Mechanisms underlying mutational signatures in human cancers

Abstract

The collective somatic mutations observed in a cancer are the outcome of multiple mutagenic processes that have been operative over the lifetime of a patient. Each process leaves a characteristic imprint--a mutational signature--on the cancer genome, which is defined by the type of DNA damage and DNA repair processes that result in base substitutions, insertions and deletions or structural variations. With the advent of whole-genome sequencing, researchers are identifying an increasing array of these signatures. Mutational signatures can be used as a physiological readout of the biological history of a cancer and also have potential use for discerning ongoing mutational processes from historical ones, thus possibly revealing new targets for anticancer therapies.

Figure 1. Active mutational processes over the course of cancer development.

Each mutational process leaves a characteristic imprint — a mutational signature — in the cancer genome and comprises both a DNA damage component and a DNA repair component. In this hypothetical cancer genome, arrows indicate the duration and intensity of exposure to a mutational process. The final mutational portrait is the sum of all of the different mutational processes (A–D) that have been active in the entire lifetime. Ongoing mutational processes reflect active biological processes in the cancer that could be exploited either as biomarkers to monitor treatment response or as therapeutic anticancer targets. By contrast, historical mutational processes are no longer active. Signature A represents deamination of methylated cytosines, which is ongoing through life. Signature B can be matched up with the signatures of tobacco smoking, Signature C can represent bursts of APOBEC (apolipoprotein B mRNA editing enzyme, catalytic polypeptide)-induced deamination, and Signature D represents a DNA repair pathway that is awry.

Figure 2. Summary of known mutational signatures, and the components of DNA damage and repair that constitute the mutational processes.

There are marked differences among the 96-element mutational signatures, which are dominated by specific elements, including enrichment of various base substitutions (shown in the graphs on the right), transcriptional strand bias (T), excess of dinucleotide mutations (D), and association with insertions and deletions (I). The asterisks mark instances at which the limits of the y axes, which represent the likelihood of specific mutations being present in a signature, are exceeded. 5m, 5′ methyl group; 6m, O⁶ methyl group; APOBEC, apolipoprotein B mRNA editing enzyme, catalytic polypeptide; REV1, DNA repair protein REV1; UV, ultraviolet.

Figure 3. DNA repair pathways and mutational consequences.

a | Base excision repair (BER) typically mediates the removal and replacement of a single base residue. Substrates include uracil residues in DNA (which are created by deamination of cytosines) and damaged bases caused by reactive oxygen species, hydrolytic reactions and methylation. A damaged base is removed by a specific DNA glycosylase; here, the uracil is removed by uracil-DNA glycosylase (UNG). The resulting apurinic or apyrimidinic site is incised by DNA-(apurinic or apyrimidinic site) lyase APEX1. The 5′-deoxyribose-phosphate (dRP) residue is removed by a dRP lyase, which leaves a one-nucleotide gap that is filled in by DNA polymerase β (Pol β). Replication before completion of repair leads to base misinsertion and potentially C∙G→T∙A mutations. b | Nucleotide excision repair (NER) can remove various helix-distorting adducts, including those caused by ultraviolet radiation and cisplatin. The distorted region is recognized either during global genome repair by XPC (DNA repair protein complementing XP-C cells)–RAD23B (not shown) or during transcription, and two incisions are made on either side of the adduct to excise the damaged DNA. The resulting 27–29-nucleotide gap is filled by Pol δ or Pol ε and, under some circumstances, Pol κ. Replication before repair may result in mutations. c | Mismatch repair (MMR) is an excision repair process that removes mismatched bases or misinserted bases in DNA. It is initiated by the DNA mismatch recognition proteins MSH2 and MSH6; a segment of DNA is excised between the mismatch and a nearby nick by the MMR endonuclease PMS2 and exonuclease 1 (EXO1). The gap that is left in the DNA is filled by Pol δ. Failed MMR results in a high mutation load in microsatellite repeat sequences. d | DNA double-strand breaks (DSBs) can be repaired by non-homologous end-joining (NHEJ), which is often mediated by microhomology at ends. DSBs caused by ionizing radiation or by enzymes that cleave DNA usually do not yield DNA ends that can be ligated directly. End-trimming and resynthesis of bases are therefore required to join breaks, which may give rise to mutations. e | An alternative strategy for DSB repair is homologous recombination (HR). HR only operates when a double-stranded copy of the sequence is available, for example, as a sister chromatid in late S or G2 phase of the cell cycle, which may give rise to tandem duplication. CSA and CSB are also known as DNA excision repair protein ERCC8 and ERCC6, respectively; DNA-PK, DNA-dependent protein kinase; indel, insertion and deletion; LIG3, DNA ligase 3; PCNA, proliferating cell nuclear antigen. Figure from REF. , Nature Publishing Group.

Figure 4. Bypass of replication forks blocked by lesions.

a | In the presence of a translesion DNA synthesis (TLS) polymerase (Pol), a lesion can be bypassed by TLS, which can result in point mutagenesis. An error-free alternative to bypass a stalled replication fork is template switching. Point mutations are marked in red. b | In the absence of a TLS Pol, a translesion bypass is not possible (although some template switching still occurs), and the stalled replication fork collapses. This leads to double-strand breaks and chromosomal instability. Figure from REF. , Nature Publishing Group.

Figure 5. Gene rearrangements in cancer.

Gene rearrangements in cancer arise primarily from DNA double-strand breaks (DSBs). a | Synthesis-dependent end-joining (SDEJ), which is involved in repairing replication-associated DSBs, results in tandem duplications. Break-induced replication (BIR) initiates synthesis on the sister chromatid after strand invasion. Reversed branch migration of the Holliday junction formed following strand invasion can release the invaded strand, which contains extra DNA material from the sister chromatid and is fused to the original end by microhomology-mediated end-joining (MMEJ), resulting in a tandem duplication. b | Sister chromatid fusion causes gene amplification by breakage–fusion–bridge cycles,. In this process, two adjacent DSBs on sister chromatids are substrates for non-homologous end-joining (NHEJ), which rejoins the sister chromatids. After replication, these are again broken to form anther fusion chromosome carrying four gene a copies. c | The V(D)J recombination-activating (RAG) proteins recognize either the correct recombination signal sequences (RSSs) or almost identical (that is, pseudo) RSSs at which they initiate DSBs; they then mediate interchromosomal translocation rather than regular recombination within the V(D)J segments. This can create an immunoglobulin H (IGH)–BCL2 (B-cell CLL/lymphoma 2) fusion gene that drives cancer. d | Activation-induced cytidine deaminase (AID) is involved in class switch recombination and deaminates cytosines to uracils in transcribed regions, which are then processed by DNA repair enzymes into a DSB. If DSBs coexist in the IGH and C-MYC genes, then they can recombine by interchromosomal translocation to produce an IGH–C-MYC fusion gene. Chr, chromosome.