Oncogenes have the most distinct codon biases in the genome and codon signatures that oppose tumor suppressor genes

Abstract

Oncogenes and tumor-suppressor genes play opposing roles in cancer biology to promote and restrict growth, respectively. Codon usage patterns interface with tRNA modifications to control translation, leading to gene-specific codon signatures with regulatory potential. As such, codon-biased translational regulation has been identified as a driver of proliferation and drug resistance in multiple cancers. We used advanced codon analytics methods to characterize and compare codon usage bias in oncogenes and tumor suppressor genes (TSGs) from humans and mice at group and gene-specific levels. We demonstrate that human oncogenes exhibit a distinct and opposing codon usage pattern to TSGs. This phenomenon is also present in mice but with less distinct oncogene bias relative to humans. Further comparison to 447 gene ontology groups demonstrated that human oncogenes have the most distinct codon usage patterns in the genome, while also highlighting that codon bias can separate functionally related genes and pathways from other biological processes. Using gene-specific codon analytics, we determined that human oncogenes have two types of extreme codon bias: a large group (N = 43) over-using G/C ending (GC3) codons and a smaller group (N = 12) over-using A/U (AU3) ending codons. While GC3 bias has been linked to increased translation in general, the AU3 finding suggests that genetic, environmental, or stress-related signals could drive the translation of this small group of oncogenes. The less extreme bias observed in mouse oncogenes and tumor suppressors likely underscores species-specific differences in oncogenic translation programs. Together, our findings highlight codon usage bias as a potential determinant of oncogene expression, provide a framework for ontology-based codon analysis, and uncover on species-specific differences in oncogene translation and codon usage biases.