G/C-ending and synonymous codon bias define functional translational programs that shape human tissue and cancer proteomes.

Abstract

Codon usage bias is a fundamental feature of the genetic code, yet its impact on messenger RNA translation is incompletely defined. Here, we integrate comparative genomics, human tissue proteomes, large cancer cell line, and patient cancer datasets to reveal a conserved codon-bias axis. Across mammals, we show that GC-biased gene conversion drives human-specific GC3 (third codon nucleotide bias score) drifts, yet the functional dichotomy is maintained: A/T-ending codons associate with proliferation and RNA processing, while G/C-ending (Third nucleotide Guanine or Cytosine) codons associate with differentiation and neuronal functions. At the isoacceptors level, synonymous codons segregate into distinct functional categories. To mechanistically connect codon usage to cancer, we introduce the ANN- and m⁷G-indices, capturing codons decoded by transfer RNA (tRNA) modifications t⁶A and m⁷G. Both indices negatively correlate with GC3 and enrich for pro-oncogenic proliferative pathways. Human tissue proteomes reveal strong codon bias discordance between RNA and protein levels, with nervous system tissues enriched for G/C-ending codons while proliferative organs are A/T-biased. Analysis of 2600 cancer cell lines and 21 cancer types revealed heterogeneous codon preferences in cancer cell lines but a global A/T-ending shift in human cancer-upregulated proteins. These findings establish synonymous codon divergence and tRNA modification indices as key determinants of translational reprogramming in health and cancer.