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Derivation of Doxorubicin Mutational Signatures in Cancer

Study design and aims: This study utilizes doxorubicin exposed cell lines to derive doxorubicin mutational signatures. To validate the methodology used (bulk whole-genome sequencing of cells exposed to drug with a pulsed dose-escalation approach), cisplatin mutational signatures are first derived and compared to previously published data (single constant dose of drug and whole-genome sequencing of single-cell clones). The primary aim of the study was to characterize the impact of doxorubicin mutagenesis on the genome. Furthermore, to assess the presence of derived doxorubicin signatures in patient samples treated with a doxorubicin-containing regimen.

Population information: The study utilizes atypical teratoid rhabdoid tumor (ATRT) (n=2) and renal medullary carcinoma (RMC) (n=2) cell lines. To acquire cisplatin and doxorubicin exposed cells, parental cells were treated with escalating doses of cisplatin and doxorubicin in a pulsed manner for between 2-12 months. This study also contains 2 cell lines derived from one patient with metastatic disease, treated with a doxorubicin-containing regimen.

Molecular technologies: Whole-genome sequencing of the bulk cell population.

Principal findings: Cisplatin mutational signatures were consistent with previously published data. This study identified two related single-base substitution (SBS) doxorubicin mutational signatures. While the two resulting signatures had some similarities, they differed in their frequencies of C > A (SBS-Doxorubicin-1) and T > C (SBS-Doxorubicin-2) substitutions. A double-base substitution (DBS) signature was also observed in association with SBS-Doxorubicin-2. This DBS signature harbored peaks at TG > CA, TG > GT, and TT > CC substitutions. Next, two INDEL signatures were derived. The first consisted of 1bp insertions and deletions at T homopolymers, >=2bp insertions at repetitive DNA, and microhomology deletions. The second consisted of >=2bp insertions at non-repetitive regions. Finally, both SBS-Doxorubicin signatures were found to be significantly present in patient samples exposed to a doxorubicin-containing regimen.

Data Available through dbGaP: This dataset contains paired-end whole genome sequencing of parental (n=4), cisplatin exposed (n=2), and doxorubicin exposed (n=4) SMARCB1-deficient cell lines, as well as cell lines derived from one patient with metastatic disease (n=2), where the patient was treated with a doxorubicin-containing regimen.