A Pooled Mutational Analysis Identifies Ionizing Radiation-Associated Mutational Signatures Conserved Between Mouse and Human Malignancies

Abstract

The mutational landscape of ionizing radiation (IR)-induced tumorigenesis may yield insights into how IR-induced genomic injury leads to cancer and the important endogenous mechanisms that safeguard genomic integrity. We previously developed mouse models of IR-induced malignancies initiated by focal, fractionated irradiation similar to clinical radiotherapy. Whole exome sequencing (WES) of these mouse model-derived malignancies revealed stable trinucleotide-based (comprised of a somatic variant and the 5’ and 3’ flanking bases) mutational signatures that were independent of tumor type or genetic background, suggestive of a unique IR-specific imprint on tumor exomes. On the basis of these findings, we hypothesized that clinically derived IR-induced malignancies from patients also harbor distinct mutational signatures mirroring those identified in our mouse models and that these signatures would be distinguishable from other mutagenic processes. WES was performed on two separate clinical IR-induced malignancies, both sarcomas arising in patients who were survivors of pediatric cancers. Matched germline and tumor DNA were analyzed. Exome capture, high throughput sequencing, read alignment, and variant calling were performed using standard industry-accepted approaches. To determine whether the signatures identified from IR-exposed subjects can be differentiated from other mutagenic signatures, we included WES data from a single ultraviolet radiation (UV)-induced human skin cancer and also a mouse model of urethane-induced cancers. For all samples, single nucleotide variants (SNVs) were analyzed using non-negative matrix factorization (NMF) to estimate trinucleotide-based mutational signatures. The two IR-induced clinical malignancies harbored 194 somatic SNVs and 361 somatic SNVs. The UV-induced cutaneous carcinoma harbored 2,113 somatic SNVs. Despite being extracted from a single tumor sample, the UV signature was virtually identical to previously published UV signature. NMF distinguished all three mutagens and in the pooled analysis IR was associated with mutational signatures common to both mouse and human malignancies. These common signatures are not highly correlated with each other, suggesting that they represent separate biological processes. These findings indicate that 1) pooled NMF analysis of malignancies induced by diverse mutagens (IR, UV and the chemical carcinogen urethane) and in different species (mouse and human) isolates the distinct signatures associated with these mutagens, 2) ionizing radiation-associated mutational signatures are conserved between mouse and human malignancies and 3) pooling of mutagenesis-matched mouse and human tumor samples enables NMF analysis and extraction of stable signatures when sample numbers are limited.