Unpaved roads: How the DNA damage response navigates endogenous genotoxins

Abstract

Accurate DNA repair is essential for cellular and organismal homeostasis, and DNA repair defects result in genetic diseases and cancer predisposition. Several environmental factors, such as ultraviolet light, damage DNA, but many other molecules with DNA damaging potential are byproducts of normal cellular processes. In this review, we highlight some of the prominent sources of endogenous DNA damage as well as their mechanisms of repair, with a special focus on repair by the homologous recombination and Fanconi anemia pathways. We also discuss how modulating DNA damage caused by endogenous factors may augment current approaches used to treat BRCA-deficient cancers. Finally, we describe how synthetic lethal interactions may be exploited to exacerbate DNA repair deficiencies and cause selective toxicity in additional types of cancers.

Keywords: BRCA; Cancer; DNA repair; FANCM; Telomeres; WRN.

Fig. 1.

Endogenous sources of DNA damage and mechanisms of repair. A. Endogenous sources of DNA damage include genomic incorporation of enzymatically or chemically modified nucleotides (denoted by square with red star), which when repaired, generate abasic sites and single-strand breaks (SSBs). Removal of genomic ribonucleotides also generates SSBs. Reactive aldehydes generate inter-strand crosslinks (ICLs) and base damage, and repetitive sequences and R-loops can interfere with replication fork progression. B. Base excision repair (BER) removes enzymatically or chemically modified nucleotides from the genome. The resulting SSBs are bound by PARP1, which promotes their repair. PARP inhibitors (PARPi) covalently trap PARP1 on chromatin, and this causes cell death in HR-deficient cancer cells. ALC1 deficiency perturbs chromatin remodeling and causes an accumulation of unrepaired BER intermediates, increases PARP trapping, and enhances PARPi toxicity in HR-deficient cells. DNPH1 or ITPA loss causes increased genomic incorporation of modified bases, and the resulting increase in SSBs generated by BER potentiate PARP trapping and enhance PARPi toxicity in HR-deficient cells. C. Reactive aldehydes damage DNA by forming ICLs. Proper ICL repair requires the Fanconi anemia (FA) pathway, but in FA-deficient cells, ICLs are converted into DSBs. Subsequent DSB repair by non-homologous end-joining (NHEJ) or microhomology-mediated end joining (MMEJ) frequently results in mutations (denoted by red stars), increased genome instability, and in FA patients, hematopoietic stem cell (HSC) dysfunction and bone marrow failure. D. In cancer cells with microsatellite instability (MSI), expansion of TA-dinucleotide repeats causes formation of non-B form DNA that stalls replication forks. Stalled forks collapse into double-strand breaks (DSBs) in WRN-deficient cells, causing cell death. E. R-loops form at sites of transcription, DSBs, and replication-transcription conflicts. Multiple DNA repair proteins, including several homologous recombination (HR) and FA factors ensure proper R-loop resolution, thereby maintaining genome stability.

Fig. 2.

DNA repair pathways that are required for viability in HR-deficient cells. A. Genomic ribonucleotides (denoted by red square) are primarily removed by ribonucleotide excision repair (RER), and to a lesser extent, by topoisomerase 1 (TOP1)-mediated cleavage. TOP1 cleavage generates SSBs with 3’ blocks (denoted by triangle), which are removed by APE2. In RNASEH2-deficient cells, ribonucleotide removal by TOP1 causes a large increase in SSBs that are bound by PARP1, which when combined with PARPi treatment, enhances PARPi toxicity in HR-deficient cells. In APEX2-deficient cells, 3’ blocks generated by TOP1 cleavage are not removed by APE2, which eventually causes replication fork collapse and cell death in HR-deficient cells. B. DSBs that are resected in HR-deficient cells rely on Polθ-dependent microhomology mediated end-joining (MMEJ) for repair. DSB repair by MMEJ is mutagenic, but promotes survival of HR-deficient cells. Polθ inhibition blocks MMEJ, causing toxicity in HR-deficient cells. C. BRCA-deficient cells contain ssDNA gaps due to incomplete DNA replication that if not stabilized, cause chromosome segregation errors in mitosis. CIP2A, in complex with TOPBP1, binds under-replicated DNA in mitotic BRCA-deficient cells to tether chromatid fragments. In the absence of CIP2A, chromatid breakage causes cell death.