Quantitative profiling of adaptation to cyclin E overproduction.

Juanita C Limas,Daniel Dominguez,Maria M Aleman,Andrea Walens,Boyang Ma,Brandon L Mouery,Dalia Fleifel,Amy M House,Jeanette Gowen Cook,Amiee N Littlejohn,Katarzyna M Kedziora

doi:10.26508/lsa.202201378

Juanita C Limas, Daniel Dominguez + Show 9 more

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https://doi.org/10.26508/lsa.202201378

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Abstract

Cyclin E/CDK2 drives cell cycle progression from G1 to S phase. Despite the toxicity of cyclin E overproduction in mammalian cells, the cyclin E gene is overexpressed in some cancers. To further understand how cells can tolerate high cyclin E, we characterized non-transformed epithelial cells subjected to chronic cyclin E overproduction. Cells overproducing cyclin E, but not cyclins D or A, briefly experienced truncated G1 phases followed by a transient period of DNA replication origin underlicensing, replication stress, and impaired proliferation. Individual cells displayed substantial intercellular heterogeneity in cell cycle dynamics and CDK activity. Each phenotype improved rapidly despite high cyclin E-associated activity. Transcriptome analysis revealed adapted cells down-regulated a cohort of G1-regulated genes. Withdrawing cyclin E from adapted cells only partially reversed underlicensing indicating that adaptation is at least partly non-genetic. This study provides evidence that mammalian cyclin E/CDK inhibits origin licensing indirectly through premature S phase onset and provides mechanistic insight into the relationship between CDKs and licensing. It serves as an example of oncogene adaptation that may recapitulate molecular changes during tumorigenesis.

Highlights

Cell cycle regulation depends on tight cyclin expression control to activate the cyclin-dependent protein kinase enzymes (CDK) that govern cell cycle progression (Evans et al, 1983)
We included cyclin A because it is an alternative activator of CDK2
CCNE1 mRNA in The Cancer Genome Atlas (TCGA) shows similar increases in some tumors compared with normal tissue

Summary

Introduction

Cell cycle regulation depends on tight cyclin expression control to activate the cyclin-dependent protein kinase enzymes (CDK) that govern cell cycle progression (Evans et al, 1983). In G1 phase, growth factors induce cyclin D which activates CDK4 and CDK6, which in turn, inactivate the E2F inhibitor, the retinoblastoma protein (RB). Rb hyperphosphorylation by cyclin E/CDK2 (and/or cyclin D/CDK4-6) (DeGregori et al, 1995; Dimova & Dyson, 2005; Narasimha et al, 2014; Sanidas et al, 2019) fully activates E2F (Zarkowska & Mittnacht, 1997; Yang et al, 2020). Cells progress from late G1 into S phase and initiate DNA replication. Cyclin E is overproduced in many cancers and tumor-derived cell lines due to gene amplification or dysregulated transcription (Barretina et al, 2012; Asghar et al, 2017; Geng et al, 2018; Chu et al, 2021), yet high cyclin E can induce replication stress, proliferation failure, and genome instability (Minella et al, 2002; Teixeira et al, 2015). The mechanisms for accommodating cyclin E overproduction are not fully understood

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