Defects in 8-oxo-guanine repair pathway cause high frequency of C > A substitutions in neuroblastoma.

Abstract

Neuroblastomas are childhood tumors with frequent fatal relapses after induction treatment, which is related to tumor evolution with additional genomic events. Our whole-genome sequencing data analysis revealed a high frequency of somatic cytosine > adenine (C > A) substitutions in primary neuroblastoma tumors, which was associated with poor survival. We showed that increased levels of C > A substitutions correlate with copy number loss (CNL) of <i>OGG1</i> or <i>MUTYH</i> Both genes encode DNA glycosylases that recognize 8-oxo-guanine (8-oxoG) lesions as a first step of 8-oxoG repair. Tumor organoid models with CNL of <i>OGG1</i> or <i>MUTYH</i> show increased 8-oxoG levels compared to wild-type cells. We used CRISPR-Cas9 genome editing to create knockout clones of <i>MUTYH</i> and <i>OGG1</i> in neuroblastoma cells. Whole-genome sequencing of single-cell <i>OGG1</i> and <i>MUTYH</i> knockout clones identified an increased accumulation of C > A substitutions. Mutational signature analysis of these <i>OGG1</i> and <i>MUTYH</i> knockout clones revealed enrichment for C > A signatures 18 and 36, respectively. Clustering analysis showed that the knockout clones group together with tumors containing <i>OGG1</i> or <i>MUTYH</i> CNL. In conclusion, we demonstrate that defects in 8-oxoG repair cause accumulation of C > A substitutions in neuroblastoma, which contributes to mutagenesis and tumor evolution.