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. Epub 2024 May 14.

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.

MeSH terms

  • AMP-Activated Protein Kinase Kinases* / genetics
  • AMP-Activated Protein Kinase Kinases* / metabolism
  • CRISPR-Cas Systems
  • Cell Line, Tumor
  • Cell Proliferation
  • Clustered Regularly Interspaced Short Palindromic Repeats / genetics
  • Humans
  • Lung Neoplasms / genetics
  • Lung Neoplasms / metabolism
  • Lung Neoplasms / pathology
  • Phosphatidylinositol 3-Kinases* / genetics
  • Phosphatidylinositol 3-Kinases* / metabolism
  • Protein Serine-Threonine Kinases* / genetics
  • Protein Serine-Threonine Kinases* / metabolism
  • Spheroids, Cellular* / metabolism