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Tissue-specific codon optimality influences gene expression. In cancer, synonymous mutations often increase optimal codons, promoting tumor growth and potentially serving as a biomarker for certain cancers.

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Area of Science:

  • Genomics
  • Molecular Biology
  • Cancer Research

Background:

  • Codon optimality impacts mRNA stability and expression across organisms.
  • Tissue-specific codon optimality and its role in cancer have been underexplored.
  • Somatic synonymous mutations can alter codon optimality in cancer.

Purpose of the Study:

  • To determine tissue-specific codon optimality in human tissues.
  • To investigate how codon optimality is perturbed by somatic synonymous mutations in human cancers.
  • To assess the role of altered codon optimality in tumorigenesis and as a potential therapeutic target.

Main Methods:

  • Analysis of mRNA expression data from the Genotype-Tissue Expression (GTEx) project for 29 human tissues.
  • Application of tissue-specific codon optimality to somatic synonymous mutations in 8532 tumor samples and 416 normal cells.
  • Correlation analysis between codon optimality, differentiation, proliferation, and cancer progression.

Main Results:

  • Optimal codons correlate with cellular differentiation, while non-optimal codons correlate with proliferation.
  • Tissue specificity of codon optimality is prominent in amino acids with high genetic code degeneracy.
  • Synonymous mutations frequently increase optimal codons in tumor cells and cancer-related genes.
  • Elevated optimal codon gain promotes tumor cell proliferation in specific cancer types and may serve as a prognostic biomarker in triple-negative breast cancer.

Conclusions:

  • This study establishes tissue-specific codon optimality profiles for human tissues.
  • Synonymous mutations in cancer significantly alter codon optimality, favoring optimal codons.
  • Optimal codon gain plays a role in cancer development and presents potential therapeutic avenues.