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Hosseini SF, Javanshir-Giv S, Soleimani H, Mollaei H, Sadri F, Rezaei Z. The importance of hsa-miR-28 in human malignancies. Biomed Pharmacother 2023; 161:114453. [PMID: 36868012 DOI: 10.1016/j.biopha.2023.114453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/24/2023] [Accepted: 02/26/2023] [Indexed: 03/05/2023] Open
Abstract
MicroRNA production in tumorigenesis is dysregulated by a variety of processes, such as proliferation and removal of microRNA genes, aberrant transcriptional regulation of microRNAs, disrupted epigenetic alterations, and failures in the miRNA biogenesis machinery. Under some circumstances, miRNAs may act as tumorigenic and maybe anti-oncogenes. Tumor aspects such as maintaining proliferating signals, bypassing development suppressors, delaying apoptosis, stimulating metastasis and invasion, and promoting angiogenesis have been linked to dysfunctional and dysregulated miRNAs. MiRNAs have been found as possible biomarkers for human cancer in a great deal of research, which requires additional evaluation and confirmation. It is known that hsa-miR-28 can function as an oncogene or tumor suppressor in many malignancies, and it does this by modulating the expression of several genes and the downstream signaling network. MiR-28-5p and miR-28-3p, which originate from the same RNA hairpin precursor miR-28, have essential roles in a variety of cancers. This review outlines the function and mechanisms of miR-28-3p and miR-28-5p in human cancers and illustrates the miR-28 family's potential utility as a diagnostic biomarker for prognosis and early detection of cancers.
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Affiliation(s)
- Seyede Fatemeh Hosseini
- Faculty Member, Tabas School of Nursing, Birjand University of Medical Sciences, Birjand, Iran
| | - Setareh Javanshir-Giv
- Faculty of Medicine, Department of Biochemistry, Birjand University of Medical Sciences, Birjand, Iran; Department of Clinical Biochemistry, Afzalipour School of Medicine & Physiology Research Center, Kerman University of Medical Sciences, Kerman, Iran
| | - Hanieh Soleimani
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran
| | - Homa Mollaei
- Department of Biology, Faculty of Sciences, University of Birjand, Birjand, Iran
| | - Farzad Sadri
- Student Research Committee, Birjand University of Medical Sciences, Birjand, Iran.
| | - Zohreh Rezaei
- Department of Biology, University of Sistan and Baluchestan, Zahedan, Iran; Cellular and Molecular Research Center, Birjand University of Medical Sciences, Birjand, Iran.
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202
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Yin P, Xue Y. CircRNA hsa_circ_0006859 inhibits the osteogenic differentiation of BMSCs and aggravates osteoporosis by targeting miR-642b-5p/miR-483-3p and upregulating EFNA2/DOCK3. Int Immunopharmacol 2023; 116:109844. [PMID: 36764273 DOI: 10.1016/j.intimp.2023.109844] [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: 07/01/2022] [Revised: 01/14/2023] [Accepted: 01/31/2023] [Indexed: 02/11/2023]
Abstract
Hsa_circ_0006859 has been found as a possible biomarker for postmenopausal osteoporosis (PMOP) with an effect on the osteogenic differentiation of bone marrow mesenchymal stem cells (BMSCs), but the underlying mechanism is unclear. Bioinformatics analysis was used to identify dysregulated RNAs involved in osteoporosis based on public datasets. Function assays were used to determine the functions of hsa_circ_0006859 on cell proliferation and osteogenic differentiation in vitro. It was found that hsa_circ_0006859 was upregulated in OVX mice-derived BMSCs, but lowly expressed during osteogenic differentiation. Overexpressing hsa_circ_0006859 inhibited the cell proliferation and osteogenesis of BMSCs and hFOB 1.19 cells, vice versa. Bilateral ovariectomy (OVX) was used to induce PMOP in mice. The interactions among circ_0006859, miR-642b-5p/miR-483-3p, and EFNA2/DOCK3 were determined using the RIP assay. Silencing circ_0006859 relieved PMOP in mice. Mechanistically, circ_0006859 bound to miR-642b-5p/miR-483-3p directly, while miR-642b-5p and miR-483-3p respectively targeted EFNA2 and DOCK3. Hsa_circ_0006859 downregulated the expression of miR-642b-5p/miR-483-3p to upregulate EFNA2/DOCK3. Additionally, miR-642b-5p/miR-483-3p targeted EFNA2/DOCK3 to inhibit BMSCs osteogenic differentiation and facilitate osteoporosis progression by inactivating the Wnt signaling. In conclusion, hsa_circ_0006859 is involved in PMOP by targeting miR-642b-5p/EFNA2 and miR-483-3p/DOCK3 axes to maintain the Wnt-signaling pathway, which may be a novel possible therapeutic targets and biomarkers for PMOP.
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Affiliation(s)
- Peng Yin
- Department of Orthopaedic Surgery, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin Medical University General Hospital, China.
| | - Yuan Xue
- Department of Orthopaedic Surgery, Tianjin Key Laboratory of Spine and Spinal Cord, Tianjin Medical University General Hospital, China.
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203
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Huang L, Guo B, Yan J, Wei H, Liu S, Li Y. CircHSPG2 knockdown attenuates hypoxia-induced apoptosis, inflammation, and oxidative stress in human AC16 cardiomyocytes by regulating the miR-1184/MAP3K2 axis. Cell Stress Chaperones 2023; 28:177-190. [PMID: 36810972 PMCID: PMC10050264 DOI: 10.1007/s12192-023-01328-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/02/2023] [Accepted: 02/03/2023] [Indexed: 02/24/2023] Open
Abstract
Circular RNAs (circRNAs) have been identified as vital regulators in cardiovascular diseases, including acute myocardial infarction (AMI). In this study, the function and mechanism of circRNA heparan sulfate proteoglycan 2 (circHSPG2) in hypoxia-induced injury in AC16 cardiomyocytes were investigated. AC16 cells were stimulated with hypoxia to establish an AMI cell model in vitro. Real-time quantitative PCR and western blot assays were performed to quantify the expression levels of circHSPG2, microRNA-1184 (miR-1184), and mitogen-activated protein kinase kinase kinase 2 (MAP3K2). Counting Kit-8 (CCK-8) assay was used to measure cell viability. Flow cytometry was performed to detect cell cycle and apoptosis. Enzyme-linked immunosorbent assay (ELISA) was used to determine the expression of inflammatory factors. Dual-luciferase reporter, RNA immunoprecipitation (RIP), and RNA pull-down assays were used to analyze the relationship between miR-1184 and circHSPG2 or MAP3K2. In AMI serum, circHSPG2 and MAP3K2 mRNA were highly expressed and miR-1184 was down-regulated. Hypoxia treatment elevated HIF1α expression and repressed cell growth and glycolysis. Moreover, hypoxia promoted cell apoptosis, inflammation, and oxidative stress in AC16 cells. Hypoxia-induced circHSPG2 expression in AC16 cells. CircHSPG2 knockdown alleviated hypoxia-induced AC16 cell injury. CircHSPG2 directly targeted miR-1184, and miR-1184 targeted and suppressed MAP3K2. Inhibition of miR-1184 or overexpression of MAP3K2 abolished the alleviated effect of circHSPG2 knockdown on hypoxia-induced AC16 cell injury. Overexpression of miR-1184 relieved hypoxia-induced impairment in AC16 cells by MAP3K2. CircHSPG2 could regulate MAP3K2 expression through miR-1184. CircHSPG2 knockdown protected AC16 cells from hypoxia-induced injury by regulating the miR-1184/MAP3K2 cascade.
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Affiliation(s)
- Liu Huang
- Department of Cardiovascular Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, China
| | - Bingyan Guo
- Department of Cardiovascular Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, China
| | - Jie Yan
- Department of Cardiovascular Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, China
| | - Huiqing Wei
- Department of Cardiovascular Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, China
| | - Suyun Liu
- Department of Cardiovascular Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, China
| | - Yongjun Li
- Department of Cardiovascular Medicine, The Second Hospital of Hebei Medical University, No. 215 Heping West Road, Shijiazhuang, 050000, China.
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204
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Liu J, Liu B. CircTNPO3 promotes hepatocellular carcinoma progression by sponging miR-199b-5p and regulating STRN expression. Kaohsiung J Med Sci 2023; 39:221-233. [PMID: 36524450 DOI: 10.1002/kjm2.12631] [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: 03/24/2022] [Revised: 10/12/2022] [Accepted: 11/13/2022] [Indexed: 12/23/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the most common primary liver tumor, which seriously threatens human health. CircTNPO3 was up-regulated in HCC tissues. However, the regulatory mechanism of circTNPO3 in HCC was still unclear. We aimed to investigate the circTNPO3 function in the development of HCC. qRT-PCR and Western blot examined gene and protein levels. CCK8, EdU, flow cytometry, and Transwell assays were used to detect cell viability, proliferation, apoptosis, and invasion abilities. Dual-luciferase reporter and RIP assays determined the relationship between circTNPO3, miR-199b-5p, and striatin (STRN). The effect of CircTNPO3 on HCC progress was investigated in vivo. CircTNPO3 and STRN were significantly increased, while miR-199b-5p was repressed in HCC tissues or cells. Afterward, miR-199b-5p was negatively correlated with STRN. circTNPO3 was positively correlated with STRN. Knockdown of circTNPO3 inhibited cell viability, proliferation, invasion, and promoted apoptosis, while circTNPO3 overexpression had the opposite results. Furthermore, miR-199b-5p inhibition could eliminate the regulatory effect of sh-circTNPO3 on the proliferation and apoptosis in HCC cells. CircTNPO3 positively regulated STRN expression by targeting miR-199b-5p. MiR-199b-5p suppressed HCC progression by inhibiting STRN expression. Tumor formation in nude mice showed that knockdown of circTNPO3 significantly inhibited tumor growth and suppressed ki-67 levels. CircTNPO3 promoted HCC progression through regulating STRN expression by sponging miR-199b-5p, which provided a strategy for HCC treatment.
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Affiliation(s)
- Jing Liu
- Department of Infection Disease, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
| | - BingJie Liu
- Department of Infection Disease, The First Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, Hunan, China
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205
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Cao W, Zhang N, He X, Xing Y, Yang N. Long non-coding RNAs in retinal neovascularization: current research and future directions. Graefes Arch Clin Exp Ophthalmol 2023; 261:615-626. [PMID: 36171459 DOI: 10.1007/s00417-022-05843-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 09/05/2022] [Accepted: 09/20/2022] [Indexed: 12/17/2022] Open
Abstract
PURPOSE Retinal neovascularization (RNV) is an intractable pathological hallmark of numerous ocular blinding diseases, including diabetic retinopathy, retinal vein occlusion, and retinopathy of prematurity. However, current therapeutic methods have potential side effects and limited efficacy. Thus, further studies on the pathogenesis of RNV-related disorders and novel therapeutic targets are critically required. Long non-coding RNAs (lncRNAs) have various functions and participate in almost all biological processes in living cells, such as translation, transcription, signal transduction, and cell cycle control. In addition, recent research has demonstrated critical modulatory roles of various lncRNAs in RNV. In this review, we summarize current knowledge about the expression and regulatory functions of lncRNAs related to the progression of pathological RNV. METHODS We searched databases such as PubMed and Web of Science to gather and review information from the published literature. CONCLUSIONS In general, lncRNA MEG3 attenuates RNV, thus protecting the retina from excessive and dysregulated angiogenesis under high glucose stress. In contrast, lncRNAs MALAT1, MIAT, ANRIL, HOTAIR, HOTTIP, and SNHG16, have been identified as causative molecules in the pathological progression of RNV. Comprehensive and in-depth studies of the roles of lncRNAs in RNV indicate that targeting lncRNAs may be an alternative therapeutic approach in the near future, enabling new options for attenuating RNV progression and treating RNV-related retinal diseases.
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Affiliation(s)
- Wenye Cao
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Ningzhi Zhang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Xuejun He
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China
| | - Yiqiao Xing
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
| | - Ning Yang
- Department of Ophthalmology, Renmin Hospital of Wuhan University, Jiefang Road #238, Wuhan, 430060, Hubei, China.
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206
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Jin M, Liu Y, Hu G, Li X, Jia N, Cui X, Li Z, Ai L, Xie M, Xue F, Yang Y, Li W, Zhang M, Yu Q. Establishment of a schizophrenia classifier based on peripheral blood signatures and investigation of pathogenic miRNA-mRNA regulation. J Psychiatr Res 2023; 159:172-184. [PMID: 36738648 DOI: 10.1016/j.jpsychires.2023.01.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 01/04/2023] [Accepted: 01/26/2023] [Indexed: 01/30/2023]
Abstract
To date, the diagnosis of schizophrenia (SCZ) mainly relies on patients' or guardians' self-reports and clinical observation, and the pathogenesis of SCZ remains elusive. In this study, we sought to develop a reliable classifier for diagnosing SCZ patients and provide clues to the etiology and pathogenesis of SCZ. Based on the high throughput sequencing analysis of peripheral blood miRNA expression profile and weighted gene co-expression network analysis (WGCNA) in our previous study, we selected eleven hub miRNAs for validation by qRT-PCR in 51 SCZ patients and 51 controls. miR-939-5p, miR-4732-3p let-7d-3p, and miR-142-3p were confirmed to be significantly up-regulated, and miR-30e-3p and miR-23a-3p were down-regulated in SCZ patients. miR-30e-3p with the most considerable fold change and statistically significance was selected for targeting validation. We first performed bioinformatics prediction followed by qRT-PCR and verified the up-regulation of potential target mRNAs (ABI1, NMT1, HMGB1) expression. Next, we found that the expression level of ABI1 was significantly up-regulated in SH-SY5Y cells transfected with miR-30e-3p mimics. Lastly, we conducted a luciferase assay in 293T cells confirming that miR-30e-3p could directly bind with the 3'untranslated region (3'-UTR) of ABI1, revealing that miR-30e-3p might play a role in the polymerization of neuronal actin and the reconstruction of the cytoskeleton via the downstream regulation of ABI1. In addition, we constructed a classifier by a series of bioinformatics algorithms and evaluated its diagnostic performance. It appears that the classifier consists of miRNAs and mRNAs possess a better discrimination performance than individual miRNA or mRNA in SCZ.
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Affiliation(s)
- Mengdi Jin
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Yane Liu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Guoyan Hu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Xinwei Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Ningning Jia
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Xingyao Cui
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Zhijun Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Lizhe Ai
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Mengtong Xie
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Fengyu Xue
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Yuqing Yang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Weizhen Li
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Min Zhang
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China
| | - Qiong Yu
- Department of Epidemiology and Biostatistics, School of Public Health, Jilin University, Changchun, 130021, China.
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207
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Yang Y, Lang P, Zhang X, Wu X, Cao S, Zhao C, Shen R, Ling X, Yang Y, Zhang J. Molecular characterization of extracellular vesicles derived from follicular fluid of women with and without PCOS: integrating analysis of differential miRNAs and proteins reveals vital molecules involving in PCOS. J Assist Reprod Genet 2023; 40:537-552. [PMID: 36695944 PMCID: PMC10033803 DOI: 10.1007/s10815-023-02724-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 01/10/2023] [Indexed: 01/26/2023] Open
Abstract
PURPOSE To elucidate the characterization of extracellular vesicles (EVs) in the follicular fluid-derived extracellular vesicles (FF-EVs) and discover critical molecules and signaling pathways associating with the etiology and pathobiology of PCOS, the differentially expressed miRNAs (DEmiRNAs) and differentially expressed proteins profiles (DEPs) were initially explored and combinedly analyzed. METHODS First, the miRNA and protein expression profiles of FF-EVs in PCOS patients and control patients were compared by RNA-sequencing and tandem mass tagging (TMT) proteomic methods. Subsequently, Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes were used to analyze the biological function of target genes of DEmiRNAs and DEPs. Finally, to discover the functional miRNA-target gene-protein interaction pairs involved in PCOS, DEmiRs target gene datasets and DEPs datasets were used integratedly. RESULTS A total of 6 DEmiRNAs and 32 DEPs were identified in FF-EVs in patients with PCOS. Bioinformatics analysis revealed that DEmiRNAs target genes are mainly involved in thiamine metabolism, insulin secretion, GnRH, and Apelin signaling pathway, which are closely related to the occurrence of PCOS. DEPs also closely related to hormone metabolism processes such as steroid hormone biosynthesis. In the analysis integrating DEmiRNAs target genes and DEPs, two molecules, GRAMD1B and STPLC2, attracted our attention that are closely associated with cholesterol transport and ceramide biosynthesis, respectively. CONCLUSION Dysregulated miRNAs and proteins in FF-EVs, mainly involving in hormone metabolism, insulin secretion, neurotransmitters regulation, adipokine expression, and secretion, may be closely related to PCOS. The effects of GRAMD1B and STPLC2 on PCOS deserve further study.
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Affiliation(s)
- Yuqin Yang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Peng Lang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiaolan Zhang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xun Wu
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Shanren Cao
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Chun Zhao
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Rong Shen
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Xiufeng Ling
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China
| | - Ye Yang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
| | - Junqiang Zhang
- Department of Reproductive Medicine, Women's Hospital of Nanjing Medical University, Nanjing Maternity and Child Health Care Hospital, Nanjing, China.
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208
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Guo P, Yi H, Han M, Liu X, Chen K, Qing J, Yang F. Dexmedetomidine alleviates myocardial ischemia-reperfusion injury by down-regulating miR-34b-3p to activate the Jagged1/Notch signaling pathway. Int Immunopharmacol 2023; 116:109766. [PMID: 36764271 DOI: 10.1016/j.intimp.2023.109766] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/16/2023] [Accepted: 01/19/2023] [Indexed: 02/10/2023]
Abstract
BACKGROUND Myocardial ischemia/reperfusion (I/R) injury is a fatal event that usually occurs after reperfusion therapy for myocardial infarction. Dexmedetomidine (Dex) has been shown to be beneficial in the treatment of myocardial infarction, however, its underlying mechanism for regulating I/R injury is unclear. METHODS H9c2 cell and rat models of I/R injury were established via oxygen-glucose deprivation reoxygenation (OGD/R) and occlusion of the left anterior descending branch of coronary artery, respectively. Flow cytometry, MTT, or DHE assay detected cell activity, ROS, or apoptosis, respectively. The expression levels of miR-34b-3p and related mRNAs were determined using qRT-PCR. Related protein expression levels were detected by Western blotting and ELISA test. The interaction between miR-34b-3p and Jagged1 was assessed by dual luciferase reporter and RIP assays. The morphology of cardiac tissue was examined by TTC, HE, and TUNEL labeling. RESULTS Dex markedly inhibited the inflammatory damage and apoptosis caused by OGD/R in H9c2 cells. MiR-34b-3p and Jagged1 levels were increased and decreased in myocardial I/R injury model, respectively, while Dex reversed this effect. Moreover, miR-34b-3p was firstly reported to directly bind and decrease Jagged1 expression, thereby inhibiting Notch signaling pathway. Transfection of agomiR-34b-3p or Jagged1 silencing eliminated Dex's defensive impact on OGD/R-induced cardiomyocytes damage. Dex relieved the myocardial I/R injury of rats via inhibiting miR-34b-3p and further activating Notch signaling pathway. CONCLUSION Dex protected myocardium from I/R injury via suppressing miR-34b-3p to activate Jagged1-mediated Notch signaling pathway. Our findings revealed a novel mechanism underlying of Dex on myocardial I/R injury.
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Affiliation(s)
- Peng Guo
- Department of Anesthesiology, The First People's Hospital of Huaihua, Huaihua 418000, Hunan Province, PR China
| | - Han Yi
- Department of Anesthesiology, The Second People's Hospital of Yueyang, Yueyang 414000, Hunan Province, PR China
| | - Mingming Han
- Department of Anesthesiology, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei 230036, Anhui Province, PR China; Department of Anesthesiology and Critical Care Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Xinxin Liu
- Department of Anesthesiology, The First People's Hospital of Huaihua, Huaihua 418000, Hunan Province, PR China
| | - Kemin Chen
- Department of Anesthesiology, The First Affiliated Hospital of University of South China, Hengyang 421001, Hunan Province, PR China
| | - Jie Qing
- Department of Anesthesiology, The First Affiliated Hospital of University of South China, Hengyang 421001, Hunan Province, PR China
| | - Fengrui Yang
- Department of Anesthesiology, The First People's Hospital of Huaihua, Huaihua 418000, Hunan Province, PR China; Department of Anesthesiology and Critical Care Medicine, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA; Department of Anesthesiology, The First Affiliated Hospital of University of South China, Hengyang 421001, Hunan Province, PR China.
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209
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Pradhan A, Aneja A, Ghosh S, Devvanshi H, C D, Sahu R, Ross C, Kshetrapal P, Maitra A, Das S. Association of exosomal miR-96-5p and miR-146a-5p with the disease severity in dengue virus infection. J Med Virol 2023; 95:e28614. [PMID: 36840403 DOI: 10.1002/jmv.28614] [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: 11/10/2022] [Revised: 01/31/2023] [Accepted: 02/19/2023] [Indexed: 02/26/2023]
Abstract
Exosomes are small extracellular vesicles secreted by cells and have a major role in cell-to-cell signaling. As dengue infection progresses from a mild to a severe form of infection, the exosome's microRNA (miRNA) composition might change, which may contribute to pathogenesis. In this study, a comprehensive analysis of serum exosomal miRNAs was performed and their involvement in dengue virus-induced disease progression in an Indian cohort was assessed. Small RNA-seq showed 50 differentially expressed exosomal miRNAs that were significantly dysregulated during dengue infection. After extensive validation, miR-96-5p was found to be significantly upregulated, whereas miR-146a-5p was significantly downregulated with the progression of disease to severe form. Interestingly, a strong positive correlation was found between the expression levels of miR-96-5p and miR-146a-5p and the platelet levels of the patients. Further, study of miR-146a-5p showed that it regulates the expression of the proteins which are involved in the immune responses. These results suggest that miR-96-5p and miR-146a-5p could be used as diagnostic and prognostic markers for dengue disease progression, in addition to the already available biochemical and pathological parameters.
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Affiliation(s)
- Aunji Pradhan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Ashish Aneja
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Sahana Ghosh
- National Institute of Biomedical Genomics, Kalyani, India
| | - Himadri Devvanshi
- Translational Health Science and Technology Institute, Faridabad, India
| | - Deepika C
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Risabh Sahu
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
| | - Celil Ross
- St. John's Medical College, Bangalore, India
| | | | - Arindam Maitra
- National Institute of Biomedical Genomics, Kalyani, India
| | - Saumitra Das
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India
- National Institute of Biomedical Genomics, Kalyani, India
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210
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Ji X, Lv C, Huang J, Dong W, Sun W, Zhang H. ALKBH5-induced circular RNA NRIP1 promotes glycolysis in thyroid cancer cells by targeting PKM2. Cancer Sci 2023. [PMID: 36851875 DOI: 10.1111/cas.15772] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/14/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023] Open
Abstract
Although circular RNAs (circRNAs) are involved in cell proliferation, differentiation, apoptosis, and invasion, the underlying regulatory mechanisms of circRNAs in thyroid cancer have not been fully elucidated. This article aimed to study the role of circRNA regulated by N6-methyladenosine modification in papillary thyroid cancer (PTC). Quantitative real-time PCR, western blotting, and immunohistochemistry were used to investigate the expressions of circRNA nuclear receptor-interacting protein 1 (circNRIP1) in PTC tissues and adjacent noncancerous thyroid tissues. In vitro and in vivo assays were carried out to assess the effects of circNRIP1 on PTC glycolysis and growth. The N6-methyladenosine mechanisms of circNRIP1 were evaluated by methylated RNA immunoprecipitation sequencing, luciferase reporter gene, and RNA stability assays. Results showed that circNRIP1 levels were significantly upregulated in PTC tissues. Furthermore, elevated circNRIP1 levels in PTC patients were correlated with high tumor lymph node metastasis stage and larger tumor sizes. Functionally, circNRIP1 significantly promoted glycolysis, PTC cell proliferation in vitro, and tumorigenesis in vivo. Mechanistically, circNRIP1 acted as a sponge for microRNA (miR)-541-5p and miR-3064-5p and jointly upregulated pyruvate kinase M2 (PKM2) expression. Knockdown of m6 A demethylase α-ketoglutarate-dependent dioxygenase alkB homolog 5 (ALKBH5) significantly enhanced circNRIP1 m6 A modification and upregulated its expression. These results show that ALKBH5 knockdown upregulates circNRIP1, thus promoting glycolysis in PTC cells. Therefore, circNRIP1 can be a prognostic biomarker and therapeutic target for PTC by acting as a sponge for oncogenic miR-541-5p and miR-3064-5p to upregulate PKM2 expression.
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Affiliation(s)
- Xiaoyu Ji
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Chengzhou Lv
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Jiapeng Huang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Wenwu Dong
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Wei Sun
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
| | - Hao Zhang
- Department of Thyroid Surgery, The First Hospital of China Medical University, Shenyang, China
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211
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Škrlec I. Circadian system microRNAs - Role in the development of cardiovascular diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2023; 137:225-267. [PMID: 37709378 DOI: 10.1016/bs.apcsb.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/09/2023]
Abstract
Circadian rhythm regulates numerous physiological processes, and disruption of the circadian clock can lead to cardiovascular disease. Cardiovascular disease is the leading cause of morbidity and mortality worldwide. Small non-coding RNAs, microRNAs (miRNAs), are involved in regulating gene expression, both those important for the cardiovascular system and key circadian clock genes. Epigenetic mechanisms based on miRNAs are essential for fine-tuning circadian physiology. Indeed, some miRNAs depend on circadian periodicity, others are under the influence of light, and still others are under the influence of core clock genes. Dysregulation of miRNAs involved in circadian rhythm modulation has been associated with inflammatory conditions of the endothelium and atherosclerosis, which can lead to coronary heart disease and myocardial infarction. Epigenetic processes are reversible through their association with environmental factors, enabling innovative preventive and therapeutic strategies for cardiovascular disease. Here, is a review of recent findings on how miRNAs modulate circadian rhythm desynchronization in cardiovascular disease. In the era of personalized medicine, the possibility of treatment with miRNA antagomirs should be time-dependent to correspond to chronotherapy and achieve the most significant efficacy.
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Affiliation(s)
- Ivana Škrlec
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, Osijek, Croatia.
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212
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Krasnodębski C, Sawuła A, Kaźmierczak U, Żuk M. Oligo-Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants. Int J Mol Sci 2023; 24:ijms24054466. [PMID: 36901895 PMCID: PMC10002457 DOI: 10.3390/ijms24054466] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 02/15/2023] [Accepted: 02/22/2023] [Indexed: 03/12/2023] Open
Abstract
Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides' action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.
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Affiliation(s)
- Cezary Krasnodębski
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Agnieszka Sawuła
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
| | - Urszula Kaźmierczak
- Department of Cellular Molecular Biology, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14A, 50-383 Wroclaw, Poland
| | - Magdalena Żuk
- Department of Genetic Biochemistry, Faculty of Biotechnology, University of Wroclaw, Przybyszewskiego 63/77, 51-148 Wroclaw, Poland
- Correspondence:
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213
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La Y, Ma X, Bao P, Chu M, Guo X, Liang C, Yan P. Identification and profiling of microRNAs during yak's testicular development. BMC Vet Res 2023; 19:53. [PMID: 36803968 PMCID: PMC9940382 DOI: 10.1186/s12917-023-03602-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 02/01/2023] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND Normal testicular development is highly crucial for male reproduction and is a precondition for spermatogenesis that is the production of spermatozoa in the testes. MiRNAs have been implicated in several testicular biological processes, including cell proliferation, spermatogenesis, hormone secretion, metabolism and reproductive regulation. In the present study, we used deep sequencing data to study the functions of miRNAs during testicular development and spermatogenesis, by analyzing the expression patterns of small RNAs in 6-, 18- and 30-month-old yak testis tissues. RESULTS A total of 737 known and 359 novel miRNAs were obtained from 6-, 18- and 30-month-old yak testes. In all, we obtained 12, 142 and 139 differentially expressed (DE) miRNAs in 30- vs. 18-, 18- vs. 6-, and 30- vs. 6-month-old testes, respectively. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis of all DE miRNA target genes revealed BMP2, TGFB2, GDF6, SMAD6, TGFBR2 and other target genes as participants in different biological processes, including TGF-β, GnRH, Wnt, PI3K-Akt, MAPK signaling pathways and several other reproductive pathways. In addition, quantitative reverse transcriptase-polymerase chain reaction (qRT-PCR) was used to detect the expression of seven randomly selected miRNAs in 6-, 18- and 30-month-old testes, and the results were consistent with the sequencing data. CONCLUSIONS The differential expression of miRNAs in yak testes at different development stages was characterized and investigated using deep sequencing technology. We believe that the results will contribute to further understanding the functions of miRNAs in regulating the development of yak testes and improving the reproductive performance of male yaks.
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Affiliation(s)
- Yongfu La
- grid.464362.1Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiaoming Ma
- grid.464362.1Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Pengjia Bao
- grid.464362.1Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Min Chu
- grid.464362.1Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xian Guo
- grid.464362.1Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China ,grid.410727.70000 0001 0526 1937Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Chunnian Liang
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China. .,Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China. .,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China.
| | - Ping Yan
- Animal Science Department, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China. .,Key Laboratory of Animal Genetics and Breeding On Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Chinese Academy of Agricultural Sciences, Lanzhou, China. .,Key Laboratory for Yak Genetics, Breeding, and Reproduction Engineering of Gansu Province, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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miR-103-3p Regulates the Differentiation and Autophagy of Myoblasts by Targeting MAP4. Int J Mol Sci 2023; 24:ijms24044130. [PMID: 36835542 PMCID: PMC9959477 DOI: 10.3390/ijms24044130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
Skeletal muscle is the most abundant tissue in mammals, and myogenesis and differentiation require a series of regulatory factors such as microRNAs (miRNAs). In this study, we found that miR-103-3p was highly expressed in the skeletal muscle of mice, and the effects of miR-103-3p on skeletal muscle development were explored using myoblast C2C12 cells as a model. The results showed that miR-103-3p could significantly reduce myotube formation and restrain the differentiation of C2C12 cells. Additionally, miR-103-3p obviously prevented the production of autolysosomes and inhibited the autophagy of C2C12 cells. Moreover, bioinformatics prediction and dual-luciferase reporter assays confirmed that miR-103-3p could directly target the microtubule-associated protein 4 (MAP4) gene. The effects of MAP4 on the differentiation and autophagy of myoblasts were then elucidated. MAP4 promoted both the differentiation and autophagy of C2C12 cells, which was contrary to the role of miR-103-3p. Further research revealed that MAP4 colocalized with LC3 in C2C12 cell cytoplasm, and the immunoprecipitation assay showed that MAP4 interacted with autophagy marker LC3 to regulate the autophagy of C2C12 cells. Overall, these results indicated that miR-103-3p regulated the differentiation and autophagy of myoblasts by targeting MAP4. These findings enrich the understanding of the regulatory network of miRNAs involved in the myogenesis of skeletal muscle.
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215
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Wu J, Shi Y, Xing M, Deng M, Cao W, Guo Q, Zou W. CircRalgapa1 facilitates morphine tolerance via miR-873a-5p/A20 axis in mice. Neuropharmacology 2023; 224:109353. [PMID: 36455645 DOI: 10.1016/j.neuropharm.2022.109353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Revised: 11/08/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Morphine tolerance (MT) caused by long-term use of morphine is a major medical problem. The underlying molecular mechanisms of morphine tolerance remain unclear. Here, we establish the morphine tolerance model in mice and verify whether a novel circRNA, circRalgapa1 is involved in morphine tolerance and its specific molecular mechanism. We show that the expression of circRalgapa1 in the spinal cord is significantly down-expressed in the spinal cord of morphine-tolerant mice. CircRalgapa1 is mainly located in the neuronal cytoplasm and co-localizes with miR-873a-5p. Mechanically, circRalgapa1 acts as competing endogenous RNAs (ceRNAs) to regulate the inhibitory of miR-873a-5p on A20 (also known as tumor necrosis factor α-induced protein 3, TNFAIP3). Functionally, overexpression of circRalgapa1 by intrathecal injection of adeno-associated virus (AAV- circRalgapa1) attenuated the formation of morphine tolerance and partially reversed the development of morphine tolerance. Moreover, overexpression of miR-873a-5p blocked the effect of AAV-circRalgapa1 on alleviating morphine tolerance in mice. In conclusion, chronic morphine administration-mediated down-regulation of circRalgapa1 in the spinal cord contributes to morphine tolerance via miR-873a-5p/A20 axis in mice. Overexpression of circRalgapa1 may be a promising RNA-based therapy for morphine tolerance.
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Affiliation(s)
- Jing Wu
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yufei Shi
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Manyu Xing
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Meiling Deng
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wei Cao
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qulian Guo
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wangyuan Zou
- Department of Anesthesiology, Xiangya Hospital, Central South University, Changsha, Hunan, China; National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Central South University, Changsha, China.
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216
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Studies on the role of non-coding RNAs in controlling the activity of T cells in asthma. Noncoding RNA Res 2023; 8:211-217. [PMID: 36865391 PMCID: PMC9972402 DOI: 10.1016/j.ncrna.2023.02.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 02/17/2023] Open
Abstract
Bronchial asthma, commonly known as asthma, is a chronic inflammatory disease characterized by airway inflammation, increased responsiveness and changes in airway structure. T cells, particularly T helper cells, play a crucial role in the disease. Non-coding RNAs, which are RNAs that do not code for proteins, mainly include microRNAs, long non-coding RNAs, and circular RNAs, play a role in regulating various biological processes. Studies have shown that non-coding RNAs have an important role in the activation and transformation of T cells and other biological processes in asthma. The specific mechanisms and clinical applications are worth further examination. This article reviews the recent research on the role of microRNAs, long non-coding RNAs and circular RNAs in T cells in asthma.
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217
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Wang S, Li N, Meng X. Silencing of the circ-Arhgap5 RNA protects neuronal PC12 cells against injury and depends on the miR-29a-3p/Rock1 axis. Metab Brain Dis 2023; 38:1285-1296. [PMID: 36790698 DOI: 10.1007/s11011-023-01178-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 01/23/2023] [Indexed: 02/16/2023]
Abstract
Circular RNAs (circRNAs) are abundantly expressed in human central nervous system. Here, we explored the role of circ_Arhgap5 in cerebral ischemia/reperfusion (I/R)-induced nerve injury in PC12 cells and its associated mechanism. Cell proliferation ability was assessed by 5-Ethynyl-2'-deoxyuridine (Edu) assay and 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. Flow cytometry (FCM) was applied to assess cell apoptotic rate. Cell death was analyzed by lactate dehydrogenase (LDH) assay. Oxygen-glucose deprivation and reoxygenation (OGD/R) up-regulates the expression of circRNA Rho GTPase activating protein 5 (circ_Arhgap5; mmu_circ_0000377) in PC12 cells. OGD/R exposure inhibited the proliferation and induced the apoptosis of PC12 cells, and the silence of circ_Arhgap5 attenuated OGD/R-induced injury in PC12 cells. miR-29a-3p was identified as a target of circ_Arhgap5 in PC12 cells. Circ_Arhgap5 knockdown-mediated protective effects in OGD/R-induced PC12 cells were reversed by the interference of miR-29a-3p. miR-29a-3p interacted with the 3' untranslated region (3'UTR) of Rho-associated coiled-coil-containing protein kinase 1 (Rock1), and circ_Arhgap5 can positively regulate Rock1 expression by sponging miR-29a-3p in PC12 cells. miR-29a-3p overexpression protected PC12 cells against OGD/R-induced damage by down-regulating Rock1. In conclusion, circ_Arhgap5 silencing protected PC12 cells from OGD/R-induced injury through mediating miR-29a-3p/Rock1 axis.
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Affiliation(s)
- Shengyuan Wang
- Department of Hyperbaric Oxygen, The Sixth Medical Center of PLA General Hospital, 6 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Na Li
- Department of Hyperbaric Oxygen, The Sixth Medical Center of PLA General Hospital, 6 Fucheng Road, Haidian District, Beijing, 100048, China
| | - Xiangen Meng
- Department of Hyperbaric Oxygen, The Sixth Medical Center of PLA General Hospital, 6 Fucheng Road, Haidian District, Beijing, 100048, China.
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218
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Zhang X, Luo M, Jiang B, Zhu W, Min Q, Hu J, Liu T, Fu J, Shi X, Wang P, Wang L, Dong Z. microRNA regulation of skin pigmentation in golden-back mutant of crucian carp from a rice-fish integrated farming system. BMC Genomics 2023; 24:70. [PMID: 36765276 PMCID: PMC9912656 DOI: 10.1186/s12864-023-09168-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
BACKGROUND MicroRNAs (miRNAs) are endogenous small non-coding RNAs (21-25 nucleotides) that act as essential components of several biological processes. Golden-back crucian carp (GBCrC, Carassius auratus) is a naturally mutant species of carp that has two distinct body skin color types (golden and greenish-grey), making it an excellent model for research on the genetic basis of pigmentation. Here, we performed small RNA (sRNA) analysis on the two different skin colors via Illumina sequencing. RESULTS A total of 679 known miRNAs and 254 novel miRNAs were identified, of which 32 were detected as miRNAs with significant differential expression (DEMs). 23,577 genes were projected to be the targets of 32 DEMs, primarily those involved in melanogenesis, adrenergic signaling in cardiomyocytes, MAPK signaling pathway and wnt signaling pathway by functional enrichment. Furthermore, we built an interaction module of mRNAs, proteins and miRNAs based on 10 up-regulated and 13 down-regulated miRNAs in golden skin. In addition to transcriptional destabilization and translational suppression, we discovered that miRNAs and their target genes were expressed in the same trend at both the transcriptional and translational levels. Finally, we discovered that miR-196d could be indirectly implicated in regulating melanocyte synthesis and motility in the skin by targeting to myh7 (myosin-7) gene through the luciferase reporter assay, antagomir silencing in vivo and qRT-PCR techniques. CONCLUSIONS Our study gives a systematic examination of the miRNA profiles expressed in the skin of GBCrC, assisting in the comprehension of the intricate molecular regulation of body color polymorphism and providing insights for C. auratus breeding research.
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Affiliation(s)
- Xianbo Zhang
- Guizhou Fisheries Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang, Guizhou, China
| | - Mingkun Luo
- grid.43308.3c0000 0000 9413 3760Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, Jiangsu, China
| | - Bingjie Jiang
- grid.27871.3b0000 0000 9750 7019Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China
| | - Wenbin Zhu
- grid.43308.3c0000 0000 9413 3760Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, Jiangsu, China
| | - Qianwen Min
- Guizhou Fisheries Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang, Guizhou, China
| | - Jinli Hu
- Guizhou Fisheries Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang, Guizhou, China
| | - Ting Liu
- Guizhou Fisheries Research Institute, Guizhou Academy of Agriculture Sciences, Guiyang, Guizhou, China
| | - Jianjun Fu
- grid.43308.3c0000 0000 9413 3760Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, Jiangsu, China
| | - Xiulan Shi
- grid.27871.3b0000 0000 9750 7019Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China
| | - Pan Wang
- grid.412514.70000 0000 9833 2433College of Fisheries and Life Science, Shanghai Ocean University, Shanghai, China
| | - Lanmei Wang
- grid.43308.3c0000 0000 9413 3760Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, Jiangsu, China
| | - Zaijie Dong
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center of Chinese Academy of Fishery Sciences, Ministry of Agriculture and Rural Affairs, Wuxi, Jiangsu, China. .,Wuxi Fisheries College, Nanjing Agricultural University, Wuxi, Jiangsu, China.
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219
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Gao Y, Cao H, Huang D, Zheng L, Nie Z, Zhang S. RNA-Binding Proteins in Bladder Cancer. Cancers (Basel) 2023; 15:cancers15041150. [PMID: 36831493 PMCID: PMC9953953 DOI: 10.3390/cancers15041150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/09/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
RNA-binding proteins (RBPs) are key regulators of transcription and translation, with highly dynamic spatio-temporal regulation. They are usually involved in the regulation of RNA splicing, polyadenylation, and mRNA stability and mediate processes such as mRNA localization and translation, thereby affecting the RNA life cycle and causing the production of abnormal protein phenotypes that lead to tumorigenesis and development. Accumulating evidence supports that RBPs play critical roles in vital life processes, such as bladder cancer initiation, progression, metastasis, and drug resistance. Uncovering the regulatory mechanisms of RBPs in bladder cancer is aimed at addressing the occurrence and progression of bladder cancer and finding new therapies for cancer treatment. This article reviews the effects and mechanisms of several RBPs on bladder cancer and summarizes the different types of RBPs involved in the progression of bladder cancer and the potential molecular mechanisms by which they are regulated, with a view to providing information for basic and clinical researchers.
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220
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miRNA-Induced Downregulation of IPMK in Macrophages Mediates Lipopolysaccharide-Triggered TLR4 Signaling. Biomolecules 2023; 13:biom13020332. [PMID: 36830701 PMCID: PMC9952907 DOI: 10.3390/biom13020332] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 01/27/2023] [Accepted: 02/07/2023] [Indexed: 02/11/2023] Open
Abstract
Inositol polyphosphate multikinase (IPMK) is a pleiotropic enzyme responsible for the production of inositol polyphosphates and phosphoinositide. IPMK in macrophages was identified as a key factor for the full activation of the Toll-like receptor 4 (TLR4) signaling pathway and inflammation by directly interacting with tumor necrosis factor receptor-associated factor 6 (TRAF6). Here, dynamic changes of IPMK levels in lipopolysaccharide (LPS)-stimulated macrophages and their functional significance were investigated. Both the mRNA and protein levels of IPMK were acutely decreased in mouse and human macrophages when cells were stimulated with LPS for between 1 and 6 h. Analysis of the 3' untranslated region (UTR) of mouse IPMK mRNA revealed a highly conserved binding site for miR-181c. Transfection of miR-181c mimics into RAW 264.7 macrophages led to decreased IPMK 3'UTR-luciferase reporter activity and lowered endogenous IPMK levels. When the genomic deletion of a 33-bp fragment containing a putative miR-181c-binding site was introduced within the IPMK 3'UTR of RAW 264.7 macrophages (264.7Δ3'UTR), LPS-triggered downregulation of IPMK levels was prevented. LPS treatment in 264.7Δ3'UTR macrophages decreased TLR4-induced signaling and the expression of proinflammatory cytokines. In response to LPS stimulation, K63-linked ubiquitination of TRAF6 was impaired in 264.7Δ3'UTR macrophages, suggesting an action of IPMK in the suppression of TRAF6 activation. Therefore, our findings reveal that LPS-mediated suppression of IPMK regulates the full activation of TLR4 signaling and inflammation in macrophages.
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221
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Zhu H, Leung SW. MicroRNA biomarkers of type 2 diabetes: evidence synthesis from meta-analyses and pathway modelling. Diabetologia 2023; 66:288-299. [PMID: 36269347 PMCID: PMC9807484 DOI: 10.1007/s00125-022-05809-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 08/10/2022] [Indexed: 01/07/2023]
Abstract
AIMS/HYPOTHESIS MicroRNAs are being sought as biomarkers for the early identification of type 2 diabetes. This study aimed to synthesise the evidence from microRNA-type 2 diabetes association studies and microRNA-regulated type 2 diabetes pathway delineation studies that met stringent quality criteria to identify and validate microRNAs of both statistical and biological significance as type 2 diabetes biomarkers. METHODS Eligible controlled studies on microRNA expression profiling of type 2 diabetes were retrieved from PubMed, ScienceDirect and Web of Science. MicroRNA-regulated type 2 diabetes pathway delineation studies were conducted by integrating and cross-verifying the data from miRTarBase, TransmiR, miRecords, TargetScanHuman, the Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Retraction Watch database. Before meta-analysis, quality assessment was performed according to the corresponding reporting guidelines for evidence-based medicine. To select the most statistically significant microRNAs, we conducted extensive meta-analyses according to the latest methodology. Subgroup and sensitivity analyses were carried out to further examine the microRNA candidates for their tissue specificity and blood fraction specificity and the robustness of the evidence. Signalling pathway impact analysis of dysregulated microRNAs identified from meta-analyses was performed to select biologically significant microRNAs that were enriched in our newly built microRNA-regulated pathways. RESULTS Of the 404 differentially expressed microRNAs identified in the 156 controlled profiling studies with a combined sample size of >15,000, only 60 were both consistently and significantly dysregulated in human type 2 diabetes. No microRNAs were both consistently and significantly dysregulated in multiple tissues according to subgroup analyses. In total, 58 microRNAs were found to be robust in sensitivity analyses. A total of 1966 pathway delineation studies were identified, including 3290 microRNA-target interactions, which were further combined with KEGG pathways, producing 225 microRNA-regulated pathways. Impact analysis found that 16 dysregulated microRNAs identified from extensive meta-analyses were statistically significantly enriched in the augmented KEGG type 2 diabetes pathway. CONCLUSIONS/INTERPRETATION Sixteen microRNAs met the criteria for biomarker selection. In terms of both significance and relevance, the order of priority for verification of these microRNAs is as follows: miR-29a-3p, miR-221-3p, miR-126-3p, miR-26a-5p, miR-503-5p, miR-100-5p, miR-101-3p, mIR-103a-3p, miR-122-5p, miR-199a-3p, miR-30b-5p, miR-130a-3p, miR-143-3p, miR-145-5p, miR-19a-3p and miR-311-3p. REGISTRATION PROSPERO registration number CRD42017081659.
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Affiliation(s)
- Hongmei Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Macao, China
- Centre of Gastrointestinal and Minimally Invasive Surgery, Department of General Surgery, Third People's Hospital of Chengdu, Chengdu, China
- Medical Research Centre, Third People's Hospital of Chengdu, Affiliated Hospital of Southwest Jiaotong University, Chengdu, China
| | - Siu-Wai Leung
- Edinburgh Bayes Centre for AI Research in Shenzhen, College of Science and Engineering, University of Edinburgh, Edinburgh, UK.
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222
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Ma Y, Liu Y, Shu B, Yang J, Lv L, Zhou L, Wang L, Shi Z. CircMAP3K4 protects human lens epithelial cells from H 2O 2-induced dysfunction by targeting miR-193a-3p/PLCD3 axis in age-related cataract. Cell Cycle 2023; 22:303-315. [PMID: 36071682 PMCID: PMC9851233 DOI: 10.1080/15384101.2022.2114587] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 07/28/2022] [Accepted: 08/11/2022] [Indexed: 01/22/2023] Open
Abstract
Circular RNAs (circRNAs) have shown pivotal regulatory roles in multiple human ocular diseases, including age-related cataract (ARC). Here, we explored the role of circRNA mitogen-activated protein kinase kinase kinase 4 (circMAP3K4, hsa_circ_0078619) in ARC pathology and its associated mechanism. The expression of RNAs and proteins was examined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR) and western blot assay. Cell viability, senescence, proliferation, and apoptosis were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay, senescence-associated-β-galactosidase (SA-β-Gal) staining, 5-ethynyl-20-deoxyuridine (EdU) assay, and flow cytometry. The oxidative stress status of SRA01/04 cells was analyzed using the commercial kits. The interaction between microRNA-193a-3p (miR-193a-3p) and circMAP3K4 or phospholipase C delta 3 (PLCD3) was verified by dual-luciferase reporter assay, RNA immunoprecipitation (RIP) assay, and RNA-pull down assay. CircMAP3K4 was significantly down-regulated in ARC patients and H2O2-induced SRA01/04 cells. H2O2 treatment restrained the viability and proliferation and promoted the senescence, apoptosis, and oxidative stress of SRA01/04 cells, and circMAP3K4 overexpression protected SRA01/04 cells from H2O2-induced dysfunction. MiR-193a-3p was a direct target of circMAP3K4, and circMAP3K4 overexpression-mediated protective effects in H2O2-induced SRA01/04 cells were largely reversed by the accumulation of miR-193a-3p. MiR-193a-3p interacted with the 3' untranslated region (3'UTR) of PLCD3, and PLCD3 knockdown largely overturned miR-193a-3p silencing-induced protective effects in H2O2-induced SRA01/04 cells. CircMAP3K4 up-regulated the expression of PLCD3 via sponging miR-193a-3p in SRA01/04 cells. In conclusion, circMAP3K4 protected SRA01/04 cells from H2O2-induced dysfunction in ARC through mediating miR-193a-3p/PLCD3 axis.
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Affiliation(s)
- Yu Ma
- Department of Ophthalmology, Zhengzhou University, Affiliated Hospital 5, Zhengzhou, Henan, China
| | - Yi Liu
- College of Medical Technology and Engineering, Zhengzhou Railway Vocational Technology College, Zhengzhou, China
| | - Baotong Shu
- Department of Medical Technology, Henan Medical College, Zhengzhou, Henan, China
| | - Jianguo Yang
- Department of ophtalmology, Ningbo Eye Hospital West Branch, Ningbo, China
| | - Liang Lv
- Department of Ophthalmology, Zhengzhou University, Affiliated Hospital 5, Zhengzhou, Henan, China
| | - Lixiao Zhou
- Department of Ophthalmology, Zhengzhou University, Affiliated Hospital 5, Zhengzhou, Henan, China
| | - Lichun Wang
- Department of Ophthalmology, Zhengzhou Second People’s Hospital, Zhengzhou, China
| | - Zongli Shi
- Department of ophtalmology, Chang Zhou Banshang Eye Hospital, Changzhou, China
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Pan X, Yu Q, Chen S, Li Y, Jiao T, Li W, Zhang C, Kureshi A, Cheng L, Xu Q. Dissecting contributions of representative heavy metal components in PM 2.5 to its cytotoxicity. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 251:114562. [PMID: 36680992 DOI: 10.1016/j.ecoenv.2023.114562] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 06/17/2023]
Abstract
PM2.5 is a complex pollutant that is a pervasive threat to human health. The health risks and toxicity mechanisms of PM2.5 components must be identified to alleviate the corresponding risks. In this study, a reductionism approach based on model PM2.5 particles was used to investigate the contributions of the most harmful components in PM2.5 to its toxicity. Human liver and kidney cells were used as models. The results showed that Cr(VI) was the most critical toxic component among other components (Pb, As, and benzo[a]pyrene) in human liver and kidney cells. PM2.5-Cr(VI) induced oxidative stress, which led to cytotoxicity by inducing cell cycle arrest in the S-phase in HepG2 and HEK293 cells. The presented findings can provide valuable insights into the toxicity levels of PM2.5 components, which can help clarify the potential health risks from PM2.5 exposure.
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Affiliation(s)
- Xiujiao Pan
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China; Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Qianhui Yu
- School of Environmental Science and Engineering, Shandong University, Jinan 250100, China
| | - Shenshu Chen
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Yaqing Li
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Taifeng Jiao
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Wenyue Li
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Chuchu Zhang
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Aliye Kureshi
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China
| | - Lianghong Cheng
- Guangdong Nantian Institute of Forensic Science, Shenzhen 518003, China.
| | - Qiyong Xu
- School of Environment and Energy, Peking University Shenzhen Graduate School, Shenzhen 518055, China.
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Peña-Flores JA, Enríquez-Espinoza D, Muela-Campos D, Álvarez-Ramírez A, Sáenz A, Barraza-Gómez AA, Bravo K, Estrada-Macías ME, González-Alvarado K. Functional Relevance of the Long Intergenic Non-Coding RNA Regulator of Reprogramming (Linc-ROR) in Cancer Proliferation, Metastasis, and Drug Resistance. Noncoding RNA 2023; 9:ncrna9010012. [PMID: 36827545 PMCID: PMC9965135 DOI: 10.3390/ncrna9010012] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 01/28/2023] [Accepted: 01/30/2023] [Indexed: 02/04/2023] Open
Abstract
Cancer is responsible for more than 10 million deaths every year. Metastasis and drug resistance lead to a poor survival rate and are a major therapeutic challenge. Substantial evidence demonstrates that an increasing number of long non-coding RNAs are dysregulated in cancer, including the long intergenic non-coding RNA, regulator of reprogramming (linc-ROR), which mostly exerts its role as an onco-lncRNA acting as a competing endogenous RNA that sequesters micro RNAs. Although the properties of linc-ROR in relation to some cancers have been reviewed in the past, active research appends evidence constantly to a better comprehension of the role of linc-ROR in different stages of cancer. Moreover, the molecular details and some recent papers have been omitted or partially reported, thus the importance of this review aimed to contribute to the up-to-date understanding of linc-ROR and its implication in cancer tumorigenesis, progression, metastasis, and chemoresistance. As the involvement of linc-ROR in cancer is elucidated, an improvement in diagnostic and prognostic tools could promote and advance in targeted and specific therapies in precision oncology.
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225
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Zhang Q, Yin J, Zou Y. MiR-568 mitigated cardiomyocytes apoptosis, oxidative stress response and cardiac dysfunction via targeting SMURF2 in heart failure rats. Heart Vessels 2023; 38:857-868. [PMID: 36717388 DOI: 10.1007/s00380-022-02231-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/28/2022] [Indexed: 02/01/2023]
Abstract
Chronic heart failure (CHF), a conventional, complex, and severe syndrome, is generally defined by myocardial output inadequate to satisfy the metabolic requirements of body tissues. Recently, miR-568 was identified to be down-regulated in CHF patients' sera and negatively correlated with left ventricular mass index in symptomatic CHF patients with systolic dysfunction. Nevertheless, the role of miR-568 during CHF development remains obscure. The current study is aimed to investigate the role of miR-568 in CHF. The MTT assay, flow cytometry analysis, RT-qPCR analysis, western blot analysis and luciferase reporter assays were conducted to figure out the function and potential mechanism of miR-568 in vitro. Rats were operated with aortic coarctation to establish CHF animal model. The effects of miR-568 and SMURF2 on CHF rats were evaluated by hematoxylin-eosin staining, Masson's staining, serum index testing, cardiac ultrasound detection, and TUNEL staining assays. We discovered that miR-568 level was downregulated by H2O2 treatment in cardiomyocytes. In mechanism, miR-568 directly targeted and negatively regulated SMURF2. In function, SMURF2 overexpression reversed the effects of miR-568 on cardiac function and histological changes in vivo. Additionally, SMURF2 overexpression reversed the effects of miR-568 on the content of LDH, AST, CK and CK-MB in vivo. Moreover, SMURF2 overexpression reversed the effects of miR-568 on oxidative stress response in vivo. MiR-568 mitigated cardiomyocytes apoptosis, oxidative stress response and cardiac dysfunction via targeting SMURF2 in CHF rats. This discovery may serve as a potential biomarker for CHF treatment.
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Affiliation(s)
- Qian Zhang
- Department of Cardiology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, No. 168, Hong Kong Road, Jiang'an District, Wuhan, 430015, Hubei, China
| | - Jun Yin
- Department of Cardiology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, No. 168, Hong Kong Road, Jiang'an District, Wuhan, 430015, Hubei, China
| | - Yong Zou
- Department of Cardiology, The Sixth Hospital of Wuhan, Affiliated Hospital of Jianghan University, No. 168, Hong Kong Road, Jiang'an District, Wuhan, 430015, Hubei, China.
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226
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Circ_0006667 contributes to high glucose-induced retinal pigment epithelial cell dysfunction by mediating miR-7-5p/TGFA axis in diabetic retinopathy. Int Ophthalmol 2023:10.1007/s10792-023-02636-y. [PMID: 36715959 DOI: 10.1007/s10792-023-02636-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 01/10/2023] [Indexed: 01/31/2023]
Abstract
BACKGROUND Diabetic retinopathy (DR) is a common complication of diabetes mellitus and it can lead to visual impairment and blindness. The loss of retinal pigment epithelial (RPE) cells is associated with the etiology of DR. Moreover, dysregulated circular RNAs (circRNAs) are implicated in DR progression. Therefore, this project aims to explore the role and potential mechanism of circ_0006667 in DR. METHODS RPE cells (ARPE-19) were stimulated with high glucose (33 mM; HG group) for 24 h to establish the DR cell model. Circ_0006667, microRNA-7-5p (miR-7-5p), and transforming growth factor alpha (TGFA) expression was determined by reverse transcription-quantitative polymerase chain reaction (RT-qPCR). Cell viability, proliferation, and apoptosis were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT), 5-ethynyl-2'-deoxyuridine (EdU), and flow cytometry. CyclinD1, Cleaved-caspase-3, and TGFA protein levels were detected using western blot. Using Circinteractome and starBase analysis, the binding miR-7-5p and circ_0006667 or TGFA was predicted, and then validated using dual-luciferase reporter and RNA Immunoprecipitation (RIP). RESULTS Circ_0006667 expression was up-regulated in DR patients and HG-induced ARPE-19 cells. HG stimulation suppressed ARPE-19 cell proliferation and promoted cell apoptosis and inflammation, which were alleviated via circ_0006667 silence. Circ_0006667 acted as a molecular sponge for miR-7-5p, and circ_0006667 absence-mediated protective effects in HG-induced ARPE-19 cells were largely overturned by the interference of miR-7-5p. miR-7-5p directly targeted TGFA, and miR-7-5p overexpression protected ARPE-19 cells from HG-induced dysfunction largely by down-regulating TGFA. Circ_0006667 can up-regulate the expression of TGFA by sponging miR-7-5p in ARPE-19 cells. CONCLUSION Circ_0006667 silencing protected ARPE-19 cells from HG-induced dysfunction by mediating miR-7-5p/TGFA axis.
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Raymond WS, Ghaffari S, Aguilera LU, Ron E, Morisaki T, Fox ZR, May MP, Stasevich TJ, Munsky B. Using Mechanistic Models and Machine Learning to Design Single-Color Multiplexed Nascent Chain Tracking Experiments. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.25.525583. [PMID: 36747627 PMCID: PMC9900927 DOI: 10.1101/2023.01.25.525583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
mRNA translation is the ubiquitous cellular process of reading messenger-RNA strands into functional proteins. Over the past decade, large strides in microscopy techniques have allowed observation of mRNA translation at a single-molecule resolution for self-consistent time-series measurements in live cells. Dubbed Nascent chain tracking (NCT), these methods have explored many temporal dynamics in mRNA translation uncaptured by other experimental methods such as ribosomal profiling, smFISH, pSILAC, BONCAT, or FUNCAT-PLA. However, NCT is currently restricted to the observation of one or two mRNA species at a time due to limits in the number of resolvable fluorescent tags. In this work, we propose a hybrid computational pipeline, where detailed mechanistic simulations produce realistic NCT videos, and machine learning is used to assess potential experimental designs for their ability to resolve multiple mRNA species using a single fluorescent color for all species. Through simulation, we show that with careful application, this hybrid design strategy could in principle be used to extend the number of mRNA species that could be watched simultaneously within the same cell. We present a simulated example NCT experiment with seven different mRNA species within the same simulated cell and use our ML labeling to identify these spots with 90% accuracy using only two distinct fluorescent tags. The proposed extension to the NCT color palette should allow experimentalists to access a plethora of new experimental design possibilities, especially for cell signalling applications requiring simultaneous study of multiple mRNAs.
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Affiliation(s)
- William S. Raymond
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Sadaf Ghaffari
- Department of Computer Science, Colorado State University, Fort Collins, Colorado, USA
| | - Luis U. Aguilera
- Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Eric Ron
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Tatsuya Morisaki
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Zachary R. Fox
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA,Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Michael P. May
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA
| | - Timothy J. Stasevich
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA,Cell Biology Unit, Institute of Innovative Research, Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama, Japan
| | - Brian Munsky
- School of Biomedical Engineering, Colorado State University, Fort Collins, Colorado, USA,Department of Chemical and Biological Engineering, Colorado State University, Fort Collins, Colorado, USA,Corresponding Author: Brian Munsky -
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228
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Hao D, Li Y, Shi J, Jiang J. Circ_0110498 facilitates the cisplatin resistance of non-small cell lung cancer by mediating the miR-1287-5p/RBBP4 axis. Thorac Cancer 2023; 14:662-672. [PMID: 36691322 PMCID: PMC9981309 DOI: 10.1111/1759-7714.14787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/12/2022] [Accepted: 12/16/2022] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Circular RNAs (circRNAs) play vital roles in non-small cell lung cancer (NSCLC) progression. Our research analyzed the role of circ_0110498 on the cisplatin (DDP) resistance of NSCLC. METHODS Cell glycolysis was analyzed by measuring glucose consumption and lactate production. Protein expression was determined by western blot analysis. The expression of circ_0110498, microRNA (miR)-1287-5p and RBBP4 was detected by RT-qPCR assay. Cell counting kit-8, colony formation and transwell assays, together with flow cytometry were conducted to analyze cell DDP resistance, proliferation, metastasis and apoptosis. RESULTS Circ_0110498 expression was elevated in DDP-resistant NSCLC tissues and cells. Circ_0110498 silencing not only suppressed the DDP resistance of NSCLC cells by inhibiting cell growth, metastasis and glycolysis, but also enhanced the DDP sensitivity of NSCLC tumors. MiR-1287-5p was sponged by circ_0110498, and its inhibitor also reversed the effect of circ_0110498 silencing on the DDP resistance of NSCLC cells. MiR-1287-5p interacted with RBBP4, and RBBP4 overexpression partly reversed the inhibitory effect of miR-1287-5p on the DDP resistance of NSCLC cells. CONCLUSION Circ_0110498 facilitated DDP resistance partly through mediating the miR-1287-5p/RBBP4 signaling in NSCLC.
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Affiliation(s)
- Dexun Hao
- Department of Geriatric Respiratory and SleepThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou CityChina
| | - Yanshuang Li
- Department of AnesthesiologyThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou CityChina
| | - Jiang Shi
- Department of Geriatric Respiratory and SleepThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou CityChina
| | - Junguang Jiang
- Department of Geriatric Respiratory and SleepThe First Affiliated Hospital of Zhengzhou UniversityZhengzhou CityChina
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Xie Y, Zhang Y, Liu X, Cao L, Han M, Wang C, Chen J, Zhang X. miR‑151a‑5p promotes the proliferation and metastasis of colorectal carcinoma cells by targeting AGMAT. Oncol Rep 2023; 49:50. [PMID: 36704851 PMCID: PMC9887461 DOI: 10.3892/or.2023.8487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 01/11/2023] [Indexed: 01/22/2023] Open
Abstract
Colorectal carcinoma (CRC) is one of the most common types of digestive cancer. It has been reported that the ectopic expression of microRNAs (miRs) plays a critical role in the occurrence and progression of CRC. In addition, it has also been suggested that miR‑151a‑5p may serve as a useful biomarker for the early detection and treatment of different types of cancer and particularly CRC. However, the specific effects and underlying mechanisms of miR‑151a‑5p in CRC remain elusive. The results of the current study demonstrated that miR‑151a‑5p was upregulated in CRC cell lines and clinical tissues derived from patients with CRC. Functionally, the results showed that miR‑151a‑5p significantly promoted CRC cell proliferation, migration and invasion. Additionally, dual luciferase reporter assays verified that agmatinase (AGMAT) was a direct target of miR‑151a‑5p and it was positively associated with miR‑151a‑5p expression. Mechanistically, miR‑151a‑5p could enhance the epithelial‑mesenchymal transition of CRC cells. Taken together, the results of the current study revealed a novel molecular mechanism indicating that the miR‑151a‑5p/AGMAT axis could serve a crucial role in the regulation of CRC and could therefore be considered as a potential therapeutic strategy for CRC.
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Affiliation(s)
- Yaya Xie
- Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, Fengxian, Shanghai 201499, P.R. China,School of Medical, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China
| | - Yue Zhang
- School of Medical, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China,Hanzhong Central Hospital of Shaanxi, Hanzhong, Shaanxi 723000, P.R. China
| | - Xianju Liu
- Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, Fengxian, Shanghai 201499, P.R. China,School of Medical, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China
| | - Lijun Cao
- Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, Fengxian, Shanghai 201499, P.R. China,School of Medical, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China
| | - Mengting Han
- School of Medical, Anhui University of Science and Technology, Huainan, Anhui 232001, P.R. China
| | - Chunmei Wang
- Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, Fengxian, Shanghai 201499, P.R. China
| | - Jinlian Chen
- Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, Fengxian, Shanghai 201499, P.R. China,Correspondence to: Dr Xingxing Zhang or Dr Jinlian Chen, Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Fengxian, Shanghai 201499, P.R. China, E-mail:
| | - Xingxing Zhang
- Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, Fengxian, Shanghai 201499, P.R. China,Correspondence to: Dr Xingxing Zhang or Dr Jinlian Chen, Department of Gastroenterology, Anhui University of Science and Technology Affiliated Fengxian Hospital, 6600 Nanfeng Road, Fengxian, Shanghai 201499, P.R. China, E-mail:
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Chen JW, Shrestha L, Green G, Leier A, Marquez-Lago TT. The hitchhikers' guide to RNA sequencing and functional analysis. Brief Bioinform 2023; 24:bbac529. [PMID: 36617463 PMCID: PMC9851315 DOI: 10.1093/bib/bbac529] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 10/18/2022] [Accepted: 11/07/2022] [Indexed: 01/10/2023] Open
Abstract
DNA and RNA sequencing technologies have revolutionized biology and biomedical sciences, sequencing full genomes and transcriptomes at very high speeds and reasonably low costs. RNA sequencing (RNA-Seq) enables transcript identification and quantification, but once sequencing has concluded researchers can be easily overwhelmed with questions such as how to go from raw data to differential expression (DE), pathway analysis and interpretation. Several pipelines and procedures have been developed to this effect. Even though there is no unique way to perform RNA-Seq analysis, it usually follows these steps: 1) raw reads quality check, 2) alignment of reads to a reference genome, 3) aligned reads' summarization according to an annotation file, 4) DE analysis and 5) gene set analysis and/or functional enrichment analysis. Each step requires researchers to make decisions, and the wide variety of options and resulting large volumes of data often lead to interpretation challenges. There also seems to be insufficient guidance on how best to obtain relevant information and derive actionable knowledge from transcription experiments. In this paper, we explain RNA-Seq steps in detail and outline differences and similarities of different popular options, as well as advantages and disadvantages. We also discuss non-coding RNA analysis, multi-omics, meta-transcriptomics and the use of artificial intelligence methods complementing the arsenal of tools available to researchers. Lastly, we perform a complete analysis from raw reads to DE and functional enrichment analysis, visually illustrating how results are not absolute truths and how algorithmic decisions can greatly impact results and interpretation.
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Affiliation(s)
- Jiung-Wen Chen
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Lisa Shrestha
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
| | - George Green
- Department of Biology, University of Alabama at Birmingham, Birmingham, AL, USA
| | - André Leier
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
| | - Tatiana T Marquez-Lago
- Department of Genetics, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Cell, Developmental and Integrative Biology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
- Department of Microbiology, University of Alabama at Birmingham, School of Medicine, Birmingham, AL, USA
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231
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Ruiz Esparza Garrido R, Gutiérrez M, Ángel Velázquez Flores M. Circulating cervical cancer biomarkers potentially useful in medical attention (Review). Mol Clin Oncol 2023; 18:13. [PMID: 36761385 PMCID: PMC9892968 DOI: 10.3892/mco.2023.2609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 12/27/2022] [Indexed: 01/19/2023] Open
Abstract
Cervical cancer (CC) is a public health problem worldwide, including Mexico. This type of cancer is the fourth most frequent in women worldwide; in Mexico it is the second most common type in women after breast cancer. The diagnosis of CC is based mainly on Pap smears and colposcopy and the identification of molecular tools that serve as a support for these methods is urgent. Regarding this, differential expressions of specific circulating biomolecules has been detected and, based on this, they have been postulated as potential biomarkers for CC diagnosis, prognosis, and/or to identify the response to treatments. Importantly, the combined analysis of these molecules considerably improves their efficacy as biomarkers and their potential use in the medical attention is promising.
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Affiliation(s)
- Ruth Ruiz Esparza Garrido
- Investigadora por México, Non-coding RNAs Laboratory, Medical Research Unit in Human Genetics, Children's Hospital ‘Dr. Silvestre Frenk Freund’, National Medical Center XXI Century, Mexican Institute of Social (Instituto Mexicano del Seguro Social, IMSS), Doctores, Mexico City 06720, Mexico
| | - Mercedes Gutiérrez
- ATSO PHARMA Laboratory, Jardines del Pedregal, Álvaro Obregón, Mexico City 01900, Mexico
| | - Miguel Ángel Velázquez Flores
- Non-coding RNAs Laboratory, Medical Research Unit in Human Genetics, Children's Hospital ‘Dr. Silvestre Frenk Freund’, National Medical Center XXI Century, Mexican Institute of Social (Instituto Mexicano del Seguro Social, IMSS), Doctores, Mexico City 06720, Mexico,Correspondence to: Dr Miguel Ángel Velázquez Flores, Non-coding RNAs Laboratory, Medical Research Unit in Human Genetics, Children's Hospital ‘Dr. Silvestre Frenk Freund’, National Medical Center XXI Century, Mexican Institute of Social Security, 330 Cuauhtémoc Avenue, Doctores, Mexico City 06720, Mexico
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232
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Non-invasive diagnosis of endometriosis: Immunologic and genetic markers. Clin Chim Acta 2023; 538:70-86. [PMID: 36375526 DOI: 10.1016/j.cca.2022.11.013] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
Endometriosis, a benign gynecologic and chronic inflammatory disease, is defined by the presence of endometrial tissue outside the uterus characterized mainly by pelvic pain and infertility. Because endometriosis affects approximately 10% of females, it represents a significant socioeconomic burden worldwide having tremendous impact on daily quality of life. Accurate and prompt diagnosis is crucial for the management of this debilitating disorder. Unfortunately, diagnosis is typically delayed to lack of specific symptoms and readily accessible biomarkers. Although histopathologic examination remains the current gold standard, this approach is highly invasive and not applicable for early screening. Recent work has focused on the identification of reliable biomarkers including immunologic, ie, immune cells, antibodies and cytokines, as well as genetic and biochemical markers, ie, microRNAs, lncRNAs, circulating and mitochondrial nucleic acids, along with some hormones, glycoproteins and signaling molecules. Confirmatory research studies are, however, needed to more fully establish these markers in the diagnosis, progression and staging of these endometrial lesions.
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233
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Zhao X, Liang B, Li C, Wang W. Expression Regulation and Trafficking of Aquaporins. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1398:39-51. [PMID: 36717485 DOI: 10.1007/978-981-19-7415-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Aquaporins (AQPs) mediate the bidirectional water flow driven by an osmotic gradient. Either gating or trafficking allows for rapid and specific AQP regulation in a tissue-dependent manner. The regulatory mechanisms of AQP2 are discussed mainly in this chapter, as the mechanisms controlling the regulation and trafficking of AQP2 have been very well studied. The targeting of AQP2 to the apical plasma membrane of collecting duct principal cells is mainly regulated by the action of arginine vasopressin (AVP) on the type 2 AVP receptor (V2R), which cause increased intracellular cAMP or elevated intracellular calcium levels. Activation of these intracellular signaling pathways results in vesicles bearing AQP2 transport, docking and fusion with the apical membrane, which increase density of AQP2 on the membrane. The removal of AQP2 from the membrane requires dynamic cytoskeletal remodeling. AQP2 is degraded through the ubiquitin proteasome pathway and lysosomal proteolysis pathway. Finally, we review updated findings in transcriptional and epigenetic regulation of AQP2.
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Affiliation(s)
- Xiaoduo Zhao
- Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Baien Liang
- Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China
| | - Chunling Li
- Department of Physiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
| | - Weidong Wang
- Department of Pathophysiology, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, China.
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234
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Blatnik MC, Gallagher TL, Amacher SL. Keeping development on time: Insights into post-transcriptional mechanisms driving oscillatory gene expression during vertebrate segmentation. WILEY INTERDISCIPLINARY REVIEWS. RNA 2023; 14:e1751. [PMID: 35851751 PMCID: PMC9840655 DOI: 10.1002/wrna.1751] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 06/13/2022] [Accepted: 06/20/2022] [Indexed: 01/31/2023]
Abstract
Biological time keeping, or the duration and tempo at which biological processes occur, is a phenomenon that drives dynamic molecular and morphological changes that manifest throughout many facets of life. In some cases, the molecular mechanisms regulating the timing of biological transitions are driven by genetic oscillations, or periodic increases and decreases in expression of genes described collectively as a "molecular clock." In vertebrate animals, molecular clocks play a crucial role in fundamental patterning and cell differentiation processes throughout development. For example, during early vertebrate embryogenesis, the segmentation clock regulates the patterning of the embryonic mesoderm into segmented blocks of tissue called somites, which later give rise to axial skeletal muscle and vertebrae. Segmentation clock oscillations are characterized by rapid cycles of mRNA and protein expression. For segmentation clock oscillations to persist, the transcript and protein molecules of clock genes must be short-lived. Faithful, rhythmic, genetic oscillations are sustained by precise regulation at many levels, including post-transcriptional regulation, and such mechanisms are essential for proper vertebrate development. This article is categorized under: RNA Export and Localization > RNA Localization RNA Turnover and Surveillance > Regulation of RNA Stability Translation > Regulation.
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Affiliation(s)
- Monica C. Blatnik
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Thomas L. Gallagher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
| | - Sharon L. Amacher
- The Ohio State University, Department of Molecular Genetics, Columbus, Ohio, 43210-1132, United States
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235
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Okusha Y, Calderwood SK. Transfection and Thermotolerance Methods for Analysis of miR-570 Targeting the HSP Chaperone Network. Methods Mol Biol 2023; 2693:73-79. [PMID: 37540427 DOI: 10.1007/978-1-0716-3342-7_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
Heat shock proteins (HSPs) are key stress proteins induced in cells exposed to proteotoxic insult and are critical for thermotolerance. The dynamic network of chaperone interactions, known as the chaperome, contributes significantly to the proteotoxic cell response and the malignant phenotype in cancer. We identified a potent microRNA, miR-570 that could bind the 3'untranslated regions of multiple HSP mRNAs and inhibit HSP synthesis. Here, we will introduce the transfection and thermotolerance methods for analysis of miR-570 targeting the HSP chaperone network.
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Affiliation(s)
- Yuka Okusha
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
- JSPS Overseas Research Fellow, Tokyo, Japan
| | - Stuart K Calderwood
- Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA.
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236
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Yu T, Du H, Sun C. Circ-ABCC4 contributes to prostate cancer progression and radioresistance by mediating miR-1253/SOX4 cascade. Anticancer Drugs 2023; 34:155-165. [PMID: 36539368 PMCID: PMC9760474 DOI: 10.1097/cad.0000000000001361] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 03/25/2022] [Indexed: 12/24/2022]
Abstract
Circular RNAs (circRNAs) exert pivotal functions in many malignancies. However, the roles of circ-ABCC4 in prostate cancer (PCa) radioresistance and progression remain largely unclear. Cell viability, proliferation, apoptosis, invasion, and radioresistance were evaluated by 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, 5-ethynyl-2'-deoxyuridine, flow cytometry, transwell invasion, and colony formation assays. Tumor xenograft experiment was conducted to assess circ-ABCC4 role in xenograft growth in vivo. Dual-luciferase reporter assay was implemented to test the target relation of microRNA-1253 (miR-1253) and circ-ABCC4 or SRY-box transcription factor 4 (SOX4). Circ-ABCC4 enrichment was prominently raised in PCa tissue specimens and cells. Circ-ABCC4 depletion blocked PCa cell viability, proliferation, invasion, and radioresistance and triggered apoptosis. Circ-ABCC4 silencing aggravated irradiation-induced inhibitory effect on xenografts growth. miR-1253 was a downstream molecule of circ-ABCC4, and circ-ABCC4 depletion-mediated anti-cancer impacts in PCa cells were partly counteracted by decreasing miR-1253 abundance. miR-1253 targeted SOX4 mRNA, and miR-1253 blocked PCa cell malignant phenotypes partly by targeting SOX4. Circ-ABCC4 could enhance SOX4 abundance by absorbing miR-1253. Circ-ABCC4 exerted a pro-tumor activity by facilitating PCa cell viability, proliferation, invasion, and radioresistance and suppressing apoptosis.
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Affiliation(s)
- Tao Yu
- Department of Urology, Weihai Central Hospital, Weihai
| | - Hong Du
- Department of Urology, Weihai Central Hospital, Weihai
| | - Changhai Sun
- Department of Urology, Qingdao Women’s and Children’s Hospital, Qingdao, Shandong, China
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237
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Khlebodarova TM, Demenkov PS, Ivanisenko TV, Antropova EA, Lavrik IN, Ivanisenko VA. Primary and Secondary micro-RNA Modulation the Extrinsic Pathway of Apoptosis in Hepatocellular Carcinoma. Mol Biol 2023; 57:165-175. [PMID: 37128213 PMCID: PMC10131518 DOI: 10.1134/s0026893323020103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 09/09/2022] [Accepted: 09/09/2022] [Indexed: 05/03/2023]
Abstract
Abstract-One of the most common malignant liver diseases is hepatocellular carcinoma, which has a high recurrence rate and a low five-year survival rate. It is very heterogeneous both in structure and between patients, which complicates the diagnosis, prognosis and response to treatment. In this regard, an individualized, patient-centered approach becomes important, in which the use of mimetics and hsa-miRNA inhibitors involved in the pathogenesis of the disease may be determinative. From this point of view hsa-miRNAs are of interest, their aberrant expression is associated with poor prognosis for patients and is associated with tumor progression due to dysregulation of programmed cell death (apoptosis). However, the effect of hsa-miRNA on tumor development depends not only on its direct effect on expression of genes, the primary targets, but also on secondary targets mediated by regulatory pathways. While the former are actively studied, the role of secondary targets of these hsa-miRNAs in modulating apoptosis is still unclear. The present work summarizes data on hsa-miRNAs whose primary targets are key genes of the extrinsic pathway of apoptosis. Their aberrant expression is associated with early disease relapse and poor patient outcome. For these hsa-miRNAs, using the software package ANDSystem, we reconstructed the regulation of the expression of secondary targets and analyzed their impact on the activity of the extrinsic pathway of apoptosis. The potential effect of hsa-miRNAs mediated by action on secondary targets is shown to negatively correlate with the number of primary targets. It is also shown that hsa-miR-373, hsa-miR-106b and hsa-miR-96 have the highest priority as markers of hepatocellular carcinoma, whose action on secondary targets enhances their anti-apoptotic effect.
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Affiliation(s)
- T. M. Khlebodarova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - P. S. Demenkov
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - T. V. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - E. A. Antropova
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - I. N. Lavrik
- Translational Inflammation Research, Medical Faculty, Otto von Guericke University Magdeburg, 39106 Magdeburg, Germany
| | - V. A. Ivanisenko
- Institute of Cytology and Genetics, Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
- Kurchatov Genomic Center, Institute of Cytology and Genetics Siberian Branch, Russian Academy of Sciences, 630090 Novosibirsk, Russia
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Dong X, Nao J. Relationship between the therapeutic potential of various plant-derived bioactive compounds and their related microRNAs in neurological disorders. PHYTOMEDICINE : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 108:154501. [PMID: 36368284 DOI: 10.1016/j.phymed.2022.154501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/26/2022] [Accepted: 10/02/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND Neurological disorders, such as ischemic stroke, spinal cord injury, neurodegenerative diseases, and glioblastoma often lead to long-term disability and death. MicroRNAs (miRNAs) are small single-stranded non-coding RNAs of approximately 22 nucleotides, known to participate in both normal and pathological development, making them ideal therapeutic targets for clinical intervention. Several recent studies have suggested that plant-derived bioactive compounds (PDBCs) can have anti-atherosclerosis, antioxidant, and anti-inflammatory effects by regulating miRNAs. Thus, miRNAs are novel targets for the action of PDBCs. PURPOSE The aim of this review was to evaluate the current status of PDBCs targeted miRNAs by dissecting their development status through a literature review. METHODS A manual and electronic search was performed for English articles available from inception up to June 2022 reporting PDBCs and their regulating relationship with miRNAs for the therapeutic potential of neurological disorders. Information was retrieved from scientific databases including PubMed, ScienceDirect, Web of Science, Google Scholar and Chemical Abstracts Services. Keywords used for the search engines were "miRNAs" AND "Plant-derived bioactive compounds" in conjunction with "(native weeds OR alien invasive)" AND "traditional herbal medicine". RESULTS A total of 37 articles were retrieved on PDBCs and their related miRNAs in neurological disorders. These PDBCs from traditional herbal medicine may play a therapeutic role in neurological disorders in a variety of mechanisms by regulating the corresponding miRNAs. These mechanisms mainly include inhibiting oxidative stress, anti-neuroinflammation, anti-autophagy, and anti-apoptosis. PDBC are a group of chemically distinct compounds derived from medicinal plants, some of which have therapeutic effects on neurological disorders. CONCLUSION The emergence of miRNAs as pathological regulatory factors provides a new direction for the study of bioactive compounds in Traditional Chinese medicine and the elucidating of their epigenetic effects. Elucidating the regulatory relationship between bioactive compounds and miRNAs may help to identify new therapeutic targets and promoting the application of these compounds in precision medicine through their targeted molecular activity.
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Affiliation(s)
- Xiaoyu Dong
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning 110004, PR China
| | - Jianfei Nao
- Department of Neurology, Shengjing Hospital of China Medical University, 36 Sanhao Street, Heping District, Shenyang, Liaoning 110004, PR China.
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239
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Liang C, Wu W, He X, Xue F, Feng D. Circ_0138960 knockdown alleviates lipopolysaccharide-induced inflammatory response and injury in human dental pulp cells by targeting miR-545-5p/MYD88 axis in pulpitis. J Dent Sci 2023; 18:191-202. [PMID: 36643232 PMCID: PMC9831794 DOI: 10.1016/j.jds.2022.06.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 06/17/2022] [Indexed: 01/18/2023] Open
Abstract
Background/purpose Circular RNAs (circRNAs) have been shown to play important regulatory roles in many human diseases, yet their functions in pulpitis remain to be clarified. This study was designed to investigate the function of circ_0138960 in pulpitis progression and its underlying mechanism. Material and methods Cell viability and proliferation were analyzed by 3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay and 5-Ethynyl-2'-deoxyuridine (EdU) assay. Flow cytometry and enzyme-linked immunosorbent assay (ELISA) were conducted to analyze cell apoptosis rate and the release of inflammatory cytokines. The activity of superoxide dismutase (SOD) was analyzed using a SOD assay kit. Dual-luciferase reporter and RNA-pull down assays were performed to verify the interaction between microRNA-545-5p (miR-545-5p) and circ_0138960 or myeloid differentiation primary response gene 88 (MYD88). Results Lipopolysaccharide (LPS) treatment restrained the proliferation and promoted the apoptosis, inflammation, and oxidative stress of human dental pulp cells (hDPCs). LPS treatment dose-dependently up-regulated circ_0138960 expression in hDPCs. Circ_0138960 knockdown overturned LPS-induced inflammation and injury in hDPCs. Circ_0138960 could act as a molecular sponge for miR-545-5p, and circ_0138960 knockdown protected hDPCs from LPS-induced effects by up-regulating miR-545-5p. miR-545-5p directly interacted with the 3' untranslated region (3'UTR) of MYD88, and MYD88 overexpression reversed miR-545-5p-mediated effects in LPS-treated hDPCs. Circ_0138960 positively regulated MYD88 expression by sponging miR-545-5p in hDPCs. LPS could activate nuclear factor kappa-B (NF-κB) signaling by targeting circ_0138960/miR-545-5p/MYD88 axis in hDPCs. Conclusion Circ_0138960 knockdown attenuated LPS-induced inflammatory response and injury in hDPCs by targeting the miR-545-5p/MYD88/NF-κB axis.
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Affiliation(s)
| | | | | | | | - Daxing Feng
- Corresponding author. Department of Stomatology, The Second Affiliated Hospital of Hainan Medical University, No. 10, Haifu Road, Haikou 570100, China.
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Role of Transcription Factor Nrf2 in Pyroptosis in Spinal Cord Injury by Regulating GSDMD. Neurochem Res 2023; 48:172-187. [PMID: 36040608 DOI: 10.1007/s11064-022-03719-5] [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: 01/07/2022] [Revised: 07/26/2022] [Accepted: 08/01/2022] [Indexed: 02/07/2023]
Abstract
Spinal cord injury (SCI) is a prevalent disease that debilitates millions of people. Nuclear factor E2-related factor 2 (Nrf2) is an important regulator of SCI. The current study sought to elaborate on the effects of Nrf2 on gasdermin D (GSDMD)-mediated microglia pyroptosis to repair SCI. The SCI rat model was established via the percussion of the T10 spinal cord and in vitro SCI model was established on BV-2 cells via lipopolysaccharide (LPS)/adenosine triphosphate (ATP) treatment. Nrf2 expression in SCI rats and BV-2 cells was overexpressed via pcDNA3.1-Nrf2 injection. Functional assays were carried out to evaluate SCI rat pathological injury, BV-2 cell viability, the release of lactate dehydrogenase (LDH), and pyroptotic factors. The binding relations of Nrf2 and microRNA (miR)-146a and miR-146a and GSDMD were verified. BV-2 pyroptosis was analyzed after the combined experiment of miR-146a-inhibitor and pcDNA3.1-GSDMD. Our experiments revealed that Nrf2 was downregulated in SCI, and Nrf2 overexpression relieved SCI pathological injury, promoted BV-2 cell viability, inhibited the release of LDH, and repressed pyroptosis. Mechanically, Nrf2 bound to the miR-146a promoter and promoted miR-146a expression, and miR-146a targeted GSDMD transcription. Rescue experiments revealed that miR-146a knockdown or GSDMD overexpression annulled the inhibitory function of Nrf2 overexpression in LPS/ATP-induced microglia pyroptosis. Overall, our findings initially highlighted that Nrf2 inhibited GSDMD-mediated microglia pyroptosis and accelerated SCI repair by repressing miR-146a.
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Kołosowska KA, Schratt G, Winterer J. microRNA-dependent regulation of gene expression in GABAergic interneurons. Front Cell Neurosci 2023; 17:1188574. [PMID: 37213213 PMCID: PMC10196030 DOI: 10.3389/fncel.2023.1188574] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 04/20/2023] [Indexed: 05/23/2023] Open
Abstract
Information processing within neuronal circuits relies on their proper development and a balanced interplay between principal and local inhibitory interneurons within those circuits. Gamma-aminobutyric acid (GABA)ergic inhibitory interneurons are a remarkably heterogeneous population, comprising subclasses based on their morphological, electrophysiological, and molecular features, with differential connectivity and activity patterns. microRNA (miRNA)-dependent post-transcriptional control of gene expression represents an important regulatory mechanism for neuronal development and plasticity. miRNAs are a large group of small non-coding RNAs (21-24 nucleotides) acting as negative regulators of mRNA translation and stability. However, while miRNA-dependent gene regulation in principal neurons has been described heretofore in several studies, an understanding of the role of miRNAs in inhibitory interneurons is only beginning to emerge. Recent research demonstrated that miRNAs are differentially expressed in interneuron subclasses, are vitally important for migration, maturation, and survival of interneurons during embryonic development and are crucial for cognitive function and memory formation. In this review, we discuss recent progress in understanding miRNA-dependent regulation of gene expression in interneuron development and function. We aim to shed light onto mechanisms by which miRNAs in GABAergic interneurons contribute to sculpting neuronal circuits, and how their dysregulation may underlie the emergence of numerous neurodevelopmental and neuropsychiatric disorders.
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Affiliation(s)
| | - Gerhard Schratt
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
| | - Jochen Winterer
- Lab of Systems Neuroscience, Department of Health Science and Technology, Institute for Neuroscience, Swiss Federal Institute of Technology ETH, Zurich, Switzerland
- *Correspondence: Jochen Winterer,
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242
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Li Y, Arce A, Lucci T, Rasmussen RA, Lucks JB. Dynamic RNA synthetic biology: new principles, practices and potential. RNA Biol 2023; 20:817-829. [PMID: 38044595 PMCID: PMC10730207 DOI: 10.1080/15476286.2023.2269508] [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: 10/28/2023] [Accepted: 08/23/2023] [Indexed: 12/05/2023] Open
Abstract
An increased appreciation of the role of RNA dynamics in governing RNA function is ushering in a new wave of dynamic RNA synthetic biology. Here, we review recent advances in engineering dynamic RNA systems across the molecular, circuit and cellular scales for important societal-scale applications in environmental and human health, and bioproduction. For each scale, we introduce the core concepts of dynamic RNA folding and function at that scale, and then discuss technologies incorporating these concepts, covering new approaches to engineering riboswitches, ribozymes, RNA origami, RNA strand displacement circuits, biomaterials, biomolecular condensates, extracellular vesicles and synthetic cells. Considering the dynamic nature of RNA within the engineering design process promises to spark the next wave of innovation that will expand the scope and impact of RNA biotechnologies.
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Affiliation(s)
- Yueyi Li
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Anibal Arce
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Tyler Lucci
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
| | - Rebecca A. Rasmussen
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
| | - Julius B. Lucks
- Department of Chemical and Biological Engineering, Northwestern University, Evanston, IL, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, USA
- Interdisciplinary Biological Sciences Graduate Program, Northwestern University, Evanston, IL, USA
- Center for Water Research, Northwestern University, Evanston, IL, USA
- Center for Engineering Sustainability and Resilience, Northwestern University, Evanston, IL, USA
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Zou L, Feng Q, Xia W, Zhu C. Bioinformatics analysis of the common targets of miR-223-3p, miR-122-5p, and miR-93-5p in polycystic ovarian syndrome. Front Genet 2023; 14:1097706. [PMID: 36873932 PMCID: PMC9977968 DOI: 10.3389/fgene.2023.1097706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2022] [Accepted: 02/06/2023] [Indexed: 02/18/2023] Open
Abstract
Polycystic ovarian syndrome (PCOS) is one of the most common gynecological endocrine disorders. MicroRNAs (miRNAs) play extensive roles in the pathogenesis of PCOS and can serve as potential diagnostic markers. However, most studies focused on the regulatory mechanisms of individual miRNAs, and the combined regulatory effects of multiple miRNAs remain unclear. The aim of this study was to identify the common targets of miR-223-3p, miR-122-5p, and miR-93-5p; and assess the transcript levels of some of these targets in PCOS rat ovaries. Transcriptome profiles of granulosa cells from PCOS patients were obtained from the Gene Expression Omnibus (GEO) database to identify differentially expressed genes (DEGs). A total of 1,144 DEGs were screened, 204 of which were upregulated and 940 were downregulated. According to the miRWalk algorithm, 4,284 genes were targeted by all three miRNAs at the same time, and intersection with DEGs was used to obtain candidate target genes. A total of 265 candidate target genes were screened, and the detected target genes were subjected to Gene ontology (GO) and KEGG pathway enrichment, followed by PPI network analysis. Then, qRT-PCR was used to determine the levels of 12 genes in PCOS rat ovaries. The expressions of 10 of these genes were found to be consistent with our bioinformatics results. In conclusion, JMJD1C, PLCG2, SMAD3, FOSL2, TGFB1, TRIB1, GAS7, TRIM25, NFYA, and CALCRL may participate in the development of PCOS. Our findings contribute to the identification of biomarkers that may promote the effective prevention and treatment of PCOS in the future.
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Affiliation(s)
- Liping Zou
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Qiwen Feng
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Wei Xia
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Changhong Zhu
- Institute of Reproductive Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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Xu G, Liu J, He J, He H, Su X, Gui Q. LOC554202 contributes to chordoma progression by sponging miR-377-3p and up-regulating SMAD3. Anticancer Drugs 2023; 34:15-28. [PMID: 36206143 PMCID: PMC9760475 DOI: 10.1097/cad.0000000000001327] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 03/21/2022] [Indexed: 12/31/2022]
Abstract
Chordoma is a rare malignant bone tumor originating from the remnants of the notochord. Here, the role of long noncoding LOC554202 in chordoma progression and its associated mechanism were explored. Cell proliferation was analyzed by 3-(4, 5-dimethylthiazol-2-yl)-2, 5 diphenyltetrazolium bromide and colony formation assays. Flow cytometry was conducted to analyze cell apoptosis rate. The migration and invasion of chordoma cells were analyzed by transwell migration and invasion assays and wound healing assays. A xenograft tumor model was established in nude mice to explore the role of LOC554202 in regulating tumor growth in vivo . The interaction between microRNA-377-3p (miR-377-3p) and LOC554202 or sekelsky mothers against d PP (SMAD) family member 3 (SMAD3) was verified by dual-luciferase reporter and RNA immunoprecipitation assays. The glycolytic rate of chordoma cells was analyzed using glucose assay kit, lactic acid kit and ApoSENSOR ADP/ATP ratio assay kit. LOC554202 expression was upregulated in chordoma tissues and cell lines. LOC554202 silencing suppressed the proliferation, migration and invasion and induced the apoptosis of chordoma cells. LOC554202 knockdown restrained xenograft tumor growth in vivo . miR-377-3p was confirmed as a target of LOC554202, and miR-377-3p silencing largely overturned LOC554202 knockdown-mediated anti-tumor effects in chordoma cells. miR-377-3p interacted with the 3' untranslated region (3'UTR) of SMAD3 and miR-377-3p overexpression-mediated antitumor effects in chordoma cells were largely attenuated by SMAD3 overexpression. LOC554202 could positively regulate SMAD3 expression by sponging miR-377-3p in chordoma cells. LOC554202 contributed to the glycolysis of chordoma cells by targeting binding to miR-377-3p/SMAD3 axis. LOC554202 facilitated the proliferation, migration, invasion and glycolysis and inhibited the apoptosis of chordoma cells by mediating miR-377-3p/SMAD3 axis.
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Affiliation(s)
- Guang Xu
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jingnan Liu
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Jun He
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Haibo He
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Xiaotao Su
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
| | - Qianhuan Gui
- Department of Spinal Surgery, The Affiliated Nanhua Hospital, Hengyang Medical College, University of South China, Hengyang, Hunan, China
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NF-κB1 p50 stabilizes HIF-1α protein through suppression of ATG7-dependent autophagy. Cell Death Dis 2022; 13:1076. [PMID: 36575197 PMCID: PMC9794792 DOI: 10.1038/s41419-022-05521-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 12/12/2022] [Accepted: 12/14/2022] [Indexed: 12/28/2022]
Abstract
The function and underlying mechanisms of p50 in the regulation of protein expression is much less studied because of its lacking of transactivation domain. In this study, we discovered a novel function of p50 in its stabilization of hypoxia-inducible factor 1α (HIF-1α) protein under the condition of cells exposed to arsenic exposure. In p50-deficient (p50-/-) cells, the HIF-1α protein expression was impaired upon arsenic exposure, and such defect could be rescued by reconstitutional expression of p50. Mechanistic study revealed that the inhibition of autophagy-related gene 7 (ATG7)-dependent autophagy was in charge of p50-mediated HIF-1α protein stabilization following arsenic exposure. Moreover, p50 deletion promoted nucleolin (NCL) protein translation to enhance ATG7 mRNA transcription via directly binding transcription factor Sp1 mRNA and increase its stability. We further discovered that p50-mediated miR-494 upregulation gave rise to the inhibition of p50-mediated NCL translation by interacting with its 3'-UTR. These novel findings provide a great insight into the understanding of biomedical significance of p50 protein in arsenite-associated disease development and therapy.
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246
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Tumor Cell-Derived Exosomal circ-PRKCI Promotes Proliferation of Renal Cell Carcinoma via Regulating miR-545-3p/CCND1 Axis. Cancers (Basel) 2022; 15:cancers15010123. [PMID: 36612120 PMCID: PMC9817713 DOI: 10.3390/cancers15010123] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/16/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022] Open
Abstract
Renal cell carcinoma (RCC) originates from the epithelial cells of the renal tubules and has a high degree of malignancy and heterogeneity. Recent studies have found that exosomes regulate intercellular communication via transferring various bioactive molecules, such as circular RNAs (circRNAs), which are critical for cancer progression. However, the role of tumor cell-derived exosomal circRNAs in RCC remains unclear. In this study, we reported the high expression of circ-PRKCI in RCC tissues and serum exosomes. We also found that circ-PRKCI could be transferred exosomally from highly malignant RCC cells to relatively less malignant RCC cells. Tumor cell-derived exosomal circ-PRKCI promoted the proliferation, migration, and invasion of RCC cells, while inhibiting their apoptosis. Mechanistically, we found that circ-PRKCI promoted the proliferation of RCC via the miR-545-3p/CCND1 signaling pathway. Our study is the first to report the potential mechanisms of tumor cell-derived exosomal circ-PRKCI in RCC. In conclusion, this study will provide a new understanding about the molecular mechanisms of RCC progression.
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Imrat, Labala RK, Behara AK, Jeyaram K. Selective extracellular secretion of small double-stranded RNA by Tetragenococcus halophilus. Funct Integr Genomics 2022; 23:10. [PMID: 36542169 DOI: 10.1007/s10142-022-00934-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Revised: 11/23/2022] [Accepted: 11/24/2022] [Indexed: 12/24/2022]
Abstract
Small double-stranded RNAs (dsRNAs) abundantly produced by lactic acid bacteria demonstrate immunomodulatory activity and antiviral protective immunity. However, the extracellular secretion of dsRNA from lactic acid bacteria and their compositional and functional differences compared to the intracellular dsRNA is unknown. In this study, we compared the intracellular and secreted extracellular dsRNA of the lactic acid bacteria, Tetragenococcus halophilus, commonly present in fermented foods, by growing in RNA-free and RNase-free media. We used RNA deep sequencing and in-silico analysis to annotate potential regulatory functions for the comparison. A time series sampling of T. halophilus culture demonstrated growth phase-dependent dynamics in extracellular dsRNA secretion with no major change in the intracellular dsRNA profile. The RNA deep sequencing resulted in thousands of diverse dsRNA fragments with 14-21 nucleotides in size from T. halophilus culture. Over 70% of the secreted extracellular dsRNAs were unique in their sequences compared to the intracellular dsRNAs. Furthermore, the extracellular dsRNA abundantly contains sequences that are not T. halophilus genome encoded, not detected intracellularly and showed higher hits on human transcriptome during in-silico analysis, which suggests the presence of extrachromosomal mobile regulatory elements. Further analysis showed significant enrichment of dsRNA target genes of human transcriptome on cancer pathways and transcription process, indicating the extracellular dsRNA of T. halophilus is different not only at the sequence level but also in function. Studying the bacterial extracellular dsRNA is a promising area of future research, particularly for developing postbiotic fermented functional foods and understanding the impact of commensal gut bacteria on human health.
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Affiliation(s)
- Imrat
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India.,Department of Biotechnology, Gauhati University, Guwahati, 781014, Assam, India
| | - Rajendra Kumar Labala
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India
| | - Abhisek Kumar Behara
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India
| | - Kumaraswamy Jeyaram
- Microbial Resources Division, Institute of Bioresources and Sustainable Development (IBSD), Takyelpat Institutional Area, Imphal, 795001, Manipur, India.,IBSD Regional Centre, Tadong, Gangtok, 737102, Sikkim, India
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248
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Peng S, Liu C, Fan X, Zhu J, Zhang S, Zhou X, Wang T, Gao F, Zhu W. Analysis of aberrant miRNA-mRNA interaction networks in prostate cancer to conjecture its molecular mechanisms. Cancer Biomark 2022; 35:395-407. [PMID: 36373308 DOI: 10.3233/cbm-220051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND MicroRNAs (miRNAs) capable of post-transcriptionally regulating mRNA expression are essential to tumor occurrence and progression. OBJECTIVE This study aims to find negatively regulatory miRNA-mRNA pairs in prostate adenocarcinoma (PRAD). METHODS Combining The Cancer Genome Atlas (TCGA) RNA-Seq data with Gene Expression Omnibus (GEO) mRNA/miRNA expression profiles, differently expressed miRNA/mRNA (DE-miRNAs/DE-mRNAs) were identified. MiRNA-mRNA pairs were screened by miRTarBase and TarBase, databases collecting experimentally confirmed miRNA-mRNA pairs, and verified in 30 paired prostate specimens by real-time reverse transcription polymerase chain reaction (RT-qPCR). The diagnostic values of miRNA-mRNA pairs were measured by receiver operation characteristic (ROC) curve and Decision Curve Analysis (DCA). DAVID-mirPath database and Connectivity Map were employed in GO/KEGG analysis and compounds research. Interactions between miRNA-mRNA pairs and phenotypic features were analyzed with correlation heatmap in hiplot. RESULTS Based on TCGA RNA-Seq data, 22 miRNA and 14 mRNA GEO datasets, 67 (20 down and 47 up) miRNAs and 351 (139 up and 212 down) mRNAs were selected. After screening from 2 databases, 8 miRNA (up)-mRNA (down) and 7 miRNA (down)-mRNA (up) pairs were identified with Pearson's correlation in TCGA. By external validation, miR-221-3p (down)/GALNT3 (up) and miR-20a-5p (up)/FRMD6 (down) were chosen. The model combing 4 signatures possessed better diagnostic value. These two miRNA-mRNA pairs were significantly connected with immune cells fraction and tumor immune microenvironment. CONCLUSIONS The diagnostic model containing 2 negatively regulatory miRNA-mRNA pairs was established to distinguish PRADs from normal controls.
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Affiliation(s)
- Shuang Peng
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Cheng Liu
- Department of Gastroenterology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xingchen Fan
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Jingfeng Zhu
- Department of Nephrology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Shiyu Zhang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xin Zhou
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Tongshan Wang
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Feng Gao
- Department of Osteology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Wei Zhu
- Department of Oncology, First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
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Chen X, Tang YY, Yin H, Sun X, Zhang X, Xu N. A survey of the full-length transcriptome of Gracilariopsis lemaneiformis using single-molecule long-read sequencing. BMC PLANT BIOLOGY 2022; 22:597. [PMID: 36536287 PMCID: PMC9762032 DOI: 10.1186/s12870-022-03992-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Accepted: 12/09/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Posttranscriptional processing of precursor mRNAs contributes to transcriptome and protein diversity and gene regulatory mechanisms in eukaryotes. However, this posttranscriptional mechanism has not been studied in the marine macroalgae Gracilariopsis lemaneiformis, which is the most cultivated red seaweed species in China. RESULTS In the present study, third-generation sequencing (Pacific Biosciences single-molecule real-time long-read sequencing, SMRT-Seq) was used to sequence the full-length transcriptome of G. lemaneiformis to identify alternatively spliced transcripts and alternative polyadenylation (APA) sites in this species. RNAs were isolated from G. lemaneiformis under various treatments including abiotic stresses and exogenous phytohormones, and then equally pooled for SMRT-Seq. In summary, 346,544 full-length nonchimeric reads were generated, from which 13,630 unique full-length transcripts were obtained in G. lemaneiformis. Compared with the known splicing events in the gene models, more than 3000 new alternative splicing (AS) events were identified in the SMRT-Seq reads. Additionally, 810 genes were found to have poly (A) sites and 91 microRNAs (miRNAs), 961 long noncoding RNAs and 1721 novel genes were identified in G. lemaneiformis. Moreover, validation experiments showed that abiotic stresses and phytohormones could induce some specific AS events, especially intron retain isoforms, cause some alterations to the relative ratios of transcripts annotated to the same gene, and generate novel 3' ends because of differential APA. The growth of G. lemaneiformis was inhibited by Cu stress, while this inhibition was alleviated by ACC treatment. RNA-Seq analysis further revealed that 211 differential alternative splicing (DAS) events and 142 DAS events was obtained in CK vs Cu and Cu vs Cu + ACC, respectively, suggesting that AS of functional genes could be regulated by Cu stress and ACC. Compared with Cu stress, the expression of transcripts with DAS events mainly involved in the carbon fixation in photosynthetic organisms and oxidative phosphorylation pathway was upregulated in Cu + ACC treatment, revealing that ACC alleviated the growth inhibition by Cu stress by increasing carbon fixation and oxidative phosphorylation. CONCLUSIONS Our results provide the first comprehensive picture of the full-length transcriptome and posttranscriptional mechanism in red macroalgae, including transcripts that appeared in the presence of common abiotic stresses and phytohormones, which will improve the gene annotations of Gracilariopsis and contribute to the study of gene regulation in this important cultivated seaweed.
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Affiliation(s)
- Xiaojiao Chen
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Yue Yao Tang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Haodong Yin
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xue Sun
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Xiaoqian Zhang
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China
| | - Nianjun Xu
- Key Laboratory of Marine Biotechnology of Zhejiang Province, School of Marine Sciences, Ningbo University, Ningbo, 315211, Zhejiang, China.
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Challenging Cellular Homeostasis: Spatial and Temporal Regulation of miRNAs. Int J Mol Sci 2022; 23:ijms232416152. [PMID: 36555797 PMCID: PMC9787707 DOI: 10.3390/ijms232416152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Mature microRNAs (miRNAs) are single-stranded non-coding RNA (ncRNA) molecules that act in post-transcriptional regulation in animals and plants. A mature miRNA is the end product of consecutive, highly regulated processing steps of the primary miRNA transcript. Following base-paring of the mature miRNA with its mRNA target, translation is inhibited, and the targeted mRNA is degraded. There are hundreds of miRNAs in each cell that work together to regulate cellular key processes, including development, differentiation, cell cycle, apoptosis, inflammation, viral infection, and more. In this review, we present an overlooked layer of cellular regulation that addresses cell dynamics affecting miRNA accessibility. We discuss the regulation of miRNA local storage and translocation among cell compartments. The local amounts of the miRNAs and their targets dictate their actual availability, which determines the ability to fine-tune cell responses to abrupt or chronic changes. We emphasize that changes in miRNA storage and compactization occur under induced stress and changing conditions. Furthermore, we demonstrate shared principles on cell physiology, governed by miRNA under oxidative stress, tumorigenesis, viral infection, or synaptic plasticity. The evidence presented in this review article highlights the importance of spatial and temporal miRNA regulation for cell physiology. We argue that limiting the research to mature miRNAs within the cytosol undermines our understanding of the efficacy of miRNAs to regulate cell fate under stress conditions.
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