Table 3

Predictive genomic and epigenetic biomarkers of replicative stress in pre-clinical development

BiomarkerFunctionReferences
ATR/ATM inhibition
ATR/ATM lossATR/ATM lead to activation of checkpoint kinases CHK1/2 which trigger cell cycle arrest. Loss of ATR/ATM leads to loss of cell cycle checkpoint control.11 55
ARID1A deficiencyARID1A is recruited to DNA breaks through interaction with ATR and has a role in NHEJ as well as HR DNA repair. Loss of ARID1A impairs conduction of ATR-mediated DDR signalling required for HR and reduces G2/M checkpoint control.16 17
KRAS or MYC mutationOncogenic Ras expression activates ATR-CHK1 pathway.
Oncogenic Myc activates CDK2.
7 15
P53 mutationp53 is phosphorylated and stabilized by ATM/ATR, CHK1/CHK2, and is crucial for the G1 checkpoint. p53 deficiency leads to defective G1 checkpoint and increases tumor reliance on G2 checkpoint to maintain genomic integrity.55
Reduced RAD51C/D expressionLoss of RAD51C and D impairs CHK2 phosphorylation.58
CCNE1 amplificationCyclin E-CDK2 complexes trigger S phase entry from G1. Increased cyclin E levels result in early S phase entry, increasing replicative stress.59
APOBEC3B amplificationCytidine deaminase overexpression shown to increase replicative stress.60
Homologous recombination repair protein deficiency: BRCA1/2, FANCA, PALB2, RAD51C/D, FANCD2, FANCC mutationDeficiencies in homologous recombination repair lead to reduced efficacy in repairing DSBs generated from checkpoint inhibitors. BRCA and Rad51 further function to protect newly synthesized DNA on replicative stress.2
WEE1 inhibition
P53 mutationp53 deficiency leads to defective G1 checkpoint and increases tumor reliance on G2 checkpoint to maintain genomic integrity.42
CCNE1 amplificationCyclin E-CDK2 complexes trigger S phase entry from G1.
Increased cyclin E levels result in early S phase entry, increasing replicative stress.
59
KRAS mutationOncogenic Ras expression activates ATR-CHK1 pathway.15
Loss of WEE1 coupled with loss of SETD2 (the sole methyltransferase for H3K36me3)Critical interactions between SETD2 loss and WEE1 inhibition results in synthetic lethality from reduced RRM2 protein levels and increased replicative stress. WEE1 inhibition also leads to firing of inactive DNA replicative origins, heightening replicative stress further.61
CHK1 inhibition
MYC amplificationMYC amplification increases CDK2 activation.7
RB lossLoss of Rb disrupts coordination between replication origin licensing and promotes inappropriate and premature mitotic entry.11
F-box/WD repeat-containing protein 7 (FBXW7) lossTumor suppressor that facilitates degradation of oncoproteins such as cyclin E, c-Myc, Mcl-1, mTOR. Loss of FBXW7 may therefore affect cyclin E/CDK2 activity.62
  • ATM, ataxia telangiectasia-mutated; ATR, ataxia telangiectasia and Rad3 related; CHK1, checkpoint kinase 1; DDR, DNA damage response; G2, Gap 2; H3K36me3, Histone H3 trimethylation at lysine 36; HR, homologous recombination ; M, Mitosis; NHEJ, Non-homologous end joining ; RRM2, Ribonucleoside-diphosphate reductase subunit M2; SETD2, SET Domain Containing 2; WEE1, WEE1-like protein kinase.