Hypermutation in human cancer genomes: footprints and mechanisms

Abstract

A role for somatic mutations in carcinogenesis is well accepted, but the degree to which mutation rates influence cancer initiation and development is under continuous debate. Recently accumulated genomic data have revealed that thousands of tumour samples are riddled by hypermutation, broadening support for the idea that many cancers acquire a mutator phenotype. This major expansion of cancer mutation data sets has provided unprecedented statistical power for the analysis of mutation spectra, which has confirmed several classical sources of mutation in cancer, highlighted new prominent mutation sources (such as apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) enzymes) and empowered the search for cancer drivers. The confluence of cancer mutation genomics and mechanistic insight provides great promise for understanding the basic development of cancer through mutations.

Figure 1

Lesions in single-strand (ss) DNA can result in clusters of strand coordinated mutations. Lesions are shown as stars. In the case of base specific damage, e.g. cytidine deamination by APOBEC enzyme(s), lesions would be in the same type of DNA base (i.e., C) of the same strand. Trans-lesion DNA synthesis (TLS) will introduce mutations in the complementary strand, which can be then fixed in DNA by a subsequent round of synthesis (step shown in a(iii), b(iii), c(iii), d(ii), e(ii)). This will result in strand-coordination of mutations changing only Cs (red) of the initially damaged strand and only Gs (green) mutated in the complementary strand. (a). (i) ssDNA formed by 5’→3’ resection at double strand DNA breaks (DSBs); (ii) one of several DSB repair mechanisms restores double-strand (ds) DNA at the position of break. (b). ssDNA formed by migrating loop and uncoupled strand copying during break-induced replication^, . (c). Telomere uncapping (REFS^, and therein). (d). ssDNA formed during replication (shown is ssDNA in lagging strand; a similar chain of events may be associated with the leading strand). Lesions may result in mutations (ii) or be repaired via mechanism of fork regression which displaces a short stretch of complementary strand and pairs damaged ssDNA of the gap with the intact region of the complementary nascent strand (iii). The latter provides a template for excision repair of lesions generated in the ssDNA gap (iv). (e). (i) and (ii) Lesions in transient ssDNA formed by mRNA-DNA pairing (R-loops) can lead to mutation clusters. (iii) and (iv) Mutations will be prevented, if re-annealing of DNA strands followed by excision repair occurs before replication.

Figure 2

Mutation patterns and mechanistic knowledge used to define an APOBEC mutation signature and produce sample-specific statistics evaluating mutagenesis. Robust mutation signatures can be developed by identifying groups of spatially clustered mutations (red lines and highlights on (b) and (c)) likely to have been induced by a single mutagenic mechanism. Additional features used to implicate the causative factor: (a). Proximity to sites of chromosomal rearrangement (purple connector line). (b). Strand-coordination (example with sequence context of a C-coordinated cluster from multiple myeloma,see also Figure 1 and text), motif preference (grey fill), and substitution specificity. For example, the co-localization of strand-coordinated clustered cytosine substitutions with rearrangement breakpoints implicates the involvement of double strand DNA break (DSB) repair in formation of the mutations. The frequent involvement of single-strand (ss) DNA intermediates during such DSB repair events combined with an over-representation of TCA and TCT sequences among the mutations corresponds to the biochemical characteristics of a subset of APOBEC cytidine deaminases within ssDNA. Both cytosine to thymine and cytosine to guanine substitutions are also over-represented. (c). Mechanism of downstream processing of deoxyuridine (deamination product of deoxycytidine) explaining mutations specificity in clusters : (i). Glycolytic conversion of deoxyuridine to an abasic site (ii) creates a block to DNA synthesis during gap filling. The concerted action of DNA Pol delta and DNA Pol zeta (iii) or DNA Pol delta, DNA Pol zeta, and REV1 (iv) makes mutagenic insertion of either adenine or cytosine opposite of the abasic site, respectively, resulting in C to T and C to G mutations (v,vi). (d) Combining APOBEC enzymes’ favoured sequence motifs and base substitution preferences creates a refined mutation signature and allows calculation of sample-specific statistics evaluating mutagenesis – enrichment (E) by APOBEC signature mutations over the presence of APOBEC mutation motif in surrounding nucleotide context. TCW/WGA indicates the APOBEC targeted sequences of TCT, TCA, and their complements as in. Nucleotides involved in mutation event are shown in red.

Figure 3

Sources of hypermutation in cancer. (i and iii) Hypermutation can occur through alterations in the equilibrium between the formation of lesions (stars) and error-free lesion repair (left of grey dashed line) or changes in the equilibrium between the rate of replication errors and DNA polymerase proofreading (star at the 3’end of the leading strand) or mismatch repair (MMR) (shown as removal of bulged mis-pairing behind the fork) (right of grey dashed line). Low levels of lesions and replication errors and/or high efficiency of error free lesion repair, proofreading and MMR results in low mutation frequency (ii), however reduction in repair and/or increase in lesions or in replication error levels may lead to hypermutation (iv).