Defective base excision repair in the response to DNA damaging agents in triple negative breast cancer

Abstract

DNA repair defects have been increasingly focused on as therapeutic targets. In hormone-positive breast cancer, XRCC1-deficient tumors have been identified and proposed as targets for combination therapies that damage DNA and inhibit DNA repair pathways. XRCC1 is a scaffold protein that functions in base excision repair (BER) by mediating essential interactions between DNA glycosylases, AP endonuclease, poly(ADP-ribose) polymerase 1, DNA polymerase β (POL β), and DNA ligases. Loss of XRCC1 confers BER defects and hypersensitivity to DNA damaging agents. BER defects have not been evaluated in triple negative breast cancers (TNBC), for which new therapeutic targets and therapies are needed. To evaluate the potential of XRCC1 as an indicator of BER defects in TNBC, we examined XRCC1 expression in the TCGA database and its expression and localization in TNBC cell lines. The TCGA database revealed high XRCC1 expression in TNBC tumors and TNBC cell lines show variable, but mostly high expression of XRCC1. XRCC1 localized outside of the nucleus in some TNBC cell lines, altering their ability to repair base lesions and single-strand breaks. Subcellular localization of POL β also varied and did not correlate with XRCC1 localization. Basal levels of DNA damage correlated with observed changes in XRCC1 expression, localization, and measure repair capacity. The results confirmed that XRCC1 expression changes indicate DNA repair capacity changes but emphasize that basal DNA damage levels along with protein localization are better indicators of DNA repair defects. Given the observed over-expression of XRCC1 in TNBC preclinical models and tumors, XRCC1 expression levels should be assessed when evaluating treatment responses of TNBC preclinical model cells.

Exploiting DNA repair defects in triple negative breast cancer to improve cell killing

“…22 HCC1806 and MDA-468 cells showed higher levels of HR and HR-related gene expression ( Figure 4), consistent with the high protein expression of BRCA1 observed previously. 13 As no other deficits in HR gene or protein expression were observed in the four cell lines, the BRCA1 protein level likely drives the observed HR defects in MDA-157 and MDA-231 cells.…”

“…The greatest sensitivity to ATR inhibition was observed in HCC1806 (IC 50 , 1.1 μM) and MDA-231 cells (IC 50 , 3.4 μM), and these cell lines contained more defects in BER and NER pathways ( Figures 1 and 2 ). 13 …”

“…Competent repair of the THF abasic site mimic was achieved by all of the cell lines and is supported by the high expression of APE1, PARP1, and XRCC1 across the cell line panel (Figure 1). 13,17 In general, mRNA levels of BER proteins lacked correlation with protein levels, and the functional assessment of BER did not track with any single DNA repair protein or transcript.…”

“…In BER, defects in the glycosylase-driven repair of DNA lesions were observed previously and correspond to the low gene expression of the different DNA glycosylases, POL β and DNA ligases in the TNBC cells lines ( Figure 1 ). 13 , 17 These BER defects also increase the sensitivity of the cell lines to methyl methanesulfonate (MMS) and potassium bromate (KBrO 3 ), which induce alkylation and oxidative DNA damage addressed by DNA glycosylases ( Figure 5 ). Competent repair of the THF abasic site mimic was achieved by all of the cell lines and is supported by the high expression of APE1, PARP1, and XRCC1 across the cell line panel ( Figure 1 ).…”

“…The high gene and protein expression of PARP1 and XRCC1 in the cell line panel is consistent with TCGA datasets and findings from the I-SPY trials, where PARP inhibitor monotherapy has only shown modest efficacy. 13 , 34 The functional analysis of BER substrates indicates that BER deficiency in TNBC is significantly linked to oxidative or alkylating glycosylases through low protein production. 13 , 17 Therefore, combining PARP inhibitors with therapies that generate reactive oxygen species and strain the defective glycosylase activities would offer more targeted therapies for TNBC.…”