Analysis of synonymous codon usage bias in human monocytes, B, and T lymphocytes based on transcriptome data

Codon usage bias (CUB) analysis has drawn considerable attention throughout the years due to its effect on cell physiology. Meanwhile, in the immune system, any imbalance in its regulation and protein expression that can be caused by CUB may lead to immune system disorder. The objective of this study is to analyze the global CUB in protein-coding genes of human monocytes, B and T lymphocytes and identify factors that influence the codon usage pattern. The RNA-Seq datasets were used to investigate the extent of CUB in selected immune cells as well as in human protein-coding genes (HPCG) that is used as a reference. Several indices of codon usage and multivariate statistical methods were applied to analyze the differences in CUB within the datasets. Results revealed that the protein-coding genes expressed in monocytes, B and T lymphocytes showed distinctive nucleotide composition and CUB patterns based on several codon usage bias indices, namely Relative Synonymous Codon Usage (RSCU), Effective Number of Codons (ENC) and Codon Adaptation Index (CAI). Multivariate analysis of the CUB indices suggested that mutational bias may be the major factor affecting CUB in monocytes, while in B and T lymphocytes, the main influential factor may be the translational selection. Generally, this study revealed interesting differences in CUB and factors that shaped the CUB of protein-coding genes in monocytes, B and T lymphocytes. Moreover, this study also provided new insights into understanding the role of CUB in the human immune system.