Analysis of tRNA halves (tsRNAs) in serum from cattle challenged with bovine viral diarrhea virus

Differential expression of tRNA-derived small RNAs in Juvenile and adult sheep skin: implications for developmental and immune regulation

BACKGROUND

tRNA fragments (tRFs) are small non-coding RNAs generated from cleaved tRNA molecules, playing key roles in gene regulation and cellular processes. Produced by ribonucleases like angiogenin and Dicer, tRFs vary in length and function in gene silencing and stress responses. They interact with Argonaute proteins and affect mRNA levels, and are emerging as potential diagnostic and therapeutic targets for diseases such as cancer and neurodegenerative disorders. Given that the skin is the largest organ in mammals, it serves as an ideal model for studying development and various diseases. Therefore, this study investigates tRF expression in sheep skin tissues to understand their regulatory roles during growth and development.

RESULTS

This study analyzed skin tissue from five 1-month-old lambs and five 24-month-old adult Tan sheep using small RNA sequencing and proteomics. Raw sequencing data were filtered and aligned to identify various tsRNAs, while proteomic data were assessed for differential expression. Principal Component Analysis (PCA) revealed distinct separation between juvenile and adult samples based on tsRNA expression patterns, indicating intra-group similarity and inter-group differences. Differentially expressed tsRNAs were identified, with 19 highly expressed tsRNAs at 1 month of age. Proteomic screening identified 932 highly expressed and 835 lowly expressed proteins in the 1-month-old group, with functional enrichment highlighting immunity and inflammation pathways. Predictive analysis of tsRNA target genes intersected with 20 differentially expressed proteins involved in mitochondrial metabolism and stress response.

CONCLUSION

This study reveals that tsRNAs significantly influence developmental and immune processes in sheep, with distinct expression patterns between juveniles and adults. Future research should validate these findings and further elucidate the functional mechanisms of tsRNA regulation.

Redefining the approach to rare diseases: the experience of "Casa dos Raros" in Brazil

Rare diseases include 6,000-8,000 different conditions, over 70% of them having a genetic cause. Most cases have early manifestations (in childhood and adolescence), and just a small fraction (around 5%) has specific therapies available. Nevertheless, appropriate management measures contribute to improve the quality of life of patients and families. They affect up to 3.5-5.9% of the world's population and are recently attracting attention from international agencies such as the United Nations and the World Health Organization. In Brazil, a condition is considered rare when there are no more than 65 people affected in each 100,000 inhabitants and it is estimated that around 12 million people in the country may present one of these conditions, which represents a significant burden to the family and to the health care system. Despite concrete advances observed in the last decades, there are still significant unmet needs for persons living with rare diseases in Brazil. With the main aim of shortening the journey of patients with rare diseases in Brazil, we envisioned a model that involves comprehensive clinical and laboratorial multiprofessional evaluations, with intensive use of telemedicine and genomics. The model includes a strong activity in education, training and research, and has several parallel initiatives (biobank, registry, undiagnosed disease program, information services, extramural diagnostic support), in addition to strategic partnerships, that make the overall project stronger. This report describes the system in place at the pilot unit of Casa dos Raros (that started activities in 2023, in Porto Alegre, Brazil) and the stimulating preliminary results, which indicate a significant reduction in the diagnostic journey. This model, that operates as a charity and does not charge any fees to patients and families, will be replicated in other regions of Brazil, with the opening of a second unit planned to occur in the near future in Sao Paulo.

Transfer RNA-derived fragment production in calves challenged with Mycoplasma bovis or co-infected with bovine viral diarrhea virus and Mycoplasma bovis in several tissues and blood

Understanding the molecular mechanisms underlying immune response can allow informed decisions in drug or vaccine development, and aid in the identification of biomarkers to predict exposure or evaluate treatment efficacy. The objective of this study was to identify differentially expressed transfer RNA-derived fragments (tRFs) in calves challenged with Mycoplasma bovis (M. bovis) or co-infected with M. bovis and bovine viral diarrhea virus (BVDV). Serum, white blood cells (WBC), liver, mesenteric lymph node (MLN), tracheal-bronchial lymph node (TBLN), spleen, and thymus were collected from Control (n = 2), M. bovis (MB; n = 3), and co-infected (Dual; n = 3) animals, and small RNAs extracted for sequencing. An average of 94% of reads were derived from 5` halves and/or 5` tRFs in serum, liver, WBC, TBLN, spleen, MLN, and thymus. The expression of tRFs in lymphatic tissues (MLN, TBLN, Thymus, Spleen) were highly correlated with each other (r ≥ 0.82), but not with serum and WBC. A total of 25 and 65 differentially expressed tRFs were observed in liver and thymus, respectively. There were no differentially expressed tRFs found in other tissues analyzed. Nineteen thymus tRFs were differentially expressed in Dual compared to Control and MB, and the predicted targets of these tRFs were associated with MAPK signaling pathways and ERK1 and ERK2 cascades. The differentially expressed tRFs found in thymus and liver may underlie mechanisms of thymic depletion or liver inflammation previously observed in BVDV. Additional studies should be pursued to investigate differential expression of the predicted tRF targets.

Transfer RNA‑derived small RNAs: A class of potential biomarkers in multiple cancers (Review)

Transfer (t)RNA-derived small RNAs (tsRNAs) are a class of novel non-coding small RNAs that are created via precise cleavage of tRNAs or tRNA precursors by different enzymes. tsRNAs are specific biological molecules that serve essential roles in cell proliferation, apoptosis, transcriptional regulation, post-transcriptional modification and translational regulation. Additionally, tsRNAs participate in the pathogenesis of several diseases, particularly in the development of malignant tumors. At present, the process of discovering and understanding the functions of tsRNAs is still in its early stages. The present review introduces the known biological functions and mechanisms of tsRNAs, and discusses the tsRNAs progression in several types of cancers as well as the possibility of tsRNAs becoming novel tumor biomarkers. Furthermore, tsRNAs may promote and hinder tumor formation according to different mechanisms and act as oncogenic or oncostatic molecules. Therefore, tsRNAs may be future potential tumor biomarkers or therapeutic targets.

A novel tRNA-derived fragment tRF-17-18VBY9M works as a potential diagnostic biomarker for gastric cancer

BACKGROUND

Gastric cancer (GC) is one of the most prevalent malignant tumors worldwide. The low effectiveness of common biomarkers for the detection of early GC makes it essential to seek new biomarkers to improve diagnostic efficacy. tsRNAs (transfer RNA-derived small RNAs) are related to the growth of malignant tumors. In this article, we focused on whether tsRNAs may be employed as biomarkers for GC.

METHODS

tRF-17-18VBY9M was screened in the tsRFun database as a research object. The methodological efficacy of tRF-17-18VBY9M was evaluated using Sanger sequencing, agarose gel electrophoresis assays, and gradient dilution. The χ2 test was applied to assess the interaction between tRF-17-18VBY9M expression and clinicopathologic characteristics. The receiver operating characteristic (ROC) curve was utilized to investigate the clinical efficiency of tRF-17-18VBY9M in GC.

RESULTS

The Chi-square test demonstrated that high-expressed tRF-17-18VBY9M was closely associated with the T stage, tumor node metastasis stage (TNM), lymph node metastasis, and neurological/vascular invasion. ROC curve analysis revealed that the diagnostic value of tRF-17-18VBY9M in GC was superior to carcinoembryonic antigen (CEA), carbohydrate antigen 199 (CA199), and carbohydrate antigen 724 (CA724).

CONCLUSION

tRF-17-18VBY9M is up-regulated in both GC sera and tissues. Differential tRF-17-18VBY9M expression distinguishes GC patients from healthy donors and gastritis patients, which suggests tRF-17-18VBY9M could act as a diagnostic biomarker in GC.

Systematic Analysis of tRNA-Derived Small RNAs Reveals the Effects of Xuefu-Zhuyu Decoction on the Hippocampi of Rats after Traumatic Brain Injury

Background

Traumatic brain injury (TBI) is one of the most common neurosurgical diseases and refers to brain function impairment or brain pathological changes induced by external causes. A traditional Chinese medicine, Xuefu-Zhuyu Decoction (XFZYD), has been indicated to harbor therapeutic properties against TBI. Transfer RNA (tRNA)-derived small RNAs, that is, tsRNAs (a group of small RNAs derived from tRNAs), are multifunctional regulatory noncoding RNAs generated under pressure and implicated in the progression of TBI.

Methods

A TBI model was successfully constructed using rats. We further performed sequencing and omics analyses to identify novel tsRNAs as drug targets for XFZYD therapy against TBI in the rat hippocampus. qPCR assays were used to further verify the experimental results. Gene Ontology (GO) was used to analyze the signaling pathways of downstream target genes of tsRNAs in the XFZYD-regulated TBI model. qPCR was used to detect the influence of overexpressed tsRNA mimics/inhibitors on their target genes in PC12 cells.

Results

Our RNA-Seq data illustrate that 11 tsRNAs were mediated by XFZYD. The experimental data revealed AS-tDR-002004 and AS-tDR-002583 as potential targets for XFZYD therapy and showed that they influenced TBI via the cadherin signaling pathway, cocaine addiction, circadian entrainment, and the nicotine pharmacodynamics pathway. We also confirmed that Pi4kb, Mlh3, Pcdh9, and Ppp1cb were target genes of 2 XFZYD-regulated tsRNAs in the hippocampus of a rat model and PC12 cells. Furthermore, biological function analysis revealed the potential therapeutic effects of tsRNAs, and the results showed that Mapk1 and Gnai1 were related genes for XFZYD therapy against TBI.

Conclusion

Our work successfully illuminates the efficiency of XFZYD in the treatment of TBI. The experimental data revealed AS-tDR-002004 and AS-tDR-002583 as potential targets for XFZYD therapy and showed that they influenced TBI via the cadherin signaling pathway, cocaine addiction, circadian entrainment, and the nicotine pharmacodynamics pathway in a TBI rat model.

tiRNAs: Insights into Their Biogenesis, Functions, and Future Applications in Livestock Research

Transfer RNA (tRNA)-derived small RNAs (tsRNAs) belong to a group of transfer ribonucleic acid (tRNA)-derived fragments that have recently gained interest as molecules with specific biological functions. Their involvement in the regulation of physiological processes and pathological phenotypes suggests molecular roles similar to those of miRNAs. tsRNA biogenesis under specific physiological conditions will offer new perspectives in understanding diseases, and may provide new sources for biological marker design to determine and monitor the health status of farm animals. In this review, we focus on the latest discoveries about tsRNAs and give special attention to molecules initially thought to be mainly associated with tRNA-derived stress-induced RNAs (tiRNAs). We present an outline of their biological functions, offer a collection of useful databases, and discuss future research perspectives and applications in livestock basic and applied research.

Transfer RNA-Derived Small RNAs: Novel Regulators and Biomarkers of Cancers

Transfer RNA-derived small RNAs (tsRNAs) are conventional non-coding RNAs (ncRNAs) with a length between18 and 40 nucleotides (nt) playing a crucial role in treating various human diseases including tumours. Nowadays, with the use of high-throughput sequencing technologies, it has been proven that certain tsRNAs are dysregulated in multiple tumour tissues as well as in the blood serum of cancer patients. Meanwhile, data retrieved from the literature show that tsRNAs are correlated with the regulation of the hallmarks of cancer, modification of tumour microenvironment, and modulation of drug resistance. On the other side, the emerging role of tsRNAs as biomarkers for cancer diagnosis and prognosis is promising. In this review, we focus on the specific characteristics and biological functions of tsRNAs with a focus on their impact on various tumours and discuss the possibility of tsRNAs as novel potential biomarkers for cancer diagnosis and prognosis.

Recent Advances on the Bovine Viral Diarrhea Virus Molecular Pathogenesis, Immune Response, and Vaccines Development

The bovine viral diarrhea virus (BVDV) consists of two species and various subspecies of closely related viruses of varying antigenicity, cytopathology, and virulence-induced pathogenesis. Despite the great ongoing efforts to control and prevent BVDV outbreaks and the emergence of new variants, outbreaks still reported throughout the world. In this review, we are focusing on the molecular biology of BVDV, its molecular pathogenesis, and the immune response of the host against the viral infection. Special attention was paid to discuss some immune evasion strategies adopted by the BVDV to hijack the host immune system to ensure the success of virus replication. Vaccination is one of the main strategies for prophylaxis and contributes to the control and eradication of many viral diseases including BVDV. We discussed the recent advances of various types of currently available classical and modern BVDV vaccines. However, with the emergence of new strains and variants of the virus, it is urgent to find some other novel targets for BVDV vaccines that may overcome the drawbacks of some of the currently used vaccines. Effective vaccination strategy mainly based on the preparation of vaccines from the homologous circulating strains. The BVDV-E2 protein plays important role in viral infection and pathogenesis. We mapped some important potential neutralizing epitopes among some BVDV genomes especially the E2 protein. These novel epitopes could be promising targets against the currently circulating strains of BVDV. More research is needed to further explore the actual roles of these epitopes as novel targets for the development of novel vaccines against BVDV. These potential vaccines may contribute to the global eradication campaign of the BVDV.

Extracellular tRNAs and tRNA-derived fragments

Fragmentation of tRNAs generates a family of small RNAs collectively known as tRNA-derived fragments. These fragments vary in sequence and size but have been shown to regulate many processes involved in cell homoeostasis and adaptations to stress. Additionally, the field of extracellular RNAs (exRNAs) is rapidly growing because exRNAs are a promising source of biomarkers in liquid biopsies, and because exRNAs seem to play key roles in intercellular and interspecies communication. Herein, we review recent descriptions of tRNA-derived fragments in the extracellular space in all domains of life, both in biofluids and in cell culture. The purpose of this review is to find consensus on which tRNA-derived fragments are more prominent in each extracellular fraction (including extracellular vesicles, lipoproteins and ribonucleoprotein complexes). We highlight what is becoming clear and what is still controversial in this field, in order to stimulate future hypothesis-driven studies which could clarify the role of full-length tRNAs and tRNA-derived fragments in the extracellular space.

Emerging Roles of tRNAs in RNA Virus Infections

Viruses rely on the host cell translation machinery for efficient synthesis of their own proteins. Emerging evidence highlights different roles for host transfer RNAs (tRNAs) in the process of virus replication. For instance, different RNA viruses manipulate host tRNA pools to favor viral protein translation. Interestingly, specific host tRNAs are used as reverse transcription primers and are packaged into retroviral virions. Recent data also demonstrate the formation of tRNA-derived fragments (tRFs) upon infection to facilitate viral replication. Here, we comprehensively discuss how RNA viruses exploit distinct aspects of the host tRNA biology for their benefit. In light of the recent advances in the field, we propose that host tRNA-related pathways and mechanisms represent promising cellular targets for the development of novel antiviral strategies.

Profiling of tRNA Halves and YRNA Fragments in Serum and Tissue From Oral Squamous Cell Carcinoma Patients Identify Key Role of 5' tRNA-Val-CAC-2-1 Half

Oral squamous cell carcinoma (OSCC) is the most common type of head and neck cancer and, as indicated by The Oral Cancer Foundation, kills at an alarming rate of roughly one person per hour. With this study, we aimed at better understanding disease mechanisms and identifying minimally invasive disease biomarkers by profiling novel small non-coding RNAs (specifically, tRNA halves and YRNA fragments) in both serum and tumor tissue from humans. Small RNA-Sequencing identified multiple 5' tRNA halves and 5' YRNA fragments that displayed significant differential expression levels in circulation and/or tumor tissue, as compared to control counterparts. In addition, by implementing a modification of weighted gene coexpression network analysis, we identified an upregulated genetic module comprised of 5' tRNA halves and miRNAs (miRNAs were described in previous study using the same samples) with significant association with the cancer trait. By consequently implementing miRNA-overtargeting network analysis, the biological function of the module (and by "guilt by association," the function of the 5' tRNA-Val-CAC-2-1 half) was found to involve the transcriptional targeting of specific genes involved in the negative regulation of the G1/S transition of the mitotic cell cycle. These findings suggest that 5' tRNA-Val-CAC-2-1 half (reduced in serum of OSCC patients and elevated in the tumor tissue) could potentially serve as an OSCC circulating biomarker and/or target for novel anticancer therapies. To our knowledge, this is the first time that the specific molecular function of a 5'-tRNA half is specifically pinpointed in OSCC.