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Zhang X, Zhang X, Huang X, Iqbal J, McKeithan TW, Chan WC, Vose JM, Bi C, Zhu X, Fu K. MiR-17∼92 is involved in NF-κB activation via targeting the ubiquitin-editing proteins to mediate RIP1 complex polyubiquitinations in ABC-DLBCL. Clin Immunol 2024; 265:110297. [PMID: 38909971 DOI: 10.1016/j.clim.2024.110297] [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: 12/17/2023] [Revised: 05/20/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Activated B-cell-like diffuse large B-cell lymphoma (ABC-DLBCL) is an aggressive lymphoma characterized by constitutive NF-κB activation, but whether miR-17∼92 contributes to this activation remains unclear. Herein, we sought to evaluate the role of miR-17∼92 in the process of NF-κB activation in ABC-DLBCL. We found that the expression of miR-17∼92 primary transcript was positively correlated with NF-κB activity, miR-17∼92 activated the NF-κB signaling in ABC-DLBCL, and its over-expression promoted ABC-DLBCL cell growth, accelerated cell G1 to S phase transition and enhanced cell resistance to NF-κB inhibitor. Importantly, miR-17∼92 promoted NF-κB activation through directly targeting multiple ubiquitin-editing regulators to lead to increase the K63-linked polyubiquitination and decrease the K48-linked polyubiquitination of RIP1 complex in ABC-DLBCL. We further found that miR-17∼92 selectively activated IκB-α and NF-κB p65 but not NF-κB p52/p100, and high miR-17∼92 expression was also associated with poorer outcome in ABC-DLBCL patients. Overall, our results showed that miR-17∼92 selectively activated the canonical NF-κB signaling via targeting ubiquitin-editing regulators to lead to constitutively NF-κB activation and poorer outcome in ABC-DLBCL. These findings uncovered an innovative function of miR-17∼92 and previously unappreciated regulatory mechanism of NF-κB activation in ABC-DLBCL. Targeting miR-17∼92 may thus provide a novel bio-therapeutic strategy for ABC-DLBCL patients.
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Affiliation(s)
- Xiaoyan Zhang
- Department of Pediatrics, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China; Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Xuan Zhang
- Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Xin Huang
- Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Javeed Iqbal
- Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Timothy W McKeithan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Wing C Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA, USA
| | - Julie M Vose
- Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Chengfeng Bi
- Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
| | - Xiaofan Zhu
- Department of Pediatrics, State Key Laboratory of Experimental Hematology, National Clinical Research Center for Blood Diseases, Institute of Hematology & Blood Diseases Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Tianjin, China.
| | - Kai Fu
- Departments of Pathology and Microbiology, and Internal Medicine, University of Nebraska Medical Center, Omaha, NE, USA.
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2
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Zhou W, Tang M, He D, Shen Y, Huang Z, Xia W, Wu Z, Wei W, Zheng H, Wang Q, Shi W, Jiang J. Hypoxia promotes metastasis by relieving miR-598-3p-restricted glycolysis in gastric cancer. J Transl Med 2024; 22:283. [PMID: 38491378 PMCID: PMC10943772 DOI: 10.1186/s12967-024-04957-7] [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: 10/16/2023] [Accepted: 02/05/2024] [Indexed: 03/18/2024] Open
Abstract
The activation of glycolysis, particularly in the context of reprogrammed energy metabolism, is increasingly recognized as a significant characteristic of cancer. However, the precise mechanisms by which glycolysis is promoted in metastatic gastric cancer cells under normal oxygen conditions remain poorly understood. MicroRNAs (miRNAs) play a crucial role in the development of malignant phenotypes in gastric cancer. Nevertheless, our understanding of the specific involvement of miRNAs in hypoxia-induced metabolic shifting and the subsequent metastatic processes is limited. Hypoxia-induced downregulation of miR-598-3p mechanistically leads to the upregulation of RMP and IGF1r, thereby promoting glycolysis. Either overexpression of miR-598-3p or R406 treatment effectively suppresses the metastasis of gastric cancer cells both in vitro and in vivo. Collectively, the depletion of miR-598-3p alters glucose metabolism from oxidative phosphorylation to glycolysis, thereby exacerbating the malignancy of gastric cancer cells. The present findings indicate a potential target for the development of therapeutics against gastric cancers with increased miR-598-3p expression.
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Affiliation(s)
- Wei Zhou
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
| | - Mengyuan Tang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
- Department of Immunology, Soochow University, SuZhou, 215004, Jiangsu, China
| | - Dan He
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
| | - Yi Shen
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
| | - Ziwei Huang
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
| | - Wenxin Xia
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
| | - Zhiyun Wu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
| | - Wenxiang Wei
- Department of Cell Biology, Soochow University, SuZhou, 215004, Jiangsu, China
| | - Hui Zheng
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China
- Institutes of Biology and Medical Science (IBMS), Soochow University, SuZhou, 215004, Jiangsu, China
| | - Qi Wang
- Department of Biological Treatment, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China.
| | - Weifeng Shi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China.
| | - Jingting Jiang
- Department of Biological Treatment, The Third Affiliated Hospital of Soochow University, ChangZhou, 213003, Jiangsu, China.
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Kaur S, Verma H, Kaur S, Gangwar P, Yadav A, Yadav B, Rao R, Dhiman M, Mantha AK. Understanding the multifaceted role of miRNAs in Alzheimer's disease pathology. Metab Brain Dis 2024; 39:217-237. [PMID: 37505443 DOI: 10.1007/s11011-023-01265-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023]
Abstract
Small non-coding RNAs (miRNAs) regulate gene expression by binding to mRNA and mediating its degradation or inhibiting translation. Since miRNAs can regulate the expression of several genes, they have multiple roles to play in biological processes and human diseases. The majority of miRNAs are known to be expressed in the brain and are involved in synaptic functions, thus marking their presence and role in major neurodegenerative disorders, including Alzheimer's disease (AD). In AD, amyloid beta (Aβ) plaques and neurofibrillary tangles (NFTs) are known to be the major hallmarks. The clearance of Aβ and tau is known to be associated with miRNA dysregulation. In addition, the β-site APP cleaving enzyme (BACE 1), which cleaves APP to form Aβ, is also found to be regulated by miRNAs, thus directly affecting Aβ accumulation. Growing evidences suggest that neuroinflammation can be an initial event in AD pathology, and miRNAs have been linked with the regulation of neuroinflammation. Inflammatory disorders have also been associated with AD pathology, and exosomes associated with miRNAs are known to regulate brain inflammation, suggesting for the role of systemic miRNAs in AD pathology. Several miRNAs have been related in AD, years before the clinical symptoms appear, most of which are associated with regulating the cell cycle, immune system, stress responses, cellular senescence, nerve growth factor (NGF) signaling, and synaptic regulation. Phytochemicals, especially polyphenols, alter the expression of various miRNAs by binding to miRNAs or binding to the transcriptional activators of miRNAs, thus control/alter various metabolic pathways. Awing to the sundry biological processes being regulated by miRNAs in the brain and regulation of expression of miRNAs via phytochemicals, miRNAs and the regulatory bioactive phytochemicals can serve as therapeutic agents in the treatment and management of AD.
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Affiliation(s)
- Sharanjot Kaur
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Harkomal Verma
- Department of Zoology, School of Basic Sciences, Central University of Punjab, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Sukhchain Kaur
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Prabhakar Gangwar
- Department of Zoology, School of Basic Sciences, Central University of Punjab, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Anuradha Yadav
- Department of Zoology, School of Basic Sciences, Central University of Punjab, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Bharti Yadav
- Department of Zoology, School of Basic Sciences, Central University of Punjab, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Rashmi Rao
- Department of Zoology, School of Basic Sciences, Central University of Punjab, VPO - Ghudda, Bathinda, 151 401, Punjab, India
| | - Monisha Dhiman
- Department of Microbiology, School of Basic Sciences, Central University of Punjab, Ghudda, Bathinda, Punjab, India
| | - Anil Kumar Mantha
- Department of Zoology, School of Basic Sciences, Central University of Punjab, VPO - Ghudda, Bathinda, 151 401, Punjab, India.
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Shi J, Xu J, Ma J, He F. tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis. Genome Res 2023; 33:2119-2132. [PMID: 37973194 PMCID: PMC10760521 DOI: 10.1101/gr.278128.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]
Abstract
A class of noncoding RNAs, referred to as tsRNAs, is emerging with a potential to exert a new layer in gene regulation. These RNAs are breakdown products of tRNAs, either through active processing or passive cleavage or both. Since tRNAs are part of the general machinery for translation, their expression levels and activities are tightly controlled, raising the possibility that their breakdown products, tsRNAs, may provide a link between the overall translational status of a cell to specific changes in gene regulatory network. We hypothesize that Drosophila pupation, being a special developmental stage during which there is a global limitation of nutrients, represents a system in which such a link may readily reveal itself. We show that specific tsRNAs indeed show a dynamic accumulation upon entering the pupal stage. We describe experiments to characterize the mode of tsRNA action and, through the use of such gained knowledge, conduct a genome-wide analysis to assess the functions of dynamically expressed tsRNAs. Our results show that the predicted target genes are highly enriched in biological processes specific to this stage of development including metamorphosis. We further show that tsRNA action is required for successful pupation, providing direct support to the hypothesis that tsRNAs accumulated during this stage are critical to the gene expression program at this stage of development.
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Affiliation(s)
- Junling Shi
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jiaqi Xu
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
| | - Jun Ma
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China;
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
| | - Feng He
- Center for Genetic Medicine, the Fourth Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China;
- Women's Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310058, China
- Institute of Genetics, Zhejiang University International School of Medicine, Hangzhou, Zhejiang 310058, China
- Zhejiang Provincial Key Laboratory of Genetic and Developmental Disorder, Hangzhou, Zhejiang 310058, China
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5
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Dubaic M, Peskova L, Hampl M, Weissova K, Celiker C, Shylo NA, Hruba E, Kavkova M, Zikmund T, Weatherbee SD, Kaiser J, Barta T, Buchtova M. Role of ciliopathy protein TMEM107 in eye development: insights from a mouse model and retinal organoid. Life Sci Alliance 2023; 6:e202302073. [PMID: 37863656 PMCID: PMC10589122 DOI: 10.26508/lsa.202302073] [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: 04/04/2023] [Revised: 09/27/2023] [Accepted: 09/28/2023] [Indexed: 10/22/2023] Open
Abstract
Primary cilia are cellular surface projections enriched in receptors and signaling molecules, acting as signaling hubs that respond to stimuli. Malfunctions in primary cilia have been linked to human diseases, including retinopathies and ocular defects. Here, we focus on TMEM107, a protein localized to the transition zone of primary cilia. TMEM107 mutations were found in patients with Joubert and Meckel-Gruber syndromes. A mouse model lacking Tmem107 exhibited eye defects such as anophthalmia and microphthalmia, affecting retina differentiation. Tmem107 expression during prenatal mouse development correlated with phenotype occurrence, with enhanced expression in differentiating retina and optic stalk. TMEM107 deficiency in retinal organoids resulted in the loss of primary cilia, down-regulation of retina-specific genes, and cyst formation. Knocking out TMEM107 in human ARPE-19 cells prevented primary cilia formation and impaired response to Smoothened agonist treatment because of ectopic activation of the SHH pathway. Our data suggest TMEM107 plays a crucial role in early vertebrate eye development and ciliogenesis in the differentiating retina.
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Affiliation(s)
- Marija Dubaic
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucie Peskova
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marek Hampl
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kamila Weissova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Canan Celiker
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Natalia A Shylo
- Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
- Stowers Institute for Medical Research, Kansas City, MO, USA
| | - Eva Hruba
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
| | - Michaela Kavkova
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Zikmund
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Scott D Weatherbee
- Department of Genetics, Yale University, School of Medicine, New Haven, CT, USA
- Biology Department, Fairfield University, Fairfield, CT, USA
| | - Jozef Kaiser
- https://ror.org/03613d656 CEITEC - Central European Institute of Technology, Brno University of Technology, Brno, Czech Republic
| | - Tomas Barta
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Marcela Buchtova
- Laboratory of Molecular Morphogenesis, Institute of Animal Physiology and Genetics, Czech Academy of Sciences, Brno, Czech Republic
- https://ror.org/02j46qs45 Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
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6
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Zolboot N, Xiao Y, Du JX, Ghanem MM, Choi SY, Junn MJ, Zampa F, Huang Z, MacRae IJ, Lippi G. MicroRNAs are necessary for the emergence of Purkinje cell identity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560023. [PMID: 37808721 PMCID: PMC10557743 DOI: 10.1101/2023.09.28.560023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Brain computations are dictated by the unique morphology and connectivity of neuronal subtypes, features established by closely timed developmental events. MicroRNAs (miRNAs) are critical for brain development, but current technologies lack the spatiotemporal resolution to determine how miRNAs instruct the steps leading to subtype identity. Here, we developed new tools to tackle this major gap. Fast and reversible miRNA loss-of-function revealed that miRNAs are necessary for cerebellar Purkinje cell (PC) differentiation, which previously appeared miRNA-independent, and resolved distinct miRNA critical windows in PC dendritogenesis and climbing fiber synaptogenesis, key determinants of PC identity. To identify underlying mechanisms, we generated a mouse model, which enables precise mapping of miRNAs and their targets in rare cell types. With PC-specific maps, we found that the PC-enriched miR-206 drives exuberant dendritogenesis and modulates synaptogenesis. Our results showcase vastly improved approaches for dissecting miRNA function and reveal that many critical miRNA mechanisms remain largely unexplored. Highlights Fast miRNA loss-of-function with T6B impairs postnatal Purkinje cell developmentReversible T6B reveals critical miRNA windows for dendritogenesis and synaptogenesisConditional Spy3-Ago2 mouse line enables miRNA-target network mapping in rare cellsPurkinje cell-enriched miR-206 regulates its unique dendritic and synaptic morphology.
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Al Qaryoute A, Fallatah W, Dhinoja S, Raman R, Jagadeeswaran P. Role of microRNAs and their downstream target transcription factors in zebrafish thrombopoiesis. Sci Rep 2023; 13:16066. [PMID: 37752184 PMCID: PMC10522587 DOI: 10.1038/s41598-023-42868-7] [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: 04/12/2023] [Accepted: 09/15/2023] [Indexed: 09/28/2023] Open
Abstract
Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, a comprehensive study on the microRNAs and their targets has not been undertaken. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, we identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. We knocked down each of these 15 microRNAs by the piggyback method and found knockdown of three microRNAs, mir-7148, let-7b, and mir-223 in adult zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. We also found enhanced thrombosis using arterial laser thrombosis assay in a group of zebrafish larvae after mir-7148, let-7b, and mir-223 knockdowns. These results suggested mir-7148, let-7b, and mir-223 are repressors for thrombocyte production. We then explored miRWalk database for let-7b downstream targets and then selected those that are expressed in thrombocytes, and from this list based on their role in differentiation selected 14 genes, rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8, and lbx1b that encode transcriptional regulators. The qRT-PCR analysis of expression levels of the above genes following let-7b knockdown showed changes in the expression of 13 targets. We then studied the effect of the 13 targets on thrombocyte production and identified 5 genes, irf5, tgif1, irf8, cebpa, and rorca that showed thrombocytosis and one gene, ikzf1 that showed thrombocytopenia. Furthermore, we tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223. We also identified that tgif1, cebpa, ikzf1, irf5, irf8, and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a differential expression profile in let-7b and mir-223 knockdowns but resulted in thrombocytopenia in ikzf1 knockdown in both adults and larvae we also studied an ikzf1 mutant and showed the mutant had thrombocytopenia. Taken together, these studies showed that thrombopoiesis is controlled by a network of transcription regulators that are regulated by multiple microRNAs in both positive and negative manner resulting in overall inhibition of thrombopoiesis.
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Affiliation(s)
- Ayah Al Qaryoute
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Weam Fallatah
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Sanchi Dhinoja
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Revathi Raman
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA
| | - Pudur Jagadeeswaran
- Department of Biological Sciences, University of North Texas, 1511 West Sycamore Street, Denton, TX, 76203, USA.
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Fatima K, Sadaqat M, Azeem F, Rao MJ, Albekairi NA, Alshammari A, Tahir ul Qamar M. Integrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp . revealed their role in multiple stresses. Front Genet 2023; 14:1252020. [PMID: 37799143 PMCID: PMC10547876 DOI: 10.3389/fgene.2023.1252020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 09/05/2023] [Indexed: 10/07/2023] Open
Abstract
Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier. The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.
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Affiliation(s)
- Kinza Fatima
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Sadaqat
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Farrukh Azeem
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
| | - Muhammad Junaid Rao
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Laboratory of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi, China
| | - Norah A. Albekairi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Muhammad Tahir ul Qamar
- Integrative Omics and Molecular Modeling Laboratory, Department of Bioinformatics and Biotechnology, Government College University Faisalabad (GCUF), Faisalabad, Pakistan
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Montaño-Samaniego M, Sánchez-Cedillo J, Lucas-González A, Bravo-Estupiñan DM, Alarcón-Hernández E, Rivera-Gutiérrez S, Balderas-López JA, Ibáñez-Hernández M. Targeted Expression to Liver of an antimiR-33 Sponge as a Gene Therapy Strategy against Hypercholesterolemia: In Vitro Study. Curr Issues Mol Biol 2023; 45:7043-7057. [PMID: 37754229 PMCID: PMC10527677 DOI: 10.3390/cimb45090445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 08/12/2023] [Accepted: 08/17/2023] [Indexed: 09/28/2023] Open
Abstract
Atherosclerosis is the leading cause of cardiovascular diseases in Mexico and worldwide. The membrane transporters ABCA1 and ABCG1 are involved in the reverse transport of cholesterol and stimulate the HDL synthesis in hepatocytes, therefore the deficiency of these transporters promotes the acceleration of atherosclerosis. MicroRNA-33 (miR-33) plays an important role in lipid metabolism and exerts a negative regulation on the transporters ABCA1 and ABCG1. It is known that by inhibiting the function of miR-33 with antisense RNA, HDL levels increase and atherogenic risk decreases. Therefore, in this work, a genetic construct, pPEPCK-antimiR-33-IRES2-EGFP, containing a specific antimiR-33 sponge with two binding sites for miR-33 governed under the PEPCK promoter was designed, constructed, and characterized, the identity of which was confirmed by enzymatic restriction, PCR, and sequencing. Hep G2 and Hek 293 FT cell lines, as well as a mouse hepatocyte primary cell culture were transfected with this plasmid construction showing expression specificity of the PEPCK promoter in hepatic cells. An analysis of the relative expression of miR-33 target messengers showed that the antimiR-33 sponge indirectly induces the expression of its target messengers (ABCA1 and ABCG1). This strategy could open new specific therapeutic options for hypercholesterolemia and atherosclerosis, by blocking the miR-33 specifically in hepatocytes.
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Affiliation(s)
- Mariela Montaño-Samaniego
- Laboratorio de Terapia Génica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.M.-S.); (J.S.-C.); (A.L.-G.); (D.M.B.-E.)
- Laboratorio de Técnicas Fototérmicas, Departamento de Ciencias Básicas, Unidad Politécnica Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Jorge Sánchez-Cedillo
- Laboratorio de Terapia Génica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.M.-S.); (J.S.-C.); (A.L.-G.); (D.M.B.-E.)
| | - Amellalli Lucas-González
- Laboratorio de Terapia Génica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.M.-S.); (J.S.-C.); (A.L.-G.); (D.M.B.-E.)
| | - Diana M. Bravo-Estupiñan
- Laboratorio de Terapia Génica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.M.-S.); (J.S.-C.); (A.L.-G.); (D.M.B.-E.)
- Laboratorio de Quimiosensibilidad Tumoral, Facultad de Microbiología, Universidad de Costa Rica, San Jose 11501-2060, Costa Rica
| | - Ernesto Alarcón-Hernández
- Laboratorio de Genética Molecular, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - Sandra Rivera-Gutiérrez
- Laboratorio de Microbiología Molecular, Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico;
| | - José Abraham Balderas-López
- Laboratorio de Técnicas Fototérmicas, Departamento de Ciencias Básicas, Unidad Politécnica Interdisciplinaria de Biotecnología, Instituto Politécnico Nacional, Mexico City 07340, Mexico;
| | - Miguel Ibáñez-Hernández
- Laboratorio de Terapia Génica, Departamento de Bioquímica, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Mexico City 11340, Mexico; (M.M.-S.); (J.S.-C.); (A.L.-G.); (D.M.B.-E.)
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Isenmann M, Stoddart MJ, Schmelzeisen R, Gross C, Della Bella E, Rothweiler RM. Basic Principles of RNA Interference: Nucleic Acid Types and In Vitro Intracellular Delivery Methods. MICROMACHINES 2023; 14:1321. [PMID: 37512632 PMCID: PMC10383872 DOI: 10.3390/mi14071321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/23/2023] [Accepted: 06/26/2023] [Indexed: 07/30/2023]
Abstract
Since its discovery in 1989, RNA interference (RNAi) has become a widely used tool for the in vitro downregulation of specific gene expression in molecular biological research. This basically involves a complementary RNA that binds a target sequence to affect its transcription or translation process. Currently, various small RNAs, such as small interfering RNA (siRNA), micro RNA (miRNA), small hairpin RNA (shRNA), and PIWI interacting RNA (piRNA), are available for application on in vitro cell culture, to regulate the cells' gene expression by mimicking the endogenous RNAi-machinery. In addition, several biochemical, physical, and viral methods have been established to deliver these RNAs into the cell or nucleus. Since each RNA and each delivery method entail different off-target effects, limitations, and compatibilities, it is crucial to understand their basic mode of action. This review is intended to provide an overview of different nucleic acids and delivery methods for planning, interpreting, and troubleshooting of RNAi experiments.
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Affiliation(s)
- Marie Isenmann
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Martin James Stoddart
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - Rainer Schmelzeisen
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Christian Gross
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
| | - Elena Della Bella
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
| | - René Marcel Rothweiler
- Department of Oral and Maxillofacial Surgery, Faculty of Medicine, University of Freiburg, Hugstetterstrasse 55, 79106 Freiburg, Germany
- AO Research Institute Davos, Clavadelerstrasse 8, 7270 Davos, Switzerland
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11
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Nguyen HD. An evaluation of the effects of mixed heavy metals on prediabetes and type 2 diabetes: epidemiological and toxicogenomic analysis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023:10.1007/s11356-023-28037-3. [PMID: 37326729 DOI: 10.1007/s11356-023-28037-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 05/29/2023] [Indexed: 06/17/2023]
Abstract
The link between mixed heavy metals (mercury, lead, and cadmium), prediabetes, and type 2 diabetes mellitus (T2DM), especially molecular mechanisms, is poorly understood. Thus, we aimed to identify the association between mixed heavy metals and T2DM and its components using a data set from the Korean National Health and Nutrition Examination Survey. We further analyzed the main molecular mechanisms implicated in T2DM development induced by mixed heavy metals using in-silico analysis. Our findings observed that serum mercury was associated with prediabetes, elevated glucose, and ln2-transformed glucose when using different statistical methods. "AGE-RAGE signaling pathway in diabetic complications", "non-alcoholic fatty liver disease", "metabolic Syndrome X", and three miRNAs (hsa-miR-98-5p, hsa-let-7a-5p, and hsa-miR-34a-5p) were listed as the most important molecular mechanisms related to T2DM development caused by mixed heavy metals. These miRNA sponge structures were created and examined, and they may be beneficial in the treatment of T2DM. The predicted cutoff values for three heavy metal levels linked to T2DM and its components were specifically identified. Our results imply that chronic exposure to heavy metals, particularly mercury, may contribute to the development of T2DM. To understand the changes in the pathophysiology of T2DM brought on by a combination of heavy metals, more research is required.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, 57922, Jeonnam, Republic of Korea.
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12
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Beheshtizadeh N, Salimi A, Golmohammadi M, Ansari JM, Azami M. In-silico engineering of RNA nanoplatforms to promote the diabetic wound healing. BMC Chem 2023; 17:52. [PMID: 37291669 DOI: 10.1186/s13065-023-00969-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Accepted: 05/30/2023] [Indexed: 06/10/2023] Open
Abstract
One of the most notable required features of wound healing is the enhancement of angiogenesis, which aids in the acceleration of regeneration. Poor angiogenesis during diabetic wound healing is linked to a shortage of pro-angiogenic or an increase in anti-angiogenic factors. As a result, a potential treatment method is to increase angiogenesis promoters and decrease suppressors. Incorporating microRNAs (miRNAs) and small interfering RNAs (siRNAs), two forms of quite small RNA molecules, is one way to make use of RNA interference. Several different types of antagomirs and siRNAs are now in the works to counteract the negative effects of miRNAs. The purpose of this research is to locate novel antagonists for miRNAs and siRNAs that target multiple genes to promote angiogenesis and wound healing in diabetic ulcers.In this context, we used gene ontology analysis by exploring across several datasets. Following data analysis, it was processed using a systems biology approach. The feasibility of incorporating the proposed siRNAs and miRNA antagomirs into polymeric bioresponsive nanocarriers for wound delivery was further investigated by means of a molecular dynamics (MD) simulation study. Among the three nanocarriers tested (Poly (lactic-co-glycolic acid) (PLGA), Polyethylenimine (PEI), and Chitosan (CTS), MD simulations show that the integration of PLGA/hsa-mir-422a is the most stable (total energy = -1202.62 KJ/mol, Gyration radius = 2.154 nm, and solvent-accessible surface area = 408.416 nm2). With values of -25.437 KJ/mol, 0.047 nm for the Gyration radius, and 204.563 nm2 for the SASA, the integration of the second siRNA/ Chitosan took the last place. The results of the systems biology and MD simulations show that the suggested RNA may be delivered through bioresponsive nanocarriers to speed up wound healing by boosting angiogenesis.
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Affiliation(s)
- Nima Beheshtizadeh
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
- Students? Scientific Research Center, Tehran University of Medical Sciences, Tehran, Iran.
| | - Alireza Salimi
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Advanced Technologies, School of Medicine, North Khorasan University of Medical Science, Bojnurd, Iran
| | - Mahsa Golmohammadi
- Department of Polymer Engineering and Color Technology, Amirkabir University of Technology, Tehran, Iran
| | - Javad Mohajer Ansari
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Anatomy, School of Medicine, Hormozgan University of Medical Sciences, Jomhuri Eslami Blvd, Bandar Abbas, 7919915519, Iran
| | - Mahmoud Azami
- Department of Tissue Engineering, School of Advanced Technologies in Medicine, Tehran University of Medical Sciences, Tehran, Iran.
- Regenerative Medicine group (REMED), Universal Scientific Education and Research Network (USERN), Tehran, Iran.
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13
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Sevcikova A, Fridrichova I, Nikolaieva N, Kalinkova L, Omelka R, Martiniakova M, Ciernikova S. Clinical Significance of microRNAs in Hematologic Malignancies and Hematopoietic Stem Cell Transplantation. Cancers (Basel) 2023; 15:cancers15092658. [PMID: 37174123 PMCID: PMC10177548 DOI: 10.3390/cancers15092658] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 04/14/2023] [Accepted: 05/02/2023] [Indexed: 05/15/2023] Open
Abstract
Hematologic malignancies are a group of neoplastic conditions that can develop from any stage of the hematopoiesis cascade. Small non-coding microRNAs (miRNAs) play a crucial role in the post-transcriptional regulation of gene expression. Mounting evidence highlights the role of miRNAs in malignant hematopoiesis via the regulation of oncogenes and tumor suppressors involved in proliferation, differentiation, and cell death. In this review, we provide current knowledge about dysregulated miRNA expression in the pathogenesis of hematological malignancies. We summarize data about the clinical utility of aberrant miRNA expression profiles in hematologic cancer patients and their associations with diagnosis, prognosis, and the monitoring of treatment response. Moreover, we will discuss the emerging role of miRNAs in hematopoietic stem cell transplantation (HSCT), and severe post-HSCT complications, such as graft-versus-host disease (GvHD). The therapeutical potential of the miRNA-based approach in hemato-oncology will be outlined, including studies with specific antagomiRs, mimetics, and circular RNAs (circRNAs). Since hematologic malignancies represent a full spectrum of disorders with different treatment paradigms and prognoses, the potential use of miRNAs as novel diagnostic and prognostic biomarkers might lead to improvements, resulting in a more accurate diagnosis and better patient outcomes.
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Affiliation(s)
- Aneta Sevcikova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Ivana Fridrichova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Nataliia Nikolaieva
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Lenka Kalinkova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
| | - Radoslav Omelka
- Department of Botany and Genetics, Faculty of Natural Sciences and Informatics, Constantine the Philosopher University in Nitra, 949 74 Nitra, Slovakia
| | - Monika Martiniakova
- Department of Zoology and Anthropology, Faculty of Natural Sciences and Informatics, Constantine the Philosopher University in Nitra, 949 74 Nitra, Slovakia
| | - Sona Ciernikova
- Department of Genetics, Cancer Research Institute, Biomedical Research Center of Slovak Academy of Sciences, 845 05 Bratislava, Slovakia
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Nguyen HD, Kim MS. In silico identification of molecular mechanisms for stroke risk caused by heavy metals and their mixtures: sponges and drugs involved. Neurotoxicology 2023; 96:222-239. [PMID: 37121440 DOI: 10.1016/j.neuro.2023.04.011] [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: 12/19/2022] [Revised: 03/14/2023] [Accepted: 04/26/2023] [Indexed: 05/02/2023]
Abstract
This study used various approaches and databases to evaluate the molecular processes and identify miRNA sponges and drugs associated with the development of stroke caused by heavy metals and their combinations. We found that the genes ALB (albumin), IL1B (Interleukin-1β), F2 (coagulation factor II), APOA1 (apolipoprotein A1), IL6 (Interleukin 6), and NOS2 (nitric oxide synthase 2) were linked to the development of strokes by 18 chemicals and a combination of cadmium, copper, and lead. These results may point to the significance of detoxification and neuroinflammation in stroke as well as the potential for targeting these genes in future stroke therapies. ALB and IL1B were the most common and significant genes. The "selenium micronutrient network," "vitamin B12 metabolism," and "folate metabolism" were shown to be the most significant pathways connected to the risk of stroke brought on by combined heavy metals. The two main cellular elements that may increase the risk of stroke caused by heavy metals were discovered to be "blood microparticle" and "endoplasmic reticulum lumen." We also observed an important chromosome (chr7p15.3), two transcription factors (NFKB2 [nuclear factor kappa B subunit 2] and NR1I2 [nuclear receptor subfamily 1 group, member 2]), and four microRNAs (hsa-miR-26a-5p, hsa-miR-9-5p, hsa-miR-124-3p, and hsa-miR-155-5p) associated with stroke caused by combined heavy metals. Additionally, for these miRNAs, we created and examined in silico microRNA sponge sequences. Triflusal and andrographolide have been identified as potential treatments for heavy metal-induced stroke. Taken together, heavy metals may be a significant contributor to the pathophysiology of stroke, but further investigation into the precise molecular pathways implicated in stroke pathophysiology is required to corroborate these findings.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea.
| | - Min-Sun Kim
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Suncheon 57922, Republic of Korea.
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15
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Qaryoute AA, Fallatah W, Dhinoja S, Raman R, Jagadeeswaran P. Role of MicroRNAs and their Downstream Target Transcription Factors in Zebrafish Thrombopoiesis. RESEARCH SQUARE 2023:rs.3.rs-2807790. [PMID: 37162944 PMCID: PMC10168436 DOI: 10.21203/rs.3.rs-2807790/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Previous studies have shown that human platelets and megakaryocytes carry microRNAs suggesting their role in platelet function and megakaryocyte development, respectively. However, a comprehensive study on the microRNAs and their targets has not been undertaken. Zebrafish thrombocytes could be used as a model to study their role in megakaryocyte maturation and platelet function because thrombocytes have both megakaryocyte features and platelet properties. In our laboratory, we identified 15 microRNAs in thrombocytes using single-cell RNA sequencing. We knocked down each of these 15 microRNAs by the piggyback method and found knockdown of three microRNAs, mir-7148, let-7b , and mir-223 in adult zebrafish led to an increase in the percentage of thrombocytes. Functional thrombocyte analysis using plate tilt assay showed no modulatory effect of the three microRNAs on thrombocyte aggregation/agglutination. We also found enhanced thrombosis using arterial laser thrombosis assay in a group of zebrafish larvae after mir-7148, let-7b , and mir-223 knockdowns. These results suggested mir-7148, let-7b , and mir-223 are repressors for thrombocyte production. We then explored miRWalk database for let-7b downstream targets and then selected those that are expressed in thrombocytes, and from this list based on their role in differentiation selected 14 genes, rorca, tgif1, rfx1a, deaf1, zbtb18, mafba, cebpa, spi1a, spi1b, fhl3b, ikzf1, irf5, irf8 , and lbx1b that encode transcriptional regulators. The qRT-PCR analysis of expression levels of the above genes following let-7b knockdown showed changes in the expression of 13 targets. We then studied the effect of the 13 targets on thrombocyte production and identified 5 genes, irf5, tgif1, irf8, cebpa , and rorca that showed thrombocytosis and one gene, ikzf1 that showed thrombocytopenia. Furthermore, we tested whether mir-223 regulates any of the above 13 transcription factors after mir-223 knockdown using qRT-PCR. Six of the 13 genes showed similar gene expression as observed with let-7b knockdown and 7 genes showed opposing results. Thus, our results suggested a possible regulatory network in common with both let-7b and mir-223 . We also identified that tgif1, cebpa, ikzf1, irf5 , irf8 , and ikzf1 play a role in thrombopoiesis. Since the ikzf1 gene showed a differential expression profile in let-7b and mir-223 knockdowns but resulted in thrombocytopenia in ikzf1 knockdown in both adults and larvae we also studied an ikzf1 mutant and showed the mutant had thrombocytopenia. Taken together, these studies showed that thrombopoiesis is controlled by a network of transcription regulators that are regulated by multiple microRNAs in both positive and negative manner resulting in overall inhibition of thrombopoiesis.
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Csukasi F, Bosakova M, Barta T, Martin JH, Arcedo J, Barad M, Rico-Llanos GA, Zieba J, Becerra J, Krejci P, Duran I, Krakow D. Skeletal diseases caused by mutations in PTH1R show aberrant differentiation of skeletal progenitors due to dysregulation of DEPTOR. Front Cell Dev Biol 2023; 10:963389. [PMID: 36726589 PMCID: PMC9885499 DOI: 10.3389/fcell.2022.963389] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 12/27/2022] [Indexed: 01/18/2023] Open
Abstract
Alterations in the balance between skeletogenesis and adipogenesis is a pathogenic feature in multiple skeletal disorders. Clinically, enhanced bone marrow adiposity in bones impairs mobility and increases fracture risk, reducing the quality of life of patients. The molecular mechanism that underlies the balance between skeletogenesis and adipogenesis is not completely understood but alterations in skeletal progenitor cells' differentiation pathway plays a key role. We recently demonstrated that parathyroid hormone (PTH)/PTH-related peptide (PTHrP) control the levels of DEPTOR, an inhibitor of the mechanistic target of rapamycin (mTOR), and that DEPTOR levels are altered in different skeletal diseases. Here, we show that mutations in the PTH receptor-1 (PTH1R) alter the differentiation of skeletal progenitors in two different skeletal genetic disorders and lead to accumulation of fat or cartilage in bones. Mechanistically, DEPTOR controls the subcellular localization of TAZ (transcriptional co-activator with a PDZ-binding domain), a transcriptional regulator that governs skeletal stem cells differentiation into either bone and fat. We show that DEPTOR regulation of TAZ localization is achieved through the control of Dishevelled2 (DVL2) phosphorylation. Depending on nutrient availability, DEPTOR directly interacts with PTH1R to regulate PTH/PTHrP signaling or it forms a complex with TAZ, to prevent its translocation to the nucleus and therefore inhibit its transcriptional activity. Our data point DEPTOR as a key molecule in skeletal progenitor differentiation; its dysregulation under pathologic conditions results in aberrant bone/fat balance.
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Affiliation(s)
- Fabiana Csukasi
- Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, University of Malaga, Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Michaela Bosakova
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
- Institute of Animal Physiology and Genetics of the CAS, Brno, Czechia
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czechia
| | - Tomas Barta
- Institute of Animal Physiology and Genetics of the CAS, Brno, Czechia
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
| | - Jorge H Martin
- Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
| | - Jesus Arcedo
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, University of Malaga, Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
| | - Maya Barad
- Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
| | - Gustavo A Rico-Llanos
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, University of Malaga, Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Jennifer Zieba
- Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
| | - Jose Becerra
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, University of Malaga, Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Pavel Krejci
- Department of Biology, Faculty of Medicine, Masaryk University, Brno, Czechia
- Institute of Animal Physiology and Genetics of the CAS, Brno, Czechia
- International Clinical Research Center, St. Anne's University Hospital, Brno, Czechia
| | - Ivan Duran
- Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
- Laboratory of Bioengineering and Tissue Regeneration (LABRET), Department of Cell Biology, Genetics and Physiology, University of Malaga, Institute of Biomedical Research in Malaga (IBIMA-Plataforma BIONAND), Malaga, Spain
- Biomedical Research Networking Center in Bioengineering, Biomaterials, and Nanomedicine (CIBER-BBN), Madrid, Spain
| | - Deborah Krakow
- Department of Orthopaedic Surgery, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czechia
- Department of Human Genetics, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
- Department of Obstetrics and Gynecology, David Geffen School of Medicine at University of California at Los Angeles, Los Angeles, CA, United States
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17
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Nguyen HD. Interactions between heavy metals and sleep duration among pre-and postmenopausal women: A current approach to molecular mechanisms involved. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 316:120607. [PMID: 36347409 DOI: 10.1016/j.envpol.2022.120607] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/14/2022] [Accepted: 11/03/2022] [Indexed: 06/16/2023]
Abstract
The effects of heavy metals (cadmium, lead, and mercury) and their mixtures on sleep duration in pre-and postmenopausal women, particularly the molecular mechanisms, remain unknown. Here, we assessed the interaction between heavy metals and sleep duration among pre-and postmenopausal women (n = 1134). Furthermore, molecular mechanisms related to sleep disorders induced by studied heavy metals were further analyzed to support the previous findings. We found that serum lead levels were positively related to weekend and weekday sleep duration in premenopausal women. There were interactions between serum lead and mercury and menopausal status for sleep duration. Serum lead and mercury levels were shown to be inversely related to sleep duration in postmenopausal women. Despite the lack of statistically significant associations between mixed heavy metals and sleep duration, there were increasing trends in premenopausal women's sleeping patterns and decreasing trends in postmenopausal women's sleeping patterns. In silico analysis, IL1B, hsa-21-5p, hsa-887-3p, hsa-877-3p, and NR4A1 were identified as the most relevant genes, miRNAs, and transcription factors linked with sleep disorders induced by combined heavy metals (cadmium, lead, and mercury). Furthermore, "type 1 melanocortin receptor binding," "endocrine hormone secretion," "interleukin-1 receptor antagonist activity," "altered melanocortin system," and "sleep wake disorders" were identified as the predominant molecular mechanisms involved in the pathophysiology of sleep disorders induced by the studied heavy metals. Cut off point values and miRNA sponge templates for heavy metal exposure levels relevant to sleep disorders in pre- and postmenopausal women were reported. Future research is needed to verify our findings and provide insight into the molecular processes of long-term mixed heavy metal exposure in various populations, such as children and the elderly.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, jeonnam, 57922, Republic of Korea.
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18
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Khan I, Preeti K, Fernandes V, Khatri DK, Singh SB. Role of MicroRNAs, Aptamers in Neuroinflammation and Neurodegenerative Disorders. Cell Mol Neurobiol 2022; 42:2075-2095. [PMID: 33934227 DOI: 10.1007/s10571-021-01093-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Exploring the microRNAs and aptamers for their therapeutic role as biological drugs has expanded the horizon of its applicability against various human diseases, explicitly targeting the genetic materials. RNA-based therapeutics are widely being explored for the treatment and diagnosis of multiple diseases, including neurodegenerative disorders (NDD). Latter includes microRNA, aptamers, ribozymes, and small interfering RNAs (siRNAs), which control the gene expression mainly at the transcriptional strata. One RNA transcript translates into different protein types; hence, therapies targeted at the transcriptional sphere may have prominent and more extensive effects than alternative therapeutics. Unlike conventional gene therapy, RNAs, upon delivery, can either altogether abolish or alter the synthesis of the protein of interest, therefore, regulating their activities in a controlled and diverse manner. NDDs like Alzheimer's disease, Parkinson's disease, Huntington's disease, multiple sclerosis, Prion disease, and others are characterized by deposition of misfolded protein such as amyloid-ß, tau, α-synuclein, huntingtin and prion proteins. Neuroinflammation, one of the perquisites for neurodegeneration, is induced during neurodegenerative pathogenesis. In this review, we discuss microRNAs and aptamers' role as two different RNA-based approaches for their unique ability to regulate protein production at the transcription level, hence offering many advantages over other biologicals. The microRNA acts either by alleviating the malfunctioning RNA expression or by working as a replacement to lost microRNA. On the contrary, aptamer act as a chemical antibody and forms an aptamer-target complex.
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Affiliation(s)
- Islauddin Khan
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Hyderabad, Telangana, 500037, India
| | - Kumari Preeti
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Hyderabad, Telangana, 500037, India
| | - Valencia Fernandes
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Hyderabad, Telangana, 500037, India
| | - Dharmendra Kumar Khatri
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Hyderabad, Telangana, 500037, India.
| | - Shashi Bala Singh
- Department of Pharmacology and Toxicology, National Institute of Pharmaceutical Education and Research (NIPER)-Hyderabad, Balanagar, Hyderabad, Telangana, 500037, India.
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19
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Nguyen HD, Kim MS. Cadmium, lead, and mercury mixtures interact with non-alcoholic fatty liver diseases. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 309:119780. [PMID: 35841990 DOI: 10.1016/j.envpol.2022.119780] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2022] [Revised: 06/19/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
There is a scarcity of studies on the interactions between heavy metals and non-alcoholic fatty liver disease (NAFLD). Using a variety of statistical approaches, we investigated the impact of three common heavy metals on liver enzymes and NAFLD markers in a Korean adult population. We observed that cadmium, mercury, and lead all demonstrated positive correlations with liver enzymes and NAFLD indices. Our findings were mostly robust in secondary analysis, which included three novel mixture modeling approaches (WQS, qgcomp, and BKMR) as well as in silico investigation of molecular mechanisms (genes, miRNAs, biological processes, pathways, and illnesses). The 16 genes interacted with a mixture of heavy metals, which was linked to the development of NAFLD. Co-expression was discovered in nearly half of the interactions between the 18 NAFLD-linked genes. Key molecular pathways implicated in the pathogenesis of NAFLD generated by the heavy metal combination include activated oxidative stress, altered lipid metabolism, and increased cytokines and inflammatory response. Heavy metal exposure levels were related to liver enzymes and NAFLD indices, and cutoff criteria were revealed. More studies are needed to validate our findings and gain knowledge about the effects of chronic combined heavy metal exposure on adult and child liver function and the likelihood of developing NAFLD. To reduce the occurrence of NAFLD, early preventative and regulatory actions (half-yearly screening of workers at high-risk facilities; water filtration; avoiding excessive amounts of seafood, etc.) should be taken.
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Affiliation(s)
- Hai Duc Nguyen
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Jeonnam, Republic of Korea
| | - Min-Sun Kim
- Department of Pharmacy, College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Jeonnam, Republic of Korea.
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20
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Modular scaffolding by lncRNA HOXA10-AS promotes oral cancer progression. Cell Death Dis 2022; 13:629. [PMID: 35858923 PMCID: PMC9300705 DOI: 10.1038/s41419-022-05071-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 01/21/2023]
Abstract
Recent findings have implicated long noncoding RNAs (lncRNAs) as pivotal gene regulators for diverse biological processes, despite their lack of protein-coding capabilities. Accumulating evidence suggests the significance of lncRNAs in mediating cell signaling pathways, especially those associated with tumorigenesis. Consequently, lncRNAs have emerged as novel functional regulators and indicators of cancer development and malignancy. Recent transcriptomic profiling has recognized a tumor-biased expressed lncRNA, the HOXA10-AS transcript, whose expression is associated with patient survival. Functional cell-based assays show that the HOXA10-AS transcript is essential in the regulation of oral cancer growth and metastasis. LncRNA expression is also associated with drug sensitivity. In this study, we identify that HOXA10-AS serves as a modular scaffold for TP63 mRNA processing and that such involvement regulates cancer growth. These findings provide a functional interpretation of lncRNA-mediated molecular regulation, highlighting the significance of the lncRNA transcriptome in cancer biology.
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21
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Ražná K, Harenčár Ľ, Kučka M. The Involvement of microRNAs in Plant Lignan Biosynthesis—Current View. Cells 2022; 11:cells11142151. [PMID: 35883592 PMCID: PMC9323225 DOI: 10.3390/cells11142151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 07/05/2022] [Accepted: 07/06/2022] [Indexed: 02/01/2023] Open
Abstract
Lignans, as secondary metabolites synthesized within a phenylpropanoid pathway, play various roles in plants, including their involvement in growth and plant defense processes. The health and nutritional benefits of lignans are unquestionable, and many studies have been devoted to these attributes. Although the regulatory role of miRNAs in the biosynthesis of secondary metabolites has been widely reported, there is no systematic review available on the miRNA-based regulatory mechanism of lignans biosynthesis. However, the genetic background of lignan biosynthesis in plants is well characterized. We attempted to put together a regulatory mosaic based on current knowledge describing miRNA-mediated regulation of genes, enzymes, or transcription factors involved in this biosynthesis process. At the same time, we would like to underline the fact that further research is necessary to improve our understanding of the miRNAs regulating plant lignan biosynthesis by exploitation of current approaches for functional identification of miRNAs.
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22
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Saiyed AN, Vasavada AR, Johar SRK. Recent trends in miRNA therapeutics and the application of plant miRNA for prevention and treatment of human diseases. FUTURE JOURNAL OF PHARMACEUTICAL SCIENCES 2022; 8:24. [PMID: 35382490 PMCID: PMC8972743 DOI: 10.1186/s43094-022-00413-9] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 03/21/2022] [Indexed: 02/17/2023] Open
Abstract
Background Researchers now have a new avenue to investigate when it comes to miRNA-based therapeutics. miRNAs have the potential to be valuable biomarkers for disease detection. Variations in miRNA levels may be able to predict changes in normal physiological processes. At the epigenetic level, miRNA has been identified as a promising candidate for distinguishing and treating various diseases and defects. Main body In recent pharmacology, plants miRNA-based drugs have demonstrated a potential role in drug therapeutics. The purpose of this review paper is to discuss miRNA-based therapeutics, the role of miRNA in pharmacoepigenetics modulations, plant miRNA inter-kingdom regulation, and the therapeutic value and application of plant miRNA for cross-kingdom approaches. Target prediction and complementarity with host genes, as well as cross-kingdom gene interactions with plant miRNAs, are also revealed by bioinformatics research. We also show how plant miRNA can be transmitted from one species to another by crossing kingdom boundaries in this review. Despite several unidentified barriers to plant miRNA cross-transfer, plant miRNA-based gene regulation in trans-kingdom gene regulation may soon be valued as a possible approach in plant-based drug therapeutics. Conclusion This review summarised the biochemical synthesis of miRNAs, pharmacoepigenetics, drug therapeutics and miRNA transkingdom transfer.
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Affiliation(s)
- Atiyabanu N. Saiyed
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat India
- Ph.D. scholar of Manipal Academy of Higher Education, Manipal, Karnataka India
| | - Abhay R. Vasavada
- Department of Cell and Molecular Biology, Iladevi Cataract and IOL Research Centre, Ahmedabad, Gujarat India
| | - S. R. Kaid Johar
- Department of Zoology, BMTC, Human Genetics, USSC, Gujarat University, Ahmedabad, Gujarat India
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23
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Chang CW, Wang LS, Pham NN, Shen CC, Hsu MN, Nguyen NTK, Yen CY, Lin MW, Hwu JR, Chang YH, Hu YC. Synthetic biology approach to developing all-in-one baculovirus vector using mammalian introns and miRNA binding sites. J Taiwan Inst Chem Eng 2022. [DOI: 10.1016/j.jtice.2021.104175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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24
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Abstract
MicroRNAs (miRNAs) are small noncoding elements that play essential roles in the posttranscriptional regulation of biochemical processes. miRNAs recognize and target multiple mRNAs; therefore, investigating miRNA dysregulation is an indispensable strategy to understand pathological conditions and to design innovative drugs. Targeting miRNAs in diseases improve outcomes of several therapeutic strategies thus, this present study highlights miRNA targeting methods through experimental assays and bioinformatics tools. The first part of this review focuses on experimental miRNA targeting approaches for elucidating key biochemical pathways. A growing body of evidence about the miRNA world reveals the fact that it is not possible to uncover these molecules' structural and functional characteristics related to the biological processes with a deterministic approach. Instead, a systemic point of view is needed to truly understand the facts behind the natural complexity of interactions and regulations that miRNA regulations present. This task heavily depends both on computational and experimental capabilities. Fortunately, several miRNA bioinformatics tools catering to nonexperts are available as complementary wet-lab approaches. For this purpose, this work provides recent research and information about computational tools for miRNA targeting research.
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Affiliation(s)
- Hossein Ghanbarian
- Biotechnology Department & Cellular and Molecular Biology Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mehmet Taha Yıldız
- Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey
| | - Yusuf Tutar
- Division of Biochemistry, Department of Basic Pharmaceutical Sciences, Hamidiye Faculty of Pharmacy & Division of Molecular Medicine, Hamidiye Institute of Health Sciences, University of Health Sciences-Turkey, Istanbul, Turkey.
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25
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Abstract
In this era of big data, sets of methodologies and strategies are designed to extract knowledge from huge volumes of data. However, the cost of where and how to get this information accurately and quickly is extremely important, given the diversity of genomes and the different ways of representing that information. Among the huge set of information and relationships that the genome carries, there are sequences called miRNAs (microRNAs). These sequences were described in the 1990s and are mainly involved in mechanisms of regulation and gene expression. Having this in mind, this chapter focuses on exploring the available literature and providing useful and practical guidance on the miRNA database and tools topic. For that, we organized and present this text in two ways: (a) the update reviews and articles, which best summarize and discuss the theme; and (b) our update investigation on miRNA literature and portals about databases and tools. Finally, we present the main challenge and a possible solution to improve resources and tools.
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Affiliation(s)
- Tharcísio Soares de Amorim
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Daniel Longhi Fernandes Pedro
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil
| | - Alexandre Rossi Paschoal
- Department of Computer Science and Bioinformatics and Pattern Recognition Group, Universidade Tecnológica Federal do Paraná (UTFPR), Cornélio Procópio, Brazil.
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26
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Dragomir MP, Knutsen E, Calin GA. Classical and noncanonical functions of miRNAs in cancers. Trends Genet 2021; 38:379-394. [PMID: 34728089 DOI: 10.1016/j.tig.2021.10.002] [Citation(s) in RCA: 89] [Impact Index Per Article: 29.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 10/01/2021] [Accepted: 10/05/2021] [Indexed: 12/11/2022]
Abstract
Alterations in microRNAs (miRNAs) expression are causative in the initiation and progression of human cancers. The molecular events responsible for the widespread differential expression of miRNAs in malignancy are exemplified by their location in cancer-associated genomic regions, epigenetic mechanisms, transcriptional dysregulation, chemical modifications and editing, and alterations in miRNA biogenesis proteins. The classical miRNA function is synonymous with post-transcriptional repression of target protein genes. However, several studies have reported miRNAs functioning outside this paradigm and some of these novel modes of regulation of gene expression have been implicated in cancers. Here, we summarize key aspects of miRNA involvement in cancer, with a special focus on these lesser-studied mechanisms of action.
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Affiliation(s)
- Mihnea P Dragomir
- Institute of Pathology, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany.
| | - Erik Knutsen
- Department of Medical Biology, Faculty of Health Sciences, UiT-The Arctic University of Norway, Tromsø, Norway.
| | - George A Calin
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA; Center for RNA Interference and Non-Coding RNAs, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
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27
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Radaszkiewicz T, Nosková M, Gömöryová K, Vondálová Blanářová O, Radaszkiewicz KA, Picková M, Víchová R, Gybeľ T, Kaiser K, Demková L, Kučerová L, Bárta T, Potěšil D, Zdráhal Z, Souček K, Bryja V. RNF43 inhibits WNT5A-driven signaling and suppresses melanoma invasion and resistance to the targeted therapy. eLife 2021; 10:65759. [PMID: 34702444 PMCID: PMC8550759 DOI: 10.7554/elife.65759] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 09/28/2021] [Indexed: 12/30/2022] Open
Abstract
RNF43 is an E3 ubiquitin ligase and known negative regulator of WNT/β-catenin signaling. We demonstrate that RNF43 is also a regulator of noncanonical WNT5A-induced signaling in human cells. Analysis of the RNF43 interactome using BioID and immunoprecipitation showed that RNF43 can interact with the core receptor complex components dedicated to the noncanonical Wnt pathway such as ROR1, ROR2, VANGL1, and VANGL2. RNF43 triggers VANGL2 ubiquitination and proteasomal degradation and clathrin-dependent internalization of ROR1 receptor and inhibits ROR2 activation. These activities of RNF43 are physiologically relevant and block pro-metastatic WNT5A signaling in melanoma. RNF43 inhibits responses to WNT5A, which results in the suppression of invasive properties of melanoma cells. Furthermore, RNF43 prevented WNT5A-assisted development of resistance to BRAF V600E and MEK inhibitors. Next, RNF43 acted as melanoma suppressor and improved response to targeted therapies in vivo. In line with these findings, RNF43 expression decreases during melanoma progression and RNF43-low patients have a worse prognosis. We conclude that RNF43 is a newly discovered negative regulator of WNT5A-mediated biological responses that desensitizes cells to WNT5A.
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Affiliation(s)
- Tomasz Radaszkiewicz
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Michaela Nosková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Kristína Gömöryová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Olga Vondálová Blanářová
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | | | - Markéta Picková
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,International Clinical Research Center FNUSA-ICRC, Brno, Czech Republic
| | - Ráchel Víchová
- Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
| | - Tomáš Gybeľ
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Karol Kaiser
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Lucia Demková
- Laboratory of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Lucia Kučerová
- Laboratory of Molecular Oncology, Cancer Research Institute, Biomedical Research Center of the Slovak Academy of Sciences, Bratislava, Slovakia
| | - Tomáš Bárta
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - David Potěšil
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Karel Souček
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic.,International Clinical Research Center FNUSA-ICRC, Brno, Czech Republic
| | - Vítězslav Bryja
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic.,Department of Cytokinetics, Institute of Biophysics CAS, Brno, Czech Republic
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28
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Raimondi G, Gea-Sorlí S, Otero-Mateo M, Fillat C. Inhibition of miR-222 by Oncolytic Adenovirus-Encoded miRNA Sponges Promotes Viral Oncolysis and Elicits Antitumor Effects in Pancreatic Cancer Models. Cancers (Basel) 2021; 13:3233. [PMID: 34203557 PMCID: PMC8267801 DOI: 10.3390/cancers13133233] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/17/2022] Open
Abstract
Oncolytic adenoviruses (OA) are envisioned as a therapeutic option for patients with cancer, designed to preferentially replicate in cancer cells. However, the high number of genetic alterations in tumors can generate a context in which adenoviruses have difficulties replicating. Abnormal miRNAs expression is a trademark of pancreatic cancer, with several oncogenic miRNAs playing essential roles in cancer-associated pathways. The perturbed miRNome induces reprogramming of gene expression in host cells that can impact the complex interplay between cellular processes and viral replication. We have studied the effects of overexpressed miRNAs on oncolytic adenoviral activity and identified miRNAs modulators of adenoviral oncolysis in pancreatic cancer cells. Inhibition of the highly upregulated miR-222 sensitized cancer cells to oncolysis. To provide a therapeutic application to this insight, we engineered the oncolytic adenovirus AdNuPARmE1A with miR-222 binding sites, working as sponges to withdraw the miRNA from the cellular environment. AdNuPAR-E-miR222-S mediated-decrease of miR-222 expression in pancreatic cancer cells strongly improved the viral yield and enhanced the adenoviral cytotoxic effects. Antitumoral studies confirmed a high activity for AdNuPARmE1A-miR222-S in vivo, controlling tumor progression more effectively than the scrambled control virus in xenografts. We demonstrated that the increased antitumor potency of the novel oncolytic virus resulted from the combinatory effects of miR-222 oncomiR inhibition and the restoration of miR-222 target genes activity enhancing viral fitness.
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Affiliation(s)
- Giulia Raimondi
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (G.R.); (S.G.-S.); (M.O.-M.)
| | - Sabrina Gea-Sorlí
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (G.R.); (S.G.-S.); (M.O.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
| | - Marc Otero-Mateo
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (G.R.); (S.G.-S.); (M.O.-M.)
| | - Cristina Fillat
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), 08036 Barcelona, Spain; (G.R.); (S.G.-S.); (M.O.-M.)
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), 08036 Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), 08036 Barcelona, Spain
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29
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Kang GJ, Xie A, Liu H, Dudley SC. MIR448 antagomir reduces arrhythmic risk after myocardial infarction by upregulating the cardiac sodium channel. JCI Insight 2020; 5:140759. [PMID: 33108349 PMCID: PMC7714400 DOI: 10.1172/jci.insight.140759] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/21/2020] [Indexed: 12/17/2022] Open
Abstract
Cardiac ischemia is associated with arrhythmias; however, effective therapies are currently limited. The cardiac voltage-gated sodium channel α subunit (SCN5A), encoding the Nav1.5 current, plays a key role in the cardiac electrical conduction and arrhythmic risk. Here, we show that hypoxia reduces Nav1.5 through effects on a miR, miR-448. miR-448 expression is increased in ischemic cardiomyopathy. miR-448 has a conserved binding site in 3′-UTR of SCN5A. miR-448 binding to this site suppressed SCN5A expression and sodium currents. Hypoxia-induced HIF-1α and NF-κB were major transcriptional regulators for MIR448. Moreover, hypoxia relieved MIR448 transcriptional suppression by RE1 silencing transcription factor. Therefore, miR-448 inhibition reduced arrhythmic risk after myocardial infarction. Here, we show that ischemia drove miR-448 expression, reduced Nav1.5 current, and increased arrhythmic risk. Arrhythmic risk was improved by preventing Nav1.5 downregulation, suggesting a new approach to antiarrhythmic therapy. Ischemic induction of miR-448 negatively regulates the cardiac sodium channel Nav1.5, and inhibiting miR-448 raises Nav1.5 and reduces arrhythmic risk after myocardial infarction in mice.
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30
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Bosakova M, Abraham SP, Nita A, Hruba E, Buchtova M, Taylor SP, Duran I, Martin J, Svozilova K, Barta T, Varecha M, Balek L, Kohoutek J, Radaszkiewicz T, Pusapati GV, Bryja V, Rush ET, Thiffault I, Nickerson DA, Bamshad MJ, Rohatgi R, Cohn DH, Krakow D, Krejci P. Mutations in GRK2 cause Jeune syndrome by impairing Hedgehog and canonical Wnt signaling. EMBO Mol Med 2020; 12:e11739. [PMID: 33200460 PMCID: PMC7645380 DOI: 10.15252/emmm.201911739] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2019] [Revised: 09/08/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022] Open
Abstract
Mutations in genes affecting primary cilia cause ciliopathies, a diverse group of disorders often affecting skeletal development. This includes Jeune syndrome or asphyxiating thoracic dystrophy (ATD), an autosomal recessive skeletal disorder. Unraveling the responsible molecular pathology helps illuminate mechanisms responsible for functional primary cilia. We identified two families with ATD caused by loss-of-function mutations in the gene encoding adrenergic receptor kinase 1 (ADRBK1 or GRK2). GRK2 cells from an affected individual homozygous for the p.R158* mutation resulted in loss of GRK2, and disrupted chondrocyte growth and differentiation in the cartilage growth plate. GRK2 null cells displayed normal cilia morphology, yet loss of GRK2 compromised cilia-based signaling of Hedgehog (Hh) pathway. Canonical Wnt signaling was also impaired, manifested as a failure to respond to Wnt ligand due to impaired phosphorylation of the Wnt co-receptor LRP6. We have identified GRK2 as an essential regulator of skeletogenesis and demonstrate how both Hh and Wnt signaling mechanistically contribute to skeletal ciliopathies.
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Affiliation(s)
- Michaela Bosakova
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
- Institute of Animal Physiology and Genetics of the CASBrnoCzech Republic
| | - Sara P Abraham
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
| | - Alexandru Nita
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
| | - Eva Hruba
- Institute of Animal Physiology and Genetics of the CASBrnoCzech Republic
| | - Marcela Buchtova
- Institute of Animal Physiology and Genetics of the CASBrnoCzech Republic
| | - S Paige Taylor
- Department of Orthopaedic SurgeryDavid Geffen School of Medicine at UCLALos AngelesCAUSA
| | - Ivan Duran
- Department of Orthopaedic SurgeryDavid Geffen School of Medicine at UCLALos AngelesCAUSA
| | - Jorge Martin
- Department of Orthopaedic SurgeryDavid Geffen School of Medicine at UCLALos AngelesCAUSA
| | - Katerina Svozilova
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- Institute of Animal Physiology and Genetics of the CASBrnoCzech Republic
| | - Tomas Barta
- Department of Histology and EmbryologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
| | - Miroslav Varecha
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
| | - Lukas Balek
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
| | | | - Tomasz Radaszkiewicz
- Institute of Experimental BiologyFaculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Ganesh V Pusapati
- Department of BiochemistryStanford UniversityPalo AltoCAUSA
- Department of MedicineStanford UniversityPalo AltoCAUSA
| | - Vitezslav Bryja
- Institute of Experimental BiologyFaculty of ScienceMasaryk UniversityBrnoCzech Republic
| | - Eric T Rush
- Children's Mercy Kansas City, Center for Pediatric Genomic MedicineKansas CityMOUSA
- Department of PediatricsUniversity of MissouriKansas CityMOUSA
| | - Isabelle Thiffault
- Children's Mercy Kansas City, Center for Pediatric Genomic MedicineKansas CityMOUSA
- Department of PediatricsUniversity of MissouriKansas CityMOUSA
| | | | - Michael J Bamshad
- Department of Genome SciencesUniversity of WashingtonSeattleWAUSA
- Department of PediatricsUniversity of WashingtonSeattleWAUSA
- Division of Genetic MedicineSeattle Children's HospitalSeattleWAUSA
| | | | - Rajat Rohatgi
- Department of BiochemistryStanford UniversityPalo AltoCAUSA
- Department of MedicineStanford UniversityPalo AltoCAUSA
| | - Daniel H Cohn
- Department of Orthopaedic SurgeryDavid Geffen School of Medicine at UCLALos AngelesCAUSA
- Department of Molecular Cell and Developmental BiologyUniversity of California at Los AngelesLos AngelesCAUSA
| | - Deborah Krakow
- Department of Orthopaedic SurgeryDavid Geffen School of Medicine at UCLALos AngelesCAUSA
- Department of Human GeneticsDavid Geffen School of Medicine at UCLALos AngelesCAUSA
- Department of Obstetrics and GynecologyDavid Geffen School of Medicine at UCLALos AngelesCAUSA
| | - Pavel Krejci
- Department of BiologyFaculty of MedicineMasaryk UniversityBrnoCzech Republic
- International Clinical Research CenterSt. Anne's University HospitalBrnoCzech Republic
- Institute of Animal Physiology and Genetics of the CASBrnoCzech Republic
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31
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Lee LK, Medzikovic L, Eghbali M, Eltzschig HK, Yuan X. The Role of MicroRNAs in Acute Respiratory Distress Syndrome and Sepsis, From Targets to Therapies: A Narrative Review. Anesth Analg 2020; 131:1471-1484. [PMID: 33079870 PMCID: PMC8532045 DOI: 10.1213/ane.0000000000005146] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Acute respiratory distress syndrome (ARDS) is a significant cause of morbidity and mortality in the intensive care unit (ICU) and is characterized by lung epithelial and endothelial cell injury, with increased permeability of the alveolar-capillary membrane, leading to pulmonary edema, severe hypoxia, and difficulty with ventilation. The most common cause of ARDS is sepsis, and currently, treatment of ARDS and sepsis has consisted mostly of supportive care because targeted therapies have largely been unsuccessful. The molecular mechanisms behind ARDS remain elusive. Recently, a number of microRNAs (miRNAs) identified through high-throughput screening studies in ARDS patients and preclinical animal models have suggested a role for miRNA in the pathophysiology of ARDS. miRNAs are small noncoding RNAs ranging from 18 to 24 nucleotides that regulate gene expression via inhibition of the target mRNA translation or by targeting complementary mRNA for early degradation. Unsurprisingly, some miRNAs that are differentially expressed in ARDS overlap with those important in sepsis. In addition, circulatory miRNA may be useful as biomarkers or as targets for pharmacologic therapy. This can be revolutionary in a syndrome that has neither a measurable indicator of the disease nor a targeted therapy. While there are currently no miRNA-based therapies targeted for ARDS, therapies targeting miRNA have reached phase II clinical trials for the treatment of a wide range of diseases. Further studies may yield a unique miRNA profile pattern that serves as a biomarker or as targets for miRNA-based pharmacologic therapy. In this review, we discuss miRNAs that have been found to play a role in ARDS and sepsis, the potential mechanism of how particular miRNAs may contribute to the pathophysiology of ARDS, and strategies for pharmacologically targeting miRNA as therapy.
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Affiliation(s)
- Lisa K. Lee
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California
| | - Lejla Medzikovic
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California
| | - Mansoureh Eghbali
- Department of Anesthesiology and Perioperative Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, California
| | - Holger K. Eltzschig
- Department of Anesthesiology, The University of Texas Health Science Center, McGovern Medical School, Houston, Texas
| | - Xiaoyi Yuan
- Department of Anesthesiology, The University of Texas Health Science Center, McGovern Medical School, Houston, Texas
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Peskova L, Jurcikova D, Vanova T, Krivanek J, Capandova M, Sramkova Z, Sebestikova J, Kolouskova M, Kotasova H, Streit L, Barta T. miR-183/96/182 cluster is an important morphogenetic factor targeting PAX6 expression in differentiating human retinal organoids. Stem Cells 2020; 38:1557-1567. [PMID: 32875669 DOI: 10.1002/stem.3272] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/08/2020] [Accepted: 08/11/2020] [Indexed: 11/07/2022]
Abstract
MicroRNAs (miRNAs), a class of small, noncoding RNA molecules represent important regulators of gene expression. Recent reports have implicated their role in the cell specification process acting as "fine-tuners" to ensure the precise gene expression at the specific stage of cell differentiation. Here, we used retinal organoids differentiated from human pluripotent stem cells (hPSCs) as a model to closely investigate the role of a sensory organ-specific and evolutionary conserved miR-183/96/182 cluster. Using a miRNA tough decoy approach, we inhibited the miR-183/96/182 cluster in hPSCs. Inhibition of the miRNA cluster resulted in an increased expansion of neuroepithelium leading to abnormal "bulged" neural retina in organoids, associated with upregulation of neural-specific and retinal-specific genes. Importantly, we identified PAX6, a well-known essential gene in neuroectoderm specification, as a target of the miR-183/96/182 cluster members. Taken together, the miR-183/96/182 cluster not only represents an important regulator of PAX6 expression, but it also plays a crucial role in retinal tissue morphogenesis.
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Affiliation(s)
- Lucie Peskova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Denisa Jurcikova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tereza Vanova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic
| | - Jan Krivanek
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Michaela Capandova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Zuzana Sramkova
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Jana Sebestikova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Magdalena Kolouskova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Hana Kotasova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
- International Clinical Research Center (ICRC), St. Anne's University Hospital, Brno, Czech Republic
| | - Libor Streit
- Department of Plastic and Aesthetic Surgery, St. Anne's University Hospital Brno, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Tian L, Wang SL. Exploring the potential microRNA sponge interactions of breast cancer based on some known interactions. J Bioinform Comput Biol 2020; 18:2050007. [PMID: 32530353 DOI: 10.1142/s0219720020500079] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
MicroRNA (miRNA) sponges' regulatory mechanisms play an important role in developing human cancer. Herein, we develop a new method to explore potential miRNA sponge interactions (EPMSIs) for breast cancer. Based on some known interactions, and a matching gene expression profile, EPMSIs explored other potential miRNA sponge interactions for breast cancer. Every interaction is inferred with a value representing interaction intensity. Then, we apply a clustering algorithm called BCPlaid to potential interactions. Ten modules are identified; nine of them are closely associated with biological enrichments. When we employ a classification algorithm to separate normal and tumor samples in each module, each module demonstrates powerful classification performance. Furthermore, EPMSI illustrates a new method to explore the miRNA sponge regulatory network for breast cancer by applying its superior performance.
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Affiliation(s)
- Lei Tian
- School of Information Science and Engineering, Hunan University, Changsha, China
| | - Shu-Lin Wang
- School of Information Science and Engineering, Hunan University, Changsha, China
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Breuer J, Rossbach O. Production and Purification of Artificial Circular RNA Sponges for Application in Molecular Biology and Medicine. Methods Protoc 2020; 3:mps3020042. [PMID: 32466614 PMCID: PMC7359697 DOI: 10.3390/mps3020042] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/22/2022] Open
Abstract
Characterized by their covalently closed structure and thus an elevated stability compared to linear RNA molecules, circular RNAs (circRNAs) form a novel class of mainly non-coding RNAs. Although the biological functions of naturally occurring circRNAs are largely unknown, they were reported to act as molecular sponges, sequestering microRNAs (miRNAs), resulting in a de-repression of target mRNAs. Taking these characteristics of naturally occurring circRNAs into account, artificial circRNAs could be a potential tool in molecular biology and medicine. Using the Hepatitis C virus (HCV) as a model system, this application of artificial circular RNAs was demonstrated. The virus requires cellular miRNA miR-122 for its life cycle, and circRNAs specifically engineered to efficiently sequester this miRNA impacted viral propagation. Since in this context the production of engineered circRNA remains the limiting factor, we present a method to produce and efficiently purify artificial circRNA sponges (ciRS) in vitro. In this protocol we provide insights into a small-scale and large-scale production technique of artificial circular RNA sponges relying on in vitro transcription and RNA ligation.
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Dong S, Fu X, Dong Y, Simões ML, Zhu J, Dimopoulos G. Broad spectrum immunomodulatory effects of Anopheles gambiae microRNAs and their use for transgenic suppression of Plasmodium. PLoS Pathog 2020; 16:e1008453. [PMID: 32330198 PMCID: PMC7202664 DOI: 10.1371/journal.ppat.1008453] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 05/06/2020] [Accepted: 03/03/2020] [Indexed: 11/18/2022] Open
Abstract
Malaria, caused by the protozoan parasite Plasmodium and transmitted by Anopheles mosquitoes, represents a major threat to human health. Plasmodium’s infection cycle in the Anopheles vector is critical for transmission of the parasite between humans. The midgut-stage bottleneck of infection is largely imposed by the mosquito’s innate immune system. microRNAs (miRNAs, small noncoding RNAs that bind to target RNAs to regulate gene expression) are also involved in regulating immunity and the anti-Plasmodium defense in mosquitoes. Here, we characterized the mosquito’s miRNA responses to Plasmodium infection using an improved crosslinking and immunoprecipitation (CLIP) method, termed covalent ligation of endogenous Argonaute-bound RNAs (CLEAR)-CLIP. Three candidate miRNAs’ influence on P. falciparum infection and midgut microbiota was studied through transgenically expressed miRNA sponges (miR-SPs) in midgut and fat body tissues. MiR-SPs mediated conditional depletion of aga-miR-14 or aga-miR-305, but not aga-miR-8, increased mosquito resistance to both P. falciparum and P. berghei infection, and enhanced the mosquitoes’ antibacterial defenses. Transcriptome analysis revealed that depletion of aga-miR-14 or aga-miR-305 resulted in an increased expression of multiple immunity-related and anti-Plasmodium genes in mosquito midguts. The overall fitness cost of conditionally expressed miR-SPs was low, with only one of eight fitness parameters being adversely affected. Taken together, our results demonstrate that targeting mosquito miRNA by conditional expression of miR-SPs may have potential for the development of malaria control through genetically engineered mosquitoes. Malaria is caused by the Plasmodium parasite that is transmitted by Anopheles mosquitoes. The mosquito’s innate immune system plays an important role in controlling parasite infection. We have identified mosquito microRNAs (miRNAs) that are involved in regulating mosquito immunity to parasite infection. Transgenic mosquitoes that deplete the immunity-related miRNAs aga-miR-14 or aga-miR-305 through miRNA sponges, show increased resistance to both human and rodent parasite infection, and enhanced antibacterial defenses. Depletion of aga-miR-14 or aga-miR-305 resulted in an increased expression of multiple immunity-related and anti-Plasmodium genes, and the overall fitness cost of transgenic mosquitoes upon depletion of aga-miR-14 or aga-miR-305 was negligible. We show that targeting mosquito miRNA by transgenic expression of miRNA sponges may have potential for the development of malaria control through genetically engineered mosquitoes.
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Affiliation(s)
- Shengzhang Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Xiaonan Fu
- The Interdisciplinary Ph.D. Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, Blacksburg, VA, United States of America
| | - Yuemei Dong
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Maria L. Simões
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
| | - Jinsong Zhu
- Department of Biochemistry, Virginia Tech, Blacksburg, VA, United States of America
| | - George Dimopoulos
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, United States of America
- * E-mail:
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Chen D, Li L, Wang Y, Xu R, Peng S, Zhou L, Deng Z. Ischemia-reperfusion injury of brain induces endothelial-mesenchymal transition and vascular fibrosis via activating let-7i/TGF-βR1 double-negative feedback loop. FASEB J 2020; 34:7178-7191. [PMID: 32274860 DOI: 10.1096/fj.202000201r] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Revised: 03/12/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022]
Abstract
Let-7i modulates the physical function and inflammation in endothelial cells (ECs). However, whether the let-7i of ECs involves in brain vasculature and ischemic stroke is unknown. Using inducible Cadherin5-Cre lineage-tracking mice, a loxp-RNA-sponge conditional knockdown of let-7 in ECs- induced increase of transforming growth factor-β receptor type 1 (TGF-βR1), endothelial-mesenchymal transition (endMT), vascular fibrosis, and opening of the brain-blood barrier (BBB). By this lineage-tracking mice, we found that ECs underwent endMT after transient middle cerebral artery occlusion (MCAO). Through specifically overexpressed let-7i in ECs, we found that it reduced TGF-βR1, endMT, and vascular fibrosis. Furthermore, this overexpression reduced the infarct volume and leakage of the BBB, and improved the neurological function. Further, the expression of let-7i decreased after MCAO, but was reversed by antagonist of TGF-βR1 or inhibition of Mek phosphorylation. And the inhibition of Mek attenuated the vascular fibrosis after MCAO. In summary, we concluded that ischemic stroke activates a let-7i/TGF-βR1 double-negative feedback loop, thereby inducing endMT and vascular fibrosis. These results suggest that endMT is a potential target for the treatment of cerebral vascular fibrosis.
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Affiliation(s)
- Danqi Chen
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ling Li
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ying Wang
- The First Clinical College, Southern Medical University, Guangzhou, China
| | - Ruoting Xu
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Shunli Peng
- Department of Radiation Oncology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Liang Zhou
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Zhen Deng
- Department of Neurology, Nanfang Hospital, Southern Medical University, Guangzhou, China
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Abbasi Pashaki P, Rahim F, Habibi Roudkenar M, Razavi-Toosi S, Ebrahimi A. MicroRNA Tough Decoy Knockdowns miR-195 and Represses Hypertrophy in Chondrocytes. Appl Biochem Biotechnol 2020; 191:1056-1071. [PMID: 31956957 DOI: 10.1007/s12010-020-03229-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/08/2020] [Indexed: 12/12/2022]
Abstract
Cartilage hypertrophy is a condition in which the cells are completely differentiated, and new morphological changes and mineralization prevent proper cellular functions. The occurrence of hypertrophy during differentiation fails current regenerative strategies for treatment. Strategies to minimize hypertrophy in chondrocytes are categorized into two levels of protein and gene. Among these strategies, one way to affect multiple pathways involved in the development of hypertrophy is to manage microRNA activity in cells. Recent miRNA profiling studies have shown that miR-195-5p upregulates through the transition from chondrogenic to hypertrophic state. Bioinformatics assessment of microRNA targets also indicates that several genes repressed by miR-195-5p play important roles in processes related to hypertrophy. The aim of this study was to develop a microRNA Tough Decoy to suppress miR-195-5p and investigate whether it can prevent a hypertrophic state in chondrocytes. The Tough Decoy (TUD) was designed and evaluated bioinformatically and then cloned into the pLVX-Puro plasmid. The TUD function was validated by Dual-Luciferase assay and qRT-PCR. After delivering TUD to C28/I2 chondrocytes cultured in a hypertrophic medium, hypertrophic differentiation was assessed by histochemical staining, quantitative RT-PCR of hypertrophy marker genes, and alkaline phosphatase activity. Results showed that the TUD could inhibit miRNA efficiently and downregulate hypertrophic markers such as RUNX2, alkaline phosphatase, and collagen 10 significantly compared with the control group. Alcian blue and alizarin red staining also demonstrated the optimal effect of gene constructs on tissue properties and mineralization of the TUD group. Delivering the miR-195-5p Tough Decoy to the cartilage cells can prevent the occurrence of hypertrophy in chondrocytes and could be considered as a candidate for the treatment of other diseases such as osteoarthritis.
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Affiliation(s)
| | - Fakher Rahim
- Thalassemia and Hemoglobinopathy Research Centre, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mehryar Habibi Roudkenar
- Department of Medical Biotechnology, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Smt Razavi-Toosi
- Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran
| | - Ammar Ebrahimi
- Department of Medical Biotechnology, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran. .,Medical Biotechnology Research Center, School of Paramedicine, Guilan University of Medical Sciences, Rasht, Iran.
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To KKW, Fong W, Tong CWS, Wu M, Yan W, Cho WCS. Advances in the discovery of microRNA-based anticancer therapeutics: latest tools and developments. Expert Opin Drug Discov 2019; 15:63-83. [PMID: 31739699 DOI: 10.1080/17460441.2020.1690449] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Introduction: MicroRNAs (miRNAs) are small endogenous non-coding RNAs that repress the expression of their target genes by reducing mRNA stability and/or inhibiting translation. miRNAs are known to be aberrantly regulated in cancers. Modulators of miRNA (mimics and antagonists) have emerged as novel therapeutic tools for cancer treatment.Areas covered: This review summarizes the various strategies that have been applied to correct the dysregulated miRNA in cancer cells. The authors also discuss the recent advances in the technical development and preclinical/clinical evaluation of miRNA-based therapeutic agents.Expert opinion: Application of miRNA-based therapeutics for cancer treatment is appealing because they are able to modulate multiple dysregulated genes and/or signaling pathways in cancer cells. Major obstacles hindering their clinical development include drug delivery, off-target effects, efficacious dose determination, and safety. Tumor site-specific delivery of novel miRNA therapeutics may help to minimize off-target effects and toxicity. Combination of miRNA therapeutics with other anticancer treatment modalities could provide a synergistic effect, thus allowing the use of lower dose, minimizing off-target effects, and improving the overall safety profile in cancer patients. It is critical to identify individual miRNAs with cancer type-specific and context-specific regulation of oncogenes and tumor-suppressor genes in order to facilitate the precise use of miRNA anticancer therapeutics.
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Affiliation(s)
- Kenneth K W To
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Winnie Fong
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Christy W S Tong
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Mingxia Wu
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - Wei Yan
- School of Pharmacy, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, China
| | - William C S Cho
- Department of Clinical Oncology, Queen Elizabeth Hospital, Hong Kong SAR, China
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Peskova L, Cerna K, Oppelt J, Mraz M, Barta T. Oct4-mediated reprogramming induces embryonic-like microRNA expression signatures in human fibroblasts. Sci Rep 2019; 9:15759. [PMID: 31673026 PMCID: PMC6823439 DOI: 10.1038/s41598-019-52294-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 10/16/2019] [Indexed: 12/22/2022] Open
Abstract
Oct4-mediated reprogramming has recently become a novel tool for the generation of various cell types from differentiated somatic cells. Although molecular mechanisms underlying this process are unknown, it is well documented that cells over-expressing Oct4 undergo transition from differentiated state into plastic state. This transition is associated with the acquisition of stem cells properties leading to epigenetically “open” state that is permissive to cell fate switch upon external stimuli. In order to contribute to our understanding of molecular mechanisms driving this process, we characterised human fibroblasts over-expressing Oct4 and performed comprehensive small-RNAseq analysis. Our analyses revealed new interesting aspects of Oct4-mediated cell plasticity induction. Cells over-expressing Oct4 lose their cell identity demonstrated by down-regulation of fibroblast-specific genes and up-regulation of epithelial genes. Interestingly, this process is associated with microRNA expression profile that is similar to microRNA profiles typically found in pluripotent stem cells. We also provide extensive network of microRNA families and clusters allowing us to precisely determine the miRNAome associated with the acquisition of Oct4-induced transient plastic state. Our data expands current knowledge of microRNA and their implications in cell fate alterations and contributing to understanding molecular mechanisms underlying it.
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Affiliation(s)
- Lucie Peskova
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, 625 00, Czech Republic
| | - Katerina Cerna
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic
| | - Jan Oppelt
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, 625 00, Czech Republic
| | - Marek Mraz
- CEITEC-Central European Institute of Technology, Masaryk University, Brno, 625 00, Czech Republic.,Department of Internal Medicine, Hematology and Oncology, University Hospital Brno and Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Tomas Barta
- Department of Histology and Embryology, Faculty of Medicine, Masaryk University, Brno, 625 00, Czech Republic.
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Huerta-Zavala ML, Lopez-Castillejos ES, Requenez-Contreras JL, Granados-Riveron JT, Aquino-Jarquin G. A single miRNA and miRNA sponge expression system for efficient modulation of miR-223 availability in mammalian cells. J Gene Med 2019; 21:e3100. [PMID: 31166636 DOI: 10.1002/jgm.3100] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2019] [Revised: 05/20/2019] [Accepted: 05/27/2019] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Hundreds of microRNAs (miRNAs), comprising small non-coding RNAs of 20-24 nucleotides, have been discovered, although the entirety of their biological functions is poorly understood. Overexpression or suppression approaches are commonly performed to investigate the function of specific miRNAs. In the present study, we focused on generating a lentiviral vector-based strategy that enables hsa-miR-223-3p (miR-223) overexpression and suppression in the target cells for functional analysis of this miRNA easily and rapidly. METHODS The sequence that gives rise to miR-223 and the sequence generating the sponge RNA with four binding sites for miR-223 were cloned in pLVX-shRNA2 vector. The functionality of the vector to overexpress miR-223 was evaluated by quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) assays, whereas the post-transcriptional regulation exerted by miR-223 was evaluated by luciferase reporter assays in AD-293 cells. The anti-miR-223 sponge activity with one binding site for miR-223 (pmCherry-anti-miR-223) was confirmed by qRT-PCR and the restoration of its target (IKKα) was evaluated by western blot assays in Jurkat cells. RESULTS The pLVX-miR-223 vector is functional for over-expressing miR-223 and regulates the mRNA of MDR1/ABCB1 at the post-transcriptional level in AD-293 cells. The anti-miR-223 sponge with one miR-223 binding site efficiently modulates the miR-223 availability and not the one with four sites. The over-expression of anti-miR-223 correlated with a decrease in the levels of miR-223 and, consequently, with an increase in the expression level of the IKKα protein in Jurkat cells. CONCLUSIONS This single miRNA and miRNA sponge expression system specifically alters the availability of miR-223 in mammalian cells.
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Affiliation(s)
- Mariel Lizbeth Huerta-Zavala
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - Erika Sicahui Lopez-Castillejos
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - José Luis Requenez-Contreras
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - Javier Tadeo Granados-Riveron
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
| | - Guillermo Aquino-Jarquin
- Laboratorio de Investigación en Genómica, Genética y Bioinformática, Torre de Hemato-Oncología, Hospital Infantil de México, Cuauhtémoc, CDMX, Mexico
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Zheng H, Liu J, Tycksen E, Nunley R, McAlinden A. MicroRNA-181a/b-1 over-expression enhances osteogenesis by modulating PTEN/PI3K/AKT signaling and mitochondrial metabolism. Bone 2019; 123:92-102. [PMID: 30898695 PMCID: PMC6491221 DOI: 10.1016/j.bone.2019.03.020] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 03/13/2019] [Accepted: 03/16/2019] [Indexed: 12/14/2022]
Abstract
MicroRNAs are small non-coding RNAs that play important roles in many cellular processes including proliferation, metabolism and differentiation. They function by binding to specific regions within the 3'UTR of target mRNAs resulting in suppression of protein synthesis and modulation of potentially many cellular pathways. We previously showed that miRNA expression levels differed between cells from distinct regions of developing human embryonic long bones. Specifically, we found that miR-181a-1 was significantly more highly expressed in hypertrophic chondrocytes compared to proliferating differentiated or progenitor chondrocytes, suggesting a potential role in regulating chondrocyte hypertrophy and/or endochondral bone formation. The goal of this study was to determine how miR-181a-1 together with its clustered miRNA, miR-181b-1, regulates osteogenesis. We show that over-expression of the miR-181a/b-1 cluster enhanced osteogenesis and that cellular pathways associated with protein synthesis and mitochondrial metabolism were significantly up-regulated. Metabolic assays revealed that the oxygen consumption rate and ATP-linked respiration were increased by miR-181a/b-1. To further decipher a potential mechanism causing these metabolic changes, we showed that PTEN (phosphatase and tensin homolog) levels were suppressed following miR-181a/b-1 over-expression, and that PI3K/AKT signaling was subsequently increased. Over-expression of PTEN was found to attenuate the enhancing effects of miR-181a/b-1, providing further evidence that miR-181a/b-1 regulates the PTEN/PI3K/AKT axis to enhance osteogenic differentiation and mitochondrial metabolism. These findings have important implications for the design of miR-181a/b targeting strategies to treat bone conditions such as fractures or heterotopic ossification.
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Affiliation(s)
- Hongjun Zheng
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America.
| | - Jin Liu
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America.
| | - Eric Tycksen
- Genome Technology Access Center, Washington University School of Medicine, St Louis, MO, United States of America.
| | - Ryan Nunley
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America.
| | - Audrey McAlinden
- Department of Orthopaedic Surgery, Washington University School of Medicine, St. Louis, MO, United States of America; Department of Cell Biology, Washington University School of Medicine, St. Louis, MO, United States of America; Shriners Hospital for Children - St Louis, St Louis, MO, United States of America.
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Zhang J, Liu L, Xu T, Xie Y, Zhao C, Li J, Le TD. miRspongeR: an R/Bioconductor package for the identification and analysis of miRNA sponge interaction networks and modules. BMC Bioinformatics 2019; 20:235. [PMID: 31077152 PMCID: PMC6509829 DOI: 10.1186/s12859-019-2861-y] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2018] [Accepted: 04/29/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND A microRNA (miRNA) sponge is an RNA molecule with multiple tandem miRNA response elements that can sequester miRNAs from their target mRNAs. Despite growing appreciation of the importance of miRNA sponges, our knowledge of their complex functions remains limited. Moreover, there is still a lack of miRNA sponge research tools that help researchers to quickly compare their proposed methods with other methods, apply existing methods to new datasets, or select appropriate methods for assisting in subsequent experimental design. RESULTS To fill the gap, we present an R/Bioconductor package, miRspongeR, for simplifying the procedure of identifying and analyzing miRNA sponge interaction networks and modules. It provides seven popular methods and an integrative method to identify miRNA sponge interactions. Moreover, it supports the validation of miRNA sponge interactions and the identification of miRNA sponge modules, as well as functional enrichment and survival analysis of miRNA sponge modules. CONCLUSIONS This package enables researchers to quickly evaluate their new methods, apply existing methods to new datasets, and consequently speed up miRNA sponge research.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, 671003, Yunnan, China.
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Taosheng Xu
- Institute of Intelligent Machines, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, 230031, China
| | - Yong Xie
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Chunwen Zhao
- School of Engineering, Dali University, Dali, 671003, Yunnan, China
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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Fibroblast growth factor receptor influences primary cilium length through an interaction with intestinal cell kinase. Proc Natl Acad Sci U S A 2019; 116:4316-4325. [PMID: 30782830 PMCID: PMC6410813 DOI: 10.1073/pnas.1800338116] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A properly functioning primary cilium is prerequisite for both normal development and aging of all ciliated organisms, including humans. In vertebrates, the signaling of Hedgehog family morphogens depends entirely on primary cilium. Recently, we reported that fibroblast growth factors (FGF) signaling interacts with that of Hedgehog, and that this is a consequence of FGF regulating length of the cilium and speed of processes that happen therein. In this report, we provide a molecular mechanism of such interaction, identifying intestinal cell kinase as a mediator of the FGF-induced changes in the ciliary morphology and function. This expands our understanding how FGF signaling regulates intracellular processes, and how aberrant FGF signaling contributes to diseases, such as achondroplasia and cancer. Vertebrate primary cilium is a Hedgehog signaling center but the extent of its involvement in other signaling systems is less well understood. This report delineates a mechanism by which fibroblast growth factor (FGF) controls primary cilia. Employing proteomic approaches to characterize proteins associated with the FGF-receptor, FGFR3, we identified the serine/threonine kinase intestinal cell kinase (ICK) as an FGFR interactor. ICK is involved in ciliogenesis and participates in control of ciliary length. FGF signaling partially abolished ICK’s kinase activity, through FGFR-mediated ICK phosphorylation at conserved residue Tyr15, which interfered with optimal ATP binding. Activation of the FGF signaling pathway affected both primary cilia length and function in a manner consistent with cilia effects caused by inhibition of ICK activity. Moreover, knockdown and knockout of ICK rescued the FGF-mediated effect on cilia. We provide conclusive evidence that FGF signaling controls cilia via interaction with ICK.
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Quévillon Huberdeau M, Simard MJ. A guide to microRNA‐mediated gene silencing. FEBS J 2018; 286:642-652. [DOI: 10.1111/febs.14666] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Revised: 08/23/2018] [Accepted: 09/25/2018] [Indexed: 12/21/2022]
Affiliation(s)
- Miguel Quévillon Huberdeau
- Oncology division (St‐Patrick Research Group in Basic Oncology) CHU de Québec‐Université Laval Research Center Quebec City Canada
- Laval University Cancer Research Centre Quebec City Canada
| | - Martin J. Simard
- Oncology division (St‐Patrick Research Group in Basic Oncology) CHU de Québec‐Université Laval Research Center Quebec City Canada
- Laval University Cancer Research Centre Quebec City Canada
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Bernardo BC, Gregorevic P, Ritchie RH, McMullen JR. Generation of MicroRNA-34 Sponges and Tough Decoys for the Heart: Developments and Challenges. Front Pharmacol 2018; 9:1090. [PMID: 30298011 PMCID: PMC6160554 DOI: 10.3389/fphar.2018.01090] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Accepted: 09/07/2018] [Indexed: 12/13/2022] Open
Abstract
Heart failure (HF) is a debilitating and deadly chronic disease, with almost 50% of patients with HF dying within 5 years of diagnosis. With limited effective therapies to treat or cure HF, new therapies are greatly needed. microRNAs (miRNAs) are small non-coding RNA molecules that are powerful regulators of gene expression and play a key role in almost every biological process. Disruptions in miRNA gene expression has been functionally linked to numerous diseases, including cardiovascular disease. Molecular tools for manipulating miRNA activity have been developed, and there is evidence from preclinical studies demonstrating the potential of miRNAs to be therapeutic targets for cardiovascular disease. For clinical application, miRNA sponges and tough decoys have been developed for more stable suppression and targeted delivery of the miRNA of choice. The aim of this study was to generate miRNA sponges and tough decoys to target miR-34 in the mouse heart. We present data to show that using both approaches we were unable to get significant knockdown of miR-34 or regulate miR-34 target genes in the heart in vivo. We also review recent applications of this method in the heart and discuss further considerations for optimisation in construct design and testing, and the obstacles to be overcome before they enter the clinic.
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Affiliation(s)
- Bianca C Bernardo
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Melbourne, VIC, Australia.,Department of Diabetes, Central Clinical School, Monash University, Clayton, VIC, Australia
| | - Paul Gregorevic
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Physiology, Centre for Muscle Research, The University of Melbourne, Melbourne, VIC, Australia
| | - Rebecca H Ritchie
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Diabetes, Central Clinical School, Monash University, Clayton, VIC, Australia.,Department of Pharmacology and Therapeutics, The University of Melbourne, Melbourne, VIC, Australia
| | - Julie R McMullen
- Baker Heart and Diabetes Institute, Melbourne, VIC, Australia.,Department of Diabetes, Central Clinical School, Monash University, Clayton, VIC, Australia.,Department of Medicine, Monash University, Clayton, VIC, Australia.,Department of Physiology, Monash University, Clayton, VIC, Australia.,Department of Physiology, Anatomy, and Microbiology, La Trobe University, Melbourne, VIC, Australia
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Gao Y, Karimi M, Kudreyko AA, Song W. Spare optimistic based on improved ADMM and the minimum entropy de-convolution for the early weak fault diagnosis of bearings in marine systems. ISA TRANSACTIONS 2018; 78:98-104. [PMID: 29295740 DOI: 10.1016/j.isatra.2017.12.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/27/2017] [Accepted: 12/22/2017] [Indexed: 06/07/2023]
Abstract
In the marine systems, engines represent the most important part of ships, the probability of the bearings fault is the highest in the engines, so in the bearing vibration analysis, early weak fault detection is very important for long term monitoring. In this paper, we propose a novel method to solve the early weak fault diagnosis of bearing. Firstly, we should improve the alternating direction method of multipliers (ADMM), structure of the traditional ADMM is changed, and then the improved ADMM is applied to the compressed sensing (CS) theory, which realizes the sparse optimization of bearing signal for a mount of data. After the sparse signal is reconstructed, the calculated signal is restored with the minimum entropy de-convolution (MED) to get clear fault information. Finally we adopt the sample entropy. Morphological mean square amplitude and the root mean square (RMS) to find the early fault diagnosis of bearing respectively, at the same time, we plot the Boxplot comparison chart to find the best of the three indicators. The experimental results prove that the proposed method can effectively identify the early weak fault diagnosis.
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Affiliation(s)
- Yangde Gao
- The School of Electronic and Electrical Engineering, Shanghai University of Engineering Science, 333, Long Teng Road, Shanghai, 201620, China
| | - Mohammad Karimi
- Young Researchers and Elite Club, South Tehran Branch, Islamic Azad University, Tehran, Iran
| | - Aleksey A Kudreyko
- Ufa State Petroleum Technological University, Department of Physics, Kosmonavtov 1, 450062, Ufa, Russia
| | - Wanqing Song
- The School of Electronic and Electrical Engineering, Shanghai University of Engineering Science, 333, Long Teng Road, Shanghai, 201620, China.
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Nguyen DD, Chang S. Development of Novel Therapeutic Agents by Inhibition of Oncogenic MicroRNAs. Int J Mol Sci 2017; 19:E65. [PMID: 29280958 PMCID: PMC5796015 DOI: 10.3390/ijms19010065] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2017] [Revised: 12/14/2017] [Accepted: 12/22/2017] [Indexed: 01/04/2023] Open
Abstract
MicroRNAs (miRs, miRNAs) are regulatory small noncoding RNAs, with their roles already confirmed to be important for post-transcriptional regulation of gene expression affecting cell physiology and disease development. Upregulation of a cancer-causing miRNA, known as oncogenic miRNA, has been found in many types of cancers and, therefore, represents a potential new class of targets for therapeutic inhibition. Several strategies have been developed in recent years to inhibit oncogenic miRNAs. Among them is a direct approach that targets mature oncogenic miRNA with an antisense sequence known as antimiR, which could be an oligonucleotide or miRNA sponge. In contrast, an indirect approach is to block the biogenesis of miRNA by genome editing using the CRISPR/Cas9 system or a small molecule inhibitor. The development of these inhibitors is straightforward but involves significant scientific and therapeutic challenges that need to be resolved. In this review, we summarize recent relevant studies on the development of miRNA inhibitors against cancer.
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Affiliation(s)
- Dinh-Duc Nguyen
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
| | - Suhwan Chang
- Department of Biomedical Sciences, University of Ulsan College of Medicine, Asan Medical Center, Seoul 05505, Korea.
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Zhang J, Le TD, Liu L, Li J. Inferring miRNA sponge co-regulation of protein-protein interactions in human breast cancer. BMC Bioinformatics 2017; 18:243. [PMID: 28482794 PMCID: PMC5423010 DOI: 10.1186/s12859-017-1672-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2017] [Accepted: 05/03/2017] [Indexed: 12/14/2022] Open
Abstract
Background Recent studies have shown that the crosstalk between microRNA (miRNA) sponges plays an important role in human cancers. However, the co-regulation roles of miRNA sponges in protein-protein interactions (PPIs) are still unknown. Results In this study, we propose a multi-step method called miRSCoPPI to infer miRNA sponge co-regulation of PPIs. We focus on investigating breast cancer (BRCA) related miRNA sponge co-regulation, by integrating heterogeneous data, including miRNA, long non-coding RNA (lncRNA) and messenger RNA (mRNA) expression data, experimentally validated miRNA-target interactions, PPIs and lncRNA-target interactions, and the list of breast cancer genes. We find that the inferred BRCA-related miRSCoPPI network is highly connected and scale free. The top 10% hub genes in the BRCA-related miRSCoPPI network have potential biological implications in breast cancer. By utilizing a graph clustering method, we discover 17 BRCA-related miRSCoPPI modules. Through pathway enrichment analysis of the modules, we find that several modules are significantly enriched in pathways associated with breast cancer. Moreover, 10 modules have good performance in classifying breast tumor and normal samples, and can act as module signatures for prognostication. By using putative computationally predicted miRNA-target interactions, we have consistent results with those obtained using experimentally validated miRNA-target interactions, indicating that miRSCoPPI is robust in inferring miRNA sponge co-regulation of PPIs in human breast cancer. Conclusions Taken together, the results demonstrate that miRSCoPPI is a promising tool for inferring BRCA-related miRNA sponge co-regulation of PPIs and it can help with the understanding of the co-regulation roles of miRNA sponges on the PPIs. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1672-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Junpeng Zhang
- School of Engineering, Dali University, Dali, Yunnan, 671003, People's Republic of China.
| | - Thuc Duy Le
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.,Centre for Cancer Biology, University of South Australia, Adelaide, SA, 5000, Australia
| | - Lin Liu
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia
| | - Jiuyong Li
- School of Information Technology and Mathematical Sciences, University of South Australia, Mawson Lakes, SA, 5095, Australia.
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