Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity

Abstract

The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.

Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy

“…Published data on mutator phenotypes or biochemical defects resulting from similar mutations in model organisms were also considered. It is of note that in the majority of cases, the experiments in model organisms cited as evidence of functional significance used a different DNA polymerase (e.g., Polδ rather than Polε), often a different amino acid substitution, and sometimes not the same amino acid residue [23,24,63,64,67,70–72]. In most cases, the results of these analyses led the authors to conclude that the mutations were likely to affect proofreading.…”

“…Therefore, a common approach involves creating a mimic of a tumor-associated mutation in the chromosomal DNA polymerase gene and determining the effect on replication fidelity inside the cell by measuring the spontaneous mutation rate. Although the significance of many human mutations was claimed to be confirmed by mutagenesis assays in yeast [23,24,59,60,67,71,72], to our knowledge, in only ten cases listed in Table 1 were the variants actually modeled by creating an analogous amino acid substitution in the corresponding polymerase. Most of these are POLD1 mutations.…”

Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates

“…from three independent experiments are shown below the gel. [170,357]. Beyond analysis of mutational signatures and mRNA levels, there has been a paucity of biochemical data characterizing how these enzymes act on substrates relevant to deamination of genomic DNA [119].…”

“…As a result, there is a view that the ssDNA is simply left available for A3 enzymes to catalyze deamination of cytosine [176,341,357]. To test this experimentally we set up a minimal phage replication system where the DNA polymerase of phage Φ29 can initiate rolling circle replication and strand displacement synthesis on a plasmid after random hexamer primers are annealed [358].…”

“…In cells, the ssDNA exposed during replication stress would be coated with RPA [361]. It has been assumed that A3 enzymes cannot displace RPA and that they are limited to deaminating ssDNA at gaps in the RPA coating [357]. However, RPA is displaced to enable other recombination proteins to access the ssDNA, such as Rad51 [362,363].…”