Assessing cell-specific effects of genetic variations using tRNA microarrays

Christine Polte,Marcel J. C. Bijvelds,Eric J. Sorscher,Hugo R. de Jonge,Johannes Wagner,Daniel Wedemeyer,Zoya Ignatova,John Mahoney,Kathryn E. Oliver

doi:10.1186/s12864-019-5864-1

Abstract

BackgroundBy definition, effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid. Recent examples indicate tissue-specific and transfer RNA (tRNA)-dependent effects of some genetic variations arguing against neutrality of synonymous SNVs for protein biogenesis.ResultsWe performed systematic analysis of tRNA abunandance across in various models used in cystic fibrosis (CF) research and drug development, including Fischer rat thyroid (FRT) cells, patient-derived primary human bronchial epithelia (HBE) from lung biopsies, primary human nasal epithelia (HNE) from nasal curettage, intestinal organoids, and airway progenitor-directed differentiation of human induced pluripotent stem cells (iPSCs). These were compared to an immortalized CF bronchial cell model (CFBE41o−) and two widely used laboratory cell lines, HeLa and HEK293. We discovered that specific synonymous SNVs exhibited differential effects which correlated with variable concentrations of cognate tRNAs.ConclusionsOur results highlight ways in which the presence of synonymous SNVs may alter local kinetics of mRNA translation; and thus, impact protein biogenesis and function. This effect is likely to influence results from mechansistic analysis and/or drug screeining efforts, and establishes importance of cereful model system selection based on genetic variation profile.

Highlights

By definition, effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid
We hypothesized that variations in transfer RNA (tRNA) sets may alter Cystic fibrosis transmembrane regulator (CFTR) translation profiles, and the effect of synonymous SNVs/SNPs in each system
For Induced pluripotent stem cells (iPSC), only the zero time point was reported in all panels. tRNA isoacceptors are depicted with their cognate codon and the corresponding amino acid respectively, is 1 in Fischer rat thyroid (FRT), human bronchial epithelia (HBE), HeLa and iPSC (Fig. 3b), or equal to these in CFBE41o−, it would be expected that the c

Summary

Introduction

Effect of synonymous single-nucleotide variants (SNVs) on protein folding and function are neutral, as they alter the codon and not the encoded amino acid. Recent examples indicate tissue-specific and transfer RNA (tRNA)-dependent effects of some genetic variations arguing against neutrality of synonymous SNVs for protein biogenesis. Genetic variations are the source of evolutionary diversity and are grouped into three general categories: deleterious, neutral and beneficial Fitness landscapes, both at singleprotein and whole-organism levels, are generally used to depict phenotypic manifestation of genotypes [1,2,3]. Cellular concentrations of tRNA isoacceptors vary greatly and shape behavior of synonymous codons, which in turn, has a profound effect on translation kinetics and accuracy (Fig. 1), as well as protein expression level, folding and activity [25,26,27]. We perform systematic global quantification of the tRNAomes within various human cell lines and model systems used in the study of

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Conclusion