Burns, M. B., Temiz, N. A., & Harris, R. S. (2013). Evidence for APOBEC3B mutagenesis in multiple human cancers. Nature Genetics, 45(9), 977–983.

Burns et al. (2013) — Evidence for APOBEC3B Mutagenesis in Multiple Human Cancers

Bibliographic Reference

Burns, M. B., Temiz, N. A., & Harris, R. S. (2013). Evidence for APOBEC3B mutagenesis in multiple human cancers. Nature Genetics, 45(9), 977–983. DOI: 10.1038/ng.2701.

Core Argument

APOBEC3B is a general endogenous mutagen active across multiple human cancer types, not merely a breast-cancer-specific phenomenon. By analyzing expression data, mutation frequencies, local sequence contexts, and kataegis events across 19 cancer types (4,800+ tumors, >1,000,000 somatic mutations), the authors demonstrate that six distinct cancers — bladder, cervical, lung adenocarcinoma, lung squamous cell, head/neck, and breast — show convergent evidence for APOBEC3B-dependent mutagenesis: elevated APOBEC3B expression, C/G-dominated mutation spectra, cytosine mutation contexts matching recombinant APOBEC3B’s biochemical signature, and kataegis events. This establishes APOBEC3B as a broad-spectrum mutator that shapes the mutation landscapes of multiple tumor types — a concrete molecular instantiation of Loeb’s mutator phenotype hypothesis operating across tissue boundaries.

Methods

• Data source: TCGA RNAseq and exome mutation data retrieved January–April 2013; 19 tumor types
• Expression analysis: APOBEC3B mRNA levels normalized to TBP; comparisons by Mann-Whitney U test; RT-qPCR validation for normal tissues
• Mutation analysis: >1,000,000 somatic SNVs; insertions/deletions and adjacent multiple mutations removed; converted to hg19 coordinates
• Sequence context: Trinucleotide frequencies around mutated cytosines; hierarchical clustering of cancer mutation signatures; comparison to recombinant APOBEC3B biochemical signature
• Kataegis detection: Intermutation distance analysis; strand-coordinated clusters of C mutations identified per tumor
• Correlations: Spearman’s rank correlation between APOBEC3B expression and C/G mutation fraction, overall mutation load, and kataegis frequency

Key Findings

• Six cancers converge on APOBEC3B. Bladder, cervical, lung adenocarcinoma, lung squamous cell, head/neck, and breast cancers all showed: (1) elevated APOBEC3B expression in the majority of tumors (p<0.0001 vs. normal), (2) strong C/G mutation biases, (3) cytosine mutation contexts closely matching the recombinant APOBEC3B deamination signature, and (4) evidence for kataegis events. The convergence of these four independent data types upon the same six cancer types is the paper’s central finding.

• APOBEC3B expression correlates positively with mutation burden. Across 19 cancer types, median APOBEC3B expression correlated with the proportion of mutations at C/G base pairs (p=0.0031, r=0.64), overall mutation load (p=0.0013, r=0.68), and average kataegis events per tumor (p=0.017, r=0.54). These correlations persisted despite the inclusion of all available data, including cancers with known alternative mutational sources (e.g., UV in skin, undefined sources in glioma).

• Hierarchical clustering identifies an APOBEC3B mutational signature group. Unbiased clustering of cytosine mutation spectra across the 16 possible trinucleotide contexts grouped the six implicated cancer types together, distinct from cancers dominated by other mutational processes (UV-driven skin cancer, CpG-dominated colon cancer). The clustering was driven by the 5’ TpC preference characteristic of APOBEC3B.

• Kataegis is APOBEC3B-linked and broadly distributed. Strand-coordinated cytosine mutation clusters (kataegis) were detected in multiple cancer types and their frequency correlated with APOBEC3B expression levels. The six signature cancers all showed strong evidence for kataegis with a mean of 1–4 clusters per tumor. The mechanistic model: uracil lesions processed into nicks by UNG and APE1 generate single- and double-stranded DNA breaks — intermediates in both clustered mutagenesis and larger-scale chromosomal rearrangements.

• Ten cancers show APOBEC3B upregulation exceeding breast cancer. A total of 10 cancer types showed median APOBEC3B upregulation greater than breast cancer (the intended positive control), with bladder, head/neck, lung, and cervical cancers showing particularly striking elevations. Additional cancers (uterine, rectal, stomach, ovarian) showed significant upregulation and kataegis but ambiguous trinucleotide signatures — suggestive but not conclusive for APOBEC3B involvement.

Concepts Introduced or Used

APOBEC3B, mutator-phenotype, kataegis, mutational-signature, C-to-U deamination, cytosine mutation bias, trinucleotide sequence context, hierarchical clustering, Spearman correlation, TCGA, breast-cancer, bladder-cancer, cervical-cancer, lung-cancer, head-and-neck-cancer, uracil DNA glycosylase (UNG), abasic site, translesion DNA synthesis

Entities Referenced

• APOBEC3B — The DNA cytosine deaminase identified as the primary mutator across six cancer types
• APOBEC3A, APOBEC3C, APOBEC3D, APOBEC3F, APOBEC3G, APOBEC3H — Other APOBEC family members excluded as major contributors based on expression, localization, or sequence preference
• AID — Activation-induced deaminase; acknowledged as a B-cell-specific mutator
• APOBEC1 — mRNA editing enzyme; tissue-restricted expression
• TCGA (The Cancer Genome Atlas) — Data source for all expression and mutation analyses
• UNG (uracil DNA glycosylase) — Processes uracil lesions into abasic sites, enabling translesion synthesis and strand breaks
• TBP (TATA-binding protein) — Housekeeping gene used for expression normalization
• Cancer types: bladder, cervical, lung adenocarcinoma, lung squamous cell, head/neck, breast, uterine, rectal, stomach, ovarian, prostate, renal clear cell, skin (melanoma), colon, glioma, LAML

Limitations (as stated by authors)

• APOBEC3B involvement could not be unambiguously determined for several cancers (uterine, rectal, stomach, ovarian) despite significant upregulation and kataegis evidence — trinucleotide mutation motifs were too distantly related to the recombinant enzyme signature
• Other DNA deaminase family members cannot be completely excluded, though AID is the only other member with a plausible role (restricted to B-cell cancers)
• Skin cancer has high APOBEC3B expression and kataegis but the UV-dominated dipyrimidine mutation signature likely eclipses the APOBEC deamination signature
• High-depth whole-genome sequences will be required to unambiguously distinguish APOBEC3B-dependent mechanisms from other mutational processes in ambiguous cases
• The analysis used exome data, which captures only ~1% of the genome — non-coding regions and regulatory elements may show different APOBEC3B impact patterns
• Causal direction: APOBEC3B upregulation could drive mutagenesis, or genomic instability could trigger APOBEC3B upregulation as part of an innate immune response — correlation does not establish causation

Relevance to Clonal Evolution

This paper provides the multi-cancer evidence base for APOBEC3B as a broad-spectrum endogenous mutator — a concrete molecular instantiation of the mutator-phenotype hypothesis that operates across tissue boundaries. By demonstrating that APOBEC3B upregulation correlates with increased mutation load, C/G bias, and kataegis across six distinct cancer types, it establishes a general mechanism by which tumors acquire the genetic diversity that fuels clonal-evolution. The paper’s convergence argument — expression + mutation bias + sequence context + kataegis all pointing to the same enzyme in the same six cancers — is a model of how to attribute mutational processes to specific molecular causes from genomic data alone.

Relationship to Burns 2013 Nature: The companion paper (burns2013-apobec3b-breast-cancer) established APOBEC3B as a mutator in breast cancer specifically — cell-line experiments, tumor/normal comparisons, and biochemical characterization of the recombinant enzyme. This Nature Genetics paper generalizes the finding to a pan-cancer scale using TCGA data, replacing experimental depth with statistical breadth (4,800+ tumors vs. 52 pairs). Together, they form a two-pronged argument: mechanistic depth (Nature) + population breadth (Nature Genetics).

Caveat on primacy: Petljak et al. (2022) subsequently demonstrated that APOBEC3A, not APOBEC3B, is the main driver of somatic APOBEC mutagenesis in cancer — APOBEC3B deletion does not significantly reduce SBS2/SBS13, and APOBEC3B can restrain APOBEC3A by reducing its protein levels. The Burns 2013 attribution of the primary mutational role to APOBEC3B reflects the evidence available at the time (expression levels, nuclear localization, biochemical activity) and has been revised by subsequent evidence. This is documented in APOBEC-mutagenesis §Molecular Basis.