A Kinome-Wide Synthetic Lethal CRISPR/Cas9 Screen Reveals That mTOR Inhibition Prevents Adaptive Resistance to CDK4/CDK6 Blockade in HNSCC

Author:

Goto Yusuke1ORCID,Koshizuka Keiichi1ORCID,Ando Toshinori12ORCID,Izumi Hiroki1ORCID,Wu Xingyu1ORCID,Sato Kuniaki1ORCID,Ishikawa Tomohiko1ORCID,Ford Kyle3ORCID,Feng Xiaodong1ORCID,Wang Zhiyong1ORCID,Arang Nadia1ORCID,Allevato Michael M.1ORCID,Kishore Ayush1ORCID,Mali Prashant3ORCID,Gutkind J. Silvio1ORCID

Affiliation:

1. Moores Cancer Center, University of California San Diego, La Jolla, California. 1

2. Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan. 2

3. Department of Bioengineering, University of California San Diego, San Diego, California. 3

Abstract

Abstract The comprehensive genomic analysis of the head and neck squamous cell carcinoma (HNSCC) oncogenome revealed the frequent loss of p16INK4A (CDKN2A) and amplification of cyclin D1 genes in most human papillomavirus–negative HNSCC lesions. However, cyclin-dependent kinase 4 and 6 (CDK4/6) inhibitors have shown modest effects in the clinic. The aberrant activation of the PI3K/mTOR pathway is highly prevalent in HNSCC, and recent clinical trials have shown promising clinical efficacy of mTOR inhibitors (mTORi) in the neoadjuvant and adjuvant settings but not in patients with advanced HNSCC. By implementing a kinome-wide CRISPR/Cas9 screen, we identified cell-cycle inhibition as a synthetic lethal target for mTORis. A combination of mTORi and palbociclib, a CDK4/6-specific inhibitor, showed strong synergism in HNSCC-derived cells in vitro and in vivo. Remarkably, we found that an adaptive increase in cyclin E1 (CCNE1) expression upon palbociclib treatment underlies the rapid acquired resistance to this CDK4/6 inhibitor. Mechanistically, mTORi inhibits the formation of eIF4G–CCNE1 mRNA complexes, with the consequent reduction in mRNA translation and CCNE1 protein expression. Our findings suggest that mTORi reverts the adaptive resistance to palbociclib. This provides a multimodal therapeutic option for HNSCC by cotargeting mTOR and CDK4/6, which in turn may halt the emergence of palbociclib resistance. Significance: A kinome-wide CRISPR/Cas9 screen identified cell-cycle inhibition as a synthetic lethal target of mTORis. A combination of mTORi and palbociclib, a CDK4/6-specific inhibitor, showed strong synergistic effects in HNSCC. Mechanistically, mTORis inhibited palbociclib-induced increase in CCNE1.

Publisher

American Association for Cancer Research (AACR)

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