A novel tsRNA-16902 regulating the adipogenic differentiation of human bone marrow mesenchymal stem cells

tRNA-derived small RNA changes in bone marrow stem cells under hypoxia and osteogenic conduction

BACKGROUND

Tissue engineering using bone mesenchymal stem cells (BMSCs) transplantation is a promising therapeutic for bone regeneration. However, the effect of bone regeneration remains unsatisfactory due to the BMSCs' functional abnormality influenced by hypoxia. In this study, we attempt to explore the mechanism of osteogenic differentiation of BMSCs under hypoxic conditions from the perspective of non-coding RNA regulation.

METHODS

The study employed BMSCs obtained from healthy donors and simulated hypoxia using CoCl2 stimulation. High-throughput sequencing technique was used to identify differential expression profiles of tRNA-derived small RNA (tsRNA) in three experimental groups: BMSCs-0d, BMSCs-7d and BMSCs-0d-CoCl2 . TargetScan and miRanda algorithms were used to determine tsRNA target genes, while Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analysis were employed for the prediction of biological functions. Real-time reverse transcriptase-polymerase chain reaction (Real-time RT-PCR) was carried out on four selected differentially expressed tsRNAs.

RESULTS

After the osteogenic induction and CoCl2 stimulated separately, there were 19 tsRNAs differentially expressed in BMSCs, including 14 upregulated and five downregulated. According to the analysis of biological information, these tsRNAs may regulate 311 potential target genes and mainly enrich the pathways such as metabolic pathways, Wnt signalling pathway, osteoclast differentiation, cellular senescence and mTOR signalling pathway. The results of Real-time RT-PCR for 3'tiRNA-41-GlnTTG-6, 3'tiRNA-42-LysTTT-8, 5'tiRNA-35-CysACA-1 and tRF3a-AsnGTT-9 were consistent with small RNA sequencing data.

CONCLUSION

We discovered the tsRNA that changes the process of osteogenesis and hypoxia, which provides new targets for promoting survival and regeneration functions after BMSCs transplantation.

Classification, function, and advances in tsRNA in non-neoplastic diseases

tRNA-derived small RNAs (tsRNAs) are non-coding small RNAs produced by specific endonucleases following the processing and splicing of precursor or mature tRNAs upon starvation, oxidative stress, hypoxia, and other adverse conditions. tRNAs are classified into two major categories, tRNA fragments (tRFs) and tRNA-derived stress-induced small RNAs (tiRNAs), based on differences in splice sites. With the development of high-throughput sequencing technologies in recent years, tsRNAs have been found to have important biological functions, including inhibition of apoptosis, epigenetic regulation, cell-cell communication, translation, and regulation of gene expression. Additionally, these molecules have been found to be aberrantly expressed in various diseases and to be involved in several pathological processes. In this article, the classification and nomenclature, biological functions, and potential use of tsRNAs as diagnostic biomarkers and therapeutic targets in non-neoplastic diseases are reviewed. Although tsRNA research is at its infancy, their potential in the treatment of non-tumor diseases warrants further investigation.

Differential Expression Analysis of tRNA-Derived Small RNAs from Subcutaneous Adipose Tissue of Obese and Lean Pigs

Epigenetic factors, including non-coding RNA regulation, play a vital role in the development of obesity and have been well researched. Transfer RNA-derived small RNA (tsRNA) is a class of non-coding RNA proven to be involved in various aspects of mammalian biology. Here we take pigs as a model for obesity research and use tsRNA-seq to investigate the difference in tsRNA expression in the subcutaneous adipose tissue of obese and lean pigs to elucidate the role of tsRNA in obesity development. A total of 482 tsRNAs were identified in pig adipose tissue, of which 123 were significantly differentially accumulated tsRNAs compared with the control group. The tRF-5c was the main type of these tsRNAs. The largest number of tsRNAs produced was the Gly-carrying tRNA, which produced 81 tsRNAs. Functional enrichment analysis revealed that differential tsRNAs indirectly participated in MAPK, AMPK, insulin resistance, the TNF signaling pathway, adipocytokine signaling pathway, and other signaling pathways by interacting with target genes. These are involved in bioenergetic metabolic regulatory processes, suggesting that tsRNAs may influence these pathways to mediate the regulation of energy metabolism in porcine adipocytes to promote lipid deposition, thus contributing to obesity. Our findings suggest a potential function of tsRNA in regulating obesity development.

The effect of narcotics on ferroptosis-related molecular mechanisms and signalling pathways

Ferroptosis is a novel programmed cell death form characterized by iron-mediated reactive oxygen species-induced lipid peroxidation and subsequent cell damage that is distinct from apoptosis, necroptosis, pyroptosis, and autophagy. Most studies on ferroptosis are based on its function and mechanism, but there have been relatively few studies on the effects of drugs, especially anaesthetics, on ferroptosis. Therefore, we summarized the recent literature on the effects of anaesthetics on ferroptosis to understand the underlying mechanism. In particular, we focused on the targets of various anaesthetics in different mechanisms of ferroptosis and the effects of ferroptosis induction or inhibition by narcotics on various diseases. The aims of this review are to provide a relatively reasonable drug regimen for clinicians, to explore potential ferroptosis protection drugs and targets, to reduce perioperative complications and to improve the postoperative performance of patients, especially those who are critically ill.

A Novel tiRNA-Gly-GCC-1 Promotes Progression of Urothelial Bladder Carcinoma and Directly Targets TLR4

Simple Summary

Patients with urothelial bladder carcinoma (UBC) have a poor prognosis and a high risk of progression. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA, have been identified. In our previous study, we found differential expression profiles of tsRNAs in UBC. As a result, tiRNA-Gly-GCC-1 was significantly upregulated in UBC tissue and might target the predicted target gene toll-like receptor 4 (TLR4) to play a regulatory role in UBC. Here, after lentiviral transfection in UBC cell lines, the results showed down-regulation of tiRNA-Gly-GCC-1 could inhibit cell proliferation, migration and invasion, promote cell apoptosis, and affect the cell cycle. Besides, tiRNA-Gly-GCC-1 was found to inhibit TLR4 expression by directly targeting its 3′UTR. In summary, our study demonstrated that tiRNA-Gly-GCC-1 promotes the progression of UBC and directly targets TLR4. This study provides novel insights for future investigations to explore the mechanisms and therapeutic targets for UBC.

Abstract

Background: Patients with urothelial bladder carcinoma (UBC) have a poor prognosis and a high risk of progression. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA, have been identified. In our previous study, we found tiRNA-Gly-GCC-1 was significantly upregulated in UBC tissue and might target the predicted target gene toll-like receptor 4 (TLR4) to play a regulatory role in UBC. Thus, the aim of this study was to identify the functional roles of tiRNA-Gly-GCC-1 and the relationship between tiRNA-Gly-GCC-1 and TLR4. Methods: After lentiviral transfection in 5637 and T24 cell lines, quantitative reverse transcription-PCR, Cell Counting Kit-8, IncuCyte ZOOM™ live cell imaging, flow cytometry, Transwell assays, scratch assay, and luciferase assay were performed. Results: The results showed down-regulation of tiRNA-Gly-GCC-1 inhibits cell proliferation, migration and invasion, promotes cell apoptosis, and affects the cell cycle. Besides, tiRNA-Gly-GCC-1 was found to inhibit TLR4 expression by directly targeting its 3′UTR. Conclusions: Our study demonstrated that tiRNA-Gly-GCC-1 promotes the progression of UBC and directly targets TLR4. This study provides novel insights for future investigations to explore the mechanisms and therapeutic targets for UBC.

tRNA derived small RNAs—Small players with big roles

In the past 2 decades, small non-coding RNAs derived from tRNA (tsRNAs or tRNA derived fragments; tRFs) have emerged as new powerful players in the field of small RNA mediated regulation of gene expression, translation, and epigenetic control. tRFs have been identified from evolutionarily divergent organisms from Archaea, the higher plants, to humans. Recent studies have confirmed their roles in cancers and other metabolic disorders in humans and experimental models. They have been implicated in biotic and abiotic stress responses in plants as well. In this review, we summarize the current knowledge on tRFs including types of tRFs, their biogenesis, and mechanisms of action. The review also highlights recent studies involving differential expression profiling of tRFs and elucidation of specific functions of individual tRFs from various species. We also discuss potential considerations while designing experiments involving tRFs identification and characterization and list the available bioinformatics tools for this purpose.

tRF-Val-CAC-016 modulates the transduction of CACNA1d-mediated MAPK signaling pathways to suppress the proliferation of gastric carcinoma

Background

As a new kind of non-coding RNAs (ncRNAs), tRNA derivatives play an important role in gastric carcinoma (GC). Nevertheless, the underlying mechanism tRNA derivatives were involved in was rarely illustrated.

Methods

We screened out the tRNA derivative, tRF-Val-CAC-016, based on the tsRNA sequencing and demonstrated the effect tRF-Val-CAC-016 exerted on GC proliferation in vitro and in vivo. We applied Dual-luciferase reporter assay, RIP assay, and bioinformatic analysis to discover the downstream target of tRF-Val-CAC-016. Then CACNA1d was selected, and the oncogenic characteristics were verified. Subsequently, we detected the possible regulation of the canonical MAPK signaling pathway to further explore the downstream mechanism of tRF-Val-CAC-016.

Results

As a result, we found that tRF-Val-CAC-016 was low-expressed in GC, and upregulation of tRF-Val-CAC-016 could significantly suppress the proliferation of GC cell lines. Meanwhile, tRF-Val-CAC-016 regulated the canonical MAPK signaling pathway by targeting CACNA1d.

Conclusions

tRF-Val-CAC-016 modulates the transduction of CACNA1d-mediated MAPK signaling pathways to suppress the proliferation of gastric carcinoma. This study discussed the function and mechanism of tRF-Val-CAC-016 in GC for the first time. The pioneering work has contributed to our present understanding of tRNA derivative, which might provide an alternative mean for the targeted therapy of GC.

Paternal High-Fat Diet Altered Sperm 5'tsRNA-Gly-GCC Is Associated With Enhanced Gluconeogenesis in the Offspring

Background: Paternal lifestyle, stress and environmental exposures play a crucial role in the health of offspring and are associated with non-genetic inheritance of acquired traits, however the underlying mechanisms are unclear. In this study, we aimed to find out how the sperm tsRNA involved in paternal high-fat diet induced abnormal gluconeogenesis of F1 offspring, and explore the underlying molecular mechanism of its regulation.

Method: We generated a paternal high fat diet (42% kcal fat) model to investigate the mechanism by which paternal diet affects offspring metabolism. Four-week-old C57BL/6J male mice were randomly assigned into two groups to receive either a control diet (CD; 10% kcal fat) or a high-fat (HFD; 42% kcal fat) diet for 10 weeks, and mice from each group were then mated with 8-week-old females with control diet in a 1:2 ratio to generate F1. F0 sperms were isolated and small RNAs was sequenced by high-throughput sequencing. Metabolic phenotypes were examined with both F0 and F1.

Results: A significant increase in body weight was observed with HFD-F0 mice at 8 weeks of age as compared to CD mice at the same age. F0 mice showed impaired glucose tolerance (GTT), resistance to insulin tolerance (ITT) and increased pyruvate tolerance (PTT) at 14 weeks. HFD-F1 male mice showed no significant difference in body weight. An increase in PTT was found at 13 weeks of age and no significant changes in GTT and ITT. PEPCK and G6Pase that related to gluconeogenesis increased significantly in the liver of HFD-F1 male mice. Sperm sequencing results showed that 5′tsRNA-Gly-GCC derived from tRNA-Gly-GCC-2 specifically was remarkably upregulated in sperm of HFD F0 mice. Q-PCR further showed that this tsRNA was also increased in the liver of HFD-F1 comparison with CD-F1 mice. In addition, we found that 5′tsRNA-Gly-GCC can regulate Sirt6-FoxO1 pathway and be involved in the gluconeogenesis pathway in liver.

Conclusion: 5′tsRNA-Gly-GCC that increased in HFD mice mature sperms can promote gluconeogenesis in liver by regulating Sirt6-FoxO1 pathway, which might represent a potential paternal epigenetic factor mediating the intergenerational inheritance of diet-induced metabolic alteration.

Differential Expression Profiles and Bioinformatics Analysis of tRNA-Derived Small RNAs in Muscle-Invasive Bladder Cancer in a Chinese Population

Muscle-invasive bladder cancer (MIBC) leads to a large societal burden. Recently, tRNA-derived small RNAs (tsRNAs), a novel type of noncoding RNA (ncRNAs), have been identified. However, the expression patterns and functions of tsRNAs in MIBC have not yet been identified. Here, RNA sequencing, bioinformatics, and quantitative reverse transcription- polymerase chain reaction (qRT-PCR) were used to screen the expression profiles and predict the potential roles of tsRNAs in MIBC. Of 406 tsRNAs differentially expressed in MIBC tissues, 91 tsRNAs were significantly differentially expressed. Then, four candidate tsRNAs, tiRNA-1:34-Val-CAC-2, tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1, were selected. Next, a bioinformatics analysis showed the potential target genes and tsRNA–mRNA network. The most significant and meaningful terms of gene ontology were the positive regulation of the phosphate metabolic process, lamellipodium, and protein-cysteine S-acyltransferase activity in the biological process, cellular component, and molecular function, respectively. In addition, the top four pathways were predicted by the Kyoto Encyclopedia of Genes and Genomes database (KEGG). Finally, qRT-PCR demonstrated a similar expression pattern compared to sequencing data for the candidate tsRNAs. In short, we find differential expression profiles and predict that tiRNA-1:33-Gly-GCC-1, tRF-1:32-Gly-GCC-1, and tRF-+1:T20-Ser-TGA-1 are very likely to engage in the pathophysiological process of MIBC via regulating the target genes in the key pathways.

tsRNA-5001a promotes proliferation of lung adenocarcinoma cells and is associated with postoperative recurrence in lung adenocarcinoma patients

Background

The biological role and clinical significance of transfer RNA-derived small RNAs (tsRNAs) remain largely unclear. The purpose of this study was to investigate the biological function, molecular mechanism, and clinical significance of tsRNA-5001a in lung adenocarcinoma.

Methods

The function of tsRNA-5001a on the growth of tumor cells was accessed by cell function experiments. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to detect the expression of tsRNA-5001a in paired samples of lung adenocarcinoma. Cell localization of tsRNA-5001a was performed by nuclear-cytoplasmic separation assay. Transcriptome sequencing was used to screen the molecules involved in the regulatory network of tsRNA-5001a. Independent samples t-test was used to compare the two groups. Prism software (Prism 7.0) was used to analyze the statistical results. P<0.05 was considered statistically significant.

Results

tsRNA-5001a was significantly upregulated in lung adenocarcinoma tissues. Upregulation of tsRNA-5001a was found to increase the risk of postoperative recurrences in patients with lung adenocarcinoma and was associated with poor prognosis. Function assay showed that overexpression tsRNA-5001a could significantly promote cell proliferation. In contrast, knockdown of tsRNA-5001a significantly inhibited the proliferation of lung adenocarcinoma cells. In addition, nucleoplasmic isolation assay indicated that tsRNA-5001a was located mainly in the cytoplasm. According to the results of RNA sequencing and The Cancer Genome Atlas database (TCGA database) analysis, growth arrest and DNA damage 45G (GADD45G) was screened and may be the target gene of tsRNA-5001a.

Conclusions

tsRNA-5001a promotes the proliferation of lung adenocarcinoma cells and increases the risk of postoperative recurrences in lung adenocarcinoma patients.

Effects of dexmedetomidine on the expression profile of tsRNAs in LPS-induced acute lung injury

BACKGROUND

Acute lung injury (ALI) is characterized by impaired alveolar function and excessive inflammation, which is commonly seen in clinical anesthesia and intensive care units. tRNA-derived small RNA (tsRNA) is a non-coding RNA that can be used as a potential disease diagnostic biomarker. The connection between ALI and tsRNA remains unknown. We aimed to explore the possible regulatory functions and mechanisms of tsRNAs in ALI treated with DEX.

METHODS

Firstly, we established the ALI model by LPS injection and explored the effect of dexmedetomidine (DEX) treatment on lung damage. Then, the lung tissues were obtained from the LPS and LPS + DEX group for small RNA sequencing.

RESULTS

We proved that DEX could ameliorate pulmonary injury, and decreased inflammation, pulmonary edema, and ferroptosis (MDA down-regulation and GPX4 up-regulation) in ALI. Furthermore, in the tsRNA expression profile, the top 10 down-regulated tsRNAs were tsRNA-1018, tsRNA-3045b, tsRNA-5021a, tsRNA-1020, tsRNA-5002b, tsRNA-3045b, tsRNA-1026, tsRNA-5004a, tsRNA-5005b and tsRNA-1009, and the top 10 up-regulated tsRNAs were tsRNA-3025b, tsRNA-3025a, tsRNA-5016b, tsRNA-3042b, tsRNA-3029b, tsRNA-3028b, tsRNA-5006a, tsRNA-3027b, tsRNA-3027a, and tsRNA-5009b. The enrichment analysis of GO terms and KEGG pathways pointed that target genes of DE-tsRNAs were mainly enriched in regulation of transcription-associated GO terms, NF-kappa B signaling pathway, MAPK signaling pathway, and PI3K-Akt signaling pathway. The RT-qPCR results of tsRNA-1020 and tsRNA-1018 were in accordance with small RNA sequencing data.

CONCLUSION

DEX affected the abnormal expression of tsRNAs in ALI. These aberrantly expressed tsRNAs and enriched physiological processes provide a scientific basis for the diagnosis and treatment of ALI.