Abstract 2918: Analysis of matched pre and post cisplatin-treated muscle-invasive bladder cancer reveals a candidate cisplatin mutational signature
Authors: David Liu, Daniel Keliher, Philip Abbosh, Kent Mouw, Diana Miao, Mariel Boyd, Jean Hoffman-Censits, Gopa Iyer, Sara Tolaney, Jaegil Kim, Gad Getz, Scott Carter, Joaquim Bellmunt, Elizabeth R. Plimack, Jonathan E. Rosenberg, Eliezer M. Van Allen
Journal: Cancer Research (2017)

Abstract Background: Mutational signatures of exposure to DNA damaging agents such as UV irradiation, tobacco, and temozolomide have been described; however a cisplatin mutational signature has not been identified. We analyzed mutational changes in matched pre- and post-cisplatin based neoadjuvant chemotherapy (NAC)-treated muscle-invasive bladder cancer (MIBC) samples to identify a cisplatin mutational signature. Methods: Whole exome sequencing and mutation calling was performed on matched germline and pre- and post-cisplatin based NAC (MVAC and GC) tumor samples from 46 MIBC patients with gross residual disease (≥ pT2) at cystectomy. After quality control, samples from 30 patients were analyzed. For each tumor, we characterized single nucleotide mutations (C&amp;gt;A, C&amp;gt;T, C&amp;gt;G, T&amp;gt;A, T&amp;gt;C, T&amp;gt;G) within a tri-nucleotide context, and used an optimized non-negative matrix factorization (NMF) to discover signatures of mutational processes in pre-NAC tumors, post-NAC tumors, and among mutations unique to the post-NAC samples. We compared our discovered signatures to previously described human mutational signatures and to a signature of cisplatin exposure in a DT40 (chicken lymphoblast) cell line (normalized for a human exome context). We also performed strand asymmetry analysis to search for evidence of transcription-coupled repair. Results: In both pre and post-NAC tumors we identified mutational signatures matching those attributed to APOBEC activity and nucleotide excision repair pathway defects, consistent with past studies in MIBC. In post-NAC tumors we identified an additional novel mutational signature, with modest overall cosine similarity (0.61) to the DT40 cisplatin signature, but similar C&amp;gt;A and T&amp;gt;A motifs. There was a strong correlation in inferred mutational activity (Pearson R = 0.98) when we replaced the novel signature with the DT40 signature in the post-NAC tumors, which was highly unlikely to be due to chance (p &amp;lt; 0.001, empiric null distribution). Further, we found evidence of transcriptional strand bias in C&amp;gt;A (p = 0.00025) and T&amp;gt;A (p = 4.2e-06) motifs with depletion of coding strand mutations, consistent with transcription coupled repair of platinum crosslinks at GpG and ApG motifs in the non-coding strand. Finally, we were able to rediscover the novel signature when limiting analyses to mutations unique to post-NAC tumors, consistent with mutational activity during chemotherapy. Conclusions: Analysis of matched pre- and post- cisplatin treated MIBC identified a novel signature in post-cisplatin treated samples that (1) has mutational activity similar to a preclinical cisplatin mutational signature; (2) has a transcription strand bias consistent with known repair characteristics of platinum-induced DNA damage; and (3) arises in tumors following cisplatin chemotherapy. This may represent a cisplatin-induced mutational signature in human tumors. Citation Format: David Liu, Daniel Keliher, Philip Abbosh, Kent Mouw, Diana Miao, Mariel Boyd, Jean Hoffman-Censits, Gopa Iyer, Sara Tolaney, Jaegil Kim, Gad Getz, Scott Carter, Joaquim Bellmunt, Elizabeth R. Plimack, Jonathan E. Rosenberg, Eliezer M. Van Allen. Analysis of matched pre and post cisplatin-treated muscle-invasive bladder cancer reveals a candidate cisplatin mutational signature [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2918. doi:10.1158/1538-7445.AM2017-2918