Expression of tiRNA and tRF in APP/PS1 transgenic mice and the change of related proteins expression

Abstract

Background: Transcriptomics, such as that of non-coding RNA (ncRNA), which include microRNA (miRNA), circular RNA, and the transfer RNA (tRNA)-derived fragments (tiRNA and tRF) in Alzheimer's disease (AD) have attracted much attention recently. The tiRNA and tRFs are produced when the tRNA splits at specific sites. The expression change and related function of tiRNA and tRFs in AD has not been fully investigated.Methods: In our study, APP/PS1 transgenic mice (AD mice model) and healthy control mice were used to discover the differentially expressed tiRNA and tRFs with high-throughput sequencing. Among the differentially expressed tiRNA and tRFs, we chose two tRFs (tRF-Thr-CGT-003 and tRF-Leu-CAA-004) and predicted the target messenger RNAs (mRNAs) with miRanda and Target Scan. The target mRNAs of tRF-related function and pathways were analyzed, then we performed quantitative reverse transcription polymerase chain reaction (RT-qPCR) and western blot to validate the related target mRNAs and pathways.Results: A total of 27 significantly different tiRNA and tRFs were detected between wild type (WT) and APP/PS1 groups, including 14 up-regulated and 13 down-regulated. Through analyzing the target mRNAs of all differentially expressed tiRNA and tRFs with GO enrichment, we found the target mRNAs could take part in the learning and memory biological process, synapse organization, cognition biological process, synaptic transmission, amyloid-β (Aβ) metabolic process, and so on. We then chose three differentially expressed tRFs for further qPCR validation and passed two tRFs: tRF-Thr-CGT-003 and tRF-Leu-CAA-004, that were found to regulate the calcium regulation-related proteins (the voltage-gated calcium channel γ2 subunit and the RYR1 endoplasmic reticulum calcium released protein) and the retinol metabolism-related proteins (retinoic acid metabolic enzymes CYP2S1, CYP2C68, CYP2S1). Conclusions:The APP expression and presenilin mutation in APP/PS1 mice could cause tiRNA and tRFs expression change. Among the differentially expressed tiRNA and tRFs, we found some tRFs took part in the voltage-gated calcium channel γ2 subunit expression and regulation, influencing the neuron calcium homeostasis. Moreover, we also found the tRFs may participate in the regulation of retinol metabolism. Our findings suggest that the dysregulated tiRNA and tRFs may be beneficially exploited as potential diagnostic biomarkers and/or therapeutic targets of AD.

tRNA fragment biomarkers of Neurological Disease: Challenges and Opportunities

“…Investigations using transgenic mice overexpressing a mutant chimeric mouse/human APP (APPswe) and a mutant human Presenilin 1 (PSEN1dE9) that develop age-dependent cognitive impairment and show abundant pathological A40-42 inclusions also identified dysregulated tRFs 69 . Lu et al, performed small RNA sequencing on hippocampal tissue from ~12-month-old male mice and identified dysregulated tRFs, validation confirmed that a tRF derived from ThrCGT was upregulated in AD mice compared to controls, whereas a tRF from LeuCAA was significantly downregulated 70 . Wu et al, found that microRNAs and tRFs were elevated in a publicly available sequencing dataset from 6 late onset AD patients and 6 age-matched healthy controls 71 .…”

Biogenesis, function, and landscape of tsRNAs in central nervous system diseases

“…identified 27 differentially expressed tsRNAs in the hippocampus of APP/PS1 transgenic mice and WT mice by transcriptome analysis, followed by qPCR validation of 2 tsRNAs. After bioinformatics analysis, qPCR and Western blot verification of the target genes, tRF‐Thr‐CGT‐003 and tRF‐Leu‐CAA‐004 were found to be involved in the regulation of CACNG2 and RYR1 genes related to calcium regulation 58 . Numerous studies have focused on the pathogenic role of calcium dysregulation caused by RyR channel leakage in AD 59–63 .…”

An old friend with a new face: tRNA-derived small RNAs with big regulatory potential in cancer biology

“…In another mechanism, downregulated 5’ tsRNA-Leu (referred to as tRF-Leu-CCA-004) was found to modulate the expression of members of the cytochrome P450 family leading to the speculation that it could affect protein expression [ 110 ]. In the archaea haloferax volcanii , the 5’ tsRNA Val (referred to as tRF-5Val) binds to the small ribosomal subunit and interferes with the peptidyl transferase, hence destabilising the growing polypeptide chain [ 28 ].…”