Genome-wide CRISPR screens in spheroid culture reveal that the tumor suppressor LKB1 inhibits growth via the PIKFYVE lipid kinase

  • Proc Natl Acad Sci U S A. 2024 May 21;121(21):e2403685121. doi: 10.1073/pnas.2403685121.
John R Ferrarone  1  2 ,  Jerin Thomas  1 ,  Arun M Unni  1 ,  Yuxiang Zheng  1 ,  Michal J Nagiec  1  3 ,  Eric E Gardner  1 ,  Oksana Mashadova  1 ,  Kate Li  1 ,  Nikos Koundouros  1  3 ,  Antonino Montalbano  4  5 ,  Meer Mustafa  4  5 ,  Lewis C Cantley  1  6 ,  John Blenis  1  3 ,  Neville E Sanjana  4  5 ,  Harold Varmus  1  6
Affiliations
  • 1. Meyer Cancer Center, Weill Cornell Medicine, New York, NY 10021.
  • 2. Division of Hematology and Medical Oncology, Department of Medicine, Weill Cornell Medicine, New York, NY 10021.
  • 3. Department of Pharmacology, Weill Cornell Medicine, New York, NY 10021.
  • 4. New York Genome Center, New York, NY 10013.
  • 5. Department of Biology, New York University, New York, NY 10003.
  • 6. Department of Medicine, Weill Cornell Medicine, New York, NY 10021.
PMID: 38743625 DOI: 10.1073/pnas.2403685121
Abstract

The tumor suppressor LKB1 is a serine/threonine protein kinase that is frequently mutated in human lung adenocarcinoma (LUAD). LKB1 regulates a complex signaling network that is known to control cell polarity and metabolism; however, the pathways that mediate the tumor-suppressive activity of LKB1 are incompletely defined. To identify mechanisms of LKB1-mediated growth suppression, we developed a spheroid-based Cell Culture assay to study LKB1-dependent growth. We then performed genome-wide CRISPR screens in spheroidal culture and found that LKB1 suppresses growth, in part, by activating the PIKfyve lipid kinase. Finally, we used chemical inhibitors and a pH-sensitive reporter to determine that LKB1 impairs growth by promoting the internalization of wild-type EGFR in a PIKFYVE-dependent manner.

Keywords
EGFR; LKB1; PIKFYVE; STK11.
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