Perturbation of base excision repair sensitizes breast cancer cells to APOBEC3 deaminase-mediated mutations

Abstract

Abundant APOBEC3 (A3) deaminase-mediated mutations can dominate the mutational landscape (‘mutator phenotype’) of some cancers, however, the basis of this sporadic vulnerability is unknown. We show here that elevated expression of the bifunctional DNA glycosylase, NEIL2, sensitizes breast cancer cells to A3B-mediated mutations and double-strand breaks (DSBs) by perturbing canonical base excision repair (BER). NEIL2 usurps the canonical lyase, APE1, at abasic sites in a purified BER system, rendering them poor substrates for polymerase β. However, the nicked NEIL2 product can serve as an entry site for Exo1 in vitro to generate single-stranded DNA, which would be susceptible to both A3B and DSBs. As NEIL2 or Exo1 depletion mitigates the DNA damage caused by A3B expression, we suggest that aberrant NEIL2 expression can explain certain instances of A3B-mediated mutations.

Auger Emitter Conjugated PARP Inhibitor for Therapy in Triple Negative Breast Cancers: A Comparative In-Vitro Study

“…This correlates with the Dox-NP induced enhanced uptake and retention of [ 125 I]-PARPi-01 observed in uptake assay. However, their MGMT deficiency and response to TMZ predisposes these subtypes for TMZ combination with [ 125 I]-PARPi-01 treatment [ 33 , 54 ]. Among the above mentioned cell lines the BRCAness signature has been reported to be low for BT20 and MDA-MB-231, which have still shown promising response to Auger emitter-based therapy [ 55 ].…”

Unique structural features of mammalian NEIL2 DNA glycosylase prime its activity for diverse DNA substrates and environments

“…Recent studies implicate a potential role for NEIL2 in cytosine deaminase APOBEC3-mediated mutagenesis, likely via its activity towards abasic sites (44) where data suggest NEIL2 may outcompete APE1 for the site in particular contexts. This presents interesting contribution of NEIL2 variants to the APOBEC3 mutation signature both by aberrant NEIL2 activity towards the abasic sites produced during the deamination process as well as reduced activity towards oxidized cytosine lesions.…”

The effect of APOBEC3B deaminase on double-stranded DNA

“…Breast cancer cell line Hs578T (HTB-126) was obtained from American Type Culture Collection (ATCC) and cultured as previously reported 58 . HEK293T cells (provided by Dr. Roland Owens, NIH) were maintained in DMEM with 10% FBS at 37°C in 5% CO2.…”

“…The original data for mRNA level of MGMT and housekeeping genes in four breast cancer cells shown in Supplementary Fig. S2 was adapted from Shen et al 58 .…”