Translational efficiency across healthy and tumor tissues is proliferation-related

Abstract

11Background: Different tissues express genes with particular codon usage and anticodon 12 tRNA repertoires. However, the codon-anticodon co-adaptation in humans is not completely 13 understood, as well as its effect on tissue-specific protein levels. 14 Results:We first validated the accuracy of small RNA-seq for tRNA quantification across 15 five human cell lines. We then analyzed tRNA expression in more than 8000 tumor samples 16 from TCGA, together with their paired mRNA-seq and proteomics data, to determine the 17 Relative Translation Efficiency. We thereby elucidate that the dynamic adaptation of the 18 tRNA pool is largely related to the proliferative state across tissues, which determines tissue-19 specific translation efficiency. Furthermore, the aberrant translational efficiency of ProCCA 20 and GlyGGT in cancer, among other codons, which is partly regulated by the tRNA gene 21 copy numbers and their promoter DNA methylation, is associated with poor patient survival. 22Conclusions: The distribution of tissue-specific tRNA pools over the whole cellular 23 translatome affects the subsequent translational efficiency, which functionally determines a 24 condition-specific expression program in tissues both in healthy and tumor states. 25 (14)(15)(16)(17)(18). In this context, The Cancer Genome Atlas (TCGA) has been recently used to 52 investigate the alteration of tRNA gene expression and translational machinery in cancer, 53 which may play a role in driving aberrant translation (19,20). 54To validate the use of small RNA-seq for tRNA quantification, we first compare tRNA levels 55 determined in HEK293 by well-established tRNA sequencing methods (Hydro-tRNAseq and 56 demethylase-tRNA-seq) (12,13,21), with those obtained by small RNA-seq. Then we 57 quantify the tRNA repertoire of five cell lines using Hydro-tRNAseq and perform small RNA-58 seq in parallel. Comparison of the tRNA abundance obtained by both approaches shows that 59 it is possible to accurately estimate relative tRNA abundance of cells and tissues using small 60 RNA-seq. Furthermore, we show that both types of quantification are informative enough to 61 distinguish between the five analyzed human cell lines covering multiple tissue types. In 62 consequence, we apply a tRNA-specific computational pipeline to re-analyze 8,534 small 63 RNA-seq datasets from TCGA (22). We find that the tissue-specificity of tRNA expression is 64 largely proliferation-related, even within healthy tissues. The tRNA quantification of TCGA 65 samples enables their comparison with paired and publicly available mRNA-seq, proteomic, 66 DNA methylation and copy number data, which underscores the role of tRNAs in globally 67 controlling a condition-specific translational program. We discover multiple codons, including 68ProCCA and GlyGGT, whose translational efficiency is compromised and leads to poor 69 prognosis in cancer. Finally, promoter DNA methylation and tRNA gene copy number arise 70 as two regulatory mechanisms controlling tRNA gene expression in cancer. 71 RESULT...

5′ Half of specific tRNAs feeds back to promote corresponding tRNA gene transcription in vertebrate embryos

“…S3, A and B). Similar to tRNA expression in other systems (43)(44)(45), however, some tRNA genes showed severely biased expression levels in zebrafish embryos. For example, 75 to 86% of total tRNAs at any examined developmental stages were tRNA His/GTG that has 511 gene copies in the genome (Fig.…”

Evolutionary conservation of A/T-ending codons reflects co-regulation of expression and complex formation

“…Our analysis showed that the fine-tuned regulation of transcripts enriched in A/T-ending codons could be directly related to the specific regulation of tRNAs with anticodons recognizing A/T-ending codons. Therefore, we used the Supply-to-Demand Adaptation (SDA) codon values to obtain a global estimate of translation efficiency [22]. We compared the SDA values from healthy samples for codons enriched in the negative pole component against those in the positive pole (see Figure 2D).…”

“…The observed coordination could reflect a greater variation of the tRNA pool related to A/T-ending codons than that of G/C-ending codons. Harnessing recently published data on tRNA abundance [22], we explored the variation of tRNA across healthy tissues. We found that the coefficient of variation among tissues was higher for the pool of tRNAs with A or U in the position 34 of the anticodon than for tRNAs with G or C (Figure 6A, Supplementary Table 8).…”

“…Protein-coding transcripts that play a role in cell division are coordinated in their expression and have a codon usage adapted to the tRNA abundances of proliferating cells [20][21][22]. The realization that specific codon usage is required for dynamic and coordinated changes ensuring the suitable production of certain gene products has led to the expectation that some codon signatures will be conserved along evolution.…”

Control of translation elongation in health and disease

“…However, Brf1 overexpression in a mouse model of prostate cancer accelerates the disease, indicating that increases in tRNA expression may promote certain tumours, although it is possible that this phenotype is driven by upregulation of specific tRNAs (Loveridge et al, 2019). Importantly, the tRNAs induced in cancer cells favour a pro-proliferative programme and their upregulation is associated with a worse prognosis (Gingold et al, 2014;Hernandez-Alias et al, 2019).…”