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Verheyden NA, Klostermann M, Brüggemann M, Steede H, Scholz A, Amr S, Lichtenthaeler C, Münch C, Schmid T, Zarnack K, Krueger A. A high-resolution map of functional miR-181 response elements in the thymus reveals the role of coding sequence targeting and an alternative seed match. Nucleic Acids Res 2024; 52:8515-8533. [PMID: 38783381 PMCID: PMC11317165 DOI: 10.1093/nar/gkae416] [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: 09/14/2023] [Revised: 04/25/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
MicroRNAs (miRNAs) are critical post-transcriptional regulators in many biological processes. They act by guiding RNA-induced silencing complexes to miRNA response elements (MREs) in target mRNAs, inducing translational inhibition and/or mRNA degradation. Functional MREs are expected to predominantly occur in the 3' untranslated region and involve perfect base-pairing of the miRNA seed. Here, we generate a high-resolution map of miR-181a/b-1 (miR-181) MREs to define the targeting rules of miR-181 in developing murine T cells. By combining a multi-omics approach with computational high-resolution analyses, we uncover novel miR-181 targets and demonstrate that miR-181 acts predominantly through RNA destabilization. Importantly, we discover an alternative seed match and identify a distinct set of targets with repeat elements in the coding sequence which are targeted by miR-181 and mediate translational inhibition. In conclusion, deep profiling of MREs in primary cells is critical to expand physiologically relevant targetomes and establish context-dependent miRNA targeting rules.
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Affiliation(s)
- Nikita A Verheyden
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Melina Klostermann
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Mirko Brüggemann
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Hanna M Steede
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
| | - Anica Scholz
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Shady Amr
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Chiara Lichtenthaeler
- Institute of Molecular Medicine, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, 60590 Frankfurt am Main, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences & Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt am Main, Germany
| | - Andreas Krueger
- Molecular Immunology, Justus Liebig University Gießen, 35392 Gießen, Germany
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2
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Xu Z, Sziraki A, Lee J, Zhou W, Cao J. Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. Nat Biotechnol 2024; 42:1218-1223. [PMID: 37749268 PMCID: PMC10961254 DOI: 10.1038/s41587-023-01948-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 08/15/2023] [Indexed: 09/27/2023]
Abstract
We present a combinatorial indexing method, PerturbSci-Kinetics, for capturing whole transcriptomes, nascent transcriptomes and single guide RNA (sgRNA) identities across hundreds of genetic perturbations at the single-cell level. Profiling a pooled CRISPR screen targeting various biological processes, we show the gene expression regulation during RNA synthesis, processing and degradation, miRNA biogenesis and mitochondrial mRNA processing, systematically decoding the genome-wide regulatory network that underlies RNA temporal dynamics at scale.
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Affiliation(s)
- Zihan Xu
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Andras Sziraki
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
- The David Rockefeller Graduate Program in Bioscience, The Rockefeller University, New York, NY, USA
| | - Jasper Lee
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Wei Zhou
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA
| | - Junyue Cao
- Laboratory of Single Cell Genomics and Population Dynamics, The Rockefeller University, New York, NY, USA.
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3
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Zhou X, Dai N, Yu D, Niu T, Wang S. Exploring galectin-3's role in predicting mild cognitive impairment in type 2 diabetes and its regulation by miRNAs. Front Med (Lausanne) 2024; 11:1443133. [PMID: 39144658 PMCID: PMC11322075 DOI: 10.3389/fmed.2024.1443133] [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: 06/05/2024] [Accepted: 07/22/2024] [Indexed: 08/16/2024] Open
Abstract
Objective This study aimed to investigate the role of galectin-3 (Gal-3; coded by LGALS3 gene), as a biomarker for MCI in T2DM patients and to develop and validate a predictive nomogram integrating galectin-3 with clinical risk factors for MCI prediction. Additionally, microRNA regulation of LGALS3 was explored. Methods The study employed a cross-sectional design. A total of 329 hospitalized T2DM patients were recruited and randomly allocated into a training cohort (n = 231) and a validation cohort (n = 98) using 7:3 ratio. Demographic data and neuropsychological assessments were recorded for all participants. Plasma levels of galectin-3 were measured using ELISA assay. We employed Spearman's correlation and multivariable linear regression to analyze the relationship between galectin-3 levels and cognitive performance. Furthermore, univariate and multivariate logistic regression analyses were conducted to identify independent risk factors for MCI in T2DM patients. Based on these analyses, a predictive nomogram incorporating galectin-3 and clinical predictors was developed. The model's performance was evaluated in terms of discrimination, calibration, and clinical utility. Regulatory miRNAs were identified using bioinformatics and their interactions with LGALS3 were confirmed through qRT-PCR and luciferase reporter assays. Results Galectin-3 was identified as an independent risk factor for MCI, with significant correlations to cognitive decline in T2DM patients. The developed nomogram, incorporating Gal-3, age, and education levels, demonstrated excellent predictive performance with an AUC of 0.813 in the training cohort and 0.775 in the validation cohort. The model outperformed the baseline galectin-3 model and showed a higher net benefit in clinical decision-making. Hsa-miR-128-3p was significantly downregulated in MCI patients, correlating with increased Gal-3 levels, while Luciferase assays confirmed miR-128-3p's specific binding and influence on LGALS3. Conclusion Our findings emphasize the utility of Gal-3 as a viable biomarker for early detection of MCI in T2DM patients. The validated nomogram offers a practical tool for clinical decision-making, facilitating early interventions to potentially delay the progression of cognitive impairment. Additionally, further research on miRNA128's regulation of Gal-3 levels is essential to substantiate our results.
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Affiliation(s)
- Xueling Zhou
- School of Medicine, Southeast University, Nanjing, China
- Department of Endocrinology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Ning Dai
- Department of ENT, Maanshan People’s Hospital, Maanshan, China
| | - Dandan Yu
- School of Medicine, Southeast University, Nanjing, China
- Department of Endocrinology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Tong Niu
- School of Medicine, Southeast University, Nanjing, China
- Department of Endocrinology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
| | - Shaohua Wang
- School of Medicine, Southeast University, Nanjing, China
- Department of Endocrinology, Affiliated Zhongda Hospital of Southeast University, Nanjing, China
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4
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Wang C, Fu R, Wang Y, Wei J, Yu Y, Hu L, Zhang C. miR-124-3p and miR-194-5p regulation of the PI3K/AKT pathway via ROR2 in medulloblastoma progression. Cancer Gene Ther 2024; 31:941-954. [PMID: 38632356 PMCID: PMC11192632 DOI: 10.1038/s41417-024-00762-y] [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: 12/25/2023] [Revised: 03/01/2024] [Accepted: 03/07/2024] [Indexed: 04/19/2024]
Abstract
Medulloblastoma (MB), a prevalent pediatric central nervous system tumor, is influenced by microRNAs (miRNAs) that impact tumor initiation and progression. However, the specific involvement of miRNAs in MB tumorigenesis remains unclear. Using single-cell RNA sequencing, we identified ROR2 expression in normal human fetal cerebellum. Subsequent analyses, including immunofluorescence, quantitative real-time PCR (qRT-PCR), and Western blot, assessed ROR2 expression in MB tissues and cell lines. We investigated miR-124-3p and miR-194-5p and their regulatory role in ROR2 expression through the dual-luciferase reporter, qRT-PCR, and western blot assays. Mechanistic insights were gained through functional assays exploring the impact of miR-124-3p, miR-194-5p, and ROR2 on MB growth in vitro and in vivo. We observed significantly reduced miR-124-3p and miR-194-5p expression and elevated ROR2 expression in MB tissues and cell lines. High ROR2 expression inversely correlated with overall survival in WNT and SHH subgroups of MB patients. Functionally, overexpressing miR-124-3p and miR-194-5p and inhibiting ROR2 suppressed in vitro malignant transformation and in vivo tumorigenicity. Mechanistically, miR-124-3p and miR-194-5p synergistically regulated the ROR2/PI3K/Akt pathway, influencing MB progression. Our findings indicate that miR-124-3p and miR-194-5p function as tumor suppressors, inhibiting MB progression via the ROR2/PI3K/Akt axis, suggesting a key mechanism and therapeutic targets for MB patients.
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Affiliation(s)
- Chen Wang
- Department of Pediatric Neurosurgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Runxi Fu
- Department of Pediatric Surgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- Shanghai Institute for Pediatric Research, Shanghai, China
| | - Yunkun Wang
- Department of Pediatric Neurosurgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jia Wei
- Department of Pediatric Neurosurgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Ying Yu
- Department of Pediatric Neurosurgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liuhua Hu
- Department of Cardiology, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Chenran Zhang
- Department of Pediatric Neurosurgery, Xinhua Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Gambari R, Finotti A. Therapeutic Relevance of Inducing Autophagy in β-Thalassemia. Cells 2024; 13:918. [PMID: 38891049 PMCID: PMC11171814 DOI: 10.3390/cells13110918] [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: 03/22/2024] [Revised: 05/09/2024] [Accepted: 05/22/2024] [Indexed: 06/20/2024] Open
Abstract
The β-thalassemias are inherited genetic disorders affecting the hematopoietic system. In β-thalassemias, more than 350 mutations of the adult β-globin gene cause the low or absent production of adult hemoglobin (HbA). A clinical parameter affecting the physiology of erythroid cells is the excess of free α-globin. Possible experimental strategies for a reduction in excess free α-globin chains in β-thalassemia are CRISPR-Cas9-based genome editing of the β-globin gene, forcing "de novo" HbA production and fetal hemoglobin (HbF) induction. In addition, a reduction in excess free α-globin chains in β-thalassemia can be achieved by induction of the autophagic process. This process is regulated by the Unc-51-like kinase 1 (Ulk1) gene. The interplay with the PI3K/Akt/TOR pathway, with the activity of the α-globin stabilizing protein (AHSP) and the involvement of microRNAs in autophagy and Ulk1 gene expression, is presented and discussed in the context of identifying novel biomarkers and potential therapeutic targets for β-thalassemia.
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Affiliation(s)
| | - Alessia Finotti
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy;
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Che D, Xiang X, Xie J, Chen Z, Bao Q, Cao D. Exosomes Derived from Adipose Stem Cells Enhance Angiogenesis in Diabetic Wound Via miR-146a-5p/JAZF1 Axis. Stem Cell Rev Rep 2024; 20:1026-1039. [PMID: 38393667 PMCID: PMC11087353 DOI: 10.1007/s12015-024-10685-8] [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] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Chronic trauma in diabetes is a leading cause of disability and mortality. Exosomes show promise in tissue regeneration. This study investigates the role of exosomes derived from adipose stem cells (ADSC-Exos) in angiogenesis. MiRNA-seq analysis revealed significant changes in 47 genes in human umbilical vein endothelial cells (HUVECs) treated with ADSC-Exos, with miR-146a-5p highly expressed. MiR-146a-5p mimics enhanced the pro-angiogenic effects of ADSC-Exos, while inhibitors had the opposite effect. JAZF1 was identified as a direct downstream target of miR-146a-5p through bioinformatics, qRT-PCR, and dual luciferase assay. Overexpress of JAZF1 resulted in decreased proliferation, migration, and angiogenic capacity of HUVECs, and reduced VEGFA expression. This study proposes that ADSC-Exos regulate angiogenesis partly via the miR-146a-5p/JAZF1 axis.
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Affiliation(s)
- Dehui Che
- Department of Plastic and Reconstructive, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Xinjian Xiang
- Department of Plastic and Reconstructive, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Juan Xie
- Department of Plastic and Reconstructive, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Zenghong Chen
- Department of Plastic and Reconstructive, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Qiong Bao
- Department of Plastic and Reconstructive, The Second Affiliated Hospital of Anhui Medical University, Hefei, China
| | - Dongsheng Cao
- Department of Plastic and Reconstructive, The Second Affiliated Hospital of Anhui Medical University, Hefei, China.
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Xiang C, Hong SM, Zhao B, Pi H, Du F, Lu X, Tang Y, Shen N, Yang C, Wang R. Fibroblast expression of neurotransmitter receptor HTR2A associates with inflammation in rheumatoid arthritis joint. Clin Exp Med 2024; 24:84. [PMID: 38662111 PMCID: PMC11045650 DOI: 10.1007/s10238-024-01352-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: 12/06/2023] [Accepted: 04/09/2024] [Indexed: 04/26/2024]
Abstract
The study of neuroimmune crosstalk and the involvement of neurotransmitters in inflammation and bone health has illustrated their significance in joint-related conditions. One important mode of cell-to-cell communication in the synovial fluid (SF) is through extracellular vesicles (EVs) carrying microRNAs (miRNAs). The role of neurotransmitter receptors in the pathogenesis of inflammatory joint diseases, and whether there are specific miRNAs regulating differentially expressed HTR2A, contributing to the inflammatory processes and bone metabolism is unclear. Expression of neurotransmitter receptors and their correlated inflammatory molecules were identified in rheumatoid arthritis (RA) and osteoarthritis (OA) synovium from a scRNA-seq dataset. Immunohistochemistry staining of synovial tissue (ST) from RA and OA patients was performed for validation. Expression of miRNAs targeting HTR2A carried by SF EVs was screened in low- and high-grade inflammation RA from a public dataset and validated by qPCR. HTR2A reduction by target miRNAs was verified by miRNAs mimics transfection into RA fibroblasts. HTR2A was found to be highly expressed in fibroblasts derived from RA synovial tissue. Its expression showed a positive correlation with the degree of inflammation observed. 5 miRNAs targeting HTR2A were decreased in RA SF EVs compared to OA, three of which, miR-214-3p, miR-3120-5p and miR-615-3p, mainly derived from monocytes in the SF, were validated as regulators of HTR2A expression. The findings suggest that fibroblast HTR2A may play a contributory role in inflammation and the pathogenesis of RA. Additionally, targeting miRNAs that act upon HTR2A could present novel therapeutic strategies for alleviating inflammation in RA.
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Affiliation(s)
- Chunyan Xiang
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China
| | - Soon-Min Hong
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China
| | - Bingjiao Zhao
- Department of Orthodontics, Shanghai Stomatological Hospital & School of Stomatology, Fudan University, Shanghai, China
| | - Hui Pi
- Jiangxi Provincial People's Hospital, The First Affiliated Hospital of Nanchang Medical College, Nanchang, China
| | - Fang Du
- Department of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China
| | - Xingyu Lu
- Department of Endocrinology, Xinhua Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China
| | - Yuanjia Tang
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China
| | - Nan Shen
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China.
| | - Chunxi Yang
- Department of Orthopedics, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China.
| | - Runci Wang
- Shanghai Institute of Rheumatology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University (SJTUSM), Shanghai, China.
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Li N, Sun Y, Liu Y, Wei L, Zhang J, Li N, Sun D, Jiao J, Zuo Y, Li R, Cai X, Qiao J, Meng Q. Expression profiles and characterization of microRNAs responding to chitin in Arthrobotrys oligospora. Arch Microbiol 2024; 206:220. [PMID: 38630188 DOI: 10.1007/s00203-024-03949-x] [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: 01/03/2024] [Revised: 03/25/2024] [Accepted: 04/01/2024] [Indexed: 04/19/2024]
Abstract
Extracellular proteases, such as chitinases secreted by Arthrobotrys oligospora (A. oligospora), play a crucial role in the process of nematode infection. However, post-transcriptional regulation of gene expression involving microRNAs (miRNAs) in A. oligospora remains scarcely described. Hereto, transcriptome sequencing was carried out to analyze the expression profiles of chitin-responsive miRNAs in A. oligospora. Based on the RNA-seq data, the differential expression of miRNAs (DEmiRNAs) in response to chitin was screened, identified and characterized in A. oligospora. Meanwhile, the potential target genes were predicted by the online tools miRanda and Targetscan, respectively. Furthermore, the interaction of DEmiRNA with it's target gene was validated by a dual-luciferase reporter assay system. Among 85 novel miRNAs identified, 25 miRNAs displayed significant differences in expression in A. oligospora in response to chitin. Gene Ontology (GO) analysis showed that the potential genes targeted by DEmiRNAs were enriched in the biological processes such as bio-degradation, extracellular components and cell cycle. KEGG analysis revealed that the target genes were mainly involved in Hippo, carbon and riboflavin metabolic pathway. Outstandingly, chitinase AOL_s00004g379, which is involved in the hydrolysis metabolic pathway of chitin, was confirmed to be a target gene of differential miR_70. These findings suggest that chitin-responsive miRNAs are involved in the regulation of cell proliferation, predator hyphae growth and chitinase expression through the mechanisms of post-transcriptional regulation, which provides a new perspective to the molecular mechanisms underlying miRNAs-mediated control of gene expression in A. oligospora.
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Affiliation(s)
- Ningxing Li
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Yansen Sun
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Yucheng Liu
- State key laboratory of sheep genetic improvement and healthy breeding, Institute of Animal Science and Veterinary Research, Xinjiang Academy of Agricultural and Reclamation Science, Shihezi, 832000, Xinjiang, China
| | - Lixiang Wei
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Jiahua Zhang
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Nengxiu Li
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Dianming Sun
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Jian Jiao
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Yufei Zuo
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Ruobing Li
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China
| | - Xuepeng Cai
- State key laboratory of veterinary etiological biology, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, 730046, Gansu, China
| | - Jun Qiao
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China.
| | - Qingling Meng
- College of Animal Science and Technology, Shihezi University, North Street No.4, Shihezi, 832003, Xinjiang, China.
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9
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Varsha KK, Yang X, Cannon AS, Zhong Y, Nagarkatti M, Nagarkatti P. Identification of miRNAs that target Fcγ receptor-mediated phagocytosis during macrophage activation syndrome. Front Immunol 2024; 15:1355315. [PMID: 38558807 PMCID: PMC10981272 DOI: 10.3389/fimmu.2024.1355315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 02/27/2024] [Indexed: 04/04/2024] Open
Abstract
Macrophage activation syndrome (MAS) is a life-threatening complication of systemic juvenile arthritis, accompanied by cytokine storm and hemophagocytosis. In addition, COVID-19-related hyperinflammation shares clinical features of MAS. Mechanisms that activate macrophages in MAS remain unclear. Here, we identify the role of miRNA in increased phagocytosis and interleukin-12 (IL-12) production by macrophages in a murine model of MAS. MAS significantly increased F4/80+ macrophages and phagocytosis in the mouse liver. Gene expression profile revealed the induction of Fcγ receptor-mediated phagocytosis (FGRP) and IL-12 production in the liver. Phagocytosis pathways such as High-affinity IgE receptor is known as Fc epsilon RI -signaling and pattern recognition receptors involved in the recognition of bacteria and viruses and phagosome formation were also significantly upregulated. In MAS, miR-136-5p and miR-501-3p targeted and caused increased expression of Fcgr3, Fcgr4, and Fcgr1 genes in FGRP pathway and consequent increase in phagocytosis by macrophages, whereas miR-129-1-3p and miR-150-3p targeted and induced Il-12. Transcriptome analysis of patients with MAS revealed the upregulation of FGRP and FCGR gene expression. A target analysis of gene expression data from a patient with MAS discovered that miR-136-5p targets FCGR2A and FCGR3A/3B, the human orthologs of mouse Fcgr3 and Fcgr4, and miR-501-3p targets FCGR1A, the human ortholog of mouse Fcgr1. Together, we demonstrate the novel role of miRNAs during MAS pathogenesis, thereby suggesting miRNA mimic-based therapy to control the hyperactivation of macrophages in patients with MAS as well as use overexpression of FCGR genes as a marker for MAS classification.
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Affiliation(s)
| | | | | | | | | | - Prakash Nagarkatti
- Department of Pathology, Microbiology and Immunology, School of Medicine, University of South Carolina School of Medicine, Columbia, SC, United States
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Sessa R, Trombetti S, Bianco AL, Amendola G, Catapano R, Cesaro E, Petruzziello F, D'Armiento M, Maruotti GM, Menna G, Izzo P, Grosso M. miR-1202 acts as anti-oncomiR in myeloid leukaemia by down-modulating GATA-1 S expression. Open Biol 2024; 14:230319. [PMID: 38350611 PMCID: PMC10864098 DOI: 10.1098/rsob.230319] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 11/21/2023] [Indexed: 02/15/2024] Open
Abstract
Transient abnormal myelopoiesis (TAM) is a Down syndrome-related pre-leukaemic condition characterized by somatic mutations in the haematopoietic transcription factor GATA-1 that result in exclusive production of its shorter isoform (GATA-1S). Given the common hallmark of altered miRNA expression profiles in haematological malignancies and the pro-leukaemic role of GATA-1S, we aimed to search for miRNAs potentially able to modulate the expression of GATA-1 isoforms. Starting from an in silico prediction of miRNA binding sites in the GATA-1 transcript, miR-1202 came into our sight as potential regulator of GATA-1 expression. Expression studies in K562 cells revealed that miR-1202 directly targets GATA-1, negatively regulates its expression, impairs GATA-1S production, reduces cell proliferation, and increases apoptosis sensitivity. Furthermore, data from TAM and myeloid leukaemia patients provided substantial support to our study by showing that miR-1202 down-modulation is accompanied by increased GATA-1 levels, with more marked effects on GATA-1S. These findings indicate that miR-1202 acts as an anti-oncomiR in myeloid cells and may impact leukaemogenesis at least in part by down-modulating GATA-1S levels.
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Affiliation(s)
- Raffaele Sessa
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Silvia Trombetti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- Department of Veterinary Medicine and Animal Productions, University of Naples Federico II, Naples, Italy
| | - Alessandra Lo Bianco
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Giovanni Amendola
- Department of Pediatrics and Intensive Care Unit, Umberto I Hospital, Nocera Inferiore, Italy
| | - Rosa Catapano
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Elena Cesaro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
| | - Fara Petruzziello
- Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples, Italy
| | - Maria D'Armiento
- Department of Public Health, Section of Pathology, University of Naples Federico II, Naples, Italy
| | - Giuseppe Maria Maruotti
- Gynecology and Obstetrics Unit, Department of Neuroscience, Reproductive Sciences and Dentistry, University of Naples Federico II, Naples, Italy
| | - Giuseppe Menna
- Department of Pediatric Hemato-Oncology, AORN Santobono-Pausilipon, Naples, Italy
| | - Paola Izzo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate 'Franco Salvatore', Naples, Italy
| | - Michela Grosso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Naples, Italy
- CEINGE-Biotecnologie Avanzate 'Franco Salvatore', Naples, Italy
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11
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Shan T, Liu F, Wen M, Chen Z, Li S, Wang Y, Cheng H, Zhou Y. m 6A modification negatively regulates translation by switching mRNA from polysome to P-body via IGF2BP3. Mol Cell 2023; 83:4494-4508.e6. [PMID: 38016476 DOI: 10.1016/j.molcel.2023.10.040] [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: 08/16/2022] [Revised: 07/10/2023] [Accepted: 10/26/2023] [Indexed: 11/30/2023]
Abstract
In the cytoplasm, mRNAs are dynamically partitioned into translating and non-translating pools, but the mechanism for this regulation has largely remained elusive. Here, we report that m6A regulates mRNA partitioning between polysome and P-body where a pool of non-translating mRNAs resides. By quantifying the m6A level of polysomal and cytoplasmic mRNAs with m6A-LAIC-seq and m6A-LC-MS/MS in HeLa cells, we observed that polysome-associated mRNAs are hypo-m6A-methylated, whereas those enriched in P-body are hyper-m6A-methylated. Downregulation of the m6A writer METTL14 enhances translation by switching originally hyper-m6A-modified mRNAs from P-body to polysome. Conversely, by proteomic analysis, we identify a specific m6A reader IGF2BP3 enriched in P-body, and via knockdown and molecular tethering assays, we demonstrate that IGF2BP3 is both necessary and sufficient to switch target mRNAs from polysome to P-body. These findings suggest a model for the dynamic regulation of mRNA partitioning between the translating and non-translating pools in an m6A-dependent manner.
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Affiliation(s)
- Ting Shan
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Feiyan Liu
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Miaomiao Wen
- Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Zonggui Chen
- Institute of Advanced Studies, Wuhan University, Wuhan, China
| | - Shaopeng Li
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China
| | - Yafen Wang
- School of Public Health, Wuhan University, Wuhan, China
| | - Hong Cheng
- State Key Laboratory of Molecular Biology, CAS Center for Excellence in Molecular Cell Science, Shanghai Institute of Biochemistry and Cell Biology, Chinese Academy of Sciences, University of Chinese Academy of Sciences, Shanghai, China
| | - Yu Zhou
- College of Life Sciences, TaiKang Center for Life and Medical Sciences, RNA Institute, Hubei Key Laboratory of Cell Homeostasis, Wuhan University, Wuhan, China; Institute of Advanced Studies, Wuhan University, Wuhan, China; Frontier Science Center for Immunology and Metabolism, State Key Laboratory of Virology, Wuhan University, Wuhan, China.
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12
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Huang SH, Chen SC, Wu TY, Chen CY, Yu CH. Programmable modulation of ribosomal frameshifting by mRNA targeting CRISPR-Cas12a system. iScience 2023; 26:108492. [PMID: 38125012 PMCID: PMC10730746 DOI: 10.1016/j.isci.2023.108492] [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: 05/12/2023] [Revised: 09/13/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023] Open
Abstract
Minus 1 programmed ribosomal frameshifting (-1 PRF) is a conserved translational regulation event essential for critical biological processes, including the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) replication. Efficient trans-modulation of the structured RNA element crucial to -1 PRF will endow the therapeutic application. Here, we demonstrate that CRISPR RNA can stimulate efficient -1 PRF. Assembled CRISPR-Cas12a, but not CRISPR-Cas9, complex further enhances -1 PRF efficiency through its higher capacity to stall translating ribosomes. We additionally perform CRISPR-Cas12a targeting to impair the SARS-CoV-2 frameshifting pseudoknot structure via a focused screening. We demonstrate that targeting CRISPR-Cas12a results in more than 70% suppression of -1 PRF in vitro and about 50% suppression in mammalian cells. Our results show the expanded function of the CRISPR-Cas12 system in modulating -1 PRF efficiency through stalling ribosomes and deforming frameshifting stimulatory signals, which could serve as a new strategy for future coronavirus pandemics.
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Affiliation(s)
- Shih-Hong Huang
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Shih-Cheng Chen
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- National Institute of Cancer Research, National Health Research Institutes, Tainan, Taiwan
| | | | - Cheng-Yao Chen
- YD BioLabs, Inc., Hsinchu, Taiwan
- School of Medical Laboratory Science and Biotechnology, Taipei Medical University, Taipei, Taiwan
| | - Chien-Hung Yu
- Department of Biochemistry and Molecular Biology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
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13
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Shang R, Lee S, Senavirathne G, Lai EC. microRNAs in action: biogenesis, function and regulation. Nat Rev Genet 2023; 24:816-833. [PMID: 37380761 PMCID: PMC11087887 DOI: 10.1038/s41576-023-00611-y] [Citation(s) in RCA: 81] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/27/2023] [Indexed: 06/30/2023]
Abstract
Ever since microRNAs (miRNAs) were first recognized as an extensive gene family >20 years ago, a broad community of researchers was drawn to investigate the universe of small regulatory RNAs. Although core features of miRNA biogenesis and function were revealed early on, recent years continue to uncover fundamental information on the structural and molecular dynamics of core miRNA machinery, how miRNA substrates and targets are selected from the transcriptome, new avenues for multilevel regulation of miRNA biogenesis and mechanisms for miRNA turnover. Many of these latest insights were enabled by recent technological advances, including massively parallel assays, cryogenic electron microscopy, single-molecule imaging and CRISPR-Cas9 screening. Here, we summarize the current understanding of miRNA biogenesis, function and regulation, and outline challenges to address in the future.
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Affiliation(s)
- Renfu Shang
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Seungjae Lee
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Gayan Senavirathne
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA
| | - Eric C Lai
- Developmental Biology Program, Sloan Kettering Institute, New York, NY, USA.
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14
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Zhang RN, Jing ZQ, Zhang L, Sun ZJ. Epigenetic regulation of pyroptosis in cancer: Molecular pathogenesis and targeting strategies. Cancer Lett 2023; 575:216413. [PMID: 37769798 DOI: 10.1016/j.canlet.2023.216413] [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: 07/19/2023] [Revised: 09/02/2023] [Accepted: 09/23/2023] [Indexed: 10/02/2023]
Abstract
Immune checkpoint blockade therapy has revolutionized the field of cancer treatment, leading to durable responses in patients with advanced and metastatic cancers where conventional therapies were insufficient. However, factors like immunosuppressive cells and immune checkpoint molecules within the tumor microenvironment (TME) can suppress the immune system and thus negatively affect the efficiency of immune checkpoint inhibitors. Pyroptosis, a gasdermin-induced programmed cell death, could transform "cold tumors" to "hot tumors" to improve the milieu of TME, thus enhancing the immune response and preventing tumor growth. Recently, evidence showed that epigenetics could regulate pyroptosis, which further affects tumorigenesis, suggesting that epigenetics-based tumor cells pyroptosis could be a promising therapeutic strategy. Hence, this review focuses on the pyroptotic mechanism and summarizes three common types of epigenetics, DNA methylation, histone modification, and non-coding RNA, all of which have a role in regulating the expression of transcription factors and proteins involved in pyroptosis in cancer. Especially, we discuss targeting strategies on epigenetic-regulated pyroptosis and provide insights on the future trend of cancer research which may fuel cancer therapies into a new step.
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Affiliation(s)
- Ruo-Nan Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, China
| | - Zhi-Qian Jing
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, China
| | - Lu Zhang
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, China.
| | - Zhi-Jun Sun
- State Key Laboratory of Oral & Maxillofacial Reconstruction and Regeneration, Key Laboratory of Oral Biomedicine Ministry of Education, Hubei Key Laboratory of Stomatology, School & Hospital of Stomatology, Frontier Science Center for Immunology and Metabolism, Wuhan University, China; Department of Oral Maxillofacial-Head Neck Oncology, School & Hospital of Stomatology, Wuhan University, Wuhan, China.
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15
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Bauer AN, Majumdar N, Williams F, Rajput S, Pokhrel LR, Cook PP, Akula SM. MicroRNAs: Small but Key Players in Viral Infections and Immune Responses to Viral Pathogens. BIOLOGY 2023; 12:1334. [PMID: 37887044 PMCID: PMC10604607 DOI: 10.3390/biology12101334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 09/21/2023] [Accepted: 10/11/2023] [Indexed: 10/28/2023]
Abstract
Since the discovery of microRNAs (miRNAs) in C. elegans in 1993, the field of miRNA research has grown steeply. These single-stranded non-coding RNA molecules canonically work at the post-transcriptional phase to regulate protein expression. miRNAs are known to regulate viral infection and the ensuing host immune response. Evolving research suggests miRNAs are assets in the discovery and investigation of therapeutics and diagnostics. In this review, we succinctly summarize the latest findings in (i) mechanisms underpinning miRNA regulation of viral infection, (ii) miRNA regulation of host immune response to viral pathogens, (iii) miRNA-based diagnostics and therapeutics targeting viral pathogens and challenges, and (iv) miRNA patents and the market landscape. Our findings show the differential expression of miRNA may serve as a prognostic biomarker for viral infections in regard to predicting the severity or adverse health effects associated with viral diseases. While there is huge market potential for miRNA technology, the novel approach of using miRNA mimics to enhance antiviral activity or antagonists to inhibit pro-viral miRNAs has been an ongoing research endeavor. Significant hurdles remain in terms of miRNA delivery, stability, efficacy, safety/tolerability, and specificity. Addressing these challenges may pave a path for harnessing the full potential of miRNAs in modern medicine.
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Affiliation(s)
- Anais N. Bauer
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
| | - Niska Majumdar
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
| | - Frank Williams
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
| | - Smit Rajput
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
| | - Lok R. Pokhrel
- Department of Public Health, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
| | - Paul P. Cook
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
| | - Shaw M. Akula
- Department of Microbiology & Immunology, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA; (A.N.B.); (N.M.); (F.W.)
- Department of Internal Medicine, Brody School of Medicine, East Carolina University, Greenville, NC 27834, USA;
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16
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Sapkota S, Pillman K, Dredge B, Liu D, Bracken J, Kachooei S, Chereda B, Gregory P, Bracken C, Goodall G. On the rules of engagement for microRNAs targeting protein coding regions. Nucleic Acids Res 2023; 51:9938-9951. [PMID: 37522357 PMCID: PMC10570018 DOI: 10.1093/nar/gkad645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 07/13/2023] [Accepted: 07/23/2023] [Indexed: 08/01/2023] Open
Abstract
MiRNAs post-transcriptionally repress gene expression by binding to mRNA 3'UTRs, but the extent to which they act through protein coding regions (CDS regions) is less well established. MiRNA interaction studies show a substantial proportion of binding occurs in CDS regions, however sequencing studies show much weaker effects on mRNA levels than from 3'UTR interactions, presumably due to competition from the translating ribosome. Consequently, most target prediction algorithms consider only 3'UTR interactions. However, the consequences of CDS interactions may have been underestimated, with the reporting of a novel mode of miRNA-CDS interaction requiring base pairing of the miRNA 3' end, but not the canonical seed site, leading to repression of translation with little effect on mRNA turnover. Using extensive reporter, western blotting and bioinformatic analyses, we confirm that miRNAs can indeed suppress genes through CDS-interaction in special circumstances. However, in contrast to that previously reported, we find repression requires extensive base-pairing, including of the canonical seed, but does not strictly require base pairing of the 3' miRNA terminus and is mediated through reducing mRNA levels. We conclude that suppression of endogenous genes can occur through miRNAs binding to CDS, but the requirement for extensive base-pairing likely limits the regulatory impacts to modest effects on a small subset of targets.
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Affiliation(s)
- Sunil Sapkota
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Katherine A Pillman
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
- ACRF Cancer Genomics Facility, Centre for Cancer Biology, SA Pathology, Adelaide, SA 5000, Australia
| | - B Kate Dredge
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Dawei Liu
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Julie M Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Saba Ataei Kachooei
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Bradley Chereda
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
| | - Philip A Gregory
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
| | - Cameron P Bracken
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Adelaide
| | - Gregory J Goodall
- Centre for Cancer Biology, an alliance of SA Pathology and University of South Australia, Adelaide, SA 5000, Australia
- Faculty of Health and Medical Sciences, The University of Adelaide, Adelaide, SA 5000, Australia
- School of Biological Sciences, Faculty of Sciences, Engineering and Technology, The University of Adelaide, Adelaide, SA 5000, Adelaide
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17
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Farina FM, Weber C, Santovito D. The emerging landscape of non-conventional RNA functions in atherosclerosis. Atherosclerosis 2023; 374:74-86. [PMID: 36725418 DOI: 10.1016/j.atherosclerosis.2023.01.009] [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: 08/02/2022] [Revised: 12/15/2022] [Accepted: 01/12/2023] [Indexed: 01/22/2023]
Abstract
Most of the human genome is transcribed into non-coding RNAs (ncRNAs), which encompass a heterogeneous family of transcripts including microRNAs (miRNAs), long ncRNAs (lncRNAs), circular RNAs (circRNAs), and others. Although the detailed modes of action of some classes are not fully elucidated, the common notion is that ncRNAs contribute to sculpting gene expression of eukaryotic cells at multiple levels. These range from the regulation of chromatin remodeling and transcriptional activity to post-transcriptional regulation of messenger RNA splicing, stability, and decay. Many of these functions ultimately govern the expression of coding and non-coding genes to affect diverse physiological and pathological mechanisms in vascular biology and beyond. As such, different classes of ncRNAs emerged as crucial regulators of vascular integrity as well as active players in the pathophysiology of atherosclerosis from the early stages of endothelial dysfunction to the clinically relevant complications. However, research in recent years revealed unexpected findings such as small ncRNAs being able to biophysically regulate protein function, the glycosylation of ncRNAs to be exposed on the cell surface, the release of ncRNAs in the extracellular space to act as ligands of receptors, and even the ability of non-coding portion of messenger RNAs to mediate structural functions. This evidence expanded the functional repertoire of ncRNAs far beyond gene regulation and highlighted an additional layer of biological control of cell function. In this Review, we will discuss these emerging aspects of ncRNA biology, highlight the implications for the mechanisms of vascular biology and atherosclerosis, and discuss possible translational implications.
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Affiliation(s)
- Floriana Maria Farina
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, the Netherlands; Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
| | - Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximillians-Universität (LMU), Munich, Germany; German Center for Cardiovascular Research (DZHK), Partner Site Munich Heart Alliance, Munich, Germany; Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
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18
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Xu Z, Sziraki A, Lee J, Zhou W, Cao J. PerturbSci-Kinetics: Dissecting key regulators of transcriptome kinetics through scalable single-cell RNA profiling of pooled CRISPR screens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.29.526143. [PMID: 36778497 PMCID: PMC9915486 DOI: 10.1101/2023.01.29.526143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Here we described PerturbSci-Kinetics, a novel combinatorial indexing method for capturing three-layer single-cell readout (i.e., whole transcriptomes, nascent transcriptomes, sgRNA identities) across hundreds of genetic perturbations. Through PerturbSci-Kinetics profiling of pooled CRISPR screens targeting a variety of biological processes, we were able to decipher the complexity of RNA regulations at multiple levels (e.g., synthesis, processing, degradation), and revealed key regulators involved in miRNA and mitochondrial RNA processing pathways. Our technique opens the possibility of systematically decoding the genome-wide regulatory network underlying RNA temporal dynamics at scale and cost-effectively.
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19
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Yoo M, Choi DC, Murphy A, Ahsan AM, Junn E. MicroRNA-593-5p contributes to cell death following exposure to 1-methyl-4-phenylpyridinium (MPP +) by targeting PTEN-induced putative kinase 1 (PINK1). J Biol Chem 2023; 299:104709. [PMID: 37060996 DOI: 10.1016/j.jbc.2023.104709] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Revised: 04/03/2023] [Accepted: 04/08/2023] [Indexed: 04/17/2023] Open
Abstract
Neurodegenerative diseases are characterized by a decline in neuronal function and structure, leading to neuronal death. Understanding the molecular mechanisms of neuronal death is crucial for developing therapeutics. MicroRNAs (miRs) are small non-coding RNAs that regulate gene expression by degrading target mRNAs or inhibiting translation. MiR dysregulation has been linked to many neurodegenerative diseases, but the underlying mechanisms are not well understood. As mitochondrial dysfunction is one of the common molecular mechanisms leading to neuronal death in many neurodegenerative diseases, here we studied miRs that modulate neuronal death caused by 1-methyl-4-phenylpyridinium (MPP+), an inhibitor of complex I in mitochondria. We identified miR-593-5p, levels of which were increased in SH-SY5Y human neuronal cells, after exposure to MPP+. We found that intracellular Ca2+, but not of reactive oxygen species (ROS), mediated this miR-593-5p increase. Furthermore, we found the increase in miR-593-5p was due to enhanced stability, not increased transcription or miR processing. Importantly, we show the increase in miR-593-5p contributed to MPP+-induced cell death. Our data revealed that miR-593-5p inhibits a signaling pathway involving PTEN-induced putative kinase 1 (PINK1) and Parkin, two proteins responsible for the removal of damaged mitochondria from cells, by targeting the coding sequence of PINK1 mRNA. Our findings suggest that miR-593-5p contributes to neuronal death resulting from MPP+ toxicity, in part, by impeding the PINK1/Parkin-mediated pathway that facilitates the clearance of damaged mitochondria. Taken together, our observations highlight the potential significance of inhibiting miR-593-5p as a therapeutic approach for neurodegenerative diseases.
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Affiliation(s)
- Myungsik Yoo
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Doo Chul Choi
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Aleta Murphy
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Atiq M Ahsan
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA
| | - Eunsung Junn
- RWJMS Institute for Neurological Therapeutics, Department of Neurology, Rutgers -Robert Wood Johnson Medical School, Piscataway, NJ. 08854, USA.
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20
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Luna Buitrago D, Lovering RC, Caporali A. Insights into Online microRNA Bioinformatics Tools. Noncoding RNA 2023; 9:18. [PMID: 36960963 PMCID: PMC10037614 DOI: 10.3390/ncrna9020018] [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: 01/19/2023] [Revised: 02/24/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
MicroRNAs (miRNAs) are members of the small non-coding RNA family regulating gene expression at the post-transcriptional level. MiRNAs have been found to have critical roles in various biological and pathological processes. Research in this field has significantly progressed, with increased recognition of the importance of miRNA regulation. As a result of the vast data and information available regarding miRNAs, numerous online tools have emerged to address various biological questions related to their function and influence across essential cellular processes. This review includes a brief introduction to available resources for an investigation covering aspects such as miRNA sequences, target prediction/validation, miRNAs associated with disease, pathway analysis and genetic variants within miRNAs.
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Affiliation(s)
- Diana Luna Buitrago
- BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH164TJ, UK
| | - Ruth C. Lovering
- Functional Gene Annotation, Institute of Cardiovascular Science, University College London, London WC1E 6BT, UK
| | - Andrea Caporali
- BHF Centre for Cardiovascular Science, The Queen’s Medical Research Institute, University of Edinburgh, Edinburgh EH164TJ, UK
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21
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Dang QQ, Li PH, Wang J, Zhao JY, Zhai SN, Zheng YJ, Yang DK. CircMAN1A2 contributes to nasopharyngeal carcinoma progression via enhancing the ubiquitination of ATMIN through miR-135a-3p/UBR5 axis. Hum Cell 2023; 36:657-675. [PMID: 36626032 DOI: 10.1007/s13577-022-00831-0] [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: 07/10/2022] [Accepted: 11/21/2022] [Indexed: 01/11/2023]
Abstract
Recently, the dysregulation of circRNAs has been increasingly implicated in the pathogenesis of nasopharyngeal carcinoma (NPC). Among these circRNAs, circMAN1A2 has been highlighted for the up-regulated expression in NPC, whereas the underlying mechanisms have not been clearly established. Thus, the aim of this study was to delineate the tumor-supporting role of circMAN1A2 in the oncogenesis and metastases of NPC. We validated through qRT-PCR that circMAN1A2 was highly expressed in NPC tissues and NPC cells. Survival analysis through Kaplan-Meier method showed that the overall survival, disease-free survival, and distant metastasis-free survival of patients was negatively correlated with the expression of circMAN1A2. Then, gain- and loss-of function assays demonstrated that circMAN1A2 knockdown could impede the proliferation, migration, invasion, and EMT in NPC cells. Further, we conducted dual luciferase reporter gene, RIP, and RNA pull down assays, unveiling that circMAN1A2 functioned as a sponge of miR-135a-3p, and miR-135a-3p targeted UBR5. Additionally, UBR5 interacted with ATMIN to foster the ubiquitination of ATMIN, thereby expediting the malignant behaviors of NPC cells as well as the lung and inguinal lymph node metastases of NPC tumors in vivo. Together, our study uncovered the tumor-initiating and pro-metastatic role of circMAN1A2-miR-135a-3p-UBR5-ATMIN axis in NPC regulation that may be a potential therapeutic target for human NPC.
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Affiliation(s)
- Qian-Qian Dang
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China
| | - Pei-Hong Li
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China
| | - Juan Wang
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China
| | - Jing-Yi Zhao
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China
| | - Su-Nan Zhai
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China
| | - Ying-Juan Zheng
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China.
| | - Dao-Ke Yang
- Department of Radiotherapy, the First Affiliated Hospital of Zhengzhou University, No. 1, East Jianshe Road, Zhengzhou, 450018, Henan Province, People's Republic of China.
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22
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Gao Y, Zhu Y, Sun Q, Chen D. Argonaute-dependent ribosome-associated protein quality control. Trends Cell Biol 2023; 33:260-272. [PMID: 35981909 DOI: 10.1016/j.tcb.2022.07.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 07/19/2022] [Accepted: 07/25/2022] [Indexed: 11/17/2022]
Abstract
Ribosome-associated protein quality control (RQC) is a protein surveillance mechanism that eliminates defective nascent polypeptides. The E3 ubiquitin ligase, Ltn1, is a key regulator of RQC that targets substrates for ubiquitination. Argonaute proteins (AGOs) are central players in miRNA-mediated gene silencing and have recently been shown to also regulate RQC by facilitating Ltn1. Therefore, AGOs directly coordinate post-transcriptional gene silencing and RQC, ensuring efficient gene silencing. We summarize the principles of RQC and the functions of AGOs in miRNA-mediated gene silencing, and discuss how AGOs associate with the endoplasmic reticulum (ER) to assist Ltn1 in controlling RQC. We highlight that RQC not only eliminates defective nascent polypeptides but also removes unwanted protein products when AGOs participate.
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Affiliation(s)
- Yajie Gao
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Yuanxiang Zhu
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China
| | - Qinmiao Sun
- State Key Laboratory of Membrane Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; Institute of Stem Cells and Regeneration, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dahua Chen
- Institute of Biomedical Research, Yunnan University, Kunming 650500, China.
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23
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Manjunath LE, Singh A, Som S, Eswarappa SM. Mammalian proteome expansion by stop codon readthrough. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1739. [PMID: 35570338 DOI: 10.1002/wrna.1739] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/11/2022] [Accepted: 04/16/2022] [Indexed: 12/20/2022]
Abstract
Recognition of a stop codon by translation machinery as a sense codon results in translational readthrough instead of termination. This recoding process, termed stop codon readthrough (SCR) or translational readthrough, is found in all domains of life including mammals. The context of the stop codon, local mRNA topology, and molecules that interact with the mRNA region downstream of the stop codon determine SCR. The products of SCR can have localization, stability, and function different from those of the canonical isoforms. In this review, we discuss how recent technological and computational advances have increased our understanding of the SCR process in the mammalian system. Based on the known molecular events that occur during SCR of multiple mRNAs, we propose transient molecular roadblocks on an mRNA downstream of the stop codon as a possible mechanism for the induction of SCR. We argue, with examples, that the insights gained from the natural SCR events can guide us to develop novel strategies for the treatment of diseases caused by premature stop codons. This article is categorized under: Translation > Regulation.
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Affiliation(s)
- Lekha E Manjunath
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
| | - Sandeep M Eswarappa
- Department of Biochemistry, Indian Institute of Science, Bengaluru, Karnataka, India
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24
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Komatsu S, Kitai H, Suzuki HI. Network Regulation of microRNA Biogenesis and Target Interaction. Cells 2023; 12:306. [PMID: 36672241 PMCID: PMC9856966 DOI: 10.3390/cells12020306] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/09/2023] [Accepted: 01/12/2023] [Indexed: 01/15/2023] Open
Abstract
MicroRNAs (miRNAs) are versatile, post-transcriptional regulators of gene expression. Canonical miRNAs are generated through the two-step DROSHA- and DICER-mediated processing of primary miRNA (pri-miRNA) transcripts with optimal or suboptimal features for DROSHA and DICER cleavage and loading into Argonaute (AGO) proteins, whereas multiple hairpin-structured RNAs are encoded in the genome and could be a source of non-canonical miRNAs. Recent advances in miRNA biogenesis research have revealed details of the structural basis of miRNA processing and cluster assistance mechanisms that facilitate the processing of suboptimal hairpins encoded together with optimal hairpins in polycistronic pri-miRNAs. In addition, a deeper investigation of miRNA-target interaction has provided insights into the complexity of target recognition with distinct outcomes, including target-mediated miRNA degradation (TDMD) and cooperation in target regulation by multiple miRNAs. Therefore, the coordinated or network regulation of both miRNA biogenesis and miRNA-target interaction is prevalent in miRNA biology. Alongside recent advances in the mechanistic investigation of miRNA functions, this review summarizes recent findings regarding the ordered regulation of miRNA biogenesis and miRNA-target interaction.
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Affiliation(s)
- Shintaro Komatsu
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
| | - Hiroki Kitai
- Department of Nephrology, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Division of Nephrology, Department of Medicine, Duke University School of Medicine, Durham, NC 27710, USA
| | - Hiroshi I. Suzuki
- Division of Molecular Oncology, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya 466-8550, Japan
- Institute for Glyco-Core Research (iGCORE), Nagoya University, Nagoya 464-8601, Japan
- Center for One Medicine Innovative Translational Research, Gifu University Institute for Advanced Study, Gifu 501-1193, Japan
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25
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Wu J, Han X, Yang X, Li Y, Liang Y, Sun G, Wang R, Wang P, Xie S, Feng J, Sun H. MiR-138-5p suppresses the progression of lung cancer by targeting SNIP1. Thorac Cancer 2023; 14:612-623. [PMID: 36597175 PMCID: PMC9968603 DOI: 10.1111/1759-7714.14791] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/20/2022] [Accepted: 12/22/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) play crucial roles in the development of various cancers. Here, we aimed to evaluate the roles of miR-138-5p in lung cancer progression and the value of miR-138-5p in lung cancer diagnosis. METHODS Quantitative real-time PCR was performed to examine the expressions of miR-138-5p and smad nuclear interacting protein 1 (SNIP1) mRNA. The diagnostic value of miR-138-5p was analyzed using receiver operating characteristic (ROC) curve analysis, sensitivity, and specificity. We explored the effect of miR-138-5p on cell proliferation and metastasis by CCK-8, colony formation, wound healing and transwell assays. Western blot was employed to detect the protein expression of SNIP1 and related genes. Lung cancer cell growth was evaluated in vivo using xenograft tumor assay. RESULTS MiR-138-5p was decreased in the serum of patients with non-small cell lung cancer (NSCLC) and in NSCLC cells and tissues. The area under the ROC curve of serum miR-138-5p in the diagnosis of NSCLC was 0.922. This finding indicates the high diagnostic efficiency for lung cancer. MiR-138-5p suppressed but its inhibitor promoted cell proliferation and migration compared with control treatment in vitro and in vivo. MiR-138-5p directly binds to the 3'-untranslated region of SNIP1 and negatively regulated the expression of SNIP1, thereby inhibiting the expression of cyclin D1 and c-Myc. Moreover, overexpression of SNIP1 rescues the miR-138-5p-mediated inhibition in NSCLC cells. CONCLUSIONS The results suggested that miR-138-5p suppressed lung cancer cell proliferation and migration by targeting SNIP1. Serum miR-138-5p is a novel and valuable biomarker for NSCLC diagnosis.
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Affiliation(s)
- Jiaen Wu
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina,Department of Laboratory MedicineYantai Affiliated Hospital of Binzhou Medical UniversityYantaiChina
| | - Xuejia Han
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina,Department of Laboratory MedicineYantai Affiliated Hospital of Binzhou Medical UniversityYantaiChina
| | - Xiancong Yang
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Youjie Li
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Yan Liang
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Guangbin Sun
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Ranran Wang
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Pingyu Wang
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Shuyang Xie
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
| | - Jiankai Feng
- Department of Laboratory MedicineYantai Affiliated Hospital of Binzhou Medical UniversityYantaiChina
| | - Hongfang Sun
- Department of Biochemistry and Molecular BiologyBinzhou Medical UniversityYantaiChina
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26
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Zhang H, Li X, Jia M, Ji J, Wu Z, Chen X, Yu D, Zheng Y, Zhao Y. Roles of H19/miR-29a-3p/COL1A1 axis in COE-induced lung cancer. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 313:120194. [PMID: 36150622 DOI: 10.1016/j.envpol.2022.120194] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 09/06/2022] [Accepted: 09/13/2022] [Indexed: 06/16/2023]
Abstract
Occupational lung cancer caused by coke oven emissions (COE) has attracted increasing attention, but the mechanism is not clear. Many evidences show ceRNA (competing endogenous RNA) networks play important regulatory roles in cancers. In this study, we aimed to construct and verify the ceRNA regulatory network in the occurrence of COE-induced lung squamous cell carcinoma (LUSC). We performed RNA sequencing with lung bronchial epithelial cell (16HBE) and COE induced malignant transformed cell (Rf). Furthermore, we analyzed RNA sequencing data of LUSC and adjacent tissues in the cancer genome atlas (TCGA) database. Combined our data and TCGA data to determine the differentially expressed lncRNAs, miRNAs, mRNAs. lncBASE, miRDB and miRTarBase were used to predict the binding relationship between lncRNA and miRNA, miRNA and mRNA. Based on these, we construct the ceRNA network. FREMSA, dual-luciferase reporter assay, quantitative real-time PCR (qRT-PCR), western-blot were used to verify the regulatory axis. CCK8 assay, phalloidin staining, p53 detection were used to explore the roles of this axis in the COE induced malignant transformation. Results showed 7 lncRNAs, 7 miRNAs and 146 mRNAs were identified. Among these, we constructed a ceRNA network including 1 lncRNA, 2 miRNAs and 9 mRNAs. Further verification confirmed the trend of lncRNA H19, miR-29a-3p and COL1A1 were consistent with sequencing results. H19 and COL1A1 were significantly higher in Rf than in 16HBE and miR-29a-3p was reverse. Regulatory investigation revealed H19 increased COL1A1 expression by sponging miR-29a-3p. Knockdown of H19, COL1A1 or overexpression of miR-29a-3p in Rf cells could inhibit cell proliferation, increased cell adhesion and p53 level. However, knockdown of H19 while suppressing the miR-29a-3p partially rescue the malignant phenotype of Rf caused by H19. In conclusion, all these indicated H19 functioned as a ceRNA to increase COL1A1 by sponging miR-29a-3p and promoted COE-induced cell malignant transformation.
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Affiliation(s)
- Heng Zhang
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Xinmei Li
- Department of Environment and Health, Tianjin Institute of Environmental & Operational Medicine, Key Laboratory of Risk Assessment and Control for Environment & Food Safety, Tianjin, China
| | - Mengmeng Jia
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Jing Ji
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Zhaoxu Wu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Xian Chen
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Dianke Yu
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yuxin Zheng
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China
| | - Yanjie Zhao
- Department of Toxicology, School of Public Health, Qingdao University, Qingdao, China.
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27
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Six MicroRNA Prognostic Models for Overall Survival of Lung Adenocarcinoma. Genet Res (Camb) 2022; 2022:5955052. [PMID: 36101742 PMCID: PMC9440840 DOI: 10.1155/2022/5955052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/19/2022] [Indexed: 11/17/2022] Open
Abstract
Objective The purpose of this study is to screen for microRNAs (miRNAs) associated with the prognosis of lung adenocarcinoma (LUAD) and to explore its prognosis and effects on the tumor microenvironment in patients with LUAD. Methods Gene expression data, miRNA expression data, and clinical data for two different databases, TCGA-LUAD and CPTAC-3 LUAD, were downloaded from the GDC database. The miRNA prognosis of LUAD was filtered by the Cox proportional hazard model and the Least Absolute Shrinkage and Selection Operator (LASSO) regression model. The performance of the model was validated by time-dependent receiver operating characteristics (ROC) curves. Possible biological processes associated with the miRNAs target gene were analyzed through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). Finally, the prognostic model was scored by risk, divided into high- and low-risk groups by median, and the differences in the immersion level of 21 immune cells in the high- and low-risk groups were assessed. To gain a deeper understanding of the underlying mechanism behind the model, the two most important miRNAs in the model, miR-195-3p and miR-5571-5p, were selected for HPA database validation and ceRNA network construction. Results Of the 209 variance expressions identified in the screening analysis, 145 were upregulated and 64 were downregulated by miRNAs. The prognostic models of six miRNA genes were obtained: miR-195-3p, miR-5571-5p, miR-584-3p, miR-494-3p, miR-4664-3p, and miR-1293. These six genes were significantly associated with survival rates in LUAD patients. In particular, miR-1293, miR-195-3p, and miR-5571-5p are highly correlated with OS. The higher expression of miR-195-3p and miR-5571-5p, the better survival of LUAD OS is, and these two miRNA expressions contribute the most to the model. Finally, after sorting the risk scores calculated from low to high using the prognostic model, the patients with higher scores had shorter survival time and higher frequency of death, and there were significant differences in the immersion levels of 21 immune cells in the high- and low-risk groups. ceRNA network analysis found that TM9SF3 was regulated by miR-195-3p and was highly expressed in the tissues of LUAD patients, and the prognosis of the patients was poor. Conclusions miR-195-3p, miR-5571-5p, miR-584-3p, miR-494-3p, miR-4664-3p, and miR-1293 may be used as new biomarkers for prognosis prediction of LUAD. Our results also identified a lncRNA MEG3/miR-195-3p/RAB1A/TM9SF3 regulatory axis, which may also play an important role in the progression of LUAD. Further study needs to be conducted to verify this result.
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28
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A previously unknown Argonaute 2 variant positively modulates the viability of melanoma cells. Cell Mol Life Sci 2022; 79:475. [PMID: 35943635 PMCID: PMC9363364 DOI: 10.1007/s00018-022-04496-8] [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: 05/01/2022] [Revised: 07/13/2022] [Accepted: 07/18/2022] [Indexed: 11/28/2022]
Abstract
In malignant melanoma, a highly aggressive form of skin cancer, many microRNAs are aberrantly expressed contributing to tumorigenesis and progression. Further, deregulation of microRNA processing enzymes, like the miRNA-binding protein Argonaute 2, significantly impacts microRNA function. This study characterizes a novel splice variant of Argonaut 2, AGO2-ex1/3. AGO2-ex1/3 is substantially expressed in different melanoma cell lines and patient-derived tissue samples. It is a mature mRNA, which is translated into an N-terminally truncated Argonaute 2 protein form. Molecular dynamics simulations show that the PAZ, MID, and PIWI domain largely retain their structure in AGO2-ex1/3 and that the truncation of the N-terminus leads to an increased interdomain flexibility. Expression of AGO2-ex1/3 provides a survival advantage for melanoma cells while the knockdown causes significantly reduced proliferation and increases apoptosis. RNA-sequencing revealed that in cells lacking AGO2-ex1/3 expression many miRNA target genes are deregulated, implicating a considerable role of AGO2-ex1/3 for miRNA function. This study inaugurates insights into an important role of a so far unknown splice variant of Argonaute 2 for the miRNA pathway as well as the mechanisms which drive growth and survival of melanoma cells. This knowledge provides the basis for potential new promising therapeutic targets focusing on small RNA-mediated gene regulation in melanoma.
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29
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Guo Q, Tan L, Pan J, Wu S, Huang J, Yu F, Wang J. Coronaviruses RNA interacts with host miR-500a-5p and miR-501-5p to regulate multiple pathways. Genes Dis 2022; 10:385-388. [PMID: 35958057 PMCID: PMC9355739 DOI: 10.1016/j.gendis.2022.07.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Revised: 06/28/2022] [Accepted: 07/13/2022] [Indexed: 11/24/2022] Open
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30
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Gene Identification and Potential Drug Therapy for Drug-Resistant Melanoma with Bioinformatics and Deep Learning Technology. DISEASE MARKERS 2022; 2022:2461055. [PMID: 35915735 PMCID: PMC9338845 DOI: 10.1155/2022/2461055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Revised: 06/13/2022] [Accepted: 06/21/2022] [Indexed: 11/17/2022]
Abstract
Background. Melanomas are skin malignant tumors that arise from melanocytes which are primarily treated with surgery, chemotherapy, targeted therapy, immunotherapy, radiation therapy, etc. Targeted therapy is a promising approach to treating advanced melanomas, but resistance always occurs. This study is aimed at identifying the potential target genes and candidate drugs for drug-resistant melanoma effectively with computational methods. Methods. Identification of genes associated with drug-resistant melanomas was conducted using the text mining tool pubmed2ensembl. Further gene screening was carried out by GO and KEGG pathway enrichment analyses. The PPI network was constructed using STRING database and Cytoscape. GEPIA was used to perform the survival analysis and conduct the Kaplan-Meier curve. Drugs targeted at these genes were selected in Pharmaprojects. The binding affinity scores of drug-target interactions were predicted by DeepPurpose. Results. A total of 433 genes were found associated with drug-resistant melanomas by text mining. The most statistically differential functional enriched pathways of GO and KEGG analyses contained 348 genes, and 27 hub genes were further screened out by MCODE in Cytoscape. Six genes were identified with statistical differences after survival analysis and literature review. 16 candidate drugs targeted at hub genes were found by Pharmaprojects under our restrictions. Finally, 11 ERBB2-targeted drugs with top affinity scores were predicted by DeepPurpose, including 10 ERBB2 kinase inhibitors and 1 antibody-drug conjugate. Conclusion. Text mining and bioinformatics are valuable methods for gene identification in drug discovery. DeepPurpose is an efficient and operative deep learning tool for predicting the DTI and selecting the candidate drugs.
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31
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Cheung R, Pizza G, Chabosseau P, Rolando D, Tomas A, Burgoyne T, Wu Z, Salowka A, Thapa A, Macklin A, Cao Y, Nguyen-Tu MS, Dickerson MT, Jacobson DA, Marchetti P, Shapiro J, Piemonti L, de Koning E, Leclerc I, Bouzakri K, Sakamoto K, Smith DM, Rutter GA, Martinez-Sanchez A. Glucose-Dependent miR-125b Is a Negative Regulator of β-Cell Function. Diabetes 2022; 71:1525-1545. [PMID: 35476777 PMCID: PMC9998846 DOI: 10.2337/db21-0803] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/04/2021] [Accepted: 04/11/2022] [Indexed: 11/13/2022]
Abstract
Impaired pancreatic β-cell function and insulin secretion are hallmarks of type 2 diabetes. miRNAs are short, noncoding RNAs that silence gene expression vital for the development and function of β cells. We have previously shown that β cell-specific deletion of the important energy sensor AMP-activated protein kinase (AMPK) results in increased miR-125b-5p levels. Nevertheless, the function of this miRNA in β cells is unclear. We hypothesized that miR-125b-5p expression is regulated by glucose and that this miRNA mediates some of the deleterious effects of hyperglycemia in β cells. Here, we show that islet miR-125b-5p expression is upregulated by glucose in an AMPK-dependent manner and that short-term miR-125b-5p overexpression impairs glucose-stimulated insulin secretion (GSIS) in the mouse insulinoma MIN6 cells and in human islets. An unbiased, high-throughput screen in MIN6 cells identified multiple miR-125b-5p targets, including the transporter of lysosomal hydrolases M6pr and the mitochondrial fission regulator Mtfp1. Inactivation of miR-125b-5p in the human β-cell line EndoCβ-H1 shortened mitochondria and enhanced GSIS, whereas mice overexpressing miR-125b-5p selectively in β cells (MIR125B-Tg) were hyperglycemic and glucose intolerant. MIR125B-Tg β cells contained enlarged lysosomal structures and had reduced insulin content and secretion. Collectively, we identify miR-125b as a glucose-controlled regulator of organelle dynamics that modulates insulin secretion.
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Affiliation(s)
- Rebecca Cheung
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Grazia Pizza
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Pauline Chabosseau
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Delphine Rolando
- Beta Cell Genome Regulation Laboratory, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Alejandra Tomas
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Thomas Burgoyne
- UCL Institute of Ophthalmology, University College London, London, U.K
| | - Zhiyi Wu
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Anna Salowka
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Anusha Thapa
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Annabel Macklin
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Yufei Cao
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Marie-Sophie Nguyen-Tu
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
| | - Matthew T. Dickerson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - David A. Jacobson
- Department of Molecular Physiology and Biophysics, Vanderbilt University, Nashville, TN
| | - Piero Marchetti
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
| | - James Shapiro
- Clinical Islet Laboratory and Clinical Islet Transplant Program, University of Alberta, Edmonton, Canada
| | | | - Eelco de Koning
- Department of Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | | | - Karim Bouzakri
- UMR DIATHEC, EA 7294, Centre Européen d'Etude du Diabète, Université de Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, Strasbourg, France
| | - Kei Sakamoto
- Novo Nordisk Foundation Center for Basic Metabolic Research, University of Copenhagen, Copenhagen, Denmark
| | - David M. Smith
- Emerging Innovations Unit, Discovery Sciences, R&D, AstraZeneca, Cambridge, U.K
| | - Guy A. Rutter
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
- CR-CHUM, University of Montreal, Montreal, Quebec, Canada
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore
| | - Aida Martinez-Sanchez
- Section of Cell Biology and Functional Genomics, Department of Metabolism, Digestion and Reproduction, Imperial College London, London, U.K
- Corresponding author: Aida Martinez-Sanchez,
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32
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Jiang J, Zeng T, Zhang L, Fan X, Jin Q, Ni H, Ye Y, Cheng L, Li L, Wang L, Xu S, Yang Y, Gu J, Guo B, Wang L, Li X, Qin Y, Li J, Wang J, Chen X, Wu M, Ying QL, Qin X, Wang Y, Wang Y. Optimization of Cas9 RNA sequence to reduce its unexpected effects as a microRNA sponge. Mol Cancer 2022; 21:136. [PMID: 35751058 PMCID: PMC9229757 DOI: 10.1186/s12943-022-01604-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 06/06/2022] [Indexed: 11/28/2022] Open
Abstract
Cas9 RNA functions as a miRNA sponge. Let-7 is the dominant regulated miRNA by Cas9 RNA. RNA sequence optimization of Cas9 by synonymous mutation improves its safety.
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Affiliation(s)
- Junfeng Jiang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China.,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Tao Zeng
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China.,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China.,The 901th Hospital of PLA Jiont Logistic Support Force, HeFei, 230031, China
| | - Li Zhang
- Department of Pathology, Faculty of Medical Imaging, Naval Medical University, Shanghai, 200433, China
| | - Xingfei Fan
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China.,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China
| | - Qishu Jin
- Department of Histology and Embryology, Harbin Medical University, Harbin, 150086, China
| | - Haitao Ni
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Yusheng Ye
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Lipeng Cheng
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Li Li
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Liujun Wang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Sha Xu
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Yu Yang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Juan Gu
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Bing Guo
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China
| | - Lei Wang
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China
| | - Xin Li
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China.,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China.,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China
| | - Yingyi Qin
- Department of health statistics, Naval Medical University, Shanghai, 200433, China
| | - Jiaxi Li
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Jinjiang Wang
- Department of Oncology, Tongren Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200336, China
| | - Xi Chen
- Department of Cell and Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA
| | - Minjuan Wu
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China
| | - Qi-Long Ying
- Department of Cell and Neurobiology, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at USC, Keck School of Medicine, University of Southern California, Los Angeles, California, 90033, USA.
| | - Xingjun Qin
- Department of Oral & Maxillofacial - Head & Neck Oncology, Shanghai Ninth People's Hospital, College of Stomatology, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China. .,National Clinical Research Center for Oral Diseases, Shanghai, 200011, China. .,Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai Key Laboratory of Stomatology, 639 Zhi Zao Ju Road, Shanghai, 200011, China.
| | - Yefei Wang
- Department of Ophthalmology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200011, China. .,Shanghai Key Laboratory of Orbital Diseases and Ocular Oncology, Shanghai, 200011, China.
| | - Yue Wang
- Histology and Embryology Department, Naval Medical University, Shanghai, 200433, China. .,Research Center of Developmental Biology, Shanghai Key Laboratory of Cell Engineering, Naval Medical University, 800 Xiangyin Road, Shanghai, 200433, China.
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Yin J, Zheng Z, Zeng X, Zhao Y, Ai Z, Yu M, Wu Y, Jiang J, Li J, Li S. lncRNA MALAT1 mediates osteogenic differentiation of bone mesenchymal stem cells by sponging miR-129-5p. PeerJ 2022; 10:e13355. [PMID: 35480561 PMCID: PMC9037136 DOI: 10.7717/peerj.13355] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 04/08/2022] [Indexed: 01/15/2023] Open
Abstract
Background Bone mesenchymal stem cells (BMSCs) have good osteogenic differentiation potential and have become ideal seed cells in bone tissue engineering. However, the osteogenic differentiation ability of BMSCs gradually weakens with age, and the regulatory mechanism is unclear. Method We conducted a bioinformatics analysis, dual-luciferase reporter (DLR) experiment, and RNA binding protein immunoprecipitation (RIP) to explore the hub genes that may affect BMSC functions. Results The expression level of long non-coding RNA (lncRNA) metastasis-associated lung adenocarcinoma transcript 1 (Malat1) was significantly higher in the BMSCs from elderly than younger mice, while miR-129-5p showed the opposite trend. The results of alkaline phosphatase staining, quantitative reverse transcription PCR and western blot experiments indicated that inhibiting the expression of Malat1 inhibits the osteogenic differentiation of BMSCs. This effect can be reversed by reducing the expression of miR-129-5p. Additionally, DLR and RIP experiments confirmed that Malat1 acts as a sponge for miR-129-5p. Conclusion Overall, our study findings indicated that lncRNA Malat1 may play a critical role in maintaining the osteoblast differentiation potential of BMSCs by sponging miR-129-5p.
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Affiliation(s)
- Junhao Yin
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Zhanglong Zheng
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Xiaoli Zeng
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Yijie Zhao
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China,Department of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai, China
| | - Zexin Ai
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Miao Yu
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Yang’ou Wu
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China,Department of Oral and Maxillofacial Surgery, Shanghai Xuhui District Dental Center, Jiaotong University, Shanghai, China
| | - Jirui Jiang
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
| | - Jia Li
- Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China,Department of Prosthodontics, School and Hospital of Stomatology, Tongji University, Shanghai, China
| | - Shengjiao Li
- Department of Oral and Maxillofacial Surgery, School and Hospital of Stomatology, Tongji University, Shanghai, China,Shanghai Engineering Research Center of Tooth Restoration and Regeneration, Shanghai, China
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Chakraborty S, Nath D. A Study on microRNAs Targeting the Genes Overexpressed in Lung Cancer and their Codon Usage Patterns. Mol Biotechnol 2022; 64:1095-1119. [DOI: 10.1007/s12033-022-00491-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 04/04/2022] [Indexed: 10/18/2022]
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Liu H, Chen Y, Zhou L, Jiang X, Zhou X. MicroRNA-642b-3p functions as an oncomiR in gastric cancer by down-regulating the CUB and sushi multiple domains protein 1/smad axis. Bioengineered 2022; 13:9613-9627. [PMID: 35412956 PMCID: PMC9208452 DOI: 10.1080/21655979.2022.2056813] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Aberrant expression of microRNAs (miRNAs or miRs) has been involved in the progression of gastric cancer (GC). Our analysis of GC-related gene expression profiles identified the significantly up-regulated miR-642b-3p expression, which has been reported as a mediator in various cancers but rarely mentioned in researches on GC. Herein, this study intends to investigate the role of miR-642b-3p in GC development. Bioinformatics analysis was conducted to predict the downstream target gene of miR-642b-3p. Expression patterns of miR-642b-3p and CUB and sushi multiple domains protein 1 (CSMD1) in GC tissues and cell lines was then determined. Immunofluorescence, wound healing and Transwell invasion assays were performed to observe the malignant behaviors of GC cells with altered expression of miR-642b-3p and CSMD1. Nude mice with xenograft tumors were developed for in vivo validation. miR-642b-3p expression was increased in GC tissues and cell lines. miR-642b-3p targeted CSMD1 and reduced the expression of CSMD1, thereby inhibiting the activation of Smad signaling pathway. By this mechanism, the epithelial–mesenchymal transition (EMT), invasive and migratory potentials of GC cells were repressed. Meanwhile, in vivo data verified that miR-642b-3p enhanced the tumor growth of GC cells, which was associated with blockade of CSMD1-dependent activation of the Smad signaling pathway. Overall, miR-642b-3p acts as an oncomiR promoting tumor development in GC through suppressing CSMD1 expression and inactivating the Smad signaling pathway, which may enable the development of new therapeutic strategies for treatment of GC.
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Affiliation(s)
- Haofeng Liu
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou P.R. China.,Department of General Surgery, Tumor Hospital Affiliated to Nantong University & Nantong Tumor Hospital, Nantong P.R. China
| | - Yuan Chen
- Department of General Surgery, Tumor Hospital Affiliated to Nantong University & Nantong Tumor Hospital, Nantong P.R. China
| | - Linsen Zhou
- Department of General Surgery, Yancheng First Hospital, Affiliated Hospital of Nanjing University Medical School, Yancheng P.R. China
| | - Xiaohui Jiang
- Department of General Surgery, Tumor Hospital Affiliated to Nantong University & Nantong Tumor Hospital, Nantong P.R. China
| | - Xiaojun Zhou
- Department of General Surgery, The First Affiliated Hospital of Soochow University, Suzhou P.R. China
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36
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Meng F, Wang J, Yeo Y. Nucleic acid and oligonucleotide delivery for activating innate immunity in cancer immunotherapy. J Control Release 2022; 345:586-600. [PMID: 35351528 PMCID: PMC9133138 DOI: 10.1016/j.jconrel.2022.03.045] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 12/17/2022]
Abstract
A group of nucleic acids and oligonucleotides play various roles in the innate immune system. They can stimulate pattern recognition receptors to activate innate immune cells, encode immunostimulatory proteins or peptides, or silence specific genes to block negative regulators of immune cells. Given the limitations of current cancer immunotherapy, there has been increasing interest in harnessing innate immune responses by nucleic acids and oligonucleotides. The poor biopharmaceutical properties of nucleic acids and oligonucleotides make it critical to use carriers that can protect them in circulation, retain them in the tumor microenvironment, and bring them to intracellular targets. Therefore, various gene carriers have been repurposed to deliver nucleic acids and oligonucleotides for cancer immunotherapy and improve their safety and activity. Here, we review recent studies that employed carriers to enhance the functions of nucleic acids and oligonucleotides and overall immune responses to cancer, and discuss remaining challenges and future opportunities in the development of nucleic acid-based immunotherapeutics.
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Affiliation(s)
- Fanfei Meng
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Jianping Wang
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA
| | - Yoon Yeo
- Department of Industrial and Physical Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, IN 47907, USA; Weldon School of Biomedical Engineering, Purdue University, 206 S Martin Jischke Dr., West Lafayette, IN 47907, USA.
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37
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Santovito D, Weber C. Non-canonical features of microRNAs: paradigms emerging from cardiovascular disease. Nat Rev Cardiol 2022; 19:620-638. [PMID: 35304600 DOI: 10.1038/s41569-022-00680-2] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/14/2022] [Indexed: 02/08/2023]
Abstract
Research showing that microRNAs (miRNAs) are versatile regulators of gene expression has instigated tremendous interest in cardiovascular research. The overwhelming majority of studies are predicated on the dogmatic notion that miRNAs regulate the expression of specific target mRNAs by inhibiting mRNA translation or promoting mRNA decay in the RNA-induced silencing complex (RISC). These efforts mostly identified and dissected contributions of multiple regulatory networks of miRNA-target mRNAs to cardiovascular pathogenesis. However, evidence from studies in the past decade indicates that miRNAs also operate beyond this canonical paradigm, featuring non-conventional regulatory functions and cellular localizations that have a pathophysiological role in cardiovascular disease. In this Review, we highlight the functional relevance of atypical miRNA biogenesis and localization as well as RISC heterogeneity. Moreover, we delineate remarkable non-canonical examples of miRNA functionality, including direct interactions with proteins beyond the Argonaute family and their role in transcriptional regulation in the nucleus and in mitochondria. We scrutinize the relevance of non-conventional biogenesis and non-canonical functions of miRNAs in cardiovascular homeostasis and pathology, and contextualize how uncovering these non-conventional properties can expand the scope of translational research in the cardiovascular field and beyond.
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Affiliation(s)
- Donato Santovito
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Institute for Genetic and Biomedical Research (IRGB), Unit of Milan, National Research Council, Milan, Italy.
| | - Christian Weber
- Institute for Cardiovascular Prevention (IPEK), Ludwig-Maximilians-Universität (LMU), Munich, Germany. .,German Center for Cardiovascular Research (DZHK), partner site Munich Heart Alliance, Munich, Germany. .,Department of Biochemistry, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, Netherlands. .,Munich Cluster for Systems Neurology (SyNergy), Munich, Germany.
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38
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Identification and Characterization of MicroRNAs Involving in Initial Sex Differentiation of Chlamys farreri Gonads. BIOLOGY 2022; 11:biology11030456. [PMID: 35336829 PMCID: PMC8945268 DOI: 10.3390/biology11030456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 03/10/2022] [Accepted: 03/12/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Sex formation of gonads encompasses two ancient and highly conserved biological processes, sex determination and sex differentiation. The processes are strictly regulated by a complex of gene networks. There is increasing evidence that miRNAs play key roles in many biological processes. however, information is limited in their contribution to sex differentiation in animals. In the present study, we identified the novel miRNAs involved in sex-related genes regulation and explored the miRNA–mRNA networks underlying the posttranscriptional regulation during the initial sex differentiation in Zhikong scallop, Chlamys farreri. Our findings provide an important basis for studying the sex differentiation mechanisms, as well as developing sex control techniques in bivalves. Abstract Research on expressional regulation of genes at the initial sex differentiation of gonads will help to elucidate the mechanisms of sex determination and differentiation in animals. However, information on initial sex differentiation of gonads is limited in bivalves. MicroRNAs (miRNAs) are a class of endogenous small noncoding RNAs that can regulate the target gene expression at the posttranscription level by degrading the mRNA or repressing the mRNA translation. In the present study, we investigated the small RNAs transcriptome using the testes and ovaries of Zhikong scallop Chlamys farreri juveniles with a shell height of 5.0 mm, a critical stage of initial sex differentiation of gonads. A total of 75 known mature miRNAs and 103 novel miRNAs were identified. By comparing the expression of miRNAs between the ovary and testis, 11 miRNAs were determined to be differentially expressed. GO annotations and KEGG analyses indicated that many putative target genes that matched to these differentially expressed miRNAs participated in the regulation of sex differentiation. Furthermore, two selected miRNAs, cfa-novel_miR65 and cfa-miR-87a-3p_1, were confirmed to downregulate expressions of Foxl2 (a female-critical gene) and Klf4 (a male-critical gene), respectively, using a dual-luciferase reporter analysis. Our findings provided new insights into the initial sex differentiation of gonads regulated by miRNAs in bivalves.
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39
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Naeli P, Winter T, Hackett AP, Alboushi L, Jafarnejad SM. The intricate balance between microRNA-induced mRNA decay and translational repression. FEBS J 2022; 290:2508-2524. [PMID: 35247033 DOI: 10.1111/febs.16422] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 02/08/2022] [Accepted: 03/03/2022] [Indexed: 12/23/2022]
Abstract
Post-transcriptional regulation of messenger RNAs (mRNAs) (i.e., mechanisms that control translation, stability and localization) is a critical focal point in spatiotemporal regulation of gene expression in response to changes in environmental conditions. The human genome encodes ~ 2000 microRNAs (miRNAs), each of which could control the expression of hundreds of protein-coding mRNAs by inducing translational repression and/or promoting mRNA decay. While mRNA degradation is a terminal event, translational repression is reversible and can be employed for rapid response to internal or external cues. Recent years have seen significant progress in our understanding of how miRNAs induce degradation or translational repression of the target mRNAs. Here, we review the recent findings that illustrate the cellular machinery that contributes to miRNA-induced silencing, with a focus on the factors that could influence translational repression vs. decay.
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Affiliation(s)
- Parisa Naeli
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Timothy Winter
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Angela P Hackett
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
| | - Lilas Alboushi
- Patrick G. Johnston Centre for Cancer Research, Queen's University Belfast, UK
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40
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Liang C, Huang M, Li T, Li L, Sussman H, Dai Y, Siemann DW, Xie M, Tang X. Towards an integrative understanding of cancer mechanobiology: calcium, YAP, and microRNA under biophysical forces. SOFT MATTER 2022; 18:1112-1148. [PMID: 35089300 DOI: 10.1039/d1sm01618k] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
An increasing number of studies have demonstrated the significant roles of the interplay between microenvironmental mechanics in tissues and biochemical-genetic activities in resident tumor cells at different stages of tumor progression. Mediated by molecular mechano-sensors or -transducers, biomechanical cues in tissue microenvironments are transmitted into the tumor cells and regulate biochemical responses and gene expression through mechanotransduction processes. However, the molecular interplay between the mechanotransduction processes and intracellular biochemical signaling pathways remains elusive. This paper reviews the recent advances in understanding the crosstalk between biomechanical cues and three critical biochemical effectors during tumor progression: calcium ions (Ca2+), yes-associated protein (YAP), and microRNAs (miRNAs). We address the molecular mechanisms underpinning the interplay between the mechanotransduction pathways and each of the three effectors. Furthermore, we discuss the functional interactions among the three effectors in the context of soft matter and mechanobiology. We conclude by proposing future directions on studying the tumor mechanobiology that can employ Ca2+, YAP, and miRNAs as novel strategies for cancer mechanotheraputics. This framework has the potential to bring insights into the development of novel next-generation cancer therapies to suppress and treat tumors.
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Affiliation(s)
- Chenyu Liang
- Department of Mechanical & Aerospace Engineering, Herbert Wertheim College of Engineering (HWCOE), Gainesville, FL, 32611, USA.
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
| | - Miao Huang
- Department of Mechanical & Aerospace Engineering, Herbert Wertheim College of Engineering (HWCOE), Gainesville, FL, 32611, USA.
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
| | - Tianqi Li
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), Gainesville, FL, 32611, USA.
| | - Lu Li
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), Gainesville, FL, 32611, USA.
| | - Hayley Sussman
- Department of Radiation Oncology, COM, Gainesville, FL, 32611, USA
| | - Yao Dai
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- UF Genetics Institute (UFGI), University of Florida (UF), Gainesville, FL, 32611, USA
| | - Dietmar W Siemann
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- UF Genetics Institute (UFGI), University of Florida (UF), Gainesville, FL, 32611, USA
| | - Mingyi Xie
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
- Department of Biochemistry and Molecular Biology, College of Medicine (COM), Gainesville, FL, 32611, USA.
- Department of Biomedical Engineering, College of Engineering (COE), University of Delaware (UD), Newark, DE, 19716, USA
| | - Xin Tang
- Department of Mechanical & Aerospace Engineering, Herbert Wertheim College of Engineering (HWCOE), Gainesville, FL, 32611, USA.
- UF Health Cancer Center (UFHCC), Gainesville, FL, 32611, USA
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41
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Pozzi A, Dowling DK. New Insights into Mitochondrial-Nuclear Interactions Revealed through Analysis of Small RNAs. Genome Biol Evol 2022; 14:evac023. [PMID: 35143645 PMCID: PMC8883506 DOI: 10.1093/gbe/evac023] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/02/2022] [Indexed: 11/15/2022] Open
Abstract
Mitochondrial sequence variants affect phenotypic function, often through interaction with the nuclear genome. These "mitonuclear" interactions have been linked both to evolutionary processes and human health. The study of these interactions has focused on mechanisms regulating communication between mitochondrial and nuclear proteins; the role of mitochondrial (mt) RNAs has received little attention. Here, we show that small mt-RNAs bind to the nuclear protein Argonaute 2, and that nuclear miRNAs bind to mt-mRNAs. We identify one small mt-RNA that binds to Argonaute 2 in human tissues whose expression and sequence remain unchanged across vertebrates. Although analyses of CLEAR-CLIP sequencing data sets of human and mouse did not reveal consistent interactions between small mt-RNAs and nuclear mRNAs, we found that MT-ND4 and MT-ATP6 mRNAs are bound by different nuclear miRNAs in humans and mice. Our work homes in on previously unknown interactions between nuclear and small mt-RNAs, which may play key roles in intergenomic communication.
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Affiliation(s)
- Andrea Pozzi
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
| | - Damian K Dowling
- School of Biological Sciences, Monash University, Clayton, Victoria, Australia
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42
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Kilikevicius A, Meister G, Corey DR. Reexamining assumptions about miRNA-guided gene silencing. Nucleic Acids Res 2022; 50:617-634. [PMID: 34967419 PMCID: PMC8789053 DOI: 10.1093/nar/gkab1256] [Citation(s) in RCA: 62] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 12/01/2021] [Accepted: 12/06/2021] [Indexed: 12/16/2022] Open
Abstract
MicroRNAs (miRNAs) are short endogenously expressed RNAs that have the potential to regulate the expression of any RNA. This potential has led to the publication of several thousand papers each year connecting miRNAs to many different genes and human diseases. By contrast, relatively few papers appear that investigate the molecular mechanism used by miRNAs. There is a disconnect between rigorous understanding of mechanism and the extraordinary diversity of reported roles for miRNAs. Consequences of this disconnect include confusion about the assumptions underlying the basic science of human miRNAs and slow development of therapeutics that target miRNAs. Here, we present an overview of investigations into miRNAs and their impact on gene expression. Progress in our understanding of miRNAs would be aided by a greater focus on the mechanism of miRNAs and a higher burden of evidence on researchers who seek to link expression of a particular miRNA to a biological phenotype.
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Affiliation(s)
- Audrius Kilikevicius
- Department of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, USA
| | - Gunter Meister
- Regensburg Center for Biochemistry (RCB), Laboratory for RNA Biology, University of Regensburg, Regensburg, Germany
| | - David R Corey
- Department of Pharmacology and Biochemistry, UT Southwestern Medical Center, 6001 Forest Park Road, Dallas, TX, USA
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43
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Bell J, Hendrix DA. Predicting Drosha and Dicer Cleavage Sites with DeepMirCut. Front Mol Biosci 2022; 8:799056. [PMID: 35141278 PMCID: PMC8819831 DOI: 10.3389/fmolb.2021.799056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
MicroRNAs are a class of small RNAs involved in post-transcriptional gene silencing with roles in disease and development. Many computational tools have been developed to identify novel microRNAs. However, there have been no attempts to predict cleavage sites for Drosha from primary sequence, or to identify cleavage sites using deep neural networks. Here, we present DeepMirCut, a recurrent neural network-based software that predicts both Dicer and Drosha cleavage sites. We built a microRNA primary sequence database including flanking genomic sequences for 34,713 microRNA annotations. We compare models trained on sequence data, sequence and secondary structure data, as well as input data with annotated structures. Our best model is able to predict cuts within closer average proximity than results reported for other methods. We show that a guanine nucleotide before and a uracil nucleotide after Dicer cleavage sites on the 3′ arm of the microRNA precursor had a positive effect on predictions while the opposite order (U before, G after) had a negative effect. Our analysis was also able to predict several positions where bulges had either positive or negative effects on the score. We expect that our approach and the data we have curated will enable several future studies.
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Affiliation(s)
- Jimmy Bell
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, United States
| | - David A. Hendrix
- School of Electrical Engineering and Computer Science, Oregon State University, Corvallis, OR, United States
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR, United States
- *Correspondence: David A. Hendrix,
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44
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El Fatimy R, Zhang Y, Deforzh E, Ramadas M, Saravanan H, Wei Z, Rabinovsky R, Teplyuk NM, Uhlmann EJ, Krichevsky AM. A nuclear function for an oncogenic microRNA as a modulator of snRNA and splicing. Mol Cancer 2022; 21:17. [PMID: 35033060 PMCID: PMC8760648 DOI: 10.1186/s12943-022-01494-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 12/23/2021] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND miRNAs are regulatory transcripts established as repressors of mRNA stability and translation that have been functionally implicated in carcinogenesis. miR-10b is one of the key onco-miRs associated with multiple forms of cancer. Malignant gliomas exhibit particularly striking dependence on miR-10b. However, despite the therapeutic potential of miR-10b targeting, this miRNA's poorly investigated and largely unconventional properties hamper the clinical translation. METHODS We utilized Covalent Ligation of Endogenous Argonaute-bound RNAs and their high-throughput RNA sequencing to identify miR-10b interactome and a combination of biochemical and imaging approaches for target validation. They included Crosslinking and RNA immunoprecipitation with spliceosomal proteins, a combination of miRNA FISH with protein immunofluorescence in glioma cells and patient-derived tumors, native Northern blotting, and the transcriptome-wide analysis of alternative splicing. RESULTS We demonstrate that miR-10b binds to U6 snRNA, a core component of the spliceosomal machinery. We provide evidence of the direct binding between miR-10b and U6, in situ imaging of miR-10b and U6 co-localization in glioma cells and tumors, and biochemical co-isolation of miR-10b with the components of the spliceosome. We further demonstrate that miR-10b modulates U6 N-6-adenosine methylation and pseudouridylation, U6 binding to splicing factors SART3 and PRPF8, and regulates U6 stability, conformation, and levels. These effects on U6 result in global splicing alterations, exemplified by the altered ratio of the isoforms of a small GTPase CDC42, reduced overall CDC42 levels, and downstream CDC42 -mediated effects on cell viability. CONCLUSIONS We identified U6 snRNA, the key RNA component of the spliceosome, as the top miR-10b target in glioblastoma. We, therefore, present an unexpected intersection of the miRNA and splicing machineries and a new nuclear function for a major cancer-associated miRNA.
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Affiliation(s)
- Rachid El Fatimy
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
- Current Address: Institute of Biological Sciences (ISSB-P), Mohammed VI Polytechnic University (UM6P), 43150, Benguerir, Morocco
| | - Yanhong Zhang
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Evgeny Deforzh
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Mahalakshmi Ramadas
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Harini Saravanan
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Zhiyun Wei
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
- Current Address: Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Rosalia Rabinovsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Nadiya M Teplyuk
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Erik J Uhlmann
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA
| | - Anna M Krichevsky
- Department of Neurology, Brigham and Women's Hospital and Harvard Medical School, 60 Fenwood Rd, Room 9002T, Boston, MA, 02115, USA.
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45
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Fields CJ, Li L, Hiers NM, Li T, Sheng P, Huda T, Shan J, Gay L, Gu T, Bian J, Kilberg MS, Renne R, Xie M. Sequencing of Argonaute-bound microRNA/mRNA hybrids reveals regulation of the unfolded protein response by microRNA-320a. PLoS Genet 2021; 17:e1009934. [PMID: 34914716 PMCID: PMC8675727 DOI: 10.1371/journal.pgen.1009934] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 11/08/2021] [Indexed: 11/18/2022] Open
Abstract
MicroRNAs (miRNA) are short non-coding RNAs widely implicated in gene regulation. Most metazoan miRNAs utilize the RNase III enzymes Drosha and Dicer for biogenesis. One notable exception is the RNA polymerase II transcription start sites (TSS) miRNAs whose biogenesis does not require Drosha. The functional importance of the TSS-miRNA biogenesis is uncertain. To better understand the function of TSS-miRNAs, we applied a modified Crosslinking, Ligation, and Sequencing of Hybrids on Argonaute (AGO-qCLASH) to identify the targets for TSS-miRNAs in HCT116 colorectal cancer cells with or without DROSHA knockout. We observed that miR-320a hybrids dominate in TSS-miRNA hybrids identified by AGO-qCLASH. Targets for miR-320a are enriched for the eIF2 signaling pathway, a downstream component of the unfolded protein response. Consistently, in miR-320a mimic- and antagomir- transfected cells, differentially expressed gene products are associated with eIF2 signaling. Within the AGO-qCLASH data, we identified the endoplasmic reticulum (ER) chaperone calnexin as a direct miR-320a down-regulated target, thus connecting miR-320a to the unfolded protein response. During ER stress, but not amino acid deprivation, miR-320a up-regulates ATF4, a critical transcription factor for resolving ER stress. In summary, our study investigates the targetome of the TSS-miRNAs in colorectal cancer cells and establishes miR-320a as a regulator of unfolded protein response.
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Affiliation(s)
- Christopher J. Fields
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lu Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Nicholas M. Hiers
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Tianqi Li
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Peike Sheng
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Taha Huda
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Jixiu Shan
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Lauren Gay
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Tongjun Gu
- Bioinformatics, Interdisciplinary Center for Biotechnology Research, University of Florida, Gainesville, Florida, United States of America
| | - Jiang Bian
- Department of Health Outcomes and Biomedical Informatics, University of Florida, College of Medicine, Gainesville, Florida, United States of America
| | - Michael S. Kilberg
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
| | - Rolf Renne
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- Department of Molecular Genetics and Microbiology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
| | - Mingyi Xie
- Department of Biochemistry and Molecular Biology, University of Florida, College of Medicine, Gainesville, Florida, United States of America
- UF Health Cancer Center, University of Florida, Gainesville, Florida, United States of America
- UF Genetics Institute, University of Florida, Gainesville, Florida, United States of America
- * E-mail:
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46
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Akula SM, Bolin P, Cook PP. Cellular miR-150-5p may have a crucial role to play in the biology of SARS-CoV-2 infection by regulating nsp10 gene. RNA Biol 2021; 19:1-11. [PMID: 34904915 PMCID: PMC8786335 DOI: 10.1080/15476286.2021.2010959] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The role for circulating miRNAs as biomarkers of the COVID-19 disease remains uncertain. We analysed the circulating miRNA profile in twelve COVID-19 patients with moderate-severe disease. This analysis was conducted by performing next generation sequencing (NGS) followed by real-time polymerase chain reaction (RT-qPCR). Compared with healthy controls, we detected significant changes in the circulating miRNA profile of COVID-19 patients. The miRNAs that were significantly altered in all the COVID-19 patients were miR-150-5p, miR-375, miR-122-5p, miR-494-3p, miR-3197, miR-4690-5p, miR-1915-3p, and miR-3652. Infection assays performed using miRNA mimics in HEK-293 T cells determined miR-150-5p to have a crucial role in SARS-CoV-2 infection and this was based on the following data: (i) miR-150-5p mimic lowered in vitro SARS-CoV-2 infection; (ii) miR-150-5p inhibitor reversed the effects of miR-150-5p mimic on SARS-CoV-2 infection of cells; and (iii) a novel miRNA recognition element (MRE) was identified in the coding strand of SARS-CoV-2 nsp10, the expression of which could be inhibited by miR-150-5p mimic. Our findings identified crucial miRNA footprints in COVID-19 patients with moderate-severe disease. A combination of co-transfection and Western blotting experiments also determined the ability of miR-150-5p to inhibit SARS-CoV-2 infection via directly interacting with MRE in the coding strand of nsp10. Our investigation showed that a sharp decline in the miR-150-5p plasma levels in COVID-19 patients may support enhanced SARS-CoV-2 infection. Furthermore, this study provides insight into one possible mechanism by which COVID-19-induced changes to miR-150-5p levels may promote SARS-CoV-2 infection via modulating nsp10 expression.
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Affiliation(s)
- Shaw M Akula
- Department of Microbiology & Immunology (S.m. Akula), Department of Internal Medicine (P. Bolin, P.P.Cook), Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Paul Bolin
- Department of Microbiology & Immunology (S.m. Akula), Department of Internal Medicine (P. Bolin, P.P.Cook), Brody School of Medicine at East Carolina University, Greenville, NC, USA
| | - Paul P Cook
- Department of Microbiology & Immunology (S.m. Akula), Department of Internal Medicine (P. Bolin, P.P.Cook), Brody School of Medicine at East Carolina University, Greenville, NC, USA
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Mizuno K, Tanigawa K, Misono S, Suetsugu T, Sanada H, Uchida A, Kawano M, Machida K, Asai S, Moriya S, Inoue H, Seki N. Regulation of Oncogenic Targets by Tumor-Suppressive miR-150-3p in Lung Squamous Cell Carcinoma. Biomedicines 2021; 9:biomedicines9121883. [PMID: 34944699 PMCID: PMC8698895 DOI: 10.3390/biomedicines9121883] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 12/03/2021] [Accepted: 12/09/2021] [Indexed: 01/02/2023] Open
Abstract
Several recent studies have shown that both strands of certain miRNAs derived from miRNA duplexes are involved in cancer pathogenesis. Our own recent studies revealed that both strands of the miR-150 duplex act as tumor-suppressive miRNAs in lung adenocarcinoma (LUAD) through the targeting of several oncogenes. The aim of the study here was to further investigate the tumor-suppressive roles of miR-150-3p (the passenger strand) in lung squamous cell carcinoma (LUSQ) and its control of cancer-promoting genes in LUSQ cells. The downregulation of miR-150-3p in LUSQ tissues was confirmed by data in The Cancer Genome Atlas (TCGA). The ectopic expression of miR-150-3p attenuated cancer cell aggressive features, e.g., cell cycle arrest, migration and invasive abilities. Our target search strategy successfully identified a total of 49 putative targets that were listed as subjects of miR-150-3p regulation in LUSQ cells. Interestingly, among these targets, 17 genes were categorized as related to the “cell cycle” based on Gene Ontology (GO) classification, namely CENPA, CIT, CCNE1, CCNE2, TIMELESS, BUB1, MCM4, HELLS, SKA3, CDCA2, FANCD2, NUF2, E2F2, SUV39H2, CASC5, ZWILCH and CKAP2). Moreover, we show that the expression of HELLS (helicase, lymphoid specific) is directly controlled by miR-150-3p, and its expression promotes the malignant phenotype of LUSQ cells.
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Affiliation(s)
- Keiko Mizuno
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Kengo Tanigawa
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Shunsuke Misono
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Takayuki Suetsugu
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Hiroki Sanada
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Akifumi Uchida
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Minami Kawano
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Kentaro Machida
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Shunichi Asai
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan;
| | - Shogo Moriya
- Department of Biochemistry and Genetics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan;
| | - Hiromasa Inoue
- Department of Pulmonary Medicine, Graduate School of Medical and Dental Sciences, Kagoshima University, Kagoshima 890-8520, Japan; (K.M.); (K.T.); (S.M.); (T.S.); (H.S.); (A.U.); (M.K.); (K.M.); (H.I.)
| | - Naohiko Seki
- Department of Functional Genomics, Chiba University Graduate School of Medicine, Chuo-ku, Chiba 260-8670, Japan;
- Correspondence: ; Tel.: +81-43-226-2971
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Su H, Zheng W, Pan J, Lv X, Xin S, Xu T. Circular RNA circSamd4a Regulates Antiviral Immunity in Teleost Fish by Upregulating STING through Sponging miR-29a-3p. THE JOURNAL OF IMMUNOLOGY 2021; 207:2770-2784. [PMID: 34697227 DOI: 10.4049/jimmunol.2100469] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/21/2021] [Indexed: 12/22/2022]
Abstract
Circular RNAs (circRNAs) are a subgroup of endogenous noncoding RNA that is covalently closed rings and widely expressed. In recent years, there is accumulating evidence indicating that circRNAs are a class of important regulators, which play an important role in various biological processes. However, the biological functions and regulation mechanism of circRNAs in lower vertebrates are little known. In this study, we discovered a circRNA Samd4a (circSamd4a) that is related to the antiviral immune response of teleost fish. It can act as a key regulator of the host's antiviral response and play a key role in inhibiting Sininiperca chuatsi rhabdovirus replication. Further studies have shown that circSamd4a may act as a competing endogenous RNA, which can enhance the STING-mediated NF-κB/IRF3 signaling pathway by adsorbing miR-29a-3p, thereby enhancing the antiviral immune response. Therefore, circSamd4a plays an active regulatory role in the antiviral immune response of bony fish. Our research results provide a strong foundation for circular RNA to play a regulatory role in the antiviral immune response of teleost fish.
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Affiliation(s)
- Hui Su
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Weiwei Zheng
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Jiajia Pan
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Xing Lv
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Shiying Xin
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Tianjun Xu
- Laboratory of Fish Molecular Immunology, College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China; .,Laboratory of Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.,Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources, Shanghai Ocean University, Ministry of Education, Shanghai, China; and.,National Pathogen Collection Center for Aquatic Animals, Shanghai Ocean University, Shanghai, China
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49
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Posttranscriptional modulation of KCNQ2 gene expression by the miR-106b microRNA family. Proc Natl Acad Sci U S A 2021; 118:2110200118. [PMID: 34785595 DOI: 10.1073/pnas.2110200118] [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] [Accepted: 10/04/2021] [Indexed: 12/15/2022] Open
Abstract
MicroRNAs (miRNAs) have recently emerged as important regulators of ion channel expression. We show here that select miR-106b family members repress the expression of the KCNQ2 K+ channel protein by binding to the 3'-untranslated region of KCNQ2 messenger RNA. During the first few weeks after birth, the expression of miR-106b family members rapidly decreases, whereas KCNQ2 protein level inversely increases. Overexpression of miR-106b mimics resulted in a reduction in KCNQ2 protein levels. Conversely, KCNQ2 levels were up-regulated in neurons transfected with antisense miRNA inhibitors. By constructing more specific and stable forms of miR-106b controlling systems, we further confirmed that overexpression of precursor-miR-106b-5p led to a decrease in KCNQ current density and an increase in firing frequency of hippocampal neurons, while tough decoy miR-106b-5p dramatically increased current density and decreased neuronal excitability. These results unmask a regulatory mechanism of KCNQ2 channel expression in early postnatal development and hint at a role for miR-106b up-regulation in the pathophysiology of epilepsy.
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50
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Gao S, Gao H, Dai L, Han Y, Lei Z, Wang X, Chang H, Liu S, Wang Z, Tong H, Wu H. miR-126 regulates angiogenesis in myocardial ischemia by targeting HIF-1α. Exp Cell Res 2021; 409:112925. [PMID: 34785240 DOI: 10.1016/j.yexcr.2021.112925] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 10/17/2021] [Accepted: 11/12/2021] [Indexed: 12/27/2022]
Abstract
Promoting angiogenesis by targeting various angiogenic regulators has emerged as a new treatment strategy for myocardial ischemia (MI). MicroRNA-126 (miR-126) has been identified as the main regulator of compensatory angiogenesis; however, its role in MI is unclear. A rat MI model and an EA. hy926 endothelial cell hypoxia model were constructed and it was found that miR-126 was highly expressed in both models. The knockdown of HIF-1α expression in EA. hy926 cells in turn downregulated VEGF and CD34 expression and consequently inhibited angiogenesis. MiR-126 inhibitor inhibited EA. hy926 cell migration and tube formation as well as downregulated VEGF and CD34 expression, and these were reversed by transfection of miR-126 mimics. Rescue tests using miR-126 and HIF-1α demonstrated that miR-126-mediated regulation of angiogenesis was dependent on HIF-1α. In summary, miR-126 regulates the occurrence and progression of angiogenesis during MI via HIF-1α and may be a potential new therapeutic target.
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Affiliation(s)
- Shuibo Gao
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Haixia Gao
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Liping Dai
- School of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, China
| | - Yongjun Han
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Zhen Lei
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Xinzhou Wang
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Hongbo Chang
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Shanshan Liu
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Zhentao Wang
- Institute of Cardiovascular Disease, Henan University of Chinese Medicine, Zhengzhou, 450002, China
| | - Haibin Tong
- College of Life and Environmental Science, Wenzhou University, Wenzhou, 325035, China.
| | - Hong Wu
- Second School of Clinical Medicine, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Laboratory of Cell Imaging, Henan University of Chinese Medicine, Zhengzhou, 450002, China; Institute of Cardiovascular Disease, Henan University of Chinese Medicine, Zhengzhou, 450002, China.
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