Abstract PR10: Ionizing radiation-induced tumorigenesis is associated with exome-wide mutational signatures conserved in mice and humans
Authors: Davidson Philip , Sherborne Amy , Taylor Barry , Nakamura Alice , Nakamura Jean 
Published: April 2017

Abstract
Objective: Ionizing radiation (IR) is utilized in diagnostic and therapeutic medical applications, but is also a well-recognized mutagen. The in vivo genetic events promoting malignancy formation after IR exposure are not understood in detail. The mutational landscape of 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 single nucleotide 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 (secondary cancers, distinguishable from recurrent primary cancers) from patients also harbor distinct mutational signatures mirroring those identified in our mouse models. Our goal is to determine whether IR-induced malignancies from patients harbor mutational signatures similar to experimentally derived IR-induced malignancies arising in mice.
Methods: WES was performed on genomic DNA isolated from two separate clinical IR-induced malignancies, both sarcomas arising in patients who were survivors of pediatric cancers. Radiotherapy exposure was verified by review of volumetric dosimetry. A UV-induced cutaneous squamous cell carcinoma (clinical patient sample) was included as a negative control and also analyzed by WES utilizing the same bioinformatics pipeline. Matched germline and tumor DNA were analyzed. Exome capture, high throughput sequencing (Illumina), read alignment and variant calling were performed using standard industry-accepted approaches. IR-induced tumors from mice and clinical samples were analyzed separately, then pooled into a single analysis to identify mutational signatures common to mice and humans. For all samples, single nucleotide variants (SNVs) were analyzed using non-negative matrix factorization (NMF) to estimate trinucleotide-based mutational signatures.
Results: The two IR-induced clinical malignancies harbored 194 somatic SNVs and 361 somatic SNVs. The UV-induced cutaneous carcinoma harbored 2,113 somatic SNVs. NMF analysis of the pooled somatic SNVs from human tumor samples only support the extraction of two signatures, one of which clearly is exclusive to the UV-induced skin cancer, while the other is present almost exclusively in IR-induced malignancies (the number of mutations assigned to the signatures differs between the skin cancer and IR samples with p-value = 8.3x10-179 by a likelihood ratio test). Despite being extracted from a single tumor sample, the UV signature was virtually identical to previously published UV signature. To determine whether IR-associated mutational signatures were stable across species we pooled mouse and human IR-induced tumor SNVs for NMF analysis, which identified common signatures that are not highly correlated with each other, suggesting that they represent separate biological processes.
Conclusions: IR-induced tumorigenesis is associated with stable trinucleotide-based mutational signatures that are conserved in human malignancies and mouse malignancies. These signatures are highly distinguishable from that associated with UV. These conserved signatures, developing in multiple irradiated tissue types, may reflect mutational processes associated with in vivo IR exposure and possibly demonstrate non-lethal but pathogenic somatic variants related to DNA repair.
This abstract is also being presented as Poster B42.
Citation Format: Philip Davidson, Amy Sherborne, Barry Taylor, Alice Nakamura, Jean Nakamura. Ionizing radiation-induced tumorigenesis is associated with exome-wide mutational signatures conserved in mice and humans [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr PR10.