The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells.

Shaheen Kabir,Cortni Dick,Justin Cidado,Lisa Drew,Courtney Andersen,Pei-Chun Lin,Jacob E Corn,Hong Ma,Seung Hyun Baik,Matthew A Belmonte,Therese Mitros

doi:10.7554/elife.44288

Abstract

Overexpression of anti-apoptotic proteins MCL1 and Bcl-xL are frequently observed in many cancers. Inhibitors targeting MCL1 are in clinical development, however numerous cancer models are intrinsically resistant to this approach. To discover mechanisms underlying resistance to MCL1 inhibition, we performed multiple flow-cytometry based genome-wide CRISPR screens interrogating two drugs that directly (MCL1i) or indirectly (CDK9i) target MCL1. Remarkably, both screens identified three components (CUL5, RNF7 and UBE2F) of a cullin-RING ubiquitin ligase complex (CRL5) that resensitized cells to MCL1 inhibition. We find that levels of the BH3-only pro-apoptotic proteins Bim and Noxa are proteasomally regulated by the CRL5 complex. Accumulation of Noxa caused by depletion of CRL5 components was responsible for re-sensitization to CDK9 inhibitor, but not MCL1 inhibitor. Discovery of a novel role of CRL5 in apoptosis and resistance to multiple types of anticancer agents suggests the potential to improve combination treatments.

Highlights

Cancer cells frequently manipulate the intrinsic apoptotic pathway to evade cell death and expand their proliferative capacity
Increased Bcl-xL expression correlated with the MCL1-amplified lines that were resistant to CDK9 inhibitors (CDK9i) and MCL1 inhibitors (MCL1i)
Assessing cleaved PARP (c-PARP) levels, we found that depletion of cullin 5 (CUL5), Ring Finger Protein 7 (RNF7), UBE2F or Bcl-xL significantly induced PARP cleavage when combined with CDK9i or MCL1i (Figure 3E)

Summary

Introduction

Cancer cells frequently manipulate the intrinsic apoptotic pathway to evade cell death and expand their proliferative capacity. Aberrant increases in levels of anti-apoptotic proteins in the BCL-2 family, such as amplification of MCL1, have been widely implicated in the transformation of cancer cells and the development of resistance to current therapies (Kelly and Strasser, 2011). BCL-2 family members are classified based on the conservation of their BCL-2 homology (BH) domains: multi-domain proteins BAK, BAX and BOK serve as apoptosis executors in the mitochondria; proteins containing only the BH3 domain (BH3-only) promote BAK/BAX activation. Anti-apoptotic proteins such as MCL1, Bcl-xL and BCL-2 inhibit apoptosis by antagonistic binding to pro-apoptotic BH3-only proteins as well as BAK and BAX (Czabotar et al, 2014). Amplification of MCL1 is a prognostic indicator for disease severity and progression, making it an attractive therapeutic target (Campbell et al, 2018; Yin et al, 2016)

Methods

Results

Conclusion