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Chen Y, Shao Z, Wu S. Research progress on the tsRNA biogenesis, function, and application in lung cancer. Noncoding RNA Res 2025; 10:63-69. [PMID: 39309197 PMCID: PMC11414277 DOI: 10.1016/j.ncrna.2024.09.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Revised: 08/18/2024] [Accepted: 09/01/2024] [Indexed: 09/25/2024] Open
Abstract
In recent years, there has been a mounting occurrence of lung cancer, which stands as one of the most prevalent malignancies globally. This rise in incidence poses a significant hazard to human health, making lung cancer a matter of grave concern. It has been shown that tRNA-derived small non-coding RNA (tsRNA) is involved in the development of tumors, especially lung cancer, through mechanisms such as regulating mRNA stability, influencing protein translation, and acting as epigenetic regulators. Recent studies have shown that tsRNA is abnormally expressed in the plasma and tissues of lung cancer patients, and its expression level is closely related to the malignancy degree and postoperative recurrence of lung cancer. Therefore, for lung cancer patients, tsRNA represents a promising non-invasive biomarker, exhibiting significant potential for facilitating early diagnosis and prognostic evaluation, and for achieving precision treatment of lung cancer by regulating its expression. This article focuses on the biogenesis of tsRNA and its ability to promote lung cancer cell proliferation and invasion. In addition, the specific clinical significance of tsRNA in lung cancer was discussed. Finally, we discuss the need for further improvement of small RNA sequencing technology, and the future research directions and strategies of tsRNA in lung cancer and tumor diseases were summarized.
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Affiliation(s)
- Yu Chen
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Zhuowei Shao
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
- Health Science Center, Ningbo University, Ningbo, Zhejiang, China
| | - Shibo Wu
- Department of Respiratory Medicine, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, China
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2
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He M, Yin S, Huang X, Li Y, Li B, Gong T, Liu Q. Insights into the regulatory role of bacterial sncRNA and its extracellular delivery via OMVs. Appl Microbiol Biotechnol 2024; 108:29. [PMID: 38159117 DOI: 10.1007/s00253-023-12855-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 10/11/2023] [Accepted: 10/20/2023] [Indexed: 01/03/2024]
Abstract
Small noncoding RNAs (sncRNAs) play important regulatory roles in bacterial physiological processes and host-pathogen interactions. Meanwhile, bacterial outer membrane vesicles (OMVs), as naturally secreted outer membrane structures, play a vital role in the interaction between bacteria and their living environment, including the host environment. However, most current studies focus on the biological functions of sncRNAs in bacteria or hosts, while neglecting the roles and regulatory mechanisms of the OMVs that encapsulate these sncRNAs. Therefore, this review aims to summarize the intracellular regulatory roles of bacterial sncRNAs in promoting pathogen survival by regulating virulence, modulating bacterial drug resistance, and regulating iron metabolism, and their extracellular regulatory function for influencing host immunity through host-pathogen interactions. Additionally, we introduce the key role played by OMVs, which serve as important cargoes in bacterial sncRNA-host interactions. We propose emerging pathways of sncRNA action to further discuss the mode of host-pathogen interactions, highlighting that the inhibition of sncRNA delivery by OMVs may prevent the occurrence of infection to some extent. Hence, this review lays the foundation for future prophylactic treatments against bacterial infections and strategies for addressing bacterial drug resistance. KEY POINTS: •sncRNAs have intracellular and extracellular regulatory functions in bacterial physiological processes and host-pathogen interactions. •OMVs are potential mediators between bacterial sncRNAs and host cells. •OMVs encapsulating sncRNAs have more potential biological functions.
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Affiliation(s)
- Mengdan He
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Shuanshuan Yin
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Xinlei Huang
- Gannan Medical University, Ganzhou, 341000, Jiangxi, China
| | - Yi Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China
| | - Biaoxian Li
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China
| | - Tian Gong
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
| | - Qiong Liu
- Center for Molecular Diagnosis and Precision Medicine, The Department of Clinical Laboratory, Jiangxi Provincial Center for Advanced Diagnostic Technology and Precision Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, 330006, China.
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, 330006, China.
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Chang X, Du M, Wei J, Zhang Y, Feng X, Deng B, Liu P, Wang Y. Serum tsncRNAs reveals novel potential therapeutic targets of Salvianolic Acid B on atherosclerosis. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2024; 134:155994. [PMID: 39243751 DOI: 10.1016/j.phymed.2024.155994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 07/17/2024] [Accepted: 08/26/2024] [Indexed: 09/09/2024]
Abstract
BACKGROUND Salvianolic Acid B (SalB) has been proven to delay the progression of atherosclerosis. The therapeutic mechanisms of this compound are unclear. A novel class of short non-coding RNAs, pre-transfer RNA and mature transfer RNA (tsncRNAs) may regulate gene expression. TsncRNAs-sequencing revealed novel therapeutic targets for SalB. This is the first study focusing on tsncRNAs to treat atherosclerosis using SalB. PURPOSE To explore the potential mechanism of SalB treating atherosclerosis through tsncRNAs. METHODS Five groups of mice were created at random: control group (CON), atherosclerosis model group (MOD), SalB with high dose-treated group (SABH), SalB with low dose-treated group (SABL), and Simvastatin-treated group (ST). Aortic sinus plaque, body weight and inflammatory cytokines were evaluated. The Illumina NextSeq equipment was used to do expression profiling of tsncRNAs from serum. The targets of tsncRNAs were then predicted using tRNAscan and TargetScan. The KEGG pathway and GO analysis were utilized to forecast the bioinformatics analysis. Potential tsncRNAs and associated mRNAs were validated using quantitative real-time PCR. RESULTS tRF-Glu-CTC-014 and tRF-Gly-GCC-074 were markedly increased by SalB with high dose treatment and validated with quantitative real-time PCR. Two mRNAs SRF and Arrb related to tRF-Glu-CTC-014 changed consistently. GO analysis revealed that the altered target genes of the selected tsncRNAs were most enriched in protein binding and cellular process. Moreover, KEGG pathway analysis demonstrated that altered target genes of tsncRNAs were most enriched in MAPK signaling pathway. CONCLUSION SalB can promote the expression of tRF-Glu-CTC-014 to treat atherosclerosis.
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Affiliation(s)
- Xindi Chang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Min Du
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Jing Wei
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Yifan Zhang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Xiaoteng Feng
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Bing Deng
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China
| | - Ping Liu
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
| | - Yiru Wang
- Longhua Hospital, Shanghai University of Traditional Chinese Medicine, 725 South Wan-Ping Road, Shanghai, China.
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4
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Fan Y, Pavani KC, Broeckx BJG, Smits K, Van Soom A, Peelman L. Circular RNAs from bovine blastocysts can interact with miRNAs/tsRNAs from embryonic extracellular vesicles and regulate hatching. Int J Biol Macromol 2024; 277:134018. [PMID: 39032885 DOI: 10.1016/j.ijbiomac.2024.134018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 07/05/2024] [Accepted: 07/17/2024] [Indexed: 07/23/2024]
Abstract
Circular RNAs (circRNAs) are endogenous biological macromolecules that regulate various biological processes including embryo development. However, little is known about which circRNAs are present in bovine preimplantation embryos and their respective roles. Here, we characterized the expression profile of circRNAs in bovine blastocysts for the first time. We detected 25,700 circRNAs in total, with 12,630 circRNAs uniquely expressed in blastocysts compared to degenerated embryos. CircRNA alternative splicing (AS) events were also found more frequently in blastocysts than in degenerated embryos (299 vs 258). Additionally, 410 circRNAs, among which 11 circRNAs with a high potential to encode polypeptides, were found differentially expressed between blastocysts and degenerated embryos. We further predicted and constructed a circRNA-miRNA-mRNA network, wherein differentially expressed circRNAs were shown to bind to bovine preimplantation embryo development-related miRNAs. Employing bioinformatic algorithms we found that differentially expressed circRNAs are associated with differentially expressed miRNAs and transfer RNA-derived small RNAs (tsRNAs) enclosed in embryonic extracellular vesicles (EVs). Furthermore, functional analysis revealed that knockdown of the evolutionarily conserved circAGO2 can inhibit blastocyst hatching. Overall, our study provides the first landscape of circRNAs in bovine preimplantation embryos and highlights the novel role of circRNAs as tsRNA binding partners influencing small RNA sorting and loading into EVs, with circAGO2 playing a regulatory role in bovine blastocyst hatching.
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Affiliation(s)
- Yuan Fan
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Krishna Chaitanya Pavani
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium; Department for Reproductive Medicine, Ghent University Hospital, Corneel Heymanslaan 10, 9000 Ghent, Belgium
| | - Bart J G Broeckx
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium
| | - Katrien Smits
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Ann Van Soom
- Department of Internal Medicine, Reproduction and Population Medicine, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, 9820 Merelbeke, Belgium
| | - Luc Peelman
- Department of Veterinary and Biosciences, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, 9820 Merelbeke, Belgium.
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5
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Liang Y, Ji D, Ying X, Ma R, Ji W. tsRNA modifications: An emerging layer of biological regulation in disease. J Adv Res 2024:S2090-1232(24)00401-6. [PMID: 39260796 DOI: 10.1016/j.jare.2024.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 08/02/2024] [Accepted: 09/06/2024] [Indexed: 09/13/2024] Open
Abstract
BACKGROUND Transfer RNA (tRNA)-derived small RNA (tsRNA) represents an important and increasingly valued type of small non-coding RNA (sncRNA). The investigation of tRNA and tsRNA modification crosswalks has not only provided novel insights into the information and functions of tsRNA, but has also expanded the diversity and complexity of the tsRNA biological regulation network. AIM OF REVIEW Comparing with other sncRNAs, tsRNA biogenesis show obvious correlation with RNA modifications from mature tRNA and harbor various tRNA modifications. In this review, we aim to present the current aspect of tsRNA modifications and that modified tsRNA shape different regulatory mechanisms in physiological and pathological processes. KEY SCIENTIFIC CONCEPTS OF REVIEW Strategies for studying tsRNA mechanisms include its specific generation and functional effects induced by sequence/RNA modification/secondary structure. tsRNAs could harbor more than one tRNA modifications such as 5-methylcytosine (m5C), N1-methyladenosine (m1A), pseudouridine (Ψ) and N7-methylguanosine (m7G). This review consolidates the current knowledge of tRNA modification regulating tsRNA biogenesis, outlines the functional roles of various modified tsRNA and highlights their specific contributions in various disease pathogenesis. Therefore, the improvement of tsRNA modification detection technology and the introduction of experimental methods of tsRNA modification are conducive to further broadening the understanding of tsRNA function at the level of RNA modification.
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Affiliation(s)
- Yaomin Liang
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China
| | - Ding Ji
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510220, PR China
| | - Xiaoling Ying
- Department of Urology, The Second Affiliated Hospital of Guangzhou Medical University, Guangzhou 510220, PR China
| | - Renqiang Ma
- Department of Otolaryngology-Head & Neck Surgery, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou 510220, PR China.
| | - Weidong Ji
- Center for Translational Medicine, The First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510080, PR China.
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Liu S, Holmes AD, Katzman S, Sharma U. A sperm-enriched 5'fragment of tRNA-Valine regulates preimplantation embryonic transcriptome and development. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.08.607197. [PMID: 39211093 PMCID: PMC11361008 DOI: 10.1101/2024.08.08.607197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Sperm small RNAs have been implicated in intergenerational epigenetic inheritance of paternal environmental effects; however, their biogenesis and functions remain poorly understood. We previously identified a 5' fragment of tRNA-Valine-CAC-2 (tRFValCAC) as one of the most abundant small RNA in mature sperm. tRFValCAC is specifically enriched in sperm during post-testicular maturation in the epididymis, and we found that it is delivered to sperm from epididymis epithelial cells via extracellular vesicles. Here, we investigated the mechanistic basis of tRFValCAC delivery to sperm and its functions in the early embryo. We show that tRFValCAC interacts with an RNA binding protein, heterogeneous nuclear ribonucleoprotein A/B (hnRNPAB), in the epididymis, and this interaction regulates the sorting and packing of tRFValCAC into extracellular vesicles. In the embryo, we found that tRFValCAC regulates early embryonic mRNA processing and splicing. Inhibition of tRFValCAC in preimplantation embryos altered the transcript abundance of genes involved in RNA splicing and mRNA processing. Importantly, tRFValCAC-inhibited embryos showed altered mRNA splicing, including alternative splicing of various splicing factors and genes important for proper preimplantation embryonic development. Finally, we find that inhibition of tRFValCAC in zygotes delayed preimplantation embryonic development. Together, our results reveal a novel function of a sperm-enriched tRF in regulating alternating splicing and preimplantation embryonic development and shed light on the mechanism of sperm small RNA-mediated epigenetic inheritance.
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Affiliation(s)
- Simeiyun Liu
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Andrew D. Holmes
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
| | - Sol Katzman
- Genomics Institute, University of California, Santa Cruz, California, 95064
| | - Upasna Sharma
- Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, 95064
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7
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Li X, Mills WT, Jin DS, Meffert MK. Genome-wide and cell-type-selective profiling of in vivo small noncoding RNA:target RNA interactions by chimeric RNA sequencing. CELL REPORTS METHODS 2024; 4:100836. [PMID: 39127045 PMCID: PMC11384083 DOI: 10.1016/j.crmeth.2024.100836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/30/2024] [Accepted: 07/18/2024] [Indexed: 08/12/2024]
Abstract
Small noncoding RNAs (sncRNAs) regulate biological processes by impacting post-transcriptional gene expression through repressing the translation and levels of targeted transcripts. Despite the clear biological importance of sncRNAs, approaches to unambiguously define genome-wide sncRNA:target RNA interactions remain challenging and not widely adopted. We present CIMERA-seq, a robust strategy incorporating covalent ligation of sncRNAs to their target RNAs within the RNA-induced silencing complex (RISC) and direct detection of in vivo interactions by sequencing of the resulting chimeric RNAs. Modifications are incorporated to increase the capacity for processing low-abundance samples and permit cell-type-selective profiling of sncRNA:target RNA interactions, as demonstrated in mouse brain cortex. CIMERA-seq represents a cohesive and optimized method for unambiguously characterizing the in vivo network of sncRNA:target RNA interactions in numerous biological contexts and even subcellular fractions. Genome-wide and cell-type-selective CIMERA-seq enhances researchers' ability to study gene regulation by sncRNAs in diverse model systems and tissue types.
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Affiliation(s)
- Xinbei Li
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - William T Mills
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel S Jin
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Mollie K Meffert
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA.
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Hashimoto S, Hasan MDN, Arif M, Nozaki N, Husna AA, Furusawa Y, Sogawa T, Takahashi K, Kuramoto T, Noguchi A, Takahashi M, Yamato O, Rahman MM, Miura N. Aberrantly Expressed tRNA-Val Fragments Can Distinguish Canine Hepatocellular Carcinoma from Canine Hepatocellular Adenoma. Genes (Basel) 2024; 15:1024. [PMID: 39202384 PMCID: PMC11353709 DOI: 10.3390/genes15081024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2024] [Revised: 08/01/2024] [Accepted: 08/02/2024] [Indexed: 09/03/2024] Open
Abstract
Hepatocellular adenoma (HCA) and hepatocellular carcinoma (HCC) can be difficult to differentiate but must be diagnosed correctly as treatment and prognosis for these tumors differ markedly. Relevant diagnostic biomarkers are thus needed, and those identified in dogs may have utility in human medicine because of the similarities between human and canine HCA and HCC. A tRNA-derived fragment (tRF), tRNA-Val, is a promising potential biomarker for canine mammary gland tumors but has not previously been investigated in hepatic tumors. Accordingly, we aimed to elucidate the potential utility of tRNA-Val as a biomarker for canine HCA and HCC using clinical samples (tumor tissue and plasma extracellular vesicles [EVs]) and tumor cell lines with qRT-PCR assays. We also investigated relevant functions and signaling pathways with bioinformatic analyses (Gene Ontology and Kyoto Encyclopedia of Genes and Genomes). tRNA-Val was markedly downregulated in HCC tumor tissue versus HCA tumor tissue and normal liver tissue, and a similar trend was shown in plasma EVs and HCC cell lines versus healthy controls. Based on areas under the receiver operating characteristic curves (AUCs), tRNA-Val significantly distinguished HCC (AUC = 1.00, p = 0.001) from healthy controls in plasma EVs and HCC from HCA (AUC = 0.950, p = 0.01). Bioinformatics analysis revealed that tRNA-Val may be primarily involved in DNA repair, mRNA processing, and splicing and may be linked to the N-glycan and ubiquitin-mediated proteasome pathways. This is the first report on the expression of tRNA-Val in canine HCC and HCA and its possible functions and signaling pathways. We suggest that tRNA-Val could be a promising novel biomarker to distinguish canine HCC from HCA. This study provides evidence for a greater understanding of the role played by tRNA-Val in the development of canine HCC.
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MESH Headings
- Animals
- Dogs
- Carcinoma, Hepatocellular/genetics
- Carcinoma, Hepatocellular/veterinary
- Carcinoma, Hepatocellular/pathology
- Carcinoma, Hepatocellular/metabolism
- Liver Neoplasms/genetics
- Liver Neoplasms/veterinary
- Liver Neoplasms/pathology
- Biomarkers, Tumor/genetics
- Dog Diseases/genetics
- Dog Diseases/diagnosis
- Adenoma, Liver Cell/genetics
- Adenoma, Liver Cell/veterinary
- Adenoma, Liver Cell/pathology
- Adenoma, Liver Cell/metabolism
- Adenoma, Liver Cell/diagnosis
- Gene Expression Regulation, Neoplastic
- Diagnosis, Differential
- Cell Line, Tumor
- Female
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Affiliation(s)
- Saki Hashimoto
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - MD Nazmul Hasan
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Mohammad Arif
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Nobuhiro Nozaki
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Al Asmaul Husna
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Yu Furusawa
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Takeshi Sogawa
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Kaori Takahashi
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Tomohide Kuramoto
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Aki Noguchi
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Masashi Takahashi
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Osamu Yamato
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Md Mahfuzur Rahman
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
| | - Naoki Miura
- Joint Graduate School of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
- Joint Faculty of Veterinary Medicine, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0065, Japan
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Hao Y, Li B, Yin F, Liu W. tRNA-derived small RNA (tsr007330) regulates myocardial fibrosis after myocardial infarction through NAT10-mediated ac4C acetylation of EGR3 mRNA. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167267. [PMID: 38810917 DOI: 10.1016/j.bbadis.2024.167267] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 04/27/2024] [Accepted: 05/21/2024] [Indexed: 05/31/2024]
Abstract
Small non-coding ribonucleic acids (sncRNAs) play an important role in cell regulation and are closely related to the pathogenesis of heart diseases. However, the role and molecular mechanism of transfer RNA-derived small RNAs (tsRNAs) in myocardial fibrosis after myocardial infarction (MI) remain unknown. In this study, we identified and validated sncRNAs (mainly miRNA and tsRNA) associated with myocardial fibrosis after MI through PANDORA sequencing of rat myocardial tissue. As a key enzyme of N4-acetylcytidine (ac4C) acetylation modification, N-acetyltransferase 10 (NAT10) plays an important role in regulating messenger RNA (mRNA) stability and translation efficiency. We found that NAT10 is highly expressed in infarcted myocardial tissue, and the results of acetylated RNA immunoprecipitation sequencing (acRIP-seq) analysis suggest that early growth response 3 (EGR3) may be an important molecule in the pathogenesis of NAT10-mediated myocardial fibrosis. Both in vivo and in vitro experiments have shown that inhibition of NAT10 can reduce the expression of EGR3 and alleviate myocardial fibrosis after MI. tsRNA can participate in gene regulation by inhibiting target genes. The expression of tsr007330 was decreased in myocardial infarction tissue. We found that overexpression of tsr007330 in rat myocardial tissue could antagonize NAT10, improve myocardial function in MI and alleviate myocardial fibrosis. In conclusion, tsRNAs (rno-tsr007330) may regulate the occurrence of myocardial fibrosis by regulating NAT10-mediated EGR3 mRNA acetylation. This study provides new insights into the improvement of myocardial fibrosis after MI by targeting tsRNA therapy.
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Affiliation(s)
- Yan Hao
- Harbin Medical University, Harbin, Heilongjiang 150001, China; Department of Cardiology, the fourth affiliated hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Bohan Li
- Harbin Medical University, Harbin, Heilongjiang 150001, China
| | - Feiya Yin
- University of Sydney, NSW 2006, Australia
| | - Wei Liu
- Harbin Medical University, Harbin, Heilongjiang 150001, China; Department of Geriatric Cardiovascular Division, Guangdong Provincial Geriatrics Institute, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China.
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10
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Peng J, Zhang Y, Zhou G, Shao L, Li L, Zhang Z. Circulating serum exosomes i-tRF-AspGTC and tRF-1-SerCGA as diagnostic indicators for non-small cell lung cancer. Clin Transl Oncol 2024; 26:1988-1997. [PMID: 38502292 DOI: 10.1007/s12094-024-03423-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
BACKGROUND tRF-RNA-a representative of non-coding RNA (ncRNA)-is a precursor or fragment of mature tRNA and plays a crucial regulatory role in the occurrence and development of cancer. There is currently little research on tRF-RNA as a diagnostic marker in cancer, especially for NSCLC from serum exosomes. METHOD Serum exosomes were successfully extracted from serum; their physical morphology was captured by transmission electron microscopy (TEM); appropriate particle size detection was performed using qNano; surface labeling was verified through western blotting. Serum exosomes i-tRF-AspGTC and tRF-1-SerCGA were selected through gene microarray, and qPCR was used to validate their significance in 242 patients and 201 healthy individuals. The area under the curve (AUC) was used to evaluate the diagnostic indicators of non-small cell lung cancer (NSCLC). RESULT Compared with 201 healthy individuals, i-tRF-AspGTC and tRF-1-SerCGA were significantly downregulated in 242 NSCLC patients and 95 early-stage patients. For tRF-AspGTC and tRF-1-SerCGA, the predictive diagnostic efficiency rates of AUC were 0.690 and 0.680, respectively, whereas the early diagnostic efficiency rates were 0.656 and 0.688, respectively. The result of combined diagnosis with CEA and CYFRA21-1 was 0.928, and the early diagnostic efficiency was 0.843, which is a very high biological predictive factor for NSCLC. CONCLUSION The expression of serum exosomes i-tRF-AspGTC and tRF-1-SerCGA was significantly downregulated in NSCLC patients. These exosomes could be used as predictive indicators for diagnosis or early diagnosis of NSCLC.
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Affiliation(s)
- Jiefei Peng
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
- Shandong Provincial Key Medical and Health Laboratory of Anti-drug Resistant Drug Research, Taian City Central Hospital, Taian, 271000, China
| | - Yue Zhang
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Guangfei Zhou
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Luolin Shao
- Department of Dermatology, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China
| | - Lin Li
- Pharmacy Intravenous Admixture Services, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China.
| | - Zhijun Zhang
- Department of Clinical Laboratory, The Affiliated Taian City Central Hospital of Qingdao University, Taian, 271000, China.
- Shandong Provincial Key Medical and Health Laboratory of Anti-drug Resistant Drug Research, Taian City Central Hospital, Taian, 271000, China.
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11
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Yuan W, Zhang R, Lyu H, Xiao S, Guo D, Zhang Q, Ali DW, Michalak M, Chen XZ, Zhou C, Tang J. Dysregulation of tRNA methylation in cancer: Mechanisms and targeting therapeutic strategies. Cell Death Discov 2024; 10:327. [PMID: 39019857 PMCID: PMC11254935 DOI: 10.1038/s41420-024-02097-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/04/2024] [Accepted: 07/09/2024] [Indexed: 07/19/2024] Open
Abstract
tRNA is the RNA type that undergoes the most modifications among known RNA, and in recent years, tRNA methylation has emerged as a crucial process in regulating gene translation. Dysregulation of tRNA abundance occurs in cancer cells, along with increased expression and activity of tRNA methyltransferases to raise the level of tRNA modification and stability. This leads to hijacking of translation and synthesis of multiple proteins associated with tumor proliferation, metastasis, invasion, autophagy, chemotherapy resistance, and metabolic reprogramming. In this review, we provide an overview of current research on tRNA methylation in cancer to clarify its involvement in human malignancies and establish a theoretical framework for future therapeutic interventions targeting tRNA methylation processes.
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Affiliation(s)
- Wenbin Yuan
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Rui Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Hao Lyu
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Shuai Xiao
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Dong Guo
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Qi Zhang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China
| | - Declan William Ali
- Department of Biological Sciences, University of Alberta, Edmonton, AB, Canada
| | - Marek Michalak
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada
| | - Xing-Zhen Chen
- Membrane Protein Disease Research Group, Department of Physiology, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Cefan Zhou
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
| | - Jingfeng Tang
- National "111" Center for Cellular Regulation and Molecular Pharmaceutics, Key Laboratory of Fermentation Engineering (Ministry of Education), Cooperative Innovation Center of Industrial Fermentation (Ministry of Education & Hubei Province), Hubei Key Laboratory of Industrial Microbiology, School of Life and Health Sciences, Hubei University of Technology, Wuhan, China.
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12
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Wang F, Zhou C, Zhu Y, Keshavarzi M. The microRNA Let-7 and its exosomal form: Epigenetic regulators of gynecological cancers. Cell Biol Toxicol 2024; 40:42. [PMID: 38836981 PMCID: PMC11153289 DOI: 10.1007/s10565-024-09884-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Accepted: 05/15/2024] [Indexed: 06/06/2024]
Abstract
Many types of gynecological cancer (GC) are often silent until they reach an advanced stage, and are therefore often diagnosed too late for effective treatment. Hence, there is a real need for more efficient diagnosis and treatment for patients with GC. During recent years, researchers have increasingly studied the impact of microRNAs cancer development, leading to a number of applications in detection and treatment. MicroRNAs are a particular group of tiny RNA molecules that regulate regular gene expression by affecting the translation process. The downregulation of numerous miRNAs has been observed in human malignancies. Let-7 is an example of a miRNA that controls cellular processes as well as signaling cascades to affect post-transcriptional gene expression. Recent research supports the hypothesis that enhancing let-7 expression in those cancers where it is downregulated may be a potential treatment option. Exosomes are tiny vesicles that move through body fluids and can include components like miRNAs (including let-7) that are important for communication between cells. Studies proved that exosomes are able to enhance tumor growth, angiogenesis, chemoresistance, metastasis, and immune evasion, thus suggesting their importance in GC management.
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Affiliation(s)
- Fei Wang
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Chundi Zhou
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China
| | - Yanping Zhu
- Haiyan People's Hospital, Zhejiang Province, Jiaxing, 314300, Zhejiang, China.
| | - Maryam Keshavarzi
- School of Medicine, Tehran University of Medical Sciences, Tehran, Tehran, Iran.
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13
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Manning AC, Bashir MM, Jimenez AR, Upton HE, Collins K, Lowe TM, Tucker JM. Gammaherpesvirus infection triggers the formation of tRNA fragments from premature tRNAs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.01.592122. [PMID: 38746336 PMCID: PMC11092647 DOI: 10.1101/2024.05.01.592122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Transfer RNAs (tRNAs) are fundamental for both cellular and viral gene expression during viral infection. In addition, mounting evidence supports biological function for tRNA cleavage products, including in the control of gene expression during conditions of stress and infection. We previously reported that infection with the model murine gammaherpesvirus, MHV68, leads to enhanced tRNA transcription. However, whether this has any influence on tRNA transcript processing, viral replication, or the host response is not known. Here, we combined two new approaches, sequencing library preparation by Ordered Two Template Relay (OTTR) and tRNA bioinformatic analysis by tRAX, to quantitatively profile full-length tRNAs and tRNA fragment (tRF) identities during MHV68 infection. We find that MHV68 infection triggers both pre-tRNA and mature tRNA cleavage, resulting in the accumulation of specific tRFs. OTTR-tRAX revealed not only host tRNAome changes, but also the expression patterns of virally-encoded tRNAs (virtRNAs) and virtRFs made from the MHV68 genome, including their base modification signatures. Because the transcript ends of several host tRFs matched tRNA splice junctions, we tested and confirmed the role of tRNA splicing factors TSEN2 and CLP1 in MHV68-induced tRF biogenesis. Further, we show that CLP1 kinase, and by extension tRNA splicing, is required for productive MHV68 infection. Our findings provide new insight into how gammaherpesvirus infection both impacts and relies on tRNA transcription and processing.
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Affiliation(s)
- Aidan C. Manning
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Mahmoud M. Bashir
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
| | - Ariana R. Jimenez
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
- Interdisciplinary Graduate Program in Immunology, University of Iowa, Iowa City, IA, 52242, USA
| | - Heather E. Upton
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Kathleen Collins
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Todd M. Lowe
- Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Jessica M. Tucker
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, IA, 52242, USA
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14
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Li Z, Barnaby R, Nymon A, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in cystic fibrosis. Am J Physiol Lung Cell Mol Physiol 2024; 326:L574-L588. [PMID: 38440830 PMCID: PMC11380944 DOI: 10.1152/ajplung.00018.2024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 02/15/2024] [Accepted: 02/17/2024] [Indexed: 03/06/2024] Open
Abstract
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates of P. aeruginosa. The 5' tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lungs, increased expression of the 5' tRNA-fMet halves in OMVs attenuated KC (murine homolog of IL-8) secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice and in vitro studies on CF-HBEC that tobramycin reduces inflammation by increasing 5' tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin for P. aeruginosa infection.NEW & NOTEWORTHY The experiments in this report identify a novel mechanism, whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet halves in OMVs secreted by P. aeruginosa, which reduced the OMV-LPS-induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF.
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Affiliation(s)
- Zhongyou Li
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Roxanna Barnaby
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Amanda Nymon
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Carolyn Roche
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Katja Koeppen
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Alix Ashare
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
- Pulmonary and Critical Care Medicine, Dartmouth Health Medical Center, Lebanon, New Hampshire, United States
| | - Deborah A Hogan
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Scott A Gerber
- Dartmouth Health Cancer Center, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, United States
| | - Douglas J Taatjes
- Department of Pathology and Laboratory Medicine, Center for Biomedical Shared Resources, Larner College of Medicine, University of Vermont, Burlington, Vermont, United States
| | - Thomas H Hampton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
| | - Bruce A Stanton
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Hanover, New Hampshire, United States
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15
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Muthukumar S, Li CT, Liu RJ, Bellodi C. Roles and regulation of tRNA-derived small RNAs in animals. Nat Rev Mol Cell Biol 2024; 25:359-378. [PMID: 38182846 DOI: 10.1038/s41580-023-00690-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/13/2023] [Indexed: 01/07/2024]
Abstract
A growing class of small RNAs, known as tRNA-derived RNAs (tdRs), tRNA-derived small RNAs or tRNA-derived fragments, have long been considered mere intermediates of tRNA degradation. These small RNAs have recently been implicated in an evolutionarily conserved repertoire of biological processes. In this Review, we discuss the biogenesis and molecular functions of tdRs in mammals, including tdR-mediated gene regulation in cell metabolism, immune responses, transgenerational inheritance, development and cancer. We also discuss the accumulation of tRNA-derived stress-induced RNAs as a distinct adaptive cellular response to pathophysiological conditions. Furthermore, we highlight new conceptual advances linking RNA modifications with tdR activities and discuss challenges in studying tdR biology in health and disease.
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Affiliation(s)
- Sowndarya Muthukumar
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden
| | - Cai-Tao Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | - Ru-Juan Liu
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
| | - Cristian Bellodi
- Division of Molecular Hematology, Department of Laboratory Medicine, Lund Stem Cell Center, Faculty of Medicine, Lund University, Lund, Sweden.
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16
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Zhang Q, Zhao X, Sun M, Dong D. Novel insights into transfer RNA-derived small RNA (tsRNA) in cardio-metabolic diseases. Life Sci 2024; 341:122475. [PMID: 38309576 DOI: 10.1016/j.lfs.2024.122475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 02/05/2024]
Abstract
Cardio-metabolic diseases, including a cluster of metabolic disorders and their secondary affections on cardiovascular physiology, are gradually brought to the forefront by researchers due to their high prevalence and mortality, as well as an unidentified pathogenesis. tRNA-derived small RNAs (tsRNAs), cleaved by several specific enzymes and once considered as some "metabolic junks" in the past, have been proved to possess numerous functions in human bodies. More interestingly, such a potential also seems to influence the progression of cardio-metabolic diseases to some extent. In this review, the biogenesis, classification and mechanisms of tsRNAs will be discussed based on some latest studies, and their relations with several cardio-metabolic diseases will be highlighted in sequence. Lastly, some future prospects, such as their clinical applications as biomarkers and therapeutic targets will also be mentioned, in order to provide researchers with a comprehensive understanding of the research status of tsRNAs as well as its association with cardio-metabolic diseases, thus presenting as a beacon to indicate directions for the next stage of study.
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Affiliation(s)
- Qingya Zhang
- Innovation Institute, China Medical University, Shenyang 110122, Liaoning, China
| | - Xiaopeng Zhao
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Mingli Sun
- College of Exercise and Health, Shenyang Sport University, Shenyang 110102, Liaoning, China
| | - Dan Dong
- College of Basic Medical Science, China Medical University, Shenyang 110122, Liaoning, China.
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17
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Zhao Y, Wang K, Zhao C, Liu N, Wang Z, Yang W, Cheng Z, Zhou L, Wang K. The function of tRNA-derived small RNAs in cardiovascular diseases. MOLECULAR THERAPY. NUCLEIC ACIDS 2024; 35:102114. [PMID: 38314096 PMCID: PMC10835008 DOI: 10.1016/j.omtn.2024.102114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
tRNA-derived small RNAs (tsRNAs) constitute a subgroup of small noncoding RNAs (ncRNAs) originating from tRNA molecules. Their rich content, evolutionary conservatism, high stability, and widespread existence makes them significant in disease research. These characteristics have positioned tsRNAs as key players in various physiological and pathological processes. tsRNA actively participates in regulating many cellular processes, such as cell death, proliferation, and metabolism. tsRNAs could be promising diagnostic markers for cardiovascular diseases (CVDs). tsRNAs have been identified in serums, suggesting their utility as early indicators for the diagnosis of CVDs. Moreover, the regulatory roles of tsRNAs in CVDs make them promising targets for therapeutic intervention. This review provides a succinct overview of the characteristics, classification, and regulatory functions of tsRNAs in the context of CVDs. By shedding light on the intricate roles of tsRNAs, this knowledge could pave the way for the development of innovative diagnostic tools and therapeutic strategies for CVDs.
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Affiliation(s)
- Yan Zhao
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Kai Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Chun Zhao
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Ning Liu
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zhihong Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Wenting Yang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Zewei Cheng
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
| | - Luyu Zhou
- College of Biology, Hunan University, Changsha 410082, P.R. China
| | - Kun Wang
- Institute for Translational Medicine, The Affiliated Hospital of Qingdao University, College of Medicine, Qingdao University, Qingdao 266021, P.R. China
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18
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Zhang Y, Gu X, Li Y, Huang Y, Ju S. Multiple regulatory roles of the transfer RNA-derived small RNAs in cancers. Genes Dis 2024; 11:597-613. [PMID: 37692525 PMCID: PMC10491922 DOI: 10.1016/j.gendis.2023.02.053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Accepted: 02/20/2023] [Indexed: 09/12/2023] Open
Abstract
With the development of sequencing technology, transfer RNA (tRNA)-derived small RNAs (tsRNAs) have received extensive attention as a new type of small noncoding RNAs. Based on the differences in the cleavage sites of nucleases on tRNAs, tsRNAs can be divided into two categories, tRNA halves (tiRNAs) and tRNA-derived fragments (tRFs), each with specific subcellular localizations. Additionally, the biogenesis of tsRNAs is tissue-specific and can be regulated by tRNA modifications. In this review, we first elaborated on the classification and biogenesis of tsRNAs. After summarizing the latest mechanisms of tsRNAs, including transcriptional gene silencing, post-transcriptional gene silencing, nascent RNA silencing, translation regulation, rRNA regulation, and reverse transcription regulation, we explored the representative biological functions of tsRNAs in tumors. Furthermore, this review summarized the clinical value of tsRNAs in cancers, thus providing theoretical support for their potential as novel biomarkers and therapeutic targets.
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Affiliation(s)
- Yu Zhang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Xinliang Gu
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yang Li
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
- Research Center of Clinical Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Yuejiao Huang
- Medical School of Nantong University, Nantong University, Nantong, Jiangsu 226001, China
- Department of Medical Oncology, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
| | - Shaoqing Ju
- Department of Laboratory Medicine, Affiliated Hospital of Nantong University, Nantong, Jiangsu 226001, China
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19
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La Ferlita A, Alaimo S, Nigita G, Distefano R, Beane JD, Tsichlis PN, Ferro A, Croce CM, Pulvirenti A. tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer. iScience 2024; 27:108810. [PMID: 38303722 PMCID: PMC10831894 DOI: 10.1016/j.isci.2024.108810] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 08/02/2023] [Accepted: 01/02/2024] [Indexed: 02/03/2024] Open
Abstract
tRNA-derived ncRNAs are a heterogeneous class of non-coding RNAs recently proposed to be active regulators of gene expression and be involved in many diseases, including cancer. Consequently, several online resources on tRNA-derived ncRNAs have been released. Although interesting, such resources present only basic features and do not adequately exploit the wealth of knowledge available about tRNA-derived ncRNAs. Therefore, we introduce tRFUniverse, a novel online resource for the analysis of tRNA-derived ncRNAs in human cancer. tRFUniverse presents an extensive collection of classes of tRNA-derived ncRNAs analyzed across all the TCGA and TARGET tumor cohorts, NCI-60 cell lines, and biological fluids. Moreover, public AGO CLASH/CLIP-Seq data were analyzed to identify the molecular interactions between tRNA-derived ncRNAs and other transcripts. Importantly, tRFUniverse combines in a single resource a comprehensive set of features that we believe may be helpful to investigate the involvement of tRNA-derived ncRNAs in cancer biology.
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Affiliation(s)
- Alessandro La Ferlita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Salvatore Alaimo
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Giovanni Nigita
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Rosario Distefano
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Joal D. Beane
- Department of Surgery, Division of Surgical Oncology, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Philip N. Tsichlis
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Ferro
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Alfredo Pulvirenti
- Department of Clinical and Experimental Medicine, Knowmics Lab, University of Catania, Catania, Italy
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20
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Li Z, Barnaby R, Nymon A, Roche C, Koeppen K, Ashare A, Hogan DA, Gerber SA, Taatjes DJ, Hampton TH, Stanton BA. P. aeruginosa tRNA-fMet halves secreted in outer membrane vesicles suppress lung inflammation in Cystic Fibrosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.03.578737. [PMID: 38352468 PMCID: PMC10862835 DOI: 10.1101/2024.02.03.578737] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2024]
Abstract
Although tobramycin increases lung function in people with cystic fibrosis (pwCF), the density of Pseudomonas aeruginosa (P. aeruginosa) in the lungs is only modestly reduced by tobramycin; hence, the mechanism whereby tobramycin improves lung function is not completely understood. Here, we demonstrate that tobramycin increases 5' tRNA-fMet halves in outer membrane vesicles (OMVs) secreted by laboratory and CF clinical isolates of P. aeruginosa . The 5' tRNA-fMet halves are transferred from OMVs into primary CF human bronchial epithelial cells (CF-HBEC), decreasing OMV-induced IL-8 and IP-10 secretion. In mouse lung, increased expression of the 5' tRNA-fMet halves in OMVs attenuated KC secretion and neutrophil recruitment. Furthermore, there was less IL-8 and neutrophils in bronchoalveolar lavage fluid isolated from pwCF during the period of exposure to tobramycin versus the period off tobramycin. In conclusion, we have shown in mice and in vitro studies on CF-HBEC that tobramycin reduces inflammation by increasing 5' tRNA-fMet halves in OMVs that are delivered to CF-HBEC and reduce IL-8 and neutrophilic airway inflammation. This effect is predicted to improve lung function in pwCF receiving tobramycin for P. aeruginosa infection. New and noteworthy The experiments in this report identify a novel mechanim whereby tobramycin reduces inflammation in two models of CF. Tobramycin increased the secretion of tRNA-fMet haves in OMVs secreted by P. aeruginiosa , which reduced the OMV-LPS induced inflammatory response in primary cultures of CF-HBEC and in mouse lung, an effect predicted to reduce lung damage in pwCF. Graphical abstract The anti-inflammatory effect of tobramycin mediated by 5' tRNA-fMet halves secreted in P. aeruginosa OMVs. (A) P. aeruginosa colonizes the CF lungs and secrets OMVs. OMVs diffuse through the mucus layer overlying bronchial epithelial cells and induce IL-8 secretion, which recruits neutrophils that causes lung damage. ( B ) Tobramycin increases 5' tRNA-fMet halves in OMVs secreted by P. aeruginosa . 5' tRNA-fMet halves are delivered into host cells after OMVs fuse with lipid rafts in CF-HBEC and down-regulate protein expression of MAPK10, IKBKG, and EP300, which suppresses IL-8 secretion and neutrophils in the lungs. A reduction in neutrophils in CF BALF is predicted to improve lung function and decrease lung damage.
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21
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Delaunay S, Helm M, Frye M. RNA modifications in physiology and disease: towards clinical applications. Nat Rev Genet 2024; 25:104-122. [PMID: 37714958 DOI: 10.1038/s41576-023-00645-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/25/2023] [Indexed: 09/17/2023]
Abstract
The ability of chemical modifications of single nucleotides to alter the electrostatic charge, hydrophobic surface and base pairing of RNA molecules is exploited for the clinical use of stable artificial RNAs such as mRNA vaccines and synthetic small RNA molecules - to increase or decrease the expression of therapeutic proteins. Furthermore, naturally occurring biochemical modifications of nucleotides regulate RNA metabolism and function to modulate crucial cellular processes. Studies showing the mechanisms by which RNA modifications regulate basic cell functions in higher organisms have led to greater understanding of how aberrant RNA modification profiles can cause disease in humans. Together, these basic science discoveries have unravelled the molecular and cellular functions of RNA modifications, have provided new prospects for therapeutic manipulation and have led to a range of innovative clinical approaches.
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Affiliation(s)
- Sylvain Delaunay
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany
| | - Mark Helm
- Institute of Pharmaceutical and Biomedical Sciences, Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Michaela Frye
- Deutsches Krebsforschungszentrum (DKFZ), Division of Mechanisms Regulating Gene Expression, Heidelberg, Germany.
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22
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Gutierrez-Diaz A, Hoffmann S, Gallego-Gómez JC, Bermudez-Santana CI. Systematic computational hunting for small RNAs derived from ncRNAs during dengue virus infection in endothelial HMEC-1 cells. FRONTIERS IN BIOINFORMATICS 2024; 4:1293412. [PMID: 38357577 PMCID: PMC10864640 DOI: 10.3389/fbinf.2024.1293412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 01/08/2024] [Indexed: 02/16/2024] Open
Abstract
In recent years, a population of small RNA fragments derived from non-coding RNAs (sfd-RNAs) has gained significant interest due to its functional and structural resemblance to miRNAs, adding another level of complexity to our comprehension of small-RNA-mediated gene regulation. Despite this, scientists need more tools to test the differential expression of sfd-RNAs since the current methods to detect miRNAs may not be directly applied to them. The primary reasons are the lack of accurate small RNA and ncRNA annotation, the multi-mapping read (MMR) placement, and the multicopy nature of ncRNAs in the human genome. To solve these issues, a methodology that allows the detection of differentially expressed sfd-RNAs, including canonical miRNAs, by using an integrated copy-number-corrected ncRNA annotation was implemented. This approach was coupled with sixteen different computational strategies composed of combinations of four aligners and four normalization methods to provide a rank-order of prediction for each differentially expressed sfd-RNA. By systematically addressing the three main problems, we could detect differentially expressed miRNAs and sfd-RNAs in dengue virus-infected human dermal microvascular endothelial cells. Although more biological evaluations are required, two molecular targets of the hsa-mir-103a and hsa-mir-494 (CDK5 and PI3/AKT) appear relevant for dengue virus (DENV) infections. Here, we performed a comprehensive annotation and differential expression analysis, which can be applied in other studies addressing the role of small fragment RNA populations derived from ncRNAs in virus infection.
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Affiliation(s)
- Aimer Gutierrez-Diaz
- Grupo Rnomica Teórica y Computacional, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Steve Hoffmann
- Faculty of Biosciences, Leibniz Institute on Aging—Fritz Lipmann Institute (FLI), Friedrich Schiller University Jena, Jena, Germany
| | - Juan Carlos Gallego-Gómez
- Molecular and Translational Medicine Group, Medicine Faculty Universidad de Antioquia, Medellin, Colombia
| | - Clara Isabel Bermudez-Santana
- Grupo Rnomica Teórica y Computacional, Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
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23
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Yang N, Li R, Liu R, Yang S, Zhao Y, Xiong W, Qiu L. The Emerging Function and Promise of tRNA-Derived Small RNAs in Cancer. J Cancer 2024; 15:1642-1656. [PMID: 38370372 PMCID: PMC10869971 DOI: 10.7150/jca.89219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/01/2024] [Indexed: 02/20/2024] Open
Abstract
Fragments derived from tRNA, called tRNA-derived small RNAs (tsRNAs), have attracted widespread attention in the past decade. tsRNAs are widespread in prokaryotic and eukaryotic transcriptome, which contains two main types, tRNA-derived fragments (tRFs) and tRNA-derived stress-inducing RNA (tiRNAs), derived from the precursor tRNAs or mature tRNAs. According to differences in the cleavage position, tRFs can be divided into tRF-1, tRF-2, tRF-3, tRF-5, and i-tRF, whereas tiRNAs can be divided into 5'-tiRNA and 3'-tiRNA. Studies have found that tRFs and tiRNAs are abnormally expressed in a variety of human malignant tumors, promote or inhibit the proliferation and apoptosis of cancer cells by regulating the expression of oncogene, and play an important role in the aggressive metastasis and progression of tumors. This article reviews the biological origins of various tsRNAs, introduces their functions and new concepts of related mechanisms, and focuses on the molecular mechanisms of tsRNAs in cancer, including breast cancer, prostate cancer, colorectal cancer, lung cancer, b-cell lymphoma, and chronic lymphoma cell leukemia. Lastly, this article puts forward some unresolved problems and future research prospects.
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Affiliation(s)
- Na Yang
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Ruijun Li
- College of Foreign Languages, Chuxiong Normal University, Chuxiong 675000, China
| | - Ruai Liu
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Shengjie Yang
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Yi Zhao
- The People's Hospital of ChuXiong Yi Autonomous Prefecture, Chuxiong 675000, China
| | - Wei Xiong
- College of Basic Medical Sciences, Dali University, Dali 671000, China
| | - Lu Qiu
- College of Resources, Environment and Chemistry, Chuxiong Normal University, Chuxiong 675000, China
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24
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Pliatsika V, Cherlin T, Loher P, Vlantis P, Nagarkar P, Nersisyan S, Rigoutsos I. MINRbase: a comprehensive database of nuclear- and mitochondrial-ribosomal-RNA-derived fragments (rRFs). Nucleic Acids Res 2024; 52:D229-D238. [PMID: 37843123 PMCID: PMC10767805 DOI: 10.1093/nar/gkad833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2023] [Revised: 09/17/2023] [Accepted: 09/20/2023] [Indexed: 10/17/2023] Open
Abstract
We describe the Mitochondrial and Nuclear rRNA fragment database (MINRbase), a knowledge repository aimed at facilitating the study of ribosomal RNA-derived fragments (rRFs). MINRbase provides interactive access to the profiles of 130 238 expressed rRFs arising from the four human nuclear rRNAs (18S, 5.8S, 28S, 5S), two mitochondrial rRNAs (12S, 16S) or four spacers of 45S pre-rRNA. We compiled these profiles by analyzing 11 632 datasets, including the GEUVADIS and The Cancer Genome Atlas (TCGA) repositories. MINRbase offers a user-friendly interface that lets researchers issue complex queries based on one or more criteria, such as parental rRNA identity, nucleotide sequence, rRF minimum abundance and metadata keywords (e.g. tissue type, disease). A 'summary' page for each rRF provides a granular breakdown of its expression by tissue type, disease, sex, ancestry and other variables; it also allows users to create publication-ready plots at the click of a button. MINRbase has already allowed us to generate support for three novel observations: the internal spacers of 45S are prolific producers of abundant rRFs; many abundant rRFs straddle the known boundaries of rRNAs; rRF production is regimented and depends on 'personal attributes' (sex, ancestry) and 'context' (tissue type, tissue state, disease). MINRbase is available at https://cm.jefferson.edu/MINRbase/.
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Affiliation(s)
- Venetia Pliatsika
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Tess Cherlin
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Panagiotis Vlantis
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Parth Nagarkar
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Stepan Nersisyan
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Thomas Jefferson University, Philadelphia, PA 19107, USA
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25
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Wang L, Peng B, Yan Y, Liu G, Yang D, Wang Q, Li Y, Mao Q, Chen Q. The tRF-3024b hijacks miR-192-5p to increase BCL-2-mediated resistance to cytotoxic T lymphocytes in Esophageal Squamous Cell Carcinoma. Int Immunopharmacol 2024; 126:111135. [PMID: 37977065 DOI: 10.1016/j.intimp.2023.111135] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 10/23/2023] [Accepted: 10/23/2023] [Indexed: 11/19/2023]
Abstract
The limited efficacy of immune checkpoint inhibitors (ICIs) in the treatment of advanced Esophageal Squamous Cell Carcinoma (ESCC) poses a challenge. Recent evidence suggests that tumor cells' insensitivity to cytotoxic T lymphocytes (CTLs) contributes to drug resistance against ICIs. Here, a particular tRNA-derived fragment called tRF-3024b has been identified as playing a significant role in tumor cell resistance to CTLs. Through tRF sequencing (tRF-seq), we observed a high expression of tRF-3024b in ESCC cells that survived co-culture with CTLs. Further in vitro studies demonstrated that tRF-3024b reduced the apoptosis of tumor cells when co-cultured with CTLs. The mechanism behind this resistance involves tRF-3024b promoting the expression of B-cell lymphoma-2 (BCL-2) by sequestering miR-192-5p, a microRNA that would normally inhibit BCL-2 expression. This means that tRF-3024b indirectly enhances the protective effects of BCL-2, reducing apoptosis in tumor cells. Rescue assays confirmed that the suppressive function of tRF-3024b relies on BCL-2. In summary, the tRF-3024b/miR-192-5p/BCL-2 axis sheds light on the crucial role of tRF-3024b in regulating BCL-2 expression. These findings offer valuable insights into strategies to enhance the response of ESCC to CTLs and improve the effectiveness of immunotherapy approaches in treating ESCC.
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Affiliation(s)
- Lin Wang
- Department of Oncology, Department of Geriatric Lung Cancer Laboratory, The Affiliated Geriatric Hospital of Nanjing Medical University, Nanjing, China
| | - Bo Peng
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yan Yan
- Department of Cardiology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Guangjun Liu
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Dunpeng Yang
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Qibin Wang
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Yongcheng Li
- Department of Oncology, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China.
| | - Qixing Mao
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Nanjing Medical University and Jiangsu Cancer Hospital and Jiangsu Institute of Cancer Research, Nanjing, China.
| | - Qiang Chen
- Department of Thoracic Surgery, Xuzhou Central Hospital, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, China.
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26
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Panstruga R, Spanu P. Transfer RNA and ribosomal RNA fragments - emerging players in plant-microbe interactions. THE NEW PHYTOLOGIST 2024; 241:567-577. [PMID: 37985402 DOI: 10.1111/nph.19409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 11/03/2023] [Indexed: 11/22/2023]
Abstract
According to current textbooks, the principal task of transfer and ribosomal RNAs (tRNAs and rRNAs, respectively) is synthesizing proteins. During the last decade, additional cellular roles for precisely processed tRNA and rRNAs fragments have become evident in all kingdoms of life. These RNA fragments were originally overlooked in transcriptome datasets or regarded as unspecific degradation products. Upon closer inspection, they were found to engage in a variety of cellular processes, in particular the modulation of translation and the regulation of gene expression by sequence complementarity- and Argonaute protein-dependent gene silencing. More recently, the presence of tRNA and rRNA fragments has also been recognized in the context of plant-microbe interactions, both on the plant and the microbial side. While most of these fragments are likely to affect endogenous processes, there is increasing evidence for their transfer across kingdoms in the course of such interactions; these processes may involve mutual exchange in association with extracellular vesicles. Here, we summarize the state-of-the-art understanding of tRNA and rRNA fragment's roles in the context of plant-microbe interactions, their potential biogenesis, presumed delivery routes, and presumptive modes of action.
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Affiliation(s)
- Ralph Panstruga
- RWTH Aachen University, Worringerweg 1, Aachen, 52056, Germany
| | - Pietro Spanu
- Department of Life Sciences, Imperial College London, Imperial College Road, London, SW7 2AZ, UK
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27
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Tzur Y, Winek K, Madrer N, Dubnov S, Bennett ER, Greenberg DS, Hanin G, Gammal A, Tam J, Arkin IT, Paldor I, Soreq H. Lysine tRNA fragments and miR-194-5p co-regulate hepatic steatosis via β-Klotho and perilipin 2. Mol Metab 2024; 79:101856. [PMID: 38141848 PMCID: PMC10805669 DOI: 10.1016/j.molmet.2023.101856] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 11/20/2023] [Accepted: 12/17/2023] [Indexed: 12/25/2023] Open
Abstract
OBJECTIVE Non-alcoholic fatty liver disease (NAFLD) involves hepatic accumulation of intracellular lipid droplets via incompletely understood processes. Here, we report distinct and cooperative NAFLD roles of LysTTT-5'tRF transfer RNA fragments and microRNA miR-194-5p. METHODS Combined use of diet induced obese mice with human-derived oleic acid-exposed Hep G2 cells revealed new NAFLD roles of LysTTT-5'tRF and miR-194-5p. RESULTS Unlike lean animals, dietary-induced NAFLD mice showed concurrent hepatic decrease of both LysTTT-5'tRF and miR-194-5p levels, which were restored following miR-132 antisense oligonucleotide treatment which suppresses hepatic steatosis. Moreover, exposing human-derived Hep G2 cells to oleic acid for 7 days co-suppressed miR-194-5p and LysTTT-5'tRF levels while increasing lipid accumulation. Inversely, transfecting fattened cells with a synthetic LysTTT-5'tRF mimic elevated mRNA levels of the metabolic regulator β-Klotho while decreasing triglyceride amounts by 30% within 24 h. In contradistinction, antisense suppression of miR-194-5p induced accumulation of its novel target, the NAFLD-implicated lipid droplet-coating PLIN2 protein. Further, two out of 15 steatosis-alleviating screened drug-repurposing compounds, Danazol and Latanoprost, elevated miR-194-5p or LysTTT-5'tRF levels. CONCLUSION Our findings highlight the different yet complementary roles of miR-194-5p and LysTTT-5'tRF and offer new insights into the complex roles of small non-coding RNAs and the multiple pathways involved in NAFLD pathogenesis.
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Affiliation(s)
- Yonat Tzur
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Katarzyna Winek
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel; The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Nimrod Madrer
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Serafima Dubnov
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel; The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Estelle R Bennett
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - David S Greenberg
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Geula Hanin
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Asaad Gammal
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Joseph Tam
- Obesity and Metabolism Laboratory, The Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isaiah T Arkin
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel
| | - Iddo Paldor
- Shaare Zedek Medical Center, The Neurosurgery Department, Main Building, 10th Floor, 12 Shmu'el Bait Street, Jerusalem, 9103102 Israel
| | - Hermona Soreq
- The Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel; The Edmond and Lily Safra Center of Brain Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Jerusalem, Israel.
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28
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Shi J, Xu J, Ma J, He F. tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis. Genome Res 2023; 33:2119-2132. [PMID: 37973194 PMCID: PMC10760521 DOI: 10.1101/gr.278128.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
A class of noncoding RNAs, referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which there is a global limitation of nutrients, represents a system in which such a link may readily reveal itself. We show that specific tsRNAs indeed show a dynamic accumulation upon entering the pupal stage. We describe experiments to characterize the mode of tsRNA action and, through the use of such gained knowledge, conduct a genome-wide analysis to assess the functions of dynamically expressed tsRNAs. Our results show that the predicted target genes are highly enriched in biological processes specific to this stage of development including metamorphosis. We further show that tsRNA action is required for successful pupation, providing direct support to the hypothesis that tsRNAs accumulated during this stage are critical to the gene expression program at this stage of development.
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Affiliation(s)
- Junling Shi
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jiaqi Xu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jun Ma
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China;
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Feng He
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China;
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
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29
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Hejret V, Varadarajan NM, Klimentova E, Gresova K, Giassa IC, Vanacova S, Alexiou P. Analysis of chimeric reads characterises the diverse targetome of AGO2-mediated regulation. Sci Rep 2023; 13:22895. [PMID: 38129478 PMCID: PMC10739727 DOI: 10.1038/s41598-023-49757-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
Argonaute proteins are instrumental in regulating RNA stability and translation. AGO2, the major mammalian Argonaute protein, is known to primarily associate with microRNAs, a family of small RNA 'guide' sequences, and identifies its targets primarily via a 'seed' mediated partial complementarity process. Despite numerous studies, a definitive experimental dataset of AGO2 'guide'-'target' interactions remains elusive. Our study employs two experimental methods-AGO2 CLASH and AGO2 eCLIP, to generate thousands of AGO2 target sites verified by chimeric reads. These chimeric reads contain both the AGO2 loaded small RNA 'guide' and the target sequence, providing a robust resource for modeling AGO2 binding preferences. Our novel analysis pipeline reveals thousands of AGO2 target sites driven by microRNAs and a significant number of AGO2 'guides' derived from fragments of other small RNAs such as tRNAs, YRNAs, snoRNAs, rRNAs, and more. We utilize convolutional neural networks to train machine learning models that accurately predict the binding potential for each 'guide' class and experimentally validate several interactions. In conclusion, our comprehensive analysis of the AGO2 targetome broadens our understanding of its 'guide' repertoire and potential function in development and disease. Moreover, we offer practical bioinformatic tools for future experiments and the prediction of AGO2 targets. All data and code from this study are freely available at https://github.com/ML-Bioinfo-CEITEC/HybriDetector/ .
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Affiliation(s)
- Vaclav Hejret
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic
| | - Nandan Mysore Varadarajan
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic
| | - Eva Klimentova
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, 62500, Brno, Czech Republic
| | - Katarina Gresova
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Ilektra-Chara Giassa
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Stepanka Vanacova
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic.
| | - Panagiotis Alexiou
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic.
- Department of Applied Biomedical Science, Faculty of Health Sciences, University of Malta, Msida, MSD 2080, Malta.
- Centre for Molecular Medicine & Biobanking, University of Malta, Msida, MSD 2080, Malta.
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30
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Fallet M, Wilson R, Sarkies P. Cisplatin exposure alters tRNA-derived small RNAs but does not affect epimutations in C. elegans. BMC Biol 2023; 21:276. [PMID: 38031056 PMCID: PMC10688063 DOI: 10.1186/s12915-023-01767-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 11/13/2023] [Indexed: 12/01/2023] Open
Abstract
BACKGROUND The individual lifestyle and environment of an organism can influence its phenotype and potentially the phenotype of its offspring. The different genetic and non-genetic components of the inheritance system and their mutual interactions are key mechanisms to generate inherited phenotypic changes. Epigenetic changes can be transmitted between generations independently from changes in DNA sequence. In Caenorhabditis elegans, epigenetic differences, i.e. epimutations, mediated by small non-coding RNAs, particularly 22G-RNAs, as well as chromatin have been identified, and their average persistence is three to five generations. In addition, previous research showed that some epimutations had a longer duration and concerned genes that were enriched for multiple components of xenobiotic response pathways. These results raise the possibility that environmental stresses might change the rate at which epimutations occur, with potential significance for adaptation. RESULTS In this work, we explore this question by propagating C. elegans lines either in control conditions or in moderate or high doses of cisplatin, which introduces genotoxic stress by damaging DNA. Our results show that cisplatin has a limited effect on global small non-coding RNA epimutations and epimutations in gene expression levels. However, cisplatin exposure leads to increased fluctuations in the levels of small non-coding RNAs derived from tRNA cleavage. We show that changes in tRNA-derived small RNAs may be associated with gene expression changes. CONCLUSIONS Our work shows that epimutations are not substantially altered by cisplatin exposure but identifies transient changes in tRNA-derived small RNAs as a potential source of variation induced by genotoxic stress.
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Affiliation(s)
- Manon Fallet
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Fakultetsgatan 1, 70182, Örebro, Sweden.
| | - Rachel Wilson
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Peter Sarkies
- Department of Biochemistry, Evolutionary Epigenetics Group, Dorothy Crowfoot Hodgkin Building, University of Oxford, South Parks Rd., Oxford, OX1 3QU, UK.
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31
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Karousi P, Samiotaki M, Makridakis M, Zoidakis J, Sideris DC, Scorilas A, Carell T, Kontos CK. 3'-tRF-Cys GCA overexpression in HEK-293 cells alters the global expression profile and modulates cellular processes and pathways. Funct Integr Genomics 2023; 23:341. [PMID: 37987851 PMCID: PMC10663186 DOI: 10.1007/s10142-023-01272-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 11/12/2023] [Accepted: 11/14/2023] [Indexed: 11/22/2023]
Abstract
tRNA fragments (tRFs) are small non-coding RNAs generated through specific cleavage of tRNAs and involved in various biological processes. Among the different types of tRFs, the 3'-tRFs have attracted scientific interest due to their regulatory role in gene expression. In this study, we investigated the role of 3'-tRF-CysGCA, a tRF deriving from cleavage in the T-loop of tRNACysGCA, in the regulation of gene expression in HEK-293 cells. Previous studies have shown that 3'-tRF-CysGCA is incorporated into the RISC complex and interacts with Argonaute proteins, suggesting its involvement in the regulation of gene expression. However, the general role and effect of the deregulation of 3'-tRF-CysGCA levels in human cells have not been investigated so far. To fill this gap, we stably overexpressed 3'-tRF-CysGCA in HEK-293 cells and performed transcriptomic and proteomic analyses. Moreover, we validated the interaction of this tRF with putative targets, the levels of which were found to be affected by 3'-tRF-CysGCA overexpression. Lastly, we investigated the implication of 3'-tRF-CysGCA in various pathways using extensive bioinformatics analysis. Our results indicate that 3'-tRF-CysGCA overexpression led to changes in the global gene expression profile of HEK-293 cells and that multiple cellular pathways were affected by the deregulation of the levels of this tRF. Additionally, we demonstrated that 3'-tRF-CysGCA directly interacts with thymopoietin (TMPO) transcript variant 1 (also known as LAP2α), leading to modulation of its levels. In conclusion, our findings suggest that 3'-tRF-CysGCA plays a significant role in gene expression regulation and highlight the importance of this tRF in cellular processes.
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Affiliation(s)
- Paraskevi Karousi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, Biomedical Sciences Research Center, "Alexander Fleming", Vari, Greece
| | - Manousos Makridakis
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Jerome Zoidakis
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
- Center of Systems Biology, Biomedical Research Foundation of the Academy of Athens, Athens, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Andreas Scorilas
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece
| | - Thomas Carell
- Department for Chemistry, Institute for Chemical Epigenetics, Ludwig Maximilian University of Munich, Munich, Germany
| | - Christos K Kontos
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, Panepistimiopolis, 15701, Athens, Greece.
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Kuhle B, Chen Q, Schimmel P. tRNA renovatio: Rebirth through fragmentation. Mol Cell 2023; 83:3953-3971. [PMID: 37802077 PMCID: PMC10841463 DOI: 10.1016/j.molcel.2023.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 09/12/2023] [Indexed: 10/08/2023]
Abstract
tRNA function is based on unique structures that enable mRNA decoding using anticodon trinucleotides. These structures interact with specific aminoacyl-tRNA synthetases and ribosomes using 3D shape and sequence signatures. Beyond translation, tRNAs serve as versatile signaling molecules interacting with other RNAs and proteins. Through evolutionary processes, tRNA fragmentation emerges as not merely random degradation but an act of recreation, generating specific shorter molecules called tRNA-derived small RNAs (tsRNAs). These tsRNAs exploit their linear sequences and newly arranged 3D structures for unexpected biological functions, epitomizing the tRNA "renovatio" (from Latin, meaning renewal, renovation, and rebirth). Emerging methods to uncover full tRNA/tsRNA sequences and modifications, combined with techniques to study RNA structures and to integrate AI-powered predictions, will enable comprehensive investigations of tRNA fragmentation products and new interaction potentials in relation to their biological functions. We anticipate that these directions will herald a new era for understanding biological complexity and advancing pharmaceutical engineering.
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Affiliation(s)
- Bernhard Kuhle
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA; Department of Cellular Biochemistry, University Medical Center Göttingen, Göttingen, Germany
| | - Qi Chen
- Molecular Medicine Program, Department of Human Genetics, and Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Paul Schimmel
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA, USA.
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Zhang L, Liu J, Hou Y. Classification, function, and advances in tsRNA in non-neoplastic diseases. Cell Death Dis 2023; 14:748. [PMID: 37973899 PMCID: PMC10654580 DOI: 10.1038/s41419-023-06250-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/14/2023] [Accepted: 10/25/2023] [Indexed: 11/19/2023]
Abstract
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.
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Affiliation(s)
- Liou Zhang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Jie Liu
- Translational Research Experiment Department, Science Experiment Center, China Medical University, Shenyang, China.
| | - Yang Hou
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, 110004, China.
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Jianfeng M, Mailin G, Yitang Y, Lei C, Ye Z, Lili N, Yan W, Shunhua Z, Jingyong W, Li Z, Linyuan S. tRNA-derived small RNA dataset in multiple organs of intrauterine growth-restricted pig. Sci Data 2023; 10:793. [PMID: 37949905 PMCID: PMC10638418 DOI: 10.1038/s41597-023-02715-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 11/01/2023] [Indexed: 11/12/2023] Open
Abstract
Intrauterine growth restriction (IUGR) impairs neonatal weight and causes multiple organ dysplasia. IUGR not only threatens human health but is also a significant constraint to the development of animal husbandry. However, the molecular mechanism underlying IUGR remains to be further elucidated. tRNA-derived small RNA (tsRNAs) is a regulative non-coding RNA, which has recently been reported to correlate with the onset and progression of several diseases. In this study, we investigated the tsRNAs expression profiles of IUGR pigs. A tsRNAs dataset for multiple organs in normal and IUGR pigs was generated, including muscle, liver, spleen and intestine. We further analyzed the characteristics of tsRNAs in different organs of pigs, and KEGG pathway analysis was performed to investigate possible pathways involved. This dataset will provide valuable information for further exploring the molecular mechanism of IUGR formation.
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Affiliation(s)
- Ma Jianfeng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Gan Mailin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yang Yitang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Chen Lei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhao Ye
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Niu Lili
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wang Yan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhang Shunhua
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wang Jingyong
- Chongqing Academy of Animal Science, Chongqing, China
| | - Zhu Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China.
| | - Shen Linyuan
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, China.
- Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal and Technology, Sichuan Agricultural University, Chengdu, China.
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Goldkamp AK, Lahuis CH, Hagen DE, Taxis TM. Influence of Maternal BLV Infection on miRNA and tRF Expression in Calves. Pathogens 2023; 12:1312. [PMID: 38003777 PMCID: PMC10674961 DOI: 10.3390/pathogens12111312] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 10/27/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Small non-coding RNAs, such as microRNAs (miRNA) and tRNA-derived fragments (tRF), are known to be involved in post-transcriptional gene regulation. Research has provided evidence that small RNAs may influence immune development in calves. Bovine leukosis is a disease in cattle caused by Bovine Leukemia Virus (BLV) that leads to increased susceptibility to opportunistic pathogens. No research has addressed the potential influence that a maternal BLV infection may have on gene regulation through the differential expression of miRNAs or tRFs in progeny. Blood samples from 14-day old Holstein calves born to BLV-infected dams were collected. Antibodies for BLV were assessed using ELISA and levels of BLV provirus were assessed using qPCR. Total RNA was extracted from whole blood samples for small RNA sequencing. Five miRNAs (bta-miR-1, bta-miR-206, bta-miR-133a, bta-miR-133b, and bta-miR-2450d) and five tRFs (tRF-36-8JZ8RN58X2NF79E, tRF-20-0PF05B2I, tRF-27-W4R951KHZKK, tRF-22-S3M8309NF, and tRF-26-M87SFR2W9J0) were dysregulated in calves born to BLV-infected dams. The miRNAs appear to be involved in the gene regulation of immunological responses and muscle development. The tRF subtypes and parental tRNA profiles in calves born to infected dams appear to be consistent with previous publications in adult cattle with BLV infection. These findings offer insight into how maternal BLV infection status may impact the development of offspring.
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Affiliation(s)
- Anna K. Goldkamp
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74074, USA; (A.K.G.)
| | - Ciarra H. Lahuis
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA;
| | - Darren E. Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK 74074, USA; (A.K.G.)
| | - Tasia M. Taxis
- Department of Animal Science, College of Agriculture and Natural Resources, Michigan State University, East Lansing, MI 48824, USA;
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Nguyen J, Le Q, Win PW, Hill KA, Singh SM, Castellani CA. Decoding mitochondrial-nuclear (epi)genome interactions: the emerging role of ncRNAs. Epigenomics 2023; 15:1121-1136. [PMID: 38031736 DOI: 10.2217/epi-2023-0322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2023] Open
Abstract
Bidirectional communication between the mitochondria and the nucleus is required for several physiological processes, and the nuclear epigenome is a key mediator of this relationship. ncRNAs are an emerging area of discussion for their roles in cellular function and regulation. In this review, we highlight the role of mitochondrial-encoded ncRNAs as mediators of communication between the mitochondria and the nuclear genome. We focus primarily on retrograde signaling, a process in which the mitochondrion relays ncRNAs to translate environmental stress signals to changes in nuclear gene expression, with implications on stress responses that may include disease(s). Other biological roles of mitochondrial-encoded ncRNAs, such as mitochondrial import of proteins and regulation of cell signaling, will also be discussed.
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Affiliation(s)
- Julia Nguyen
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
| | - Quinn Le
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
| | - Phyo W Win
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
| | - Kathleen A Hill
- Department of Biology, Western University, London, ON, N6A 3K7, Canada
| | - Shiva M Singh
- Department of Biology, Western University, London, ON, N6A 3K7, Canada
- Children's Health Research Institute, Lawson Research Institute, London, ON, N6C 2R5, Canada
| | - Christina A Castellani
- Department of Pathology & Laboratory Medicine, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
- Department of Epidemiology & Biostatistics, Schulich School of Medicine & Dentistry, Western University, London, ON, N6A 3K7, Canada
- Children's Health Research Institute, Lawson Research Institute, London, ON, N6C 2R5, Canada
- McKusick-Nathans Institute, Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Rafieenia F, Ebrahimi SO, Emadi ES, Taheri F, Reiisi S. Bioengineered chimeric tRNA/pre-miRNAs as prodrugs in cancer therapy. Biotechnol Prog 2023; 39:e3387. [PMID: 37608520 DOI: 10.1002/btpr.3387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Revised: 08/08/2023] [Accepted: 08/09/2023] [Indexed: 08/24/2023]
Abstract
Today, biologic prodrugs have led to targeting specific tumor markers and have increased specificity and selectivity in cancer therapy. Various studies have shown the role of ncRNAs in cancer pathology and tumorigenesis and have suggested that ncRNAs, especially miRNAs, are valuable molecules in understanding cancer biology and therapeutic processes. Most miRNAs-based research and treatment are limited to chemically synthesized miRNAs. Synthetic alterations in these miRNA mimics may affect their folding, safety profile, and even biological activity. However, despite synthetic miRNA mimics produced by automated systems, various carriers could be used to achieve efficient production of bioengineered miRNAs through economical microbial fermentation. These bioengineered miRNAs as biological prodrugs could provide a new approach for safe therapeutic methods and drug production. In this regard, bioengineered chimeric miRNAs could be selectively processed to mature miRNAs in different types of cancer cells by targeting the desired gene and regulating cancer progression. In this article, we aim to review bioengineered miRNAs and their use in cancer therapy, as well as offering advances in this area, including the use of chimeric tRNA/pre-miRNAs.
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Affiliation(s)
- Fatemeh Rafieenia
- Department of Medical Genetics, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Seyed Omar Ebrahimi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Ensieh Sadat Emadi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
| | - Forough Taheri
- Department of Genetics, Sharekord Branch, Islamic Azad University, Sharekord
| | - Somayeh Reiisi
- Department of Genetics, Faculty of Basic Sciences, Shahrekord University, Shahrekord, Iran
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Akiyama Y, Ivanov P. tRNA-derived RNAs: Biogenesis and roles in translational control. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1805. [PMID: 37406666 PMCID: PMC10766869 DOI: 10.1002/wrna.1805] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023]
Abstract
Transfer RNA (tRNA)-derived RNAs (tDRs) are a class of small non-coding RNAs that play important roles in different aspects of gene expression. These ubiquitous and heterogenous RNAs, which vary across different species and cell types, are proposed to regulate various biological processes. In this review, we will discuss aspects of their biogenesis, and specifically, their contribution into translational control. We will summarize diverse roles of tDRs and the molecular mechanisms underlying their functions in the regulation of protein synthesis and their impact on related events such as stress-induced translational reprogramming. This article is categorized under: RNA Processing > Processing of Small RNAs Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs Regulatory RNAs/RNAi/Riboswitches > Biogenesis of Effector Small RNAs.
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Affiliation(s)
- Yasutoshi Akiyama
- Laboratory of Oncology, Pharmacy Practice and Sciences, Tohoku University Graduate School of Pharmaceutical Sciences, Sendai, Japan
| | - Pavel Ivanov
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, Massachusetts, USA
- Department of Medicine, Harvard Medical School, Boston, Massachusetts, USA
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Du J, Huang T, Zheng Z, Fang S, Deng H, Liu K. Biological function and clinical application prospect of tsRNAs in digestive system biology and pathology. Cell Commun Signal 2023; 21:302. [PMID: 37904174 PMCID: PMC10614346 DOI: 10.1186/s12964-023-01341-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 09/27/2023] [Indexed: 11/01/2023] Open
Abstract
tsRNAs are small non-coding RNAs originating from tRNA that play important roles in a variety of physiological activities such as RNA silencing, ribosome biogenesis, retrotransposition, and epigenetic inheritance, as well as involvement in cellular differentiation, proliferation, and apoptosis. tsRNA-related abnormalities have a significant influence on the onset, development, and progression of numerous human diseases, including malignant tumors through affecting the cell cycle and specific signaling molecules. This review introduced origins together with tsRNAs classification, providing a summary for regulatory mechanism and physiological function while dysfunctional effect of tsRNAs in digestive system diseases, focusing on the clinical prospects of tsRNAs for diagnostic and prognostic biomarkers. Video Abstract.
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Affiliation(s)
- Juan Du
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Tianyi Huang
- Health Science Center, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Zhen Zheng
- Department of Radiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China
| | - Shuai Fang
- The Affiliated Hospital of Medical School of Ningbo University, Ningbo, Zhejiang, China
| | - Hongxia Deng
- The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
| | - Kaitai Liu
- Department of Radiation Oncology, The Affiliated Lihuili Hospital of Ningbo University, Ningbo, Zhejiang, China.
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Shi H, Xie J, Pei S, He D, Hou H, Xu S, Fu Z, Shi X. Digging out the biology properties of tRNA-derived small RNA from black hole. Front Genet 2023; 14:1232325. [PMID: 37953919 PMCID: PMC10637384 DOI: 10.3389/fgene.2023.1232325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
An unique subclass of functional non-coding RNAs generated by transfer RNA (tRNA) under stress circumstances is known as tRNA-derived small RNA (tsRNA). tsRNAs can be divided into tRNA halves and tRNA-derived fragments (tRFs) based on the different cleavage sites. Like microRNAs, tsRNAs can attach to Argonaute (AGO) proteins to target downstream mRNA in a base pairing manner, which plays a role in rRNA processing, gene silencing, protein expression and viral infection. Notably, tsRNAs can also directly bind to protein and exhibit functions in transcription, protein modification, gene expression, protein stabilization, and signaling pathways. tsRNAs can control the expression of tumor suppressor genes and participate in the initiation of cancer. It can also mediate the progression of diseases by regulating cell viability, migration ability, inflammatory factor content and autophagy ability. Precision medicine targeting tsRNAs and drug therapy of plant-derived tsRNAs are expected to be used in clinical practice. In addition, liquid biopsy technology based on tsRNAs indicates a new direction for the non-invasive diagnosis of diseases.
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Affiliation(s)
- Hengmei Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Jiaheng Xie
- Department of Burn and Plastic Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shengbin Pei
- Department of Breast Surgery, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Danni He
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Huyang Hou
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
| | - Shipeng Xu
- Department of Biomedical Engineering, University of California, Davis, Davis, CA, United States
| | - Ziyi Fu
- Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiaoyan Shi
- Department of Obstetrics and Gynecology, Women’s Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, Jiangsu, China
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Wei D, Niu B, Zhai B, Liu XB, Yao YL, Liang CC, Wang P. Expression profiles and function prediction of tRNA-derived fragments in glioma. BMC Cancer 2023; 23:1015. [PMID: 37864150 PMCID: PMC10588164 DOI: 10.1186/s12885-023-11532-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 10/16/2023] [Indexed: 10/22/2023] Open
Abstract
BACKGROUND Glioblastoma (GBM) is the most aggressive malignant primary brain tumor. The transfer RNA-derived fragments (tRFs) are a new group of small noncoding RNAs, which are dysregulated in many cancers. Until now, the expression and function of tRFs in glioma remain unknown. METHODS The expression profiles of tRF subtypes were analyzed using the Cancer Genome Atlas (TCGA)-low-grade gliomas (LGG)/GBM dataset. The target genes of tRFs were subjected to Gene Ontology, Kyoto Encyclopedia and Gene set enrichment analysis of Genes and Genomes pathway enrichment analysis. The protein-protein interaction enrichment analysis was performed by STRING. QRT-PCR was performed to detect the expressions of tRFs in human glioma cell lines U87, U373, U251, and human astrocyte cell line SVG p12. Western blot assay was used to detect to the expression of S100A11. The interaction between tRF-19-R118LOJX and S100A11 mRNA 3'UTR was detected by dual-luciferase reporter assay. The effects of tRF-19-R118LOJX, tRF-19-6SM83OJX and S100A11 on the glioma cell proliferation, migration and in vitro vasculogenic mimicry formation ability were examined by CCK-8 proliferation assay, EdU assay, HoloMonitor cell migration assay and tube formation assay, respectively. RESULTS tRF-19-R118LOJX and tRF-19-6SM83OJX are the most differentially expressed tRFs between LGG and GBM groups. The functional enrichment analysis showed that the target genes of tRF-19-R118LOJX and tRF-19-6SM83OJX are enriched in regulating blood vessel development. The upregulated target genes are linked to adverse survival outcomes in glioma patients. tRF-19-R118LOJX and tRF-19-6SM83OJX were identified to suppress glioma cell proliferation, migration, and in vitro vasculogenic mimicry formation. The mechanism of tRF-19-R118LOJX might be related to its function as an RNA silencer by targeting the S100A11 mRNA 3'UTR. CONCLUSION tRFs would become novel diagnostic biomarkers and therapeutic targets of glioma, and the mechanism might be related to its post-transcriptionally regulation of gene expression by targeting mRNA 3'UTR.
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Affiliation(s)
- Deng Wei
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Ben Niu
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Bei Zhai
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Xiao-Bai Liu
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Yi-Long Yao
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
- Department of Neurosurgery, Shengjing Hospital of China Medical University, Shenyang, 110004, China
| | - Chan-Chan Liang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China
| | - Ping Wang
- Department of Neurobiology, School of Life Sciences, China Medical University, Shenyang, 110122, China.
- Key Laboratory of Neuro-oncology in Liaoning Province, Shenyang, China.
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Chen Q, Zhou T. Emerging functional principles of tRNA-derived small RNAs and other regulatory small RNAs. J Biol Chem 2023; 299:105225. [PMID: 37673341 PMCID: PMC10562873 DOI: 10.1016/j.jbc.2023.105225] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2023] [Revised: 08/22/2023] [Accepted: 08/28/2023] [Indexed: 09/08/2023] Open
Abstract
Recent advancements in small RNA sequencing have unveiled a previously hidden world of regulatory small noncoding RNAs (sncRNAs) that extend beyond the well-studied small interfering RNAs, microRNAs, and piwi-interacting RNAs. This exploration, starting with tRNA-derived small RNAs, has led to the discovery of a diverse universe of sncRNAs derived from various longer structured RNAs such as rRNAs, small nucleolar RNAs, small nuclear RNAs, Y RNAs, and vault RNAs, with exciting uncharted functional possibilities. In this perspective, we discuss the emerging functional principles of sncRNAs beyond the well-known RNAi-like mechanisms, focusing on those that operate independent of linear sequence complementarity but rather function in an aptamer-like fashion. Aptamers use 3D structure for specific interactions with ligands and are modulated by RNA modifications and subcellular environments. Given that aptamer-like sncRNA functions are widespread and present in species lacking RNAi, they may represent an ancient functional principle that predates RNAi. We propose a rethinking of the origin of RNAi and its relationship with these aptamer-like functions in sncRNAs and how these complementary mechanisms shape biological processes. Lastly, the aptamer-like function of sncRNAs highlights the need for caution in using small RNA mimics in research and therapeutics, as their specificity is not restricted solely to linear sequence.
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Affiliation(s)
- Qi Chen
- Molecular Medicine Program, University of Utah School of Medicine, Salt Lake City, Utah, USA; Division of Urology, Department of Surgery, University of Utah School of Medicine, Salt Lake City, Utah, USA; Department of Human Genetics, University of Utah School of Medicine, Salt Lake City, Utah, USA.
| | - Tong Zhou
- Department of Physiology and Cell Biology, University of Nevada, Reno School of Medicine, Reno, Nevada, USA.
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Brogli R, Cristodero M, Schneider A, Polacek N. A ribosome-bound tRNA half stimulates mitochondrial translation during stress recovery in Trypanosoma brucei. Cell Rep 2023; 42:113112. [PMID: 37703180 DOI: 10.1016/j.celrep.2023.113112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/07/2023] [Accepted: 08/24/2023] [Indexed: 09/15/2023] Open
Abstract
The protozoan parasite Trypanosoma brucei and its disease-causing relatives are among the few organisms that barely regulate the transcription of protein-coding genes. Yet, alterations in its gene expression are essential to survive in different host environments. Recently, tRNA-derived RNAs have been implicated as regulators of many cellular processes within and beyond translation. Previously, we identified the tRNAThr-3'-half (AGU) as a ribosome-associated non-coding RNA able to enhance global translation. Here we report that the tRNAThr-3'-half is generated upon starvation inside the mitochondria. The tRNAThr-3'-half associates with mitochondrial ribosomes and stimulates translation during stress recovery, positively affecting mitochondrial activity and, consequently, cellular energy production capacity. Our results describe an organelle ribosome-associated ncRNA involved in translation regulation to boost the central hub of energy metabolism as an immediate stress recovery response.
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Affiliation(s)
- Rebecca Brogli
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; Graduate School for Cellular and Biochemical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Marina Cristodero
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - André Schneider
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland
| | - Norbert Polacek
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland.
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Cao W, Dai S, Ruan W, Long T, Zeng Z, Lei S. Pancreatic stellate cell-derived exosomal tRF-19-PNR8YPJZ promotes proliferation and mobility of pancreatic cancer through AXIN2. J Cell Mol Med 2023; 27:2533-2546. [PMID: 37488774 PMCID: PMC10468654 DOI: 10.1111/jcmm.17852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 07/05/2023] [Accepted: 07/08/2023] [Indexed: 07/26/2023] Open
Abstract
The pancreatic stellate cells (PSCs) play an important role in the development of pancreatic cancer (PC) through mechanisms that remain unclear. Exosomes secreted from PSCs act as mediators for communication in PC. This study aimed to explore the role of PSC-derived exosomal small RNAs derived from tRNAs (tDRs) in PC cells. Exosomes from PSCs were extracted and used to detect their effects on PC cell proliferation, migration and invasion. Exosomal tDRs profiling was performed to identify PSC-derived exosomal tDRs. ISH and qRT-PCR were used to examine the tRF-19-PNR8YPJZ levels and clinical value in clinical samples. The biological function of exosomal tRF-19-PNR8YPJZ was determined using the CCK-8, clone formation, wound healing and transwell assays, subcutaneous tumour formation and lung metastatic models. The relationship between the selected exosomal tRF-19-PNR8YPJZ and AXIN2 was determined by RNA sequencing, luciferase reporter assay. PSC-derived exosomes promoted the proliferation, migration, and invasion of PC cells. Novel and abundant tDRs are found to be differentially expressed in PANC-1 cells after treatment with PSC-derived exosomes, such as tRF-19-PNR8YPJZ. PC tissue samples showed markedly higher levels of tRF-19-PNR8YPJZ than normal controls. Patients with PC exhibiting high tRF-19-PNR8YPJZ expression had a highly lymph node invasion, metastasis, perineural invasion, advanced clinical stage and poor overall survival. Exosomal tRF-19-PNR8YPJZ from PSCs targeted AXIN2 in PC cells and decreased its expression, thus activating the Wnt pathway and promoting proliferation and metastasis. Exosomal tRF-19-PNR8YPJZ from PSCs promoted proliferation and metastasis in PC cells via AXIN2.
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Affiliation(s)
- Wenpeng Cao
- Department of Anatomy, School of Basic MedicineGuizhou Medical UniversityGuiyangChina
| | - Shisi Dai
- Department of Anatomy, School of Basic MedicineGuizhou Medical UniversityGuiyangChina
- Department of Anatomy, School of Basic MedicineGuizhou Nursing Vocational collegeGuiyangChina
| | - Wanyuan Ruan
- School of Clinical MedicineGuizhou Medical UniversityGuiyangChina
| | - Tingting Long
- Department of Anatomy, School of Basic MedicineGuizhou Medical UniversityGuiyangChina
| | - Zhirui Zeng
- Department of Physiology, School of Basic MedicineGuizhou Medical UniversityGuiyangChina
| | - Shan Lei
- Department of Physiology, School of Basic MedicineGuizhou Medical UniversityGuiyangChina
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45
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Tyczewska A, Grzywacz K. tRNA-derived fragments as new players in regulatory processes in yeast. Yeast 2023; 40:283-289. [PMID: 36385711 DOI: 10.1002/yea.3829] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/04/2022] [Accepted: 11/16/2022] [Indexed: 08/08/2023] Open
Abstract
For a very long time, RNA molecules were treated as transistory molecules, by which the genetic information flows from DNA to proteins; the model proposed in the 1960s accepted that proteins are both the products and the regulators of gene expression. Since then, thousands of reports proved that RNAs should be thought about as the factors that do control gene expression. The pervasive transcription has been reported in many eukaryotic organisms, illustrating a highly interwoven transcriptome organization that includes hundreds of previously unknown noncoding RNAs. The key roles of noncoding RNAs (microRNAs and small interfering RNAs) in gene expression regulation are no longer surprising, as are new classes of noncoding RNAs constantly being discovered. Transfer RNAs (tRNAs) are the second most abundant type of RNAs in the cell. Advances in high-throughput sequencing technologies exposed the existence of functional, regulatory tRNA-derived RNA fragments (tRFs), generated from precursor and mature tRNAs. These tRF molecules have been found to play central roles during stress and different pathological conditions. Herein, we present the critical assessment of the discoveries made in the field of tRNA-derived fragments in the past 15 years in various pathogenic and nonpathogenic yeast species.
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Affiliation(s)
- Agata Tyczewska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
| | - Kamilla Grzywacz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, Poznań, Poland
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Malhotra S, Miras MCM, Pappolla A, Montalban X, Comabella M. Liquid Biopsy in Neurological Diseases. Cells 2023; 12:1911. [PMID: 37508574 PMCID: PMC10378132 DOI: 10.3390/cells12141911] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/19/2023] [Accepted: 07/19/2023] [Indexed: 07/30/2023] Open
Abstract
The most recent and non-invasive approach for studying early-stage biomarkers is liquid biopsy. This implies the extraction and analysis of non-solid biological tissues (serum, plasma, saliva, urine, and cerebrospinal fluid) without undergoing invasive procedures to determine disease prognosis. Liquid biopsy can be used for the screening of several components, such as extracellular vesicles, microRNAs, cell-free DNA, cell-free mitochondrial and nuclear DNA, circulating tumour cells, circulating tumour DNA, transfer RNA, and circular DNA or RNA derived from body fluids. Its application includes early disease diagnosis, the surveillance of disease activity, and treatment response monitoring, with growing evidence for validating this methodology in cancer, liver disease, and central nervous system (CNS) disorders. This review will provide an overview of mentioned liquid biopsy components, which could serve as valuable biomarkers for the evaluation of complex neurological conditions, including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, multiple sclerosis, epilepsy, stroke, traumatic brain injury, CNS tumours, and neuroinfectious diseases. Furthermore, this review highlights the future directions and potential limitations associated with liquid biopsy.
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Affiliation(s)
- Sunny Malhotra
- Multiple Sclerosis Center of Catalonia, Department of Neurology-Neuroimmunology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Mari Carmen Martín Miras
- Multiple Sclerosis Center of Catalonia, Department of Neurology-Neuroimmunology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Agustín Pappolla
- Multiple Sclerosis Center of Catalonia, Department of Neurology-Neuroimmunology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Xavier Montalban
- Multiple Sclerosis Center of Catalonia, Department of Neurology-Neuroimmunology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
| | - Manuel Comabella
- Multiple Sclerosis Center of Catalonia, Department of Neurology-Neuroimmunology, Vall d'Hebron University Hospital, 08035 Barcelona, Spain
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Oluwayiose OA, Houle E, Whitcomb BW, Suvorov A, Rahil T, Sites CK, Krawetz SA, Visconti PE, Pilsner JR. Urinary phthalate metabolites and small non-coding RNAs from seminal plasma extracellular vesicles among men undergoing infertility treatment. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 329:121529. [PMID: 37003585 DOI: 10.1016/j.envpol.2023.121529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 02/24/2023] [Accepted: 03/27/2023] [Indexed: 05/21/2023]
Abstract
Non-coding RNA (ncRNA) cargo of extracellular vesicles (EVs) in the male reproductive tract play critical roles in semen quality and emerging evidence suggests their susceptibility to environmental factors. Male phthalate exposures have been linked to poor semen quality, sperm DNA methylation profiles and embryo development; however, there is limited evidence on their potential impact on EV ncRNAs profiles. We evaluated the association between urinary phthalate metabolites and small ncRNAs (sncRNAs) of seminal plasma EVs (spEV) among men receiving clinical infertility care. We conducted sncRNA sequencing of EVs in 96 seminal plasma samples collected from the Sperm Environmental Epigenetics and Development Study (SEEDS). Sequencing reads were mapped to human transcriptome databases using STAR. Urinary metabolite concentrations of thirteen phthalates and two DiNCH, a phthalate alternative, were measured via tandem mass spectrometry. Associations with normalized counts were assessed using EdgeR (FDR<0.05) adjusting for urinary dilution via specific gravity, age, BMI, batch, and biotype-specific total counts. Select metabolites, MEOHP, MECPP, ∑DEHP, MCPP, MCNP, MCOP, were negatively (p < 0.05) correlated with miRNA relative abundance. Similarly, nine metabolites including MEOHP, MECPP, MEHP, MCPP, MHBP, MHiNCH, MiBP, MEHHP, MCOP and ∑DEHP were associated (q < 0.05) with normalized counts from 23 unique ncRNA transcripts (7 miRNAs (pre & mature); 6 tRFs; and 10 piRNAs), most (78%) of which displayed increased expression patterns. miRNA and tRFs gene targets were enriched in vesicle-mediated transport and developmental-related ontology terms, such as tyrosine kinase, head development, and cell morphogenesis. Six genes (MAPK1, BMPR1A/2, PTEN, TGFBR2, TP53 and APP) were present in all the ontology terms and predicted to form protein association networks. piRNAs were annotated to pseudogenes of genes important in EV cargo transfer and embryonic development. This is the first study to associate phthalate exposures to altered spEV sncRNA profiles. Future studies are needed to determine their impact on reproductive outcomes.
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Affiliation(s)
- Oladele A Oluwayiose
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Emily Houle
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA
| | - Brian W Whitcomb
- Department of Biostatistics and Epidemiology, School of Public Health and Health Sciences, University of Massachusetts Amherst, 715 North Pleasant Street, Amherst, MA, USA
| | - Alexander Suvorov
- Department of Environmental Health Sciences, School of Public Health and Health Sciences, University of Massachusetts Amherst, 686 North Pleasant Street, Amherst, MA, USA
| | - Tayyab Rahil
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, UMass Chan-Baystate, 759 Chestnut Street, Springfield, MA, USA
| | - Cynthia K Sites
- Division of Reproductive Endocrinology and Infertility, Department of Obstetrics and Gynecology, UMass Chan-Baystate, 759 Chestnut Street, Springfield, MA, USA
| | - Stephen A Krawetz
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA; Center for Molecular Medicine and Genetics, Wayne State School of Medicine, USA
| | - Pablo E Visconti
- Department of Veterinary and Animal Sciences, University of Massachusetts Amherst, 661 N. Pleasant St, Amherst, MA, 01003, USA
| | - J Richard Pilsner
- C.S. Mott Center for Human Growth and Development, Department of Obstetrics and Gynecology, School of Medicine, Wayne State University, Detroit, MI, 48201, USA; Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, 48201, USA.
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48
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Chen Y, Tang Y, Hou S, Luo J, Chen J, Qiu H, Chen W, Li K, He J, Li J. Differential expression spectrum and targeted gene prediction of tRNA-derived small RNAs in idiopathic pulmonary arterial hypertension. Front Mol Biosci 2023; 10:1204740. [PMID: 37496778 PMCID: PMC10367008 DOI: 10.3389/fmolb.2023.1204740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 07/03/2023] [Indexed: 07/28/2023] Open
Abstract
Background: Idiopathic pulmonary arterial hypertension (PAH) is a potentially fatal pulmonary vascular disease with an extremely poor natural course. The limitations of current treatment and the unclear etiology and pathogenesis of idiopathic PAH require new targets and avenues of exploration involved in the pathogenesis of PAH. tRNA-derived small RNAs (tsRNAs), a new type of small non-coding RNAs, have a significant part in the progress of diverse diseases. However, the potential functions behind tsRNAs in idiopathic PAH remain unknown. Methods: Small RNA microarray was implemented on three pairs of plasma of idiopathic PAH patients and healthy controls to investigate and compare tsRNAs expression profiles. Validation samples were used for real-time polymerase chain reaction (Real-time PCR) to verify several dysregulated tsRNAs. Bioinformatic analysis was adopted to determine potential target genes and mechanisms of the validated tsRNAs in PAH. Results: Microarray detected 816 statistically significantly dysregulated tsRNAs, of which 243 tsRNAs were upregulated and 573 were downregulated in PAH. Eight validated tsRNAs in the results of Real-time PCR were concordant with the small RNA microarray: four upregulated (tRF3a-AspGTC-9, 5'tiRNA-31-GluCTC-16, i-tRF-31:54-Val-CAC-1 and tRF3b-TyrGTA-4) and four downregulated (5'tiRNA-33-LysTTT-4, i-tRF-8:32-Val-AAC-2, i-tRF-2:30-His-GTG-1, and i-tRF-15:31-Lys-CTT-1). The Gene Ontology analysis has shown that the verified tsRNAs are related to cellular macromolecule metabolic process, regulation of cellular process, and regulation of cellular metabolic process. It is disclosed that potential target genes of verified tsRNAs are widely involved in PAH pathways by Kyoto Encyclopedia of Genes and Genomes. Conclusion: This study investigated tsRNA profiles in idiopathic PAH and found that the dysregulated tsRNAs may become a novel type of biomarkers and possible targets for PAH.
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Affiliation(s)
- Yusi Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Yi Tang
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Department of Cardiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, China
| | - Sitong Hou
- Clinical Medicine, Xiangya Medical School of Central South University, Changsha, Hunan, China
| | - Jun Luo
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Jingyuan Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Haihua Qiu
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Wenjie Chen
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
| | - Kexing Li
- Department of Pharmacology, Hebei University, Baoding, Hebei, China
| | - Jin He
- Clinical Medicine Research Center of Heart Failure of Hunan Province, Department of Cardiology, Hunan Provincial People’s Hospital, The First Affiliated Hospital of Hunan Normal University, Hunan Normal University, Changsha, China
| | - Jiang Li
- Department of Cardiovascular Medicine, The Second Xiangya Hospital of Central South University, Changsha, Hunan, China
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49
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Lee S, Kim J, Valdmanis PN, Kim HK. Emerging roles of tRNA-derived small RNAs in cancer biology. Exp Mol Med 2023:10.1038/s12276-023-01038-5. [PMID: 37430089 PMCID: PMC10393972 DOI: 10.1038/s12276-023-01038-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 04/29/2023] [Accepted: 05/09/2023] [Indexed: 07/12/2023] Open
Abstract
Transfer RNAs (tRNAs) play an essential role in mRNA translation by delivering amino acids to growing polypeptide chains. Recent data demonstrate that tRNAs can be cleaved by ribonucleases, and the resultant cleavage products, tRNA-derived small RNAs (tsRNAs), have crucial roles in physiological and pathological conditions. They are classified into more than six types according to their size and cleavage positions. Since the initial discovery of the physiological functions of tsRNAs more than a decade ago, accumulating data have demonstrated that tsRNAs play critical roles in gene regulation and tumorigenesis. These tRNA-derived molecules have various regulatory functions at the transcriptional, post-transcriptional, and translational levels. More than a hundred types of modifications are found on tRNAs, affecting the biogenesis, stability, function, and biochemical properties of tsRNA. Both oncogenic and tumor suppressor functions have been reported for tsRNAs, which play important roles in the development and progression of various cancers. Abnormal expression patterns and modification of tsRNAs are associated with various diseases, including cancer and neurological disorders. In this review, we will describe the biogenesis, versatile gene regulation mechanisms, and modification-mediated regulation mechanisms of tsRNA as well as the expression patterns and potential therapeutic roles of tsRNAs in various cancers.
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Affiliation(s)
- Saebyeol Lee
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Jungeun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea
| | - Paul N Valdmanis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, 98115, USA
| | - Hak Kyun Kim
- Department of Life Science, Chung-Ang University, Seoul, 06974, Republic of Korea.
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50
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Christodoulou S, Katsaraki K, Vassiliu P, Danias N, Michalopoulos N, Tzikos G, Sideris DC, Arkadopoulos N. High Intratumoral i-tRF-Gly GCC Expression Predicts Short-Term Relapse and Poor Overall Survival of Colorectal Cancer Patients, Independent of the TNM Stage. Biomedicines 2023; 11:1945. [PMID: 37509584 PMCID: PMC10377136 DOI: 10.3390/biomedicines11071945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/22/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Colorectal cancer (CRC), one of the most prevalent types of cancer, requires the discovery of new tumor biomarkers for accurate patient prognosis. In this work, the prognostic value of the tRNA fragment i-tRF-GlyGCC in CRC was examined. Total RNA extraction from 211 CRC patient cancer tissue specimens and 83 adjacent normal tissues was conducted. Each RNA extract was subjected to in vitro polyadenylation and reverse transcription. A real-time quantitative PCR assay was used to quantify i-tRF-GlyGCC in all samples. Extensive biostatics analysis showed that i-tRF-GlyGCC levels in CRC tissues were significantly lower than in matched normal colorectal tissues. Additionally, the disease-free survival (DFS) and overall survival (OS) time intervals were considerably shorter in CRC patients with high i-tRF-GlyGCC expression. i-tRF-GlyGCC expression maintained its prognostic value independently of other established prognostic factors, as shown by the multivariate Cox regression analysis. Additionally, survival analysis after TNM stage stratification revealed that higher i-tRF-GlyGCC levels were linked to shorter DFS time intervals in patients with TNM stage II tumors, as well as an increased probability of having a worse OS for patients in TNM stage II. In conclusion, i-tRF-GlyGCC has the potential to be a useful molecular tissue biomarker in CRC, independent of other clinicopathological variables.
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Affiliation(s)
- Spyridon Christodoulou
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Katerina Katsaraki
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Panteleimon Vassiliu
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Nikolaos Danias
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Nikolaos Michalopoulos
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
| | - Georgios Tzikos
- Propaedeutic Department of Surgery, University General Hospital "AHEPA", Aristotle University of Thessaloniki, 54636 Thessaloniki, Greece
| | - Diamantis C Sideris
- Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece
| | - Nikolaos Arkadopoulos
- Fourth Department of Surgery, University General Hospital "Attikon", National and Kapodistrian University of Athens, 12462 Athens, Greece
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