authors

Nicole M Mattson¹, Anthony K N Chan^{1

2}, Kazuya Miyashita¹, Elizaveta Mukhaleva³, Wen-Han Chang¹, Lu Yang^{1

2}, Ning Ma³, Yingyu Wang³, Sheela Pangeni Pokharel^{1

2}, Mingli Li¹, Qiao Liu¹, Xiaobao Xu¹, Renee Chen¹, Priyanka Singh¹, Leisi Zhang¹, Zeinab Elsayed¹, Bryan Chen¹, Denise Keen⁴, Patrick Pirrotte^{5

6}, Steven T Rosen⁴, Jianjun Chen^{1

4}, Mark A LaBarge^{4

7}, John E Shively^{4

8}, Nagarajan Vaidehi^{3

4}, Russell C Rockne^{3

4}, Mingye Feng^{4

9}, Chun-Wei Chen^{10

11

12}

Affiliations

¹ Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
² Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA.
³ Department of Computational and Quantitative Medicine, Beckman Research Institute, City of Hope, Duarte, CA, USA.
⁴ City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
⁵ Integrated Mass Spectrometry Shared Resource, City of Hope Comprehensive Cancer Center, Duarte, CA, USA.
⁶ Cancer and Cell Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA.
⁷ Department of Population Sciences, Beckman Research Institute, City of Hope, Duarte, CA, USA.
⁸ Department of Immunology and Theranostics, Beckman Research Institute, City of Hope, Duarte, CA, USA.
⁹ Department of Immuno-Oncology, Beckman Research Institute, City of Hope, Duarte, CA, USA.
¹⁰ Department of Systems Biology, Beckman Research Institute, City of Hope, Duarte, CA, USA. cweichen@coh.org.
¹¹ Division of Epigenetic and Transcriptional Engineering, Beckman Research Institute, City of Hope, Duarte, CA, USA. cweichen@coh.org.
¹² City of Hope Comprehensive Cancer Center, Duarte, CA, USA. cweichen@coh.org.

Abstract

The plasma membrane is enriched for receptors and signaling proteins that are accessible from the extracellular space for pharmacological intervention. Here we conducted a series of CRISPR screens using human cell surface proteome and integrin family libraries in multiple cancer models. Our results identified ITGAV (integrin αV) and its heterodimer partner ITGB5 (integrin β5) as the essential integrin α/β pair for cancer cell expansion. High-density CRISPR gene tiling further pinpointed the integral pocket within the β-propeller domain of ITGAV for integrin αVβ5 dimerization. Combined with in silico compound docking, we developed a CRISPR-Tiling-Instructed Computer-Aided (CRISPR-TICA) pipeline for drug discovery and identified Cpd_AV2 as a lead inhibitor targeting the β-propeller central pocket of ITGAV. Cpd_AV2 treatment led to rapid uncoupling of integrin αVβ5 and cellular apoptosis, providing a unique class of therapeutic action that eliminates the integrin signaling via heterodimer dissociation. We also foresee the CRISPR-TICA approach to be an accessible method for future drug discovery studies.

MeSH terms

Cell Membrane
Clustered Regularly Interspaced Short Palindromic Repeats* / genetics
Humans

Abstract

MeSH terms

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