The DNA cytosine deaminase APOBEC3H haplotype I likely contributes to breast and lung cancer mutagenesis

Abstract

Cytosine mutations within TCA/T motifs are common in cancer. A likely cause is the DNA cytosine deaminase APOBEC3B (A3B). However, A3B-null breast tumours still have this mutational bias. Here we show that APOBEC3H haplotype I (A3H-I) provides a likely solution to this paradox. A3B-null tumours with this mutational bias have at least one copy of A3H-I despite little genetic linkage between these genes. Although deemed inactive previously, A3H-I has robust activity in biochemical and cellular assays, similar to A3H-II after compensation for lower protein expression levels. Gly105 in A3H-I (versus Arg105 in A3H-II) results in lower protein expression levels and increased nuclear localization, providing a mechanism for accessing genomic DNA. A3H-I also associates with clonal TCA/T-biased mutations in lung adenocarcinoma suggesting this enzyme makes broader contributions to cancer mutagenesis. These studies combine to suggest that A3B and A3H-I, together, explain the bulk of ‘APOBEC signature' mutations in cancer.

Biochemical Basis of APOBEC3 Deoxycytidine Deaminase Activity on Diverse DNA Substrates

“…It was proposed that this causes a high propensity of catalytically unfavorable ssDNA-AID binding conformations, which may afford some protection against off-target mutations in genomic DNA [188,266]. This may also be why the majority of humans carry an A3H allele for a thermodynamically unstable enzyme (haplotypes I, III, IV, or VI) although this does not completely protect from the ability of A3H to contribute to mutations that arise during cancer [59,60,174]. The relative inactivity of A3C in the majority of humans due the loss of oligomerization may also be a mechanism to decrease off-target mutations, despite its ability to access genomic DNA in cells [28,269].…”

“…In addition or alternatively, A3H hap I is able to induce mutations in breast and lung cancer cells and there is a high association of the A3H hap I allele in an A3B -/-genetic background [174]. The A3H hap I footprint is 5'CTCA and overlaps with A3A [110,174].…”

“…In addition or alternatively, A3H hap I is able to induce mutations in breast and lung cancer cells and there is a high association of the A3H hap I allele in an A3B -/-genetic background [174]. The A3H hap I footprint is 5'CTCA and overlaps with A3A [110,174]. Thus more tumor based studies are needed to differentiate the activity of A3A and A3H hap I. Interestingly, A3A has been demonstrated to deaminate methyl-cytosines (mC) with high efficiency, unlike A3H, and is able to deaminate mC in CpG islands (mCpG) [130,185].…”

“…Usually, redundant DNA repair mechanisms can remove uracils and negate most of these promutagenic lesions [13]. However, with the development of Next Generation Sequencing technology and the availability of large sequence datasets, it has become clear that mutations in many cancers have a C/G→T/A bias, and most cancer cells or tumors also overexpress of A3B or A3H hap I mRNA, suggesting that A3s are inducing somatic mutations [16,17,[171][172][173][174][175]. The uracils created by A3 mutations also can lead to C→G or C→A mutations depending on the repair pathway initiated by the abasic site after APE-mediated removal [176,177] (Figure 1.2A).…”

“…If these enzymes are expressed at the wrong time or in the wrong cell type and have access to genomic DNA in the nucleus, there is the potential for deamination of genomic cytosines that can lead to mutations and cellular transformation [170,330,331]. A3B, A3A and A3H hap I have been demonstrated to contribute to cancer mutagenesis [17,174,175,184,196]. Among these three enzymes, A3B has emerged as the leading contributor to mutagenesis [180,[332][333][334][335][336].…”