Functional profiling of nucleotide Excision repair in breast cancer

DNA Repair (Amst). 2019 Oct;82:102697. doi: 10.1016/j.dnarep.2019.102697. Epub 2019 Aug 30.


Homologous recombination deficiency conferred by alterations in BRCA1 or BRCA2 are common in breast tumors and can drive sensitivity to platinum chemotherapy and PARP inhibitors. Alterations in nucleotide excision repair (NER) activity can also impact sensitivity to DNA damaging agents, but NER activity in breast cancer has been poorly characterized. Here, we apply a novel immunofluorescence-based cellular NER assay to screen a large panel of breast epithelial and cancer cell lines. Although the majority of breast cancer models are NER proficient, we identify an example of a breast cancer cell line with profound NER deficiency. We show that NER deficiency in this model is driven by epigenetic silencing of the ERCC4 gene, leading to lack of expression of the NER nuclease XPF, and that ERCC4 methylation is also strongly correlated with ERCC4 mRNA and XPF protein expression in primary breast tumors. Re-expression of XPF in the ERCC4-deficient breast cancer rescues NER deficiency and cisplatin sensitivity, but does not impact PARP inhibitor sensitivity. These findings demonstrate the potential to use functional assays to identify novel mechanisms of DNA repair deficiency and nominate NER deficiency as a platinum sensitivity biomarker in breast cancer.

Keywords: Breast cancer; Cisplatin; Nucleotide excision repair; PARP inhibitor.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Breast Neoplasms / pathology*
  • Cell Line, Tumor
  • Cisplatin / pharmacology
  • DNA Breaks, Double-Stranded / drug effects
  • DNA Breaks, Double-Stranded / radiation effects
  • DNA Methylation / drug effects
  • DNA Methylation / radiation effects
  • DNA Repair* / drug effects
  • DNA Repair* / genetics
  • DNA Repair* / radiation effects
  • DNA-Binding Proteins / genetics
  • Gene Expression Regulation, Neoplastic / drug effects
  • Gene Expression Regulation, Neoplastic / radiation effects
  • Humans
  • Promoter Regions, Genetic / genetics
  • Ultraviolet Rays


  • DNA-Binding Proteins
  • xeroderma pigmentosum group F protein
  • Cisplatin