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Ying S, Li P, Wang J, Chen K, Zou Y, Dai M, Xu K, Feng G, Zhang C, Jiang H, Li W, Zhang Y, Zhou Q. tRF-Gln-CTG-026 ameliorates liver injury by alleviating global protein synthesis. Signal Transduct Target Ther 2023; 8:144. [PMID: 37015921 PMCID: PMC10073094 DOI: 10.1038/s41392-023-01351-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 01/23/2023] [Accepted: 01/30/2023] [Indexed: 04/06/2023] Open
Abstract
tsRNAs (tRNA-derived small RNAs), as products of the stress response, exert considerable influence on stress response and injury regulation. However, it remains largely unclear whether tsRNAs can ameliorate liver injury. Here, we demonstrate the roles of tsRNAs in alleviating liver injury by utilizing the loss of NSun2 (NOP2/Sun domain family, member 2) as a tsRNAs-generating model. Mechanistically, the loss of NSun2 reduces methyluridine-U5 (m5U) and cytosine-C5 (m5C) of tRNAs, followed by the production of various tsRNAs, especially Class I tsRNAs (tRF-1s). Through further screening, we show that tRF-Gln-CTG-026 (tG026), the optimal tRF-1, ameliorates liver injury by repressing global protein synthesis through the weakened association between TSR1 (pre-rRNA-processing protein TSR1 homolog) and pre-40S ribosome. This study indicates the potential of tsRNA-reduced global protein synthesis in liver injury and repair, suggesting a potential therapeutic strategy for liver injury.
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Affiliation(s)
- Sunyang Ying
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengcheng Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Science, Northeast Agricultural University of China, Harbin, 150030, China
| | - Jiaqiang Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Kaiqiong Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu Zou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Moyu Dai
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Xu
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Guihai Feng
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Changjian Zhang
- Central Laboratory of the Sixth Medical Center of PLA General Hospital, Beijing, 100048, China
| | - Haiping Jiang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China
| | - Ying Zhang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
| | - Qi Zhou
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Beijing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
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Suresh PS, Thankachan S, Venkatesh T. Landscape of Clinically Relevant Exosomal tRNA-Derived Non-coding RNAs. Mol Biotechnol 2023; 65:300-310. [PMID: 35997930 DOI: 10.1007/s12033-022-00546-5] [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: 03/02/2022] [Accepted: 07/05/2022] [Indexed: 11/28/2022]
Abstract
Exosomes are extra-cellular vesicles that are < 150 nm that is formed by invagination of the plasma membrane and are released as vesicles. These contain proteins, RNA, and DNA as their cargo. In recent times, the non-coding RNA (ncRNA) present within exosomes has been studied extensively in the context of sorting, localization, and their potential as biomarkers. For example, miR-1246, miR-1290, miR-21, and miR-23a are exosomal biomarkers of cancer, and YBX1 (Y-Box Binding Protein 1) is attributed to exosomal RNA sorting. Transfer RNA-derived fragments are a class of small ncRNAs that were discovered in 2009. They are classified as tRFs (tRNA-derived fragments) and tsRNAs (tRNA halves). Interestingly, these tRNA-derived ncRNAs are emerging as biomarkers in various diseases, and these are found in exosomes. To date, the literature has covered only the biomarker potential of plasma/serum tRNA-derived ncRNAs. Hence, in the current review, we discuss the exosomal tRNA-derived fragments that are clinically relevant in pathological conditions.
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Affiliation(s)
- Padmanaban S Suresh
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, 673601, India
| | - Sanu Thankachan
- School of Biotechnology, National Institute of Technology Calicut, Kozhikode, 673601, India
| | - Thejaswini Venkatesh
- Department of Biochemistry and Molecular Biology, Central University of Kerala, Kerala, 671316, Periye, Kasaragod, India.
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Choi D, Kim S, Woo J, Lee H, Kim H, Jeon JS, Noh H, Han DC, Kim SH, Cho HC, Choi JS, Bae YU, Kwon SH. Weight Change Alters the Small RNA Profile of Urinary Extracellular Vesicles in Obesity. Obes Facts 2022; 15:292-301. [PMID: 35008090 PMCID: PMC9021654 DOI: 10.1159/000521730] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/27/2021] [Indexed: 11/19/2022] Open
Abstract
INTRODUCTION Various kidney diseases reportedly show different urinary extracellular vesicle (EV) RNA profiles. Although obesity is one of the main causes of chronic kidney disease, the expression pattern of urinary EV RNA in obesity is uncertain. Our aim was to sequence the small RNA profiles of urinary EVs in obese patients before and after weight reduction and compare them to those of healthy volunteers (HVs). METHODS We recruited age-sex-matched obese patients and HVs. The small RNA profiles of urinary EVs were analyzed using RNA sequencing. To evaluate the effect of weight reduction, small RNA profiles of urinary EVs 6 months after bariatric surgery were also analyzed. RESULTS The proportion of urinary EVs transfer RNA and microRNA of obese patients differed from that of HVs. Obese patients showed differential expression of 1,343 small RNAs in urinary EVs compared to HVs (fold change ≥2 and p value <0.05). Among those, 61 small RNAs were upregulated in obese patients and downregulated after weight reduction, whereas 167 small RNAs were downregulated in obese patients and upregulated after weight reduction. RNA sequencing revealed the correlation between the specific urinary EV small RNAs and clinical parameters including body weight, low-density lipoprotein cholesterol, triglyceride, high-density lipoprotein cholesterol, serum glucose, estimated glomerular filtration rate, and albuminuria. CONCLUSION Obese patients showed distinct urinary EV small RNA profiles compared to HVs. Weight reduction altered urinary EV small-RNA profiles in obese patients.
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Affiliation(s)
- Dughyun Choi
- Division of Endocrinology and Metabolism, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Republic of Korea
| | - Sewon Kim
- Macrogen Inc., Seoul, Republic of Korea
- ROKIT Genomics, Seoul, Republic of Korea
| | | | - Haekyung Lee
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Hyoungnae Kim
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Jin Seok Jeon
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Hyunjin Noh
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Dong Cheol Han
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Sang Hyun Kim
- Department of Surgery, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
| | - Ho Chan Cho
- Department of Clinical Endocrinology, Keimyung University School of Medicine, Daegu, Republic of Korea
| | - Jong-Soo Choi
- Research Institute, Biosolyx Co. Ltd., Daegu, Republic of Korea
| | - Yun-Ui Bae
- Department of Clinical Endocrinology, Keimyung University School of Medicine, Daegu, Republic of Korea
- *Yun-Ui Bae,
| | - Soon Hyo Kwon
- Division of Nephrology, Department of Internal Medicine, Soonchunhyang University Seoul Hospital, Seoul, Republic of Korea
- **Soon Hyo Kwon,
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Kuscu C, Kiran M, Mohammed A, Kuscu C, Satpathy S, Wolen A, Bardhi E, Bajwa A, Eason JD, Maluf D, Mas V, Akalin E. Integrative Analyses of Circulating Small RNAs and Kidney Graft Transcriptome in Transplant Glomerulopathy. Int J Mol Sci 2021; 22:ijms22126218. [PMID: 34207555 PMCID: PMC8226568 DOI: 10.3390/ijms22126218] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/01/2021] [Accepted: 06/06/2021] [Indexed: 02/07/2023] Open
Abstract
Transplant glomerulopathy develops through multiple mechanisms, including donor-specific antibodies, T cells and innate immunity. This study investigates circulating small RNA profiles in serum samples of kidney transplant recipients with biopsy-proven transplant glomerulopathy. Among total small RNA population, miRNAs were the most abundant species in the serum of kidney transplant patients. In addition, fragments arising from mature tRNA and rRNA were detected. Most of the tRNA fragments were generated from 5′ ends of mature tRNA and mainly from two parental tRNAs: tRNA-Gly and tRNA-Glu. Moreover, transplant patients with transplant glomerulopathy displayed a novel tRNA fragments signature. Gene expression analysis from allograft tissues demonstrated changes in canonical pathways related to immune activation such as iCos-iCosL signaling pathway in T helper cells, Th1 and Th2 activation pathway, and dendritic cell maturation. mRNA targets of down-regulated miRNAs such as miR-1224-5p, miR-4508, miR-320, miR-378a from serum were globally upregulated in tissue. Integration of serum miRNA profiles with tissue gene expression showed that changes in serum miRNAs support the role of T-cell mediated mechanisms in ongoing allograft injury.
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Affiliation(s)
- Canan Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
- Correspondence: ; Tel.: +1-901-448-3162
| | - Manjari Kiran
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Akram Mohammed
- Center for Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA;
| | - Cem Kuscu
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Sarthak Satpathy
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India; (M.K.); (S.S.)
| | - Aaron Wolen
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Elissa Bardhi
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Amandeep Bajwa
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - James D. Eason
- Transplant Research Institute, James D. Eason Transplant Institute, Department of Surgery, School of Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA; (C.K.); (A.W.); (A.B.); (J.D.E.)
| | - Daniel Maluf
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Valeria Mas
- Department of Surgery, School of Medicine, University of Maryland, Baltimore, MD 21201, USA; (E.B.); (D.M.); (V.M.)
| | - Enver Akalin
- Montefiore Medical Center, Abdominal Transplant Program, Albert Einstein College of Medicine, Bronx, NY 10467, USA;
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Abstract
tRNA-derived small RNA (tsRNA) is a novel class of non-coding RNA that is usually produced from tRNA following endonuclease cleavage which occurs under stress conditions. There are two types of tsRNAs: tRNA-derived fragments (tRFs) and stress-induced tRNA halves (tiRNAs), which differ in their cleavage position. Many studies have demonstrated that tsRNAs are involved in various physiological and pathological processes apart from cancer and gene expression. In this review, we briefly described the biogenesis, classification, and characteristics of tsRNAs and summarized the current research progress of tsRNAs in metabolic diseases, senescence, reproduction, stress, and organ injury, and finally put forward some problems to be solved.
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Affiliation(s)
- Qiyu Pan
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
| | - Tingting Han
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
| | - Guoping Li
- The Key Laboratory of Geriatrics, Beijing Institute of Geriatrics, Beijing Hospital, NationalCenter of Gerontology, National Health Commission; Institute of Geriatric Medicine, ChineseAcademy of Medical Sciences, Beijing 100730, P. R. China
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Pan X, Geng X, Liu Y, Yu M, Mishra MK, Xu X, Ding X, Liu P, Liang M. Transfer RNA Fragments in the Kidney in Hypertension. Hypertension 2021; 77:1627-1637. [PMID: 33775129 DOI: 10.1161/hypertensionaha.121.16994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
[Figure: see text].
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Affiliation(s)
- Xiaoqing Pan
- Department of Mathematics, Shanghai Normal University, China (X.P.).,Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xuemei Geng
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Mengqian Yu
- Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Manoj K Mishra
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
| | - Xialian Xu
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Xiaoqiang Ding
- Department of Nephrology, Zhongshan Hospital, Fudan University, Shanghai Institute of Kidney and Dialysis, Shanghai Key Laboratory of Kidney and Blood Purification, Shanghai Medical Center of Kidney Disease, China (X.G., X.X., X.D.)
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.).,Department of Respiratory Medicine, Sir Run Run Shaw Hospital and Institute of Translational Medicine, Zhejiang University School of Medicine, Hangzhou, China (M.Y., P.L.)
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee (X.P., X.G., Y.L., M.K.M., P.L., M.L.)
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Pliatsika V, Loher P, Magee R, Telonis AG, Londin E, Shigematsu M, Kirino Y, Rigoutsos I. MINTbase v2.0: a comprehensive database for tRNA-derived fragments that includes nuclear and mitochondrial fragments from all The Cancer Genome Atlas projects. Nucleic Acids Res 2018; 46:D152-D159. [PMID: 29186503 PMCID: PMC5753276 DOI: 10.1093/nar/gkx1075] [Citation(s) in RCA: 138] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Revised: 10/18/2017] [Accepted: 10/27/2017] [Indexed: 12/16/2022] Open
Abstract
MINTbase is a repository that comprises nuclear and mitochondrial tRNA-derived fragments ('tRFs') found in multiple human tissues. The original version of MINTbase comprised tRFs obtained from 768 transcriptomic datasets. We used our deterministic and exhaustive tRF mining pipeline to process all of The Cancer Genome Atlas datasets (TCGA). We identified 23 413 tRFs with abundance of ≥ 1.0 reads-per-million (RPM). To facilitate further studies of tRFs by the community, we just released version 2.0 of MINTbase that contains information about 26 531 distinct human tRFs from 11 719 human datasets as of October 2017. Key new elements include: the ability to filter tRFs on-the-fly by minimum abundance thresholding; the ability to filter tRFs by tissue keywords; easy access to information about a tRF's maximum abundance and the datasets that contain it; the ability to generate relative abundance plots for tRFs across cancer types and convert them into embeddable figures; MODOMICS information about modifications of the parental tRNA, etc. Version 2.0 of MINTbase contains 15x more datasets and nearly 4x more distinct tRFs than the original version, yet continues to offer fast, interactive access to its contents. Version 2.0 is available freely at http://cm.jefferson.edu/MINTbase/.
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Affiliation(s)
- Venetia Pliatsika
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Phillipe Loher
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Rogan Magee
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Aristeidis G Telonis
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Eric Londin
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Megumi Shigematsu
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Yohei Kirino
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
| | - Isidore Rigoutsos
- Computational Medicine Center, Sidney Kimmel Medical College at Thomas Jefferson University, Jefferson Alumni Hall #M81, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA
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Khurana R, Ranches G, Schafferer S, Lukasser M, Rudnicki M, Mayer G, Hüttenhofer A. Identification of urinary exosomal noncoding RNAs as novel biomarkers in chronic kidney disease. RNA (NEW YORK, N.Y.) 2017; 23:142-152. [PMID: 27872161 PMCID: PMC5238789 DOI: 10.1261/rna.058834.116] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 11/08/2016] [Indexed: 06/06/2023]
Abstract
In chronic kidney disease (CKD), the decline in the glomerular filtration rate is associated with increased morbidity and mortality and thus poses a major challenge for healthcare systems. While the contribution of tissue-derived miRNAs and mRNAs to CKD progression has been extensively studied, little is known about the role of urinary exosomes and their association with CKD. Exosomes are small, membrane-derived endocytic vesicles that contribute to cell-to-cell communication and are present in various body fluids, such as blood or urine. Next-generation sequencing approaches have revealed that exosomes are enriched in noncoding RNAs and thus exhibit great potential for sensitive nucleic acid biomarkers in various human diseases. Therefore, in this study we aimed to identify urinary exosomal ncRNAs as novel biomarkers for diagnosis of CKD. Since up to now most approaches have focused on the class of miRNAs, we extended our analysis to several other noncoding RNA classes, such as tRNAs, tRNA fragments (tRFs), mitochondrial tRNAs, or lincRNAs. For their computational identification from RNA-seq data, we developed a novel computational pipeline, designated as ncRNASeqScan. By these analyses, in CKD patients we identified 30 differentially expressed ncRNAs, derived from urinary exosomes, as suitable biomarkers for early diagnosis. Thereby, miRNA-181a appeared as the most robust and stable potential biomarker, being significantly decreased by about 200-fold in exosomes of CKD patients compared to healthy controls. Using a cell culture system for CKD indicated that urinary exosomes might indeed originate from renal proximal tubular epithelial cells.
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MESH Headings
- Adult
- Aged
- Aged, 80 and over
- Biomarkers/urine
- Case-Control Studies
- Early Diagnosis
- Epithelial Cells/metabolism
- Epithelial Cells/pathology
- Exosomes/chemistry
- Exosomes/metabolism
- Female
- Glomerular Filtration Rate
- High-Throughput Nucleotide Sequencing
- Humans
- Kidney Tubules, Proximal/metabolism
- Kidney Tubules, Proximal/pathology
- Male
- MicroRNAs/urine
- Middle Aged
- Molecular Sequence Annotation
- RNA/urine
- RNA, Long Noncoding/urine
- RNA, Mitochondrial
- RNA, Transfer/urine
- Renal Insufficiency, Chronic/diagnosis
- Renal Insufficiency, Chronic/pathology
- Renal Insufficiency, Chronic/urine
- Sequence Analysis, RNA
- Severity of Illness Index
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Affiliation(s)
- Rimpi Khurana
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Glory Ranches
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Simon Schafferer
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Melanie Lukasser
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Michael Rudnicki
- Department of Internal Medicine IV, Nephrology and Hypertension, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Gert Mayer
- Department of Internal Medicine IV, Nephrology and Hypertension, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Hüttenhofer
- Division of Genomics and RNomics, Biocenter, Medical University Innsbruck, 6020 Innsbruck, Austria
- i-med GenomeSeq Core, 6020 Innsbruck, Austria
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9
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Duechler M, Leszczyńska G, Sochacka E, Nawrot B. Nucleoside modifications in the regulation of gene expression: focus on tRNA. Cell Mol Life Sci 2016; 73:3075-95. [PMID: 27094388 PMCID: PMC4951516 DOI: 10.1007/s00018-016-2217-y] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 03/25/2016] [Accepted: 04/04/2016] [Indexed: 01/10/2023]
Abstract
Both, DNA and RNA nucleoside modifications contribute to the complex multi-level regulation of gene expression. Modified bases in tRNAs modulate protein translation rates in a highly dynamic manner. Synonymous codons, which differ by the third nucleoside in the triplet but code for the same amino acid, may be utilized at different rates according to codon-anticodon affinity. Nucleoside modifications in the tRNA anticodon loop can favor the interaction with selected codons by stabilizing specific base pairs. Similarly, weakening of base pairing can discriminate against binding to near-cognate codons. mRNAs enriched in favored codons are translated in higher rates constituting a fine-tuning mechanism for protein synthesis. This so-called codon bias establishes a basic protein level, but sometimes it is necessary to further adjust the production rate of a particular protein to actual requirements, brought by, e.g., stages in circadian rhythms, cell cycle progression or exposure to stress. Such an adjustment is realized by the dynamic change of tRNA modifications resulting in the preferential translation of mRNAs coding for example for stress proteins to facilitate cell survival. Furthermore, tRNAs contribute in an entirely different way to another, less specific stress response consisting in modification-dependent tRNA cleavage that contributes to the general down-regulation of protein synthesis. In this review, we summarize control functions of nucleoside modifications in gene regulation with a focus on recent findings on protein synthesis control by tRNA base modifications.
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Affiliation(s)
- Markus Duechler
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland.
| | - Grażyna Leszczyńska
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Elzbieta Sochacka
- Institute of Organic Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Barbara Nawrot
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
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