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van Zonneveld AJ, Zhao Q, Rotmans JI, Bijkerk R. Circulating non-coding RNAs in chronic kidney disease and its complications. Nat Rev Nephrol 2023; 19:573-586. [PMID: 37286733 DOI: 10.1038/s41581-023-00725-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/09/2023]
Abstract
Post-transcriptional regulation by non-coding RNAs (ncRNAs) can modulate the expression of genes involved in kidney physiology and disease. A large variety of ncRNA species exist, including microRNAs, long non-coding RNAs, piwi-interacting RNAs, small nucleolar RNAs, circular RNAs and yRNAs. Despite early assumptions that some of these species may exist as by-products of cell or tissue injury, a growing body of literature suggests that these ncRNAs are functional and participate in a variety of processes. Although they function intracellularly, ncRNAs are also present in the circulation, where they are carried by extracellular vesicles, ribonucleoprotein complexes or lipoprotein complexes such as HDL. These systemic, circulating ncRNAs are derived from specific cell types and can be directly transferred to a variety of cells, including endothelial cells of the vasculature and virtually any cell type in the kidney, thereby affecting the function of the host cell and/or its response to injury. Moreover, chronic kidney disease itself, as well as injury states associated with transplantation and allograft dysfunction, is associated with a shift in the distribution of circulating ncRNAs. These findings may provide opportunities for the identification of biomarkers with which to monitor disease progression and/or the development of therapeutic interventions.
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Affiliation(s)
- Anton Jan van Zonneveld
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Qiao Zhao
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Joris I Rotmans
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Roel Bijkerk
- Department of Internal Medicine (Nephrology), Leiden University Medical Center, Leiden, the Netherlands.
- Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands.
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Shen L, Liao T, Chen Q, Lei Y, Wang L, Gu H, Qiu Y, Zheng T, Yang Y, Wei C, Chen L, Zhao Y, Niu L, Zhang S, Zhu Y, Li M, Wang J, Li X, Gan M, Zhu L. tRNA-derived small RNA, 5'tiRNA-Gly-CCC, promotes skeletal muscle regeneration through the inflammatory response. J Cachexia Sarcopenia Muscle 2023; 14:1033-1045. [PMID: 36755335 PMCID: PMC10067481 DOI: 10.1002/jcsm.13187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 12/07/2022] [Accepted: 01/16/2023] [Indexed: 02/10/2023] Open
Abstract
BACKGROUND Increasing evidence shows that tRNA-derived small RNAs (tsRNAs) are not only by-products of transfer RNAs, but they participate in numerous cellular metabolic processes. However, the role of tsRNAs in skeletal muscle regeneration remains unknown. METHODS Small RNA sequencing revealed the relationship between tsRNAs and skeletal muscle injury. The dynamic expression level of 5'tiRNA-Gly after muscle injury was confirmed by real-time quantitative PCR (q-PCR). In addition, q-PCR, flow cytometry, the 5-ethynyl-2'-deoxyuridine (Edu), cell counting kit-8, western blotting and immunofluorescence were used to explore the biological function of 5'tiRNA-Gly. Bioinformatics analysis and dual-luciferase reporter assay were used to further explore the mechanism of action under the biological function of 5'tiRNA-Gly. RESULTS Transcriptome analysis revealed that tsRNAs were significantly enriched during inflammatory response immediately after muscle injury. Interestingly, we found that 5'tiRNA-Gly was significantly up-regulated after muscle injury (P < 0.0001) and had a strong positive correlation with inflammation in vivo. In vitro experiments showed that 5'tiRNA-Gly promoted the mRNA expression of proinflammatory cytokines (IL-1β, P = 0.0468; IL-6, P = 0.0369) and the macrophages of M1 markers (TNF-α, P = 0.0102; CD80, P = 0.0056; MCP-1, P = 0.0002). On the contrary, 5'tiRNA-Gly inhibited the mRNA expression of anti-inflammatory cytokines (IL-4, P = 0.0009; IL-10, P = 0.0007; IL-13, P = 0.0008) and the mRNA expression of M2 markers (TGF-β1, P = 0.0016; ARG1, P = 0.0083). Flow cytometry showed that 5'tiRNA-Gly promoted the percentage of CD86+ macrophages (16%, P = 0.011) but inhibited that of CD206+ macrophages (10.5%, P = 0.012). Immunofluorescence showed that knockdown of 5'tiRNA-Gly increased the infiltration of M2 macrophages to the skeletal muscles (13.9%, P = 0.0023) and inhibited the expression of Pax7 (P = 0.0089) in vivo. 5'tiRNA-Gly promoted myoblast the expression of myogenic differentiation marker genes (MyoD, P = 0.0002; MyoG, P = 0.0037) and myotube formation (21.3%, P = 0.0016) but inhibited the positive rate of Edu (27.7%, P = 0.0001), cell viability (22.6%, P = 0.003) and the number of myoblasts in the G2 phase (26.3%, P = 0.0016) in vitro. Mechanistically, we found that the Tgfbr1 gene is a direct target of 5'tiRNA-Gly mediated by AGO1 and AGO3. 5'tiRNA-Gly dysregulated the expression of downstream genes related to inflammatory response, activation of satellite cells and differentiation of myoblasts through the TGF-β signalling pathway by targeting Tgfbr1. CONCLUSIONS These results reveal that 5'tiRNA-Gly potentially regulated skeletal muscle regeneration by inducing inflammation via the TGF-β signalling pathway. The findings of this study uncover a new potential target for skeletal muscle regeneration treatment.
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Affiliation(s)
- Linyuan Shen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Tianci Liao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Qiuyang Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yuhang Lei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Linghui Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Hao Gu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yanhao Qiu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Ting Zheng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yiting Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Chenggang Wei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lei Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Ye Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Lili Niu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Shunhua Zhang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Yan Zhu
- College of Life Science, China West Normal University, Nanchong, China
| | - Mingzhou Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Jinyong Wang
- Chongqing Academy of Animal Science, Chongqing, China
| | - Xuewei Li
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Mailin Gan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
| | - Li Zhu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China.,Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, Institute of Animal Genetics and Breeding, Sichuan Agricultural University, Chengdu, China
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Williams AM, Jensen DM, Pan X, Liu P, Liu J, Huls S, Regner KR, Iczkowski KA, Wang F, Li J, Gallan AJ, Wang T, Baker MA, Liu Y, Lalehzari N, Liang M. Histologically resolved small RNA maps in primary focal segmental glomerulosclerosis indicate progressive changes within glomerular and tubulointerstitial regions. Kidney Int 2022; 101:766-778. [PMID: 35114200 PMCID: PMC8940673 DOI: 10.1016/j.kint.2021.12.030] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 10/06/2021] [Accepted: 12/23/2021] [Indexed: 12/19/2022]
Abstract
Pathological heterogeneity is common in clinical tissue specimens and complicates the interpretation of molecular data obtained from the specimen. As a typical example, a kidney biopsy specimen often contains glomeruli and tubulointerstitial regions with different levels of histological injury, including some that are histologically normal. We reasoned that the molecular profiles of kidney tissue regions with specific histological injury scores could provide new insights into kidney injury progression. Therefore, we developed a strategy to perform small RNA deep sequencing analysis for individually scored glomerular and tubulointerstitial regions in formalin-fixed, paraffin-embedded kidney needle biopsies. This approach was applied to study focal segmental glomerulosclerosis (FSGS), the leading cause of nephrotic syndrome in adults. Large numbers of small RNAs, including microRNAs, 3'-tRFs, 5'-tRFs, and mitochondrial tRFs, were differentially expressed between histologically indistinguishable tissue regions from patients with FSGS and matched healthy controls. A majority of tRFs were upregulated in FSGS. Several small RNAs were differentially expressed between tissue regions with different histological scores in FSGS. Notably, with increasing levels of histological damage, miR-21-5p was upregulated progressively and miR-192-5p was downregulated progressively in glomerular and tubulointerstitial regions, respectively. This study marks the first genome scale molecular profiling conducted in histologically characterized glomerular and tubulointerstitial regions. Thus, substantial molecular changes in histologically normal kidney regions in FSGS might contribute to initiating tissue injury or represent compensatory mechanisms. In addition, several small RNAs might contribute to subsequent progression of glomerular and tubulointerstitial injury, and histologically mapping small RNA profiles may be applied to analyze tissue specimens in any disease.
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Affiliation(s)
- Anna Marie Williams
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - David M Jensen
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Xiaoqing Pan
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA; Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Pengyuan Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Jing Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Sean Huls
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kevin R Regner
- Division of Nephrology, Department of Medicine, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Kenneth A Iczkowski
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Feng Wang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Junhui Li
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Alexander J Gallan
- Department of Pathology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Tao Wang
- Division of Biostatistics, Institute of Health and Equity, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Maria Angeles Baker
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Yong Liu
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Nava Lalehzari
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA
| | - Mingyu Liang
- Center of Systems Molecular Medicine, Department of Physiology, Medical College of Wisconsin, Milwaukee, Wisconsin, USA.
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