The UVA-induced single-base mutational signature of CX5461 in human cells

Description

Drug-related UVA-induced photoreactions have been reported for several therapeutic compounds, including fluoroquinolones. CX5461 is a clinically relevant quinolone-derived anti-cancer small molecule with documented UVA-sensitising activity. Using bulk and clonal whole genome sequencing under light-protected conditions we characterized the mutational signatures in human retinal pigment epithelial cells exposed to either UVA, CX5461, or co-exposed to UVA and CX5461. We observed that treatment with CX5461 or UVA alone resulted in a low mutation (base substitution and INDEL) burden and background-like mutational profiles. In contrast, cells co-exposed to UVA with CX5461 had a markedly higher mutational burden, characterized by T>A and T>C substitutions. The CX5461+UVA-associated SBS signature we report arises only when CX5461-treated cells are exposed to UVA, and is not observed when CX5461-treated cells are shielded from light. The RPE1_subs_indels_clones_bulk.txt file contains base substitution and INDEL mutations for bulk and clone-expanded WGS data reported in this study. To identify base substitutions and indel mutations in the datasets, first whole genome sequencing reads were aligned to the hg38 reference genome using bwa-mem. Following alignment, technical artifacts were corrected by marking duplicates and recalibrating base quality using GATK best practices workflows. Short variants, including indels and single-base, dinucleotide, and trinucleotide substitutions, were called using Mutect2 in matched normal mode, where untreated control samples were designated as the matched normal samples for short variant calling. Candidate variants were subsequently filtered to remove likely germline variants, contamination and artifacts using FilterMutectCall and FilterAlignmentArtifacts. The subs_indels_RPE1_Koh_et_al_mutect2.txt file contains base substitution and INDEL mutations for RPE1 WGS data from Koh et al 2024 (https://doi.org/10.1038/s41588-023-01602-9). We obtained the sequence files for the RPE1 WGS data reported by Koh et al, and applied the alignment and variant calling steps as described above.

Institutions

• University of British Columbia

  British Columbia, Vancouver
• BC Cancer Agency

  British Columbia, Vancouver

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